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  • 1990-1994  (2,849)
  • 1980-1984
  • 1991  (2,849)
  • Life and Medical Sciences  (1,901)
  • Biochemistry and Biotechnology  (742)
  • Physical Chemistry  (205)
  • Nuclear reactions
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  • 1990-1994  (2,849)
  • 1980-1984
Year
Keywords
  • 1
    Electronic Resource
    Electronic Resource
    The origin and abundances of the chemical elements revisited (1991)
    Springer
    The astronomy and astrophysics review 3 (1991), S. 1-46 
    Details
    ISSN: 1432-0754
    Keywords: Nucleosynthesis ; Nuclear reactions ; Stars: abundances ; Interstellar Medium: abundances ; Cosmology ; Galaxies: evolution of
    Source: Springer Online Journal Archives 1860-2000
    Topics: Physics
    Notes: Summary The basic scheme of nucleosynthesis (building of heavy elements from light ones) has held up very well since it was first proposed more than 30 years ago by E.M. Burbidge, G.R. Burbidge, A.G.W. Cameron, W.A. Fowler, and F. Hoyle. Significant advances in the intervening years include (a) observations of elemental and a few isotopic ratios in many more extrasolar-system sites, including metal-poor dwarf irregular galaxies, where very little has happened, and supernovae and their remnants, where a great deal has happened, (b) recognition of the early universe as good for making all the elements up to helium, (c) resolution of heavy element burning in stars into separate carbon, neon, oxygen, and silicon burning, with fine tuning of the resulting abundances by explosive nucleosynthesis in outgoing supernova shock waves, (d) clarification of the role of Type I supernovae, (e) concordance between elements produced in short-lived and long-lived stars with those that increased quickly and slowly over the history of the galaxy, and (f) calibration of calculations of the evolution and explosion of massive stars against the detailed observations of SN 1987A. The discussion presupposes a reader (a) with some prior knowledge of astronomy at the level of recognizing what is meant by an A star and an AGB star and (b) with at least a mild interest in how we got to where we currently are.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00873456
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  • 2
    Electronic Resource
    Electronic Resource
    Alpha-actinin and actin in the outer retina: A double immunoelectron microscopic study (1991)
    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 18 (1991), S. 15-25 
    Details
    ISSN: 0886-1544
    Keywords: cytoskeleton ; microfilaments ; immunocytochemistry ; photoreceptors ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: Actin has many diverse functions in the outer retina. To help elucidate its organization in this area, we have investigated the extent of its association with the actin cross-linking protein alpha-actinin. Ultrathin sections of chicken retina were double-immunolabelled with monospecific antibodies against actin and alpha-actinin. The highest relative amount of alpha-actinin to actin label was measured in the adherens junctions between the individual retinal pigmented epithelial (RPE) cells and between the photoreceptor and Mueller cells; in the photoreceptor myoid; and in the RPE basal microvilli. The lowest amount was in the Mueller cell microvilli, the RPE apical processes, and in the photoreceptor ellipsoid. It is likely that the areas containing the highest ratio of alpha-actinin to actin labelling are where the actin filaments are most highly cross-linked into bundles and linked to the plasma membrane by alpha-actinin. Actin filaments terminate in these areas, and, except for the myoid region, they are involved in cell-cell or cell-substrate adherens junctions.
    Additional Material: 9 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/cm.970180103
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  • 3
    Electronic Resource
    Electronic Resource
    Reorganization of cytoskeletal and junctional proteins during cochlear hair cell degeneration (1991)
    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 18 (1991), S. 215-227 
    Details
    ISSN: 0886-1544
    Keywords: guinea pig ; organ of Corti ; cytokeratins ; actin ; cingulin ; phalangeal scar ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: Experiments were carried out to elucidate changes in cytoskeletal elements and intercellular junctions in the organ of Corti, when hair cells degenerate and phalangeal scars form. Hair cell damage was induced by exposing guinea pigs to high intensity noise. The spatial and temporal changes in the organization of micro-filaments, intermediate filaments, and tight junction-specific proteins were investigated using scanning and transmission electron microscopy and histochemistry. The results show that microfilaments, cytokeratins, adherens junctions, and tight junctions rearrange their distribution in damaged areas. From the temporal sequence of these changes it appears that phalangeal scars develop simultaneous with hair cell degeneration, and that the integrity of the luminal membranes in the organ of Corti is not interrupted. Each scar is formed by two supporting cells which expand and invade the sub-apical region of the dying hair cell. This region becomes cytokeratin-positive. The two supporting cells meet at the mid-line of the scar, where a new junctional complex is formed. The junctional complex consists of tight junction and adherens-type junction, but desmosomes are absent.
    Additional Material: 9 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/cm.970180307
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  • 4
    Electronic Resource
    Electronic Resource
    Decrease of internal free calcium and human sperm movement (1991)
    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 18 (1991), S. 228-240 
    Details
    ISSN: 0886-1544
    Keywords: Quin-2/AM ; spermatozoa ; calcium depletion ; motility ; flagellum ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: In order to elucidate the effects of calcium on the movement of human spermatozoa, studies were conducted using motile cells selected by swim-up migration at 37°C in 5% CO2 in air in a synthetic BWW medium containing 1.7 × 10-3 M CaCl2 or BWW without added calcium (BWW-Ca). Preliminary experiments have confirmed that the addition of EGTA (5 × 10-3; 10-2 M) to BWW medium decreased the intracellular calcium concentration ((Ca++)i) of spermatozoa, as measured in cells loaded with a fluorescent Ca++ indicator, Quin-2. Concomitant measurements of (Ca++)i and sperm movement (analysed by videomicrography at 200 f/s at room temperature) were carried out on Quin-2 loaded cells incubated in BWW-Ca medium plus EGTA (10-5 M; 10-4 M; 10-3 M). Under these conditions a decrease in (Ca++)i was observed and associated with a decrease in mean amplitude of lateral head displacement (ALH). Analysis using an automatic analyser (Hamilton Thorn at 37°C) confirmed these results: the percentage of spermatozoa swimming with ALH ≤ 6 μm is decreased when the external free calcium in BWW-Ca is decreased by the addition of 10-5 M, 10-4 M, or 10-3 M EGTA. Flagellar analysis of the sperm population characterized by ALH ≤ 6 μm showed a large proximal curvature of the tail associated with a low propagation wave velocity and a low beat frequency as compared to the spermatozoa with ALH ≤ 6 μm with similar progressive velocities. These characteristics result in a high flagellar beat efficiency (in terms of head displacement per beat). The disappearance of this pattern of movement when intracellular calcium is lowered indicates that calcium plays a complex role in the relationship between curvature and wave propagation. The ability of spermatozoa to modulate their movement in response to an alteration in the intracellular calcium level confirms the role of calcium in controlling flagellar movement in intact cells.
    Additional Material: 7 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/cm.970180308
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  • 5
    Electronic Resource
    Electronic Resource
    Microtubule binding and translocation by inner dynein arm subtype i1 (1991)
    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 18 (1991), S. 258-268 
    Details
    ISSN: 0886-1544
    Keywords: flagella ; motility ; Chlamydomonas ; cilia ; ATPase ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: Structural, biochemical, and genetic evidence has demonstrated there are three inner dynein arm subforms, I1, I2, and I3, which differ in organization and composition (see Piperno et al.: J. Cell Biol. 110:379-389, 1990). Using dynein extracted from Chlamydomonas outer dynein armless mutant pf28, we have begun to define the structural and functional properties of isolated inner arm subforms. Inner dynein arm I1 was purified either by sucrose density gradient centrifugation or microtubule binding affinity. I1, composed of heavy chains 1α and 1β, sedimented at 21S and selectively bound to and cross-linked purified microtubules in and ATP-sensitive manner. Deep etch electron microscopy revealed that the 21S sedimenting fraction contained two-headed structures in which large globular heads are connected by long, flexible-stem domains. In contrast, components derived from I2 and I3 sedimented as a mixture of 11S particles with single globular heads which did not bind to purified microtubules. Both the 21S and 11S sedimenting fractions supported microtubule translocation in in vitro motility assays. In 1 mM MgATP the I1-containing fraction produced very slow microtubulegliding velocities (0.76 μm/sec) compared to the I2, I3-containing fraction (4.1 μm/sec).
    Additional Material: 8 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/cm.970180403
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  • 6
    Electronic Resource
    Electronic Resource
    Flagellar photoresponses of Chlamydomonas cells held on micropipettes: II. Change in flagellar beat pattern (1991)
    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 18 (1991), S. 269-278 
    Details
    ISSN: 0886-1544
    Keywords: high-speed microcinematography ; photophobic response ; phototaxis ; beat frequency ; rate of flagellar movement ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: In response to step-up as well as step-down blue or white light stimuli, changes of beat pattern were observed in the two flagella of Chlamydomonas. The front amplitude was either increased or decreased, always in reverse in the two flagella. Again, two opposite combinations of step-up and step-down responses were found roughly in parallel to the two types of beat frequency changes. It is shown that positive phototaxis is probably achieved by the first type [called type (+)] and negative phototaxis by the second one [called type (-)]. Comparative measurements have revealed that frequency is not only related to the rate of flagellar movement, but also to the beat pattern. The rate of movement may change in different ways in the recovery and in the effective stroke. Though beat frequency and pattern changes are opposite in the two types, the rates of movement of the two flagella during the effective stroke are not always. In type (-) divergent changes were found in the rates of effective stroke movement, perhaps indicating the involvement of an additional mechanism.
    Additional Material: 8 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/cm.970180404
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  • 7
    Electronic Resource
    Electronic Resource
    Post-mitotic cellular reorganisation in the diatom Cymatopleura solea: The role of microtubules and the microtubule centre (1991)
    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 18 (1991), S. 279-292 
    Details
    ISSN: 0886-1544
    Keywords: morphogenesis ; diatoms ; intracellular movement ; cytoskeleton ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: Cell division in Cymatopleura requires precise and major relocations of the nucleus and chioroplast which have been followed by time-lapse cinematography and with the electron microscope. These movements are (1) the premitotic nucleus migrating to one end of the cell; (2) after cytokinesis, the daughter nuclei moving back to the cell centre, often oscillating several times while establishing their final location; (3) the single chloroplast folding over and sandwiching the central nucleus; and (4) the folded end of the chloroplast stretching back to fill the empty half of the cell. In all cases, straight, actively moving, transient strands of cytoplasm are associated with the movement of the nucleus and chloroplast, and these often appear to be pulling on the surface or the fold of the chloroplast which undergoes transient distortion.These movements are rapid and colchicine-sensitive. Ultrastructurally, they appear to be mediated by the prominent microtubule centre (MC) and its associated cytoskeleton of microtubules (MTs) although MTs do not attach directly to either nucleus or chloroplast. The MC is located close to the moving nucleus. Later, it moves ahead of the moving chloroplast and its MTs ensheath the tip. Later still, it is seen embedded in the fold of the chloroplast. In all three situations, MTs from it are seen in the strands of cytoplasm radiating from this area across the vacuole. After these events, the MC resumes its usual interphase situation on the nuclear surface.
    Additional Material: 25 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/cm.970180405
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  • 8
    Electronic Resource
    Electronic Resource
    Announcement (1991)
    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 18 (1991), S. 319-320 
    Details
    ISSN: 0886-1544
    Keywords: Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/cm.970180408
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  • 9
    Electronic Resource
    Electronic Resource
    Neural crest cell galvanotaxis: New data and a novel approach to the analysis of both galvanotaxis and chemotaxis (1991)
    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 19 (1991), S. 121-133 
    Details
    ISSN: 0886-1544
    Keywords: modeling ; electric field ; directed motility ; information theory ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: The galvanotaxis response of neural crest cells that had migrated out of the neural tube of a 56-hr-old quail embryo, onto glass coverslips was observed using time-lapse video microscopy. These cells exhibit a track velocity of about 7 μm/min and actively translocate toward the negative pole of an imposed DC electric field. This nonrandom migration could be detected for fields as low as 7 mV/mm (0.4 mV/cell lepgth). We find that this directional migration is independent of the speed of migration and have generated a rather simple mathematical equation that fits these data. We find that the number of cells that translocate at a given angle, Φ, with respect to the field is given by the equation N (Φ) = exp(a()0 + a1 cos Φ), where a1 is linearly proportional to the electric field strength for fields less than 390 mV/mm with a constant of proportionality equal to KG, the galvanotaxis constant. We show that KG = (150 mV/mm)-1, and at this field strength the cellular response is approximately half maximal. This approach to cellular translocation data analysis is generalizable to other directed movements such as chemotaxis and allows the direct comparison of different types of directed movements. This analysis requires that the response of every cell, rather than averages of cellular responses, is reported. Once an equation for N(Φ) is derived, several characteristics of the cellular response can be determined. Specifically, we describe (1) the critical field strength (390 mV/mm) below which the cellular response exhibits a simple, linear dependence on field strength (for larger field strengths, an inhibitory constant can be used to fit the data, suggesting that larger field strengths influence a second cellular target that inhibits the first); and (2) the amount of information the cell must obtain in order to generate the observed asymmetry in the translocation distribution (for a field strength of 100 mV/mm, 0.3 bits of information is required).
    Additional Material: 7 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/cm.970190207
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  • 10
    Electronic Resource
    Electronic Resource
    Pseudopodial activity at the active edge of migrating fibroblast is decreased after drug-induced microtubule depolymerization (1991)
    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 19 (1991), S. 152-158 
    Details
    ISSN: 0886-1544
    Keywords: video-enhanced contrast microscopy ; colcemid ; lamellipodia ; mitochondria ; intermediate filaments ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: It is known that depolymerization of microtubules by colcemid or other similar drugs abolishes polarization of pseudopodial activity in migrating fibroblasts. In this work the effect of colcemid on the intensity of protrusion and retraction of lamellipodia at the active edges of human fibroblasts migrating into the wound was investigated with video-enhanced contrast microscopy. To characterize the pseudopodial activity quantitatively the outlines of the active edges in the pairs of frames taken at adjacent 20-sec intervals were compared and mean areas of protrusions and retractions per unit length of the perimeter of the edge were measured. The mean rates of protrusions and retractions were 4-6 times less in colcemid-treated cells than in controls. Thus, microtubules depolymerized by colcemid, and/or intermediate filaments undergoing perinuclear collapse in the presence of this drug, are essential not only for the restriction of pseudopodial activity to one particular zone of the cell edge but also for the development of maximal activity in this zone.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/cm.970190303
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  • 11
    Electronic Resource
    Electronic Resource
    βVLDL uptake by pigeon monocyte-derived macrophages: Correlation of binding dynamics with three-dimensional ultrastructure (1991)
    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 19 (1991), S. 139-151 
    Details
    ISSN: 0886-1544
    Keywords: lipoprotein ; receptor-mediated endocytosis ; nonspecific endocytosis ; microvilli ; membrane ruffles ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: Endocytosis of pigeon beta migrating very-low-density lipoprotein (βVLDL) by monocyte-derived macrophages (monocyte/macrophages), cultured from Random Bred White Carneu (RBWC) pigeons, occurs by both coated and non-coated regions of the plasma membrane (Henson et al.: Exp. Mol. Pathol. 51:243-263, 1989). Secondary to binding, the βVLDL is translocated to lysosomes for degradation. Ultimately these events lead to foam cell formation in vitro. Utilizing video-enhanced contrast light microscopy in conjunction with whole mount intermediate-voltage transmission electron microscopy (IVEM) and high-resolution scanning EM, the dynamics of βVLDL binding have been correlated with ultrastructure. Beta VLDL conjugated to gold colloids was visualized at the surface of living cells by using Allen video-enhanced contrast-differential interference contrast microscopy (AVEC-DIC). Subsequent to AVEC-DIC, direct observation of the identical cells by IVEM and SEM was facilitated through the use of gold finder grids, and these EM observations confirmed identification of the videoobserved βVLDL particles.Upon addition of βVLDL, pigeon monocyte/macrophages underwent gross morphological changes. These changes were recorded by video as movements at the cytoplasmic periphery, and the movements involved extension of microvilli, expression of retraction fibers, and elaboration of membrane ruffles. When secondarily observed by stereo (3-D) IVEM and SEM, the identification of microvilli, retraction fibers, and membrane ruffles was confirmed and the lipoprotein-gold conjugates were associated with these ligand-induced membrane structures. Beta VLDL-gold conjugates were also associated with pit-like regions at the base of microvilli, while at the base of ruffles, βVLDL-gold conjugates were located in membrane invaginations and cytoplasmic vesicles.
    Additional Material: 7 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/cm.970190302
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  • 12
    Electronic Resource
    Electronic Resource
    Diversity of microtubular doublets in insect sperm tails: A computer-aided image analysis (1991)
    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 19 (1991), S. 282-289 
    Details
    ISSN: 0886-1544
    Keywords: sperm flagellum ; microtubular protofilaments ; dynein arms ; computer reconstruction ; computer analysis ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: Axonemal doublets of some insect spermatozoa were fixed in a mixture of glutaraldehyde and tannic acid, post-fixed in uranyl acetate, and examined by electron microscopy, in order better to characterize the protofilament pattern. Most species had outer and inner dynein arms; others had only the inner one or none. Electron micrographs show the individual protofilaments to be well resolved and to be separated by an electron dense material. A certain “noise” inherent in the electron-microscopical technique was found and is believed to be due to irregularities in fixation, embedding, and section staining, and to beam damage. The noise level was reduced by using a computer program in which similar picture elements are averaged. The resulting averaged images of the axonemal doublets show a few widened “gaps” in the wall of protofilaments. These widened gaps coincide with the location of dynein arms, spokes, or intertubular material. There were, on the other hand, no widened gaps at the level of attachement of the accessory tubules. We tentatively conclude that at least some of the proteins that associate with microtubules are inserted deep inside the microtubular wall rather than having a superficial attachement. The internal structure of the A-subtubule is rather constant in species where both sets of dynein arms are present, whereas that of the B-tubule is more variable.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/cm.970190407
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  • 13
    Electronic Resource
    Electronic Resource
    Control of ciliary orientation in ciliated sheets from Paramecium-differential distribution of sensitivity to cyclic nucleotides (1991)
    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 20 (1991), S. 38-46 
    Details
    ISSN: 0886-1544
    Keywords: cilia ; calcium ; cAMP ; differential response ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: Ciliated sheets of cell cortex were prepared from Triton-glycerol-extracted Paramecium to observe directly the change of ciliary orientation. The observation of the ciliary responses revealed the modes of ciliary control by Ca2+ and cyclic nucleotides. The cilia changed their pointing direction clockwise from 11-12 to 5 o'clock (with the anterior of the cell defined as 12 o'clock) in the horizontal plane of cell surface when Ca2+ concentration was decreased from 10-6 M to 10-7 M. Cyclic AMP competed with Ca2+ ion in determining the orientation of the cilia. On the other hand, cGMP tended to change the ciliary orientation toward 3 o'clock. Ciliary sensitivity to cyclic nucleotides depended on their location on the cell surface. The cilia on the left-hand field of the cell were more sensitive to cyclic nucleotide than those on the right-hand field. The differential distribution of ciliary sensitivity within a single cell seems to be functional in the sophisticated turning mechanism in the behavioral response of Paramecium.
    Additional Material: 8 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/cm.970200105
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  • 14
    Electronic Resource
    Electronic Resource
    Segregation of the nucleolus during mitosis in budding and fission yeast (1991)
    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 20 (1991), S. 47-54 
    Details
    ISSN: 0886-1544
    Keywords: fibrillarin ; Saccharomyces cerevisiae ; CDC ; topoisomerase ; rDNA ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: The segregation of the nucleolus during mitosis was examined in Saccharomyces cerevisiae and Schizosaccharomyces pombe by indirect immunofluorescence using antibodies directed to highly conserved anti-nucleolus antigens. In mitotic S. pombe cells, the nucleolus appears to trail the bulk of the DNA. In wild-type cells of S. cerevisiae, the nucleolus segregates alongside the bulk of the genomic DNA. Based on its distance from the centromere, we would expect the rDNA in both organisms to segregate behind the majority of the genomic DNA, if telomeric regions trail centromeric regions as in other eukaryotes. We therefore suggest that in S. cerevisiae the nucleolus is attached to other parts of the nucleus which enable it to segregate along with the bulk of the DNA. The segregation of the nucleolus in topoisomerase mutants and nuclear division mutants of S. cerevisiae was also investigated. In cdc14 mutants which arrest at late anaphase, the vast majority of the DNA is separated, but the nucleolar antigens remain extended between the mother and daughter cells. Thus, the CDC14 gene of S. cerevisiae appears to be important for the separation of the nucleolus at mitosis.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/cm.970200106
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  • 15
    Electronic Resource
    Electronic Resource
    Synchronous triggering of trout sperm is followed by an invariable set sequence of movement parameters whatever the incubation medium (1991)
    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 20 (1991), S. 55-68 
    Details
    ISSN: 0886-1544
    Keywords: motility ; spermatozoa ; calcium ; potassium ; pH ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: The movement of live trout spermatozoa is very brief (25 sec at 20°C) and conditions have been developed to get synchronous initiation of sperm motility which allowed quantification of the major parameters of sperm movement during the motility phase.Recorded flagellar beat frequencies decreased steadily from values of 55 Hz at the beginning to 20 Hz at the end of the motility phase. Sperm forward velocities followed a similar pattern from 250 to 20 μm.sec-1 in the same conditions and the diameters of sperm trajectories were reduced from 370 to 40 μm. Thus none of the characteristics of sperm movement was constant during the motile phase which ended abruptly by a straightening of the flagella.The decrease in flagellar beat frequencies and sperm velocities are much greater than what could be extrapolated from the decrease of intracellular ATP (Christen R. et al: Eur. J. Biochem, 166:667-671, 1987) or from measurements of ATP-dependence of reactivated sperm velocities (Okuno M. and Morisawa N.: In Biological Functions of Microtubules and Related Structures. New York: Academic Press, pp. 151-162, 1982). Therefore, the cessation of flagellar beating at 25 sec is not directly the result of the low concentration of intracellular ATP.The decrease in the diameters of sperm trajectories which occurred during the first part of the motility phase was correlated with [Ca]i measurements (Cosson M.P. et al, Cell Motil. Cytoskeleton, 14:424-434, 1989). The effect of Ca2+ at the axonemal level does not indicates that Ca2+ influx is previous to flagellar beating but rather suggests a classical Ca2+ regulation of the flagellar assymetry.The short duration of the motility phase and the characteristics of sperm movement were very similar in various conditions (high external K+, low pH media) where increased external Ca2+ or divalent ions were shown to overcome K+ and H+ inhibition of sperm motility, both conditions which have been shown to depolarize the plasma membrane potential (Gatti J.L. et al: J. Cell Physiol., 143:546-554, 1990).The present study of the parameters of sperm movement suggests that once motility is initiated, a defined set of axonemal events will take place whatever the external conditions.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/cm.970200107
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  • 16
    Electronic Resource
    Electronic Resource
    Epitope mapping of monoclonal antibodies against caldesmon and their effects on the binding of caldesmon to Ca++/calmodulin and to actin or actin-tropomyosin filaments (1991)
    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 20 (1991), S. 95-108 
    Details
    ISSN: 0886-1544
    Keywords: actomyosin ; smooth muscle contraction ; nonmuscle cell motility ; microinjection ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: The effects of monoclonal anti-caldesmon antibodies, C2, C9, C18, C21, and C23, on the binding of caldesmon to F-actin/F-actin-tropomyosin filaments and to Ca++/calmodulin were examined in an in vitro reconstitution system. In addition, the antibody epitopes were mapped by Western blot analysis of NTCB (2-nitro-5-thiocyanobenzoic acid) and CNBr (cyanogen bromide) fragments of caldesmon. Both C9 and C18 recognize an amino terminal fragment composed of amino acid residues 19 to 153. The C23 epitope lies within a fragment ranging from residues 230 to 386. Included in this region is a 13-residue repeat sequence. Interestingly this repetitive sequence shares sequence similarity with a sequence found in nuclear lamin A, a protein which is also recognized by C23 antibody. Therefore, it is likely that the C23 epitope corresponds to this 13-residue repeat sequence. A carboxyl-terminal 10K fragment contains the epitopes for antibodies C2 and C21. Among these antibodies, only C21 drastically inhibits the binding of caldesmon to F-actin/F-actin-tropomyosin filaments and tc Ca++/calmodulin. When the molar ratio of monoclonal antibody C21 to caldesmon reached 1.0, a maximal inhibition (90%) on the binding of caldesmon to F-actin filaments was observed. However, it required double amounts of C21 antibody to exhibit a maximal inhibition of 70% on the binding of caldesmon to F-actin-tropomyosin filaments. These results suggest that the presence of tropomyosin in F-actin enhances caldesmon's binding. Furthermore, C21 antibody also effectively inhibits the caldesmon binding to Ca++/calmodolin. The kinetics of C21 inhibition on caldesmon's binding to Ca++/calmodulin is very similar to the inhibition obtained by preincubation of caldesmon with free Ca++/calmodulin. This result suggests that there is only one Ca++/calmodulin binding domain on caldesmon and this domain appears to be very close to the C21 epitope. Apparently, the Ca++/calmodulin-binding domain and the actin-binding domain are very close to each other and may interfere with each other. In an accompanying paper, we have further demonstrated that microinjection of C21 antibody into living chicken embryo fibroblasts inhibit intracellular granule movement, suggesting an in vivo interference with the functional domains [Hegmann et al., 1991: Cell Motil. Cytoskeleton 20:109-120].
    Additional Material: 11 Ill.
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    URL: http://dx.doi.org/10.1002/cm.970200203
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    Cytoskeleton of the mouse egg and embryo: Reorganization of planar elements (1991)
    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 18 (1991), S. 143-154 
    Details
    ISSN: 0886-1544
    Keywords: mouse ; intermediate filaments ; detergent-extracted mouse eggs ; cytoskeletal networks ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: Examination of detergent-extracted mouse eggs and embryos reveals the existence of two cytoskeletal networks. One network is the typical thin filament network observed in somatic cells while the other is composed of large planar elements. These latter cytoskeletal structures, with individual widths of 60.0±6.8 nm, alter their spatial organization in a developmental stage-specific manner. The planar elements are composed of filaments with a diameter of 10 nm aligned side-by-side with these filaments exhibiting a linear periodicity of 20.0±1.6 nm. A biochemical fraction containing components of the planar elements has been prepared from different stages of development and disappearance of prominent polypep-tides from this fraction correlates with the altered spatial organization of the planar elements. Ultrastructure and biochemistry of cytoskeletal planar elements in eggs and embryos of the mouse are comparable with cytoskeletal sheets of Syrian hamster eggs and embryos, suggesting these cytoskeletal components may have a functional role in mammalian embryogenesis. Because such structures have not been identified in eggs or embryos of species other than mammals, their function may be unique to mammalian embryogenesis.
    Additional Material: 9 Ill.
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    URL: http://dx.doi.org/10.1002/cm.970180209
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  • 18
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    Ultrastructure of the human erythrocyte cytoskeleton and its attachment to the membrane (1991)
    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 19 (1991), S. 227-243 
    Details
    ISSN: 0886-1544
    Keywords: spectrin ; band 3 ; anion transporter ; membrane structure ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: We attached paraformaldehyde-fixed human erythrocyte ghosts to coated coverslips and sheared them to expose the cytoskeleton. Quick-freeze, deep-etch, rotary-replication, or tannic acid/osmium fixation and plastic embedding revealed the cytoskeleton as a dense network of intersecting straight filaments. Previous negative stain studies on spread skeletons found 5-6 spectrin tetramers intersecting at each actin oligomer, with an estimated 250 such intersections/μm2 of membrane. In contrast, we found 3-4 filaments at each intersection and ∼400 intersections/μm2 of membrane. Immunogold labeling verified that the filaments were spectrin, but their lengths (29-37 nm) were approximately one-third that of extended spectrin dimers. The length and diameter of the filaments were sufficient to accommodate spectrin dimers, but not spectrin tetraments. Our results suggest that, in situ, spectrin dimers may associations as hexamers and octamers, rather than tetramers. We present several explanations that can reconcile our observations on intact cytoskeletons with previous reports on spread material.Extracting sheared ghosts with solutions of low ionic strength removed the cytoskeleton to reveal projections from the cytoplasmic surface of the membrane. These projections contained band 3, as shown by immunogold labeling, and they aggregated to a similar extent as intramembrane particles (IMP) when the cytoskeleton was removed, suggesting a direct relationship between these structures. Quantification indicated a stoichiometry of 2 IMP for each cytoplasmic projection. Cytoplasmic projections presumably contain other proteins besides band 3 since further treatment with high ionic strength solutions extracts peripheral proteins and reduces the diameter of projections by ∼3 nm.
    Additional Material: 9 Ill.
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    URL: http://dx.doi.org/10.1002/cm.970190402
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  • 19
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    Comparative kinetics of short and long sperm in sperm dimorphic Drosophila species (1991)
    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 19 (1991), S. 269-274 
    Details
    ISSN: 0886-1544
    Keywords: minor and major waves ; beat frequeney ; wave propagation velocity ; coiling diameter ; storage effect ; differential behaviour ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: All species of the Drosophila obscura group exhibit within-ejaculate sperm length dimorphism. The present work is a contribution to the understanding of sperm competition through a comparative study of sperm kinetic parameters in four of these species. Videomicrographic observations at 200 frames per second of sperm from males and females, out of the storage organ, prior or after storage were made. Drosophila sperm display both major and minor waves. The former is analysed by measuring coiling diameter (μm) and the latter by recording both beat frequency (s-1) and wave propagation velocity (μm·s-1). Results show that the ‘behaviour’ of short and long spermatozoa noticeably differ: short sperm kinetics remains unaltered after storage while both major and minor waves of long spermatozoa are markedly modified. Thus, evidence is provided here of a sort of “differential activation” which is assumed to result in different survival abilities of short and long sperm within the storage organ of females.
    Additional Material: 2 Ill.
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    URL: http://dx.doi.org/10.1002/cm.970190405
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  • 20
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    Centripetal flow and directed reassembly of the major sperm protein (MSP) cytoskeleton in the amoeboid sperm of the nematode, Ascaris suum (1991)
    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 20 (1991), S. 228-241 
    Details
    ISSN: 0886-1544
    Keywords: fine filaments ; intracellular pH ; motility ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: The cytoskeleton of the amoeboid spermatozoa of Ascaris suum consists of major sperm protein (MSP) filaments arranged into long, branched fiber complexes that span the length of the pseudopod and treadmill rearward continuously due to assembly and disassembly at opposite ends of the complexes (Sepsenwol et al., Journal of Cell Biology 108:55-66, (1989)). Examination by video-enhanced microscopy showed that this cytoskeletal flow is tightly coupled to sperm locomotion. The fiber complexes treadmilled reaward at the same rate (10-50 μm/ min) as the cell crawled forward. Only fiber complexes with their plasmalemmal ends within a limited sector along the leading edge of the pseudopod underwent continuous assembly. Thus, the location of this sector, which occupies about 50% of the pseudopod perimeter, determined the direction of sperm locomotion. Treatment of sperm with agents that lower intracellular pH, such as, weak acids and protonophores, caused the fiber complexes to disassemble completely in 4-5 sec. Removal of these compounds resulted in reassembly of the cytoskeleton in a pattern that mimicked treadmilling in intact sperm. The fiber complexes were reconstructed by assembly at their plasmalemmal ends so that within 30-60 sec the entire filament system reformed and the cell resumed locomotion. Both cytoskeletal reassembly and treadmilling required exogenous HCO3-. These results suggest that variation in intracellular pH may help regulate cytoskeletal treadmilling and thereby play a significant role in sperm locomotion.
    Additional Material: 8 Ill.
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    URL: http://dx.doi.org/10.1002/cm.970200306
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  • 21
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    Compartmentalization and actin binding properties of ABP-50: The elongation factor-1 alpha of Dictyostelium (1991)
    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 20 (1991), S. 279-288 
    Details
    ISSN: 0886-1544
    Keywords: actin binding protein ; cytoskeleton ; amoeboid chemotaxis ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: ABP-50 is the elongation factor-1 alpha (EF-1 alpha) of Dictyostelium discoideum (Yang et al.: Nature 347:494-496, 1990). ABP-50 is also an actin filament binding and bundling protein (Demma et al.: J. Biol. Chem. 265:2286-2291, 1990). In the present study we have investigated the compartmentalization of ABP-50 in both resting and stimulated cells. Immunofluorescence microscopy shows that in addition to being colocalized with F-actin in surface extensions in unstimulated cells, ABP-50 exhibits a diffuse distribution throughout the cytosol. Upon addition of cAMP, a chemoattractant, ABP-50 becomes localized in the filopodia that are extended as a response to stimulation. Quantification of ABP-50 in Triton-insoluble and-soluble fractions of resting cells indicates that 10% of the total ABP-50 is recovered in the Triton cytoskeleton, while the remainder is in the soluble cytosolic fraction. Stimulation with cAMP increases the incorporation of ABP-50 into the Triton cytoskeleton. The peak of incorporation of ABP-50 at 90 sec is concomitant with filopod extension. Immunoprecipitation of the cytosolic ABP-50 from unstimulated cells using affinity-purified polyclonal anti ABP-50 results in the coprecipitation of non-filamentous actin with ABP-50. Purified ABP-50 binds to G-actin with a Kd of approximately 0.09 μM. The interaction between ABP-50 and G-actin is inhibited by GTP but not by GDP, while the bundling of F-actin by ABP-50 is unaffected by guanine nucleotides. We conclude that a significant amount of ABP-50 is bound to either G- or F-actin in vivo and that the interaction between ABP-50 and F-actin in the cytoskeleton is regulated by cheniotactic stimulation.
    Additional Material: 6 Ill.
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    URL: http://dx.doi.org/10.1002/cm.970200404
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  • 22
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    The calcium-induced curvature reversal of rat sperm is potentiated by cAMP and inhibited by anti-calmodulin (1991)
    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 20 (1991), S. 316-324 
    Details
    ISSN: 0886-1544
    Keywords: sperm motility ; cadmium ; flagellar curvature ; kinase A ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: Rat sperm, demembranated with 0.1% Triton X-100, were used to explore the reversal in flagellar curvature induced by calcium ion. As reported earlier (Lindemann and Goltz, Cell Motil. Cytoskeleton, 10:420-431, 1988), the radius of curvature of the flagellar midpiece of rat sperm is controlled by the free Ca2+ concentration. A reversal of the direction of curvature (judged by the asymmetric sperm head) takes place at ≈ 2.5 + 10-6 M free Ca2+.In our current study, the time course of the curvature change, after elevating free Ca2+ to 3.5 ± 10-4 M, was utilized to assess the effects of the cAMP-kinase A pathway on the calcium response. In addition, calmodulin's involvement in this response was explored using anti-calmodulin and Cd2+. The activity state of the sperm models (which could be directly influenced through cAMP) was found to control the rate of curvature change in response to increased free Ca2+. In the most extreme case, fully quiescent sperm did not respond to Ca2+ at all, and cAMP-primed sperm models completed the response to Ca2+ in two minutes or less.Anti-calmodulin demonstrated strong inhibitory effects on the curvature reversal. Cadmium ion was also extremely potent at blocking the response to Ca2+, completely eliminating the curvature reversal at 2 × 10-10 M free Cd2+.Based on these findings, it appears that the Ca2+-activated curvature reversal of rat sperm is potentiated by cAMP-dependent kinase and may be mediated through calmodulin.
    Additional Material: 7 Ill.
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    URL: http://dx.doi.org/10.1002/cm.970200407
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  • 23
    Electronic Resource
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    Masthead (1991)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 9 (1991) 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340090101
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  • 24
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    Design and synthesis of the pseudo-EF hand in calbindin D9K: Effect of amino acid substitutions in the α-helical regions (1991)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 9 (1991), S. 12-22 
    Details
    ISSN: 0887-3585
    Keywords: calbindin D9K ; pseudo-EF hand ; peptide synthesis ; peptide design ; calcium ; α-helix ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A series of 37-residue analogues of the pseudo-EF hand in bovine calbindin D9K has been synthesized by the solid phase method. In the presence of calcium an α-helical induction of up to 44% was observed for the peptide with the native sequence with a Kd for calcium binding of 0.35 mM. A number of amino acid substitutions have been carried out to study the packing of the two α-helices based on the crystal structure of the entire protein. Three strategies were employed: (1) replacement of the Leu residues, which in the crystal structure do not contribute to the hydrophobic interaction between the two helices, by Gln or Ala in order to control the orientation of the helix packing, (2) stabilization of the individual helix by introducing a Glu-…Lys+ salt bridge or by changing the N-terminal charge to compensate for the helix dipole moment, and (3) introduction of a disulfide bond between the two helices to help the packing of the helices.The mutants with the substitution of (Leu-30, Leu-32) to (Gln-30, Gln-32), (Gln-30, Ala-32), and (Ala-30, Ala-32) designed based on the strategy 1 do not show any affinity for calcium and have low α-helicity. The Leu-30 to Lys-30 mutant designed to form a salt bridge between the side chains of Glu-26 and Lys-30 has an apparent Kd for calcium of 6.8 mM. Kd of the N-terminal acetylated and succinylated mutants are 0.41 and 0.45 mM, respectively, and no increase in the α-helix content relative to that of the natural sequence peptide is observed. The disulfide containing mutants, namely Tyr-13, Leu-31 to Cys-31 and Tyr-13, Leu-31 to Cys-13, hCys-31, show apparent Kd values of 0.93 and 2.1 mM, respectively. The former mutant shows the highest α-helix content among the peptides studied in the presence and absence of calcium. While it is difficult to construct an isolated and rigid helix-loop-helix motif with peptides of this size, introduction of a disulfide bond proved to be effective for this purpose.
    Additional Material: 5 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340090103
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  • 25
    Electronic Resource
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    Rate of β-structure formation in polypeptides (1991)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 9 (1991), S. 23-27 
    Details
    ISSN: 0887-3585
    Keywords: polypeptides ; protein folding ; β-structure ; free energy barrier ; nucleation of folding ; rate-limiting step ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: An explanation is suggested for why a marginally stable β-structure folds extremely slowly; it is predicted that even a small increase in stability drastically accelerates β-folding. According to the theory, this folding is a first-order phase transition, and the rate-limiting step is nucleation. The rate-determining “nucleus” (transition state) is the smallest β-sheet that is sufficiently large to provide an overall free energy reduction during subsequent folding. If the stability of the β-structure is low, the nucleus is large and possesses a high free energy due to having a large perimeter. When the net stability of the final β-structure increases (due to either an increase of the β-sheet stability or a decrease in stability of the competing structures, e.g., α-helices), the size and energy of a nucleus decrease and the rate of folding increases exponentially. This must result in a fast folding of polypeptides enriched by β-forming residues (e.g., protein chains). The theory is developed for intramolecular β-structure, but it can also explain the overall features of intermolecular β-folding; it is applicable both to antiparallel and parallel β-sheets. The difference in folding of β-sheets, α-helices, and proteins is discussed.
    Additional Material: 4 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340090104
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  • 26
    Electronic Resource
    Electronic Resource
    Masthead (1991)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 9 (1991) 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340090201
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  • 27
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    Distribution and complementarity of hydropathy in mutisunit proteins (1991)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 9 (1991), S. 37-55 
    Details
    ISSN: 0887-3585
    Keywords: protein-protein interactions ; intersubunit binding ; hydropathy ; hydropathy complementarity ; protein interfaces ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A survey of 40 multisubunit proteins and 2 protein-protein complexes was performed to assay quantitatively the distribution of hydropathy among the exterior surface, interior, contact surface, and noncontact exterior surface of the isolated subunits. We suggest a useful way to present this distribution by using a “hydropathy level diagram.” Additionally, we have devised a function called “hydropathy complementarity” to quantitate the degree to which interacting surfaces have matching hydropathy distributions. Our survey revealed the following patters: (1) The difference in hydropathy between the interior and exterior of subunits is a fairly invariant quantity. (2) On average, the hydropathy of the contact surface is higher than that of the exterior surface, but is not greater than that of the protein as a whole. There was variation, however, among the proteins. In some instances, the contact surface was more hydrophilic than the noncontact exterior, and in a few cases the contact surface was as hydrophobic as the protein interior. (3) The average interface manifests significant hydropathy complementarity, signifying that proteins interact by placing hydrophobic centers of one surface against hydrophobic centers of the other surface, and by similarly matching hydrophilic centers. As a measure of recognition and specificity, hydropathy complementarity could be a useful tool for predicting correct docking of interacting proteins. We suggest that high hydropathy complementarity is associated with static inflexible interactions. (4) We have found that some subunits that bind predominantly through hydrophilic forces, such as hydrogen bonds, ionic pairs, and water and metal bridges, are involved in dynamic quaternary organization and allostery.
    Additional Material: 7 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340090106
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  • 28
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    Hydrogen bonds involving sulfur atoms in proteins (1991)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 9 (1991), S. 99-107 
    Details
    ISSN: 0887-3585
    Keywords: protein structure ; hydrogen bonding ; interactions of side chains ; cysteine ; methionine ; half-cystine ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Intrachain hydrogen bonds are a hallmark of globular proteins. Traditionally, these involve oxygen and nitrogen atoms. The electronic structure of sulfur is compatible with hydrogen bond formation as well. We surveyed a set of 85 high-resolution protein structures in order to evaluate the prevalence and geometry of sulfur-containing hydrogen bonds. This information should be of interest to experimentalists and theoreticians intersted in protein structure and protein engineering.
    Additional Material: 6 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340090204
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  • 29
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    Hexamers of subunit II from Limulus hemocyanin (a 48-mer) have the same quaternary structure as whole Panulirus hemocyanin molecules (1991)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 9 (1991), S. 240-247 
    Details
    ISSN: 0887-3585
    Keywords: hemocyanin ; Limulus ; Panulirus ; horseshoe crab ; spiny lobster ; molecular replacement ; X-ray ; crystallography ; protein structure ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Hemocyanins are copper-containing proteins that transport oxygen in a variety of invertebrates. Considerable evidence has accumulated that arthropodan hemocyanins are multimers of a fundamental hexameric unit. X-Ray crystallographic structure determination has revealed that the hemocyanin molecule from the spiny lobster Panulirus interruptus is a single hexamer having 32 point group symmetry. Using crystals of subunit II, one of 8 polypeptide types comprising the octahexameric hemocyanin of the horseshoe crab Limulus polyphemus, and the molecular replacement method for crystallographic phase determination we show that subunit II forms assemblies with the same hexameric quaternary structure as the whole Panulirus hemocyanin molecule. Observation of the same hexameric motif in two widely separated species provides strong additional evidence that this quaternary structural unit is a universal building block of arthropodan hemocyanins.
    Additional Material: 4 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340090403
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  • 30
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    Hydrophobic clustering in nonnative states of a protein: Interpretation of chemical shifts in NMR spectra of denatured states of lysozyme (1991)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 9 (1991), S. 248-266 
    Details
    ISSN: 0887-3585
    Keywords: protein folding ; unfolded state ; denatured state ; hydrophobic interactions ; ring current shift ; magnetization transfer NMR ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Chemical shifts of resonances of specific protons in the 1H NMR spectrum of thermally denatured hen lysozyme have been determined by exchange correlation with assigned native state resonances in 2D NOESY spectra obtained under conditions where the two states are interconverting. There are subtle but widespread deviations of the measured shifts from the values which would be anticipated for a random coil; in the case of side chain protons these are virtually all net upfield shifts and it is shown that this may be the averaged effect of interactions with aromatic rings in a partially collapsed denatured state. In a very few cases, notably that of two sequential tryptophan residues, it is possible to interpret these effects in terms of specific, local interresidue interactions. Generally, however, there is no correlation with either native state shift perturbations or with sequence proximity to aromatic groups. Diminution of most of the residual shift perturbations on reduction of the disulfide cross-links confirms that they are not simply effects of residues adjacent in the sequence. Similar effects of chemical denaturants, with the disulfides intact, demonstrate that the shift perturbations reflect an enhanced tendency to side chain clustering in the thermally denatured state. The temperature dependences of the shift perturbations suggest that this clustering is noncooperative and is driven by small, favorable enthalpy changes. While the extent of conformational averaging is clearly much greater than that observed for a homologous protein, α-lactalbumin, in its partially folded “molten globule” state, the results clearly show that thermally denatured lysozyme differs substantially from a random coil, principally in that it is partially hydrophobically collapsed.
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    URL: http://dx.doi.org/10.1002/prot.340090404
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  • 31
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    Topological mirror images in protein structure computation: An underestimated problem (1991)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 10 (1991), S. 22-32 
    Details
    ISSN: 0887-3585
    Keywords: distance geometry ; DISHAN ; DISGEO ; protein structure ; NMR ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: When calculating three-dimensional structures from NMR data, alternative solutions with very large RMS deviation can be obtained. Sometimes local or global inversions of the protein folding can be observed. We call these different solutions topological mirror images, as they keep the correct amino acid chirality. They are observed when the number of restraints is insufficient and represent different solutions from the same scalar information. Therefore they are common in small peptides where the NMR data are often limited and the secondary structure is not very well defined. They can also be observed in large molecules in regions of higher flexibility. In our experience the observation of topological mirror images is independent of the efficiency of sampling of the algorithm used. We present four examples of proteins with different size and folding. We also discuss ways to distinguish among the different solutions.
    Additional Material: 7 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340100104
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  • 32
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    The crystal structure of the “open” and the “closed” conformation of the flexible loop of trypanosomal triosephosphate isomerase (1991)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 10 (1991), S. 33-49 
    Details
    ISSN: 0887-3585
    Keywords: TIM ; molecular dynamics refinement ; loop movement ; conformational change ; crystal contacts ; sleeping sickness ; suramine ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Triosephosphate isomerase has an important loop near the active site which can exist in a “closed” and in an “open” conformation. Here we describe the structural properties of this “flexible” loop observed in two different structures of trypanosomal triosephosphate isomerase. Trypanosomal triosephosphate isomerase, crystallized in the presence of 2.4 M ammonium sulfate, packs as an asymmetric dimer of 54,000 Da in the crystallographic asymmetric unit. Due to different crystal contacts, peptide 167-180 (the flexible loop of subunit-1) is an open conformation, whereas in subunit-2, this peptide (residues 467-480) is in a closed conformation. In the closed conformation, a hydrogen bond exists between the tip of the loop and a well-defined sulfate ion which is bound to the active site of subunit-2. Such an active site sulfate is not present in subunit-1 due to crystal contacts. When the native (2.4 M ammonium sulfate) crystals are transferred to a sulfate-free mother liquor, the flexible loop of subunit-2 adopts the open conformation. From a closed starting model, this open conformation was discovered through molecular dynamics refinement without manual intervention, despite involving Cα shifts of up to 7 Å. The tip of the loop, residues 472, 473, 474, and 475, moves as a rigid body. Our analysis shows that in this crystal form the flexible loop of subunit-2 faces a solvent channel. Therefore the open and the closed conformations of this flexible loop are virtually unaffected by crystal contacts. The actual observed conformation depends only on the absence or presence of a suitable ligand in the active site.
    Additional Material: 16 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340100105
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    Cu(II)-Binding properties of a cytochrome c with a synthetic metal-binding site: His-X3-His in an α-helix (1991)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 10 (1991), S. 156-161 
    Details
    ISSN: 0887-3585
    Keywords: synthetic metalloproteins ; protein engineering ; iso-1-cytochrome c ; metal binding ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A metal-binding site consisting of two histidines positioned His-X3-His in an α-helix has been engineered into the surface of Saccharomyces cerevisiae iso-1-cytochrome c. The synthetic metal-binding cytochrome c retains its biological activity in vivo. Its ability to bind chelated Cu(II) has been characterized by partitioning in aqueous two-phase polymer systems containing a polymer-metal complex, Cu(II)IDA-PEG, and by metal-affinity chromatography. The stability constant for the complex formed between Cu(II)IDA-PEG and the cytochrome c His-X3-His site is 5.3 × 104 M-1, which corresponds to a chelate effect that contributes 1.5 kcal mol-1 to the binding energy. Incorporation of the His-X3-His site yields a synthetic metal-binding protein whose metal affinity is sensitive to environmental conditions that alter helix structure or flexibility.
    Additional Material: 4 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340100209
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    Electronic Resource
    Electronic Resource
    Proline in α-helix: Stability and conformation studied by dynamics simulation (1991)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 10 (1991), S. 219-228 
    Details
    ISSN: 0887-3585
    Keywords: proline ; α-helix ; kinked α-helix ; molecular dynamics ; computer simulation ; peptide conformation stability ; protein conformational stability ; amino acid substitution ; protein architecture ; helix start/stop signal ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Free-energy simulations have been used to estimate the change in the conformational stability of short polyalanine α-helices when one of the alanines is replaced by a proline residue. For substituting proline in the middle of the helix the change in free energy of folding (ΔΔG°) was calculated as 14 kJ/mol (3.4 kcal/mol), in excellent agreement with the one available experimental value. The helix containing proline was found to be strongly kinked; the free energy for reducing the angle of the kink from 40° to 15° was calculated, and found to be small. A tendency to alternate hydrogen bonding schemes was observed in the proline-containing helix. These observations for the oligopeptide agree well with the observation of a range of kink angles (18-35°) and variety of hydrogen bonding schemes, in the rare instances where proline occurs in helices in globular proteins. For substituting proline at the N-terminus of the helix the change in free energy of folding (ΔΔG°) was calculated as -4 kJ/mol in the first helical position (N1) and +6 kJ/mol in the second helical position (N2). The observed frequent occurrence of proline in position N1 in α-helices in proteins therefore has its origin in stability differences of secondary structure. The conclusion reached here that proline may be a better helix former in position N1 than (even) alanine, and thus be a helix initiator may be testable experimentally by measurements of fraction helical conformation of individual residues in oligopeptides of appropriate sequence. The relevance of these results in regards to the frequent occurrence of proline-containing helices in certain membrane proteins is discussed.
    Additional Material: 4 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340100306
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    Electronic Resource
    Electronic Resource
    Structure of ricin A-chain at 2.5 Å (1991)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 10 (1991), S. 251-259 
    Details
    ISSN: 0887-3585
    Keywords: Ricin A-chain ; x-ray structure ; active site ; conserved residues ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Ricin has been refined in a crystallographic sense to 2.5 Å resolution and the model for the A-chain (RTA) is described in detail. Because RTA is the first member of the class of plant toxins to be analyzed, this model probably defines the major structural characteristics of the entire family of these medically important proteins. Explanations are provided to rationalize amino acids that are conserved between RTA and a number of homologous plant and bacterial toxins. Eight invariant residues appear to be involved in creating or stabilizing the active site. In the active site Arg180 and Glu177 are hydrogen bonded to each other and also coordinate a water molecule; each of these groups may be important in the N-glycosidation reaction. Several other polar residues may play lesser roles in the mechanism, including tyrosines 80 and 123 and asparagines 78 and 209. A number of conserved hydrophobic residues are seen to cluster within several patches and probably drive the overall folding of the toxin molecule.
    Additional Material: 6 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340100309
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    Site-directed mutagenesis of ricin A-chain and implications for the mechanism of action (1991)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 10 (1991), S. 270-278 
    Details
    ISSN: 0887-3585
    Keywords: ricin A ; site-directed mutagenesis ; mechanism of action ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Ricin A-chain is an N-glycosidase that attacks ribosomal RNA at a highly conserved adenine residue. The enzyme is representative of a large family of medically significant proteins used in the design of anticancer agents and in the treatment of HIV infection. The x-ray structure has been used as a guide to create several active site mutations by directed mutagenesis of the cloned gene. Glu177 is a key catalytic residue, and conversion to Gln reduces activity 180-fold. Asn209 is shown to participate in substrate binding by kinetic analysis. Conversion to Ser increases Km sixfold but has no effect on kcat. Conversion of Tyr80 and Tyr123 to Phe decreases activity by 15- and 7-fold respectively. A mechanism of action is proposed that involves binding of the substrate adenine in a syn configuration that resembles the transition state; the putative oxycarbonium ion is probably stabilized by interaction with Glu177.
    Additional Material: 6 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340100311
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    Conformational changes in yeast phosphoglycerate kinase upon ligand binding: Fluorescence of a linked probe and chemical reactivity of genetically introduced cysteinyl residues (1991)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 10 (1991), S. 315-324 
    Details
    ISSN: 0887-3585
    Keywords: site-directed mutagenesis ; cysteine ; phosphoglycerate kinase ; IAEDANS ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The effects of ligands on the conformation of yeast phosphoglycerate kinase were explored by introducing cysteinyl residues at different positions in the molecule by site-directed mutagenesis. Thus several mutants were constructed, each containing a unique cysteinyl residue. Neither the conformation nor the enzyme activity was affected by the substitutions. The reactivity of the thiol groups and the fluorescence of N-acetyl-N′-(5-sulfo-1-naphtyl)ethylene-diamine covalently linked to these thiols were used to monitor the conformational changes induced upon ligand binding.It was found that the observed changes mainly involve the part of the protein located in the cleft, particularly the environment of residues 35 and 183. No alteration was observed on the external side of the protein. Only 3-Phosphoglycerate induced these conformational changes. However, when the fluorescent probe was attached to residue 377, the binding of the two substrates was required to induce a modification in the fluorescence of the probe. These results indicate that the substrates separately or together induce discrete molecular motions in phosphoglycerate kinase.
    Additional Material: 5 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340100405
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    Empirical solvation models can be used to differentiate native from near-native conformations of bovine pancreatic trypsin inhibitor (1991)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 10 (1991), S. 199-218 
    Details
    ISSN: 0887-3585
    Keywords: empirical potentials ; energy calculations ; surface area ; protein stability ; protein folding ; protein structure prediction ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Several hydration models for peptides and proteins based on solvent accessible surface area have been proposed previously. We have evaluated some of these models as well as four new ones in the context of near-native conformations of a protein. In addition, we propose an empirical site-site distance-dependent correction that can be used in conjuction with any of these models.The set of near-native structures consisted of 39 conformations of bovine pancreatic trypsin inhibitor (BPTI) each of which was a local minimum of an empirical energy function (ECEPP) in the absence of solvent. Root-mean-square (rms) deviations from the crystallographically determined structure were in the following ranges: 1.06-1.94 Å for all heavy atoms, 0.77-1.36 Å for all backbone heavy atoms, 0.68-1.33 Å for all α-carbon atoms, and 1.41-2.72 Å for all side-chain heavy atoms.We have found that there is considerable variation among the solvent models when evaluated in terms of concordance between the solvation free energy and the rms deviations from the crystallographically determined conformation. The solvation model for which the best concordance (0.939) with the rms deviations of the Cα atoms was found was derived from NMR coupling constants of peptides in water combined with an exponential site-site distance dependence of the potential of mean force.Our results indicate that solvation free energy parameters derived from nonpeptide free energies of hydration may not be transferrable to peptides. Parameters derived from peptide and protein data may be more applicable to conformational analysis of proteins. A general approach to derive parameters for free energy of hydration from ensemble-averaged properties of peptides in solution is described.
    Additional Material: 8 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340100305
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    Crystallographic refinement of ricin to 2.5 Å (1991)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 10 (1991), S. 240-250 
    Details
    ISSN: 0887-3585
    Keywords: ricin ; refinement ; molecular dynamics ; molecular models ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The plant cytotoxin ricin consists of two disulfide-linked chains, each of about 30,000 daltons. An initial model based on a 2.8 Å MIR electron density map has been refined against 2.5 Å data using rounds of hand rebuilding coupled with either a restrained least squares algorithm or molecular dynamics (XPLOR). The last model (9) has an R factor of 21.6% and RMS deviations from standard bond lengths and angles of 0.021 Å and 4.67°, respectively. Refinement required several peptide segments in the original model to be adjusted translationally along the electron density. A wide range of lesser changes were also made. The RMS deviation of backbone atoms between the original and model 9 was 1.89 Å. Molecular dynamics proved to be a very powerful refinement tool. However, tests showed that it could not replace human intervention in making adjustments such as local translations of the peptide chain. The R factor is not a completely satisfactory indicator of refinement progress; difference Fouriers, when observed carefully, may be a better monitor.
    Additional Material: 4 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340100308
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    Exploration of disorder in protein structures by X-ray restrained molecular dynamics (1991)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 10 (1991), S. 340-358 
    Details
    ISSN: 0887-3585
    Keywords: ribonuclease A ; crambin ; conformational disorder ; protein crystallography ; simulated annealing ; X-ray refinement ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Conformational disorder in crystal structures of ribonuclease-A and crambin is studied by including two independent structures in least-squares optimizations against X-ray data. The optimizations are carried out by X-ray restrained molecular dynamics (simulated annealing refinement) and by conventional least-squares optimization. Starting from two identical structures, the optimizations against X-ray data lead to significant deviations between the two, with rms backbone displacements of 0.45 Å for refinement of ribonuclease at 1.53 Å resolution, and 0.31 Å for crambin at 0.945 Å. More than 15 independent X-ray restrained molecular dynamics runs have been carried out for ribonuclease, and the displacements between the resulting structures are highly reproducible for most atoms. These include residues with two or more conformations with significant dihedral angle differences and alternative hydrogen bonding, as well as groups of residues that undergo displacements that are suggestive of rigid-body librations. The crystallographic R-values obtained are ≈ 13%, as compared to 15.3% for a comparable refinement with a single structure. Least-squares optimization without an intervening restrained molecular dynamics stage is sufficient to reproduce most of the observed displacements. Similar results are obtained for crambin, where the higher resolution of the X-ray data allows for refinement of unconstrained individual anisotropic temperature factors. These are shown to be correlated with the displacements in the two-structure refinements.
    Additional Material: 10 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340100407
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    Thermodynamics of ligand binding and denaturation for his64 mutants of tissue plasminogen activator kringle-2 domain (1991)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 11 (1991), S. 35-44 
    Details
    ISSN: 0887-3585
    Keywords: microcalorimetry ; thermal stability ; lysine binding ; site-directed ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The contribution of His64 to the function and stability of tissue plasminogen activator (t-PA) kringle-2 domain (His244 in t-PA numbering) has been studied by using microcalorimetric methods to compare the ligand binding and thermal denaturation behavior of wild-type kringle-2 and mutants having His64 replaced with Tyr or Phe. This site was examined because modeling studies1 suggested that the His64 side chain could play an important role in ligand binding by forming an ion-pair with the carboxylate of the ligand, L-lysine. Kringle-2 domains were expressed by secretion of the 174-263 portion of t-PA in E. coli and purified as previously described for the wild-type domain.2 Both mutant proteins retain affinity for L-lysine, although reduced three- to four-fold relative to wild-type, demonstrating that His64 does not interact with the ligand carboxylate through an ion-pair interaction or by hydrogen bonding. The H64Y substitution does result in an altered specificity of the lysine binding site with the mutant domain having greatest affinity for a ligand of 6.8 Å chain length, whereas the wild-type domain prefers an 8.8 Å long ligand. For both wild-type and mutant, the binding of the optimal chain length ligand is dominated by enthalpic effects (ΔH = -6,000 to -7,000 cal/mol) and TΔS accounts for 〈 15% of ΔG. In addition, the H64Y mutant differs from wild-type in the effect of ligand α-amino group modification on binding affinity. Based on examination of the x-ray structure recently determined for wild-type kringle-2, the specificity changes accompanying the H64Y substitution probably result from changes in side chain interactions in the lysine binding site. Thermal denaturation experiments show that the H64Y mutant is also more stable than the wild-type protein with the difference in stabilization free energy (ΔΔG) equal to 2.7 kcal/mol at 25°C and pH 3. The increased stability of the mutant appears to be related to the difference in hydrophobicity between His and Tyr.
    Additional Material: 8 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340110105
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    Electronic Resource
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    Masthead (1991)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 11 (1991) 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340110201
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    Effect of urey-bradley-shimanouchi force field on the harmonic dynamics of proteins (1991)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 11 (1991), S. 120-132 
    Details
    ISSN: 0887-3585
    Keywords: normal mode analysis ; potential energy function ; Lys-15 ; Arg-17 residues ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A normal mode analysis of bovine pancreatic trypsin inhibitor is carried out by using a Urey-Bradley-Shimanouchi potential energy function. The density of vibrational states, the magnitudes, and time scales of the atomic fluctuations are compared with experimental and theoretical results obtained by the more commonly used potential energy functions. The atomic fluctuations of Lys-15 are subject to extensive considerations as this residue is buried in the trypsin specificity pocket. It is found that Arg-17 is likely to be of importance in order to understand the way BPTI binds on trypsin.
    Additional Material: 6 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340110205
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    Asymmetric inclusion by de novo designed proteins: Fluorescence probe studies on amphiphilic α-helix bundles (1991)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 11 (1991), S. 133-141 
    Details
    ISSN: 0887-3585
    Keywords: fluorescence depolarization ; coiled-coil ; induced circular dichroism ; exciton chirality ; ANS ; acridine orange ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The inclusion feature and supersecondary structure of the de novo designed proteins which are constructed with several amphiphilic α-helices and flexible linkage parts were investigated with fluorescence probes. Five types of small proteins (or peptides) have been designed, which are composed of 2, 3, 4, 4, and 6 helices, respectively, and are linked with only linear junctions except for one of 4-helix proteins. All of these proteins have inclusion ability for hydrophobic fluorophores. Further, by the analysis of fluorescence polarization anisotropy, it was suggested that these proteins include guest molecules in compact helix bundles constructed with about 4 helices. Asymmetric inclusion of both monomer and stacked dimer of acridine orange derivatives was found by means of induced circular dichroism except for the 4-helix protein with cross-junction. The chirality of the included dimer proved to be in accordance with the chiral sense of α-helical coiled-coil. The 6-helix protein has especially high efficiency in inclusion for any fluorophores examined in this study and brings about a significant blue-shift of maximal emission for 8-anilino-1-naphthalenesulfonate.
    Additional Material: 11 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340110206
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    Collective motions in proteins: A covariance analysis of atomic fluctuations in molecular dynamics and normal mode simulations (1991)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 11 (1991), S. 205-217 
    Details
    ISSN: 0887-3585
    Keywords: molecular dynamics ; normal modes ; collective motions ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A method is described for identifying collective motions in proteins from molecular dynamics trajectories or normal mode simulations. The method makes use of the covariances of atomic positional fluctuations. It is illustrated by an analysis of the bovine pancreatic trypsin inhibitor. Comparison of the covariance and cross-correlation matrices shows that the relative motions have many similar features in the different simulations. Many regions of the protein, especially regions of secondary structure, move in a correlated manner. Anharmonic effects, which are included in the molecular dynamics simulations but not in the normal analysis, are of some importance in determining the larger scale collective motions, but not the more local fluctuations. Comparisons of molecular dynamics simulations in the present and absence of solvent indicate that the environment is of significance for the long-range motions.
    Additional Material: 7 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340110305
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    Analysis of the steric strain in the polypeptide backbone of protein molecules (1991)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 11 (1991), S. 223-229 
    Details
    ISSN: 0887-3585
    Keywords: protein structure ; crystal structure ; dihedral angles ; cis peptides ; protein active sites ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The extent to which local strain is present in the polypeptide backbone of folded protein molecules has been examined. The occurrence of steric strain associated with nonproline cis peptide bonds and energetically unfavorable main chain dihedral angles can be identified reliably from the well ordered parts of high resolution, refined crystal structures. The analysis reveals that there are relatively few sterically strained features. Those that do occur are located overwhelmingly in regions concerned with function. We attribute this to the greater precision necessary for ligand binding and catalysis, compared with the requirements of satisfactory folding.
    Additional Material: 3 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340110307
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    Crystallization and preliminary X-ray diffraction studies of human salivary α-amylase (1991)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 11 (1991), S. 230-232 
    Details
    ISSN: 0887-3585
    Keywords: parotid saliva ; enzyme ; crystals ; X-ray analysis ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Nonglycosylated α-amylase, a major component of human parotid saliva, has been crystallized by the vapor diffusion technique using 2-methyl-2,4-pentanediol as the precipitant in the presence of CaCl2 at pH 9.0. The crystals are orthorhombic, space group P212121 with unit cell dimensions of a = 53.3, b = 75.8, and c = 138.1 Å. The asymmetric unit contains one amylase molecule. The solvent content is 54%. The crystals are stable to X-rays and diffract up to 2.8 Å and appear to be suitable for X-ray diffraction studies.
    Additional Material: 2 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340110308
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    Protein-protein recognition analyzed by docking simulation (1991)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 11 (1991), S. 271-280 
    Details
    ISSN: 0887-3585
    Keywords: antigen-antibody recognition ; protease-inhibitor complexes ; simulated annealing ; energy refinement ; docking algorithm ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Antibody-lysozyme and protease-inhibitor complexes are reconstituted by docking lysozyme as a rigid body onto the combining site of the antibodies and the inhibitors onto the active site of the proteases. Simplified protein models with one sphere per residue are subjected to simulated annealing using a crude energy function where the attractive component is proportional to the interface area. The procedure finds clusters of orientations in which a steric fit between the two protein components is achieved over a large contact surface. With five out of six complexes, the native structure of the complexes determined by X-ray crystallography is among those retained. Docked complexes are then subjected to conformational energy refinement with full atomic detail. With Fab HyHEL 5 and lysozyme, a native-like complex has the lowest refined energy. It can also be retrieved when starting with the X-ray structure of free lysozyme. However, some non-native complexes cannot be rejected: they form large interfaces, have a large number of H-bonds, and few unpaired polar groups. While these are necessary features of protein-protein recognition, they are not sufficient in determining specificity.
    Additional Material: 5 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340110406
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    Computer design of bioactive molecules: A method for receptor-based de novo ligand design (1991)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 11 (1991), S. 314-328 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The design of molecules to bind specifically to protein receptors has long been a goal of computer-assisted molecular design. Given detailed structural knowledge of the target receptor, it should be possible to construct a model of a potential ligand, by algorithmic connection of small molecular fragments, that will exhibit the desired structural and electrostatic complementarity with the receptor. However, progress in this area of receptorbased, de novo ligand design has been hampered by the complexity of the construction process, in which potentially huge numbers of structures must be considered. By limiting the scope of the structure-space examined to one particular class of ligands-namely, peptides and peptide-like compounds-the problem complexity has been reduced to the point that successful, de novo design is now possible. The methodology presented employs a large template set of amino acid conformations which are iteratively pieced together in a model of the target receptor. Each stage of ligand growth is evaluated according to a molecular mechanicsbased energy function, which considers van der Waals and coulombic interactions, internal strain energy of the lengtheining ligand, and desolvation of both ligand and receptor. The search space is managed by use of a data tree which is kept under control by pruning according to the energy evaluation. Ligands grown by this procedure are subjected to follow-up evaluation in which an approximate binding enthalpy is determined. This methodology has proven useful as a precise model-builder and has also shown the ability to design bioactive ligands.
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    URL: http://dx.doi.org/10.1002/prot.340110409
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  • 50
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    Secondary structure-based profiles: Use of structure-conserving scoring tables in searching protein sequence databases for structural similarities (1991)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 10 (1991), S. 229-239 
    Details
    ISSN: 0887-3585
    Keywords: profile method ; sequence comparison ; secondary structure-based profile ; protein sequence data bases ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The profile method, for detecting distantly related proteins by sequence comparison, has been extended to incorporate secondary structure information from know X-ray structures. The sequence of a known structure is aligned to sequences of other members of a given folding class. From the known structure, the secondary structure (α-helix, β-strand or “other”) is assigned to each position of the aligned sequences. As in the standard profile method,1 a position-dependent scoring table, termed a profile, is calculated from the aligned sequences. However, rather than using the standard Dayhoff mutation table in calculating the profile, we use distinct amino acid mutation tables for residues in α-helices, β-strands or other secondary structures to calculate the profile. In addition, we also distinguish between internal and external residues. With this new secondary structure-based profile method, we created a profile for eight-stranded, antiparallel β barrels of the insecticyanin folding class. It is based on the sequences of retinol-binding protein, insecticyanin and β-lactoglobulin. Scanning the sequence database with this profile, it was possible to detect the sequence of avidin. The structure of streptavidin is known, and it appears to be distantly related to the antiparallel β barrels. Also detected is the sequence of complement component C8, which we therefore predict to be a member of this folding class.
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    URL: http://dx.doi.org/10.1002/prot.340100307
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    A model for human cardiac troponin C and for modulation of its Ca2+ affinity by drugs (1991)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 11 (1991), S. 79-94 
    Details
    ISSN: 0887-3585
    Keywords: TnC ; calmodulin ; trifluoperazine ; bepridil ; pimobendan ; calcium sensitivity ; inotropic ; muscle contraction ; energy minimization ; binding energy ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Calcium sensitizers are drugs which increase force development in striated muscle by sensitizing myofilaments to Ca2+. This can happen by increasing Ca2+ affinity of the regulatory domain of Ca2+ binding protein troponin C. High resolution crystal structures of two calcium binding proteins, calmodulin (Babu et al.: J. Mol. Biol. 203:191-204, 1988) and skeletal troponin C (Satyshur et al.: J. Biol. Chem. 263:1628-1647, 1988; Herzber et al.: J. Mol. Biol. 203:761-779, 1988), have recently been published. This makes it possible to model in detail the calcium-sensitizing action of drugs on troponin C.In this study a model of human cardiac troponin C in three-calcium state has been constructed. When calcium is bound to calcium site II of cardiac troponin C an open conformation of the protein results, which has a hydrophobic pocket surrounded by a few polar side chains. Complexation of three drugs, trifluoperazine, bepridil, and pimobendan, to the hydrophobic pocket is studied using energy minimization techniques. Two different binding modes are found, which differ in the location of a strong electrostatic interaction. In analogy with the crystal structure of skeletal troponin C it is hypothezed that in cardiac troponin C an interaction occurs between Gln-50 and Asp-88, which has a long-range effect on calcium binding. The binding modes of drugs, where a strong interaction with Asp-88 exists, can effectively prevent the interaction between Asp-88 and Gln-50 in the protein, and are proposed to be responsible for the calcium-sensitizing properties of the studied drugs.
    Additional Material: 10 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340110202
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    Thiol proteases and aldehyde dehydrogenases: Evolution from a common thiolesterase precursor? (1991)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 11 (1991), S. 176-183 
    Details
    ISSN: 0887-3585
    Keywords: active site model ; thiolester mechanism ; multiple alignment ; three-dimensional correlations ; conservation of glycines ; conservation of functional cysteines ; conservation of salt bridges ; exon boundaries ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The C-terminal 222 residues of human liver aldehyde dehydrogenase can be aligned with the C-terminal 226 residues of a thiol protease from Dictyostelium discoideum to yield 47 residue identities, including matching active site cysteine residues. A multiple alignment with three more aldehyde dehydrogenases and three more thiol proteases yields three regions with clustered residue similarities. In the tertiary structure of papain, these three regions are in close proximity although widely separated in primary structure, and many conserved residues are located in the active site groove. The three-dimensional relationships, the common thiol ester mechanisms of the enzymes, the locations of exon boundaries in the dehydrogenase and protease genes, and the conservation of internal salt-bridging and disulfide-paired residues in papain, all appear compatible with the hypothesis of an ancestral relationship between thiol proteases and aldehyde dehydrogenases.
    Additional Material: 2 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340110303
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    Alterations in microtubule assembly caused by the microtubule-active drug LY195448 (1991)
    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 19 (1991), S. 9-17 
    Details
    ISSN: 0886-1544
    Keywords: β-tubulin ; CHO ; taxol ; colcemid ; drug resistance ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: LY195448 is an experimental drug that blocks cells at metaphase (Boder et al.:Microtubules and Microtubule Inhibitors 1985: 353-361, 1985). A 4 hour exposure of NRK cells to a drug concentration of 46 μM (15 μg/ml) increased the number of mitotic cells in the population from 4.9% to 18.5%. Examination of treated cells by immunofluorescence showed increased numbers of cells blocked at prometaphase, with short microtubules extending from the spindle pole to the kinetochores. The cytoskeleton of interphase cells remained intact at these concentrations. However, the number of microtubules appeared to be reduced, and those that remained appeared kinkier and curled, particularly toward the periphery of the cells. When cytoskeletal microtubules of NRK cells were depolymerized with nocodazole, they reassembled within minutes of transfer to drug-free media. However, nocodazole-treated cells transferred to fresh media containing 15 μg/ml of LY 195448 required 2-3 times longer to reassemble cytoplasmic microtubules. Previously isolated Chinese hamster ovary cell microtubule mutants resistant to either taxol or Colcemid were tested for cross-resistance to this drug. Cell lines resistant to the depolymerizing drug Colcemid exhibited increased resistance to LY 195448 compared to wild-type cells, whereas taxol resistant cell lines were more sensitive. Of eleven newly isolated mutant CHO cell lines selected for increased resistance to LY 195448, seven exhibited an altered β-tubulin protein by two-dimensional polyacrylamide gel electrophoresis. These 11 cell lines also showed a heterogenous pattern of resistance to several microtubule-active drugs. These data demonstrate that LY 195448 is cytotoxic to mammalian cells because it inhibits microtubule assembly, most likely through a direct interaction with tubulin.
    Additional Material: 6 Ill.
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    URL: http://dx.doi.org/10.1002/cm.970190103
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    In vitro migration of Hydra nematocytes: The influence of the natural extracellular matrix (the mesoglea), of collagen type IV and type I, laminin, and fibronectin on cell attachment, migration parameters, and on patterns of cytoskeletal proteins (1991)
    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 20 (1991), S. 215-227 
    Details
    ISSN: 0886-1544
    Keywords: cell migration ; extracellular matrix ; cytoskeleton ; nematocytes ; Hydra ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: We have established an in vitro migration system for nematocytes of the fresh water cnidarian Hydra. Nematocytes display a migratory behavior on isolated sheets of the naturally occurring extracellular matrix, the mesoglea, as well as on surfaces coated with collagen type IV or laminin. Cell behavior was analyzed using video microscopic techniques. Average migration speeds of nematocytes on the mesoglea (140 μm/hr) were lower than values reported from in vivo studies (500 μm/hr). Cells on collagen IV moved at about the same average speed (115 μm/hr) as nematocytes on the natural extracellular matrix; those on laminin were considerably slower (20 μm/hr). Attachment but no movement of cells was found on glass or on surfaces coated with collagen type I and fibronectin. In addition to the differential migration speeds, nematocytes displayed distinct morphologies depending on the substratum. In order to elucidate the causes of the observed cell shape and behavior modulations induced by the offered substratum, the arrangement of major cytoskeletal proteins in Hydra nematocytes during the in vitro migration or attachment was investigated. The pattern of F-actin, myosin, and tubulin was determined by immunocytochemical techniques and confocal laser scanning microscopy in nematocytes moving on the mesoglea, on collagen IV, and on laminin, or in cells attaching to fibronectin. We found that the distribution of the cytoskeletal proteins was strikingly different in moving and in stationary cells. The patterns of cytoskeletal proteins in all nematocytes moving on the different substrata, however, was quite similar.
    Additional Material: 8 Ill.
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    URL: http://dx.doi.org/10.1002/cm.970200305
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    Regulation of growth cone motility (1991)
    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 20 (1991), S. 267-271 
    Details
    ISSN: 0886-1544
    Keywords: Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/cm.970200402
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    Properties of the spectrin-like structural element of smooth-muscle α-actinin (1991)
    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 20 (1991), S. 242-248 
    Details
    ISSN: 0886-1544
    Keywords: α-actinin ; spectrin ; α-helical coiled-coil ; segmental mobility ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: The fragment of smooth muscle α-actinin, comprising the four spectrin-like structural repeating units, has a high α-helix content, similar to that of spectrin, and a hydrodynamic frictional coefficient, indicative of an elongated, probably bent or kinked rod-like structure, as found for spectrin dimer and tetramer. The fragment exists in solution as an extremely stable dimer, which is dissociated only under denaturing conditions and is much more resistant to dissociation by urea than is the spectrin heterodimer. High-resolution proton magnetic resonance spectra reveal that a part of the polypeptide chain gives rise to sharp resonances; this is also true of spectrin and it implies that the individual structural repeating units contain segmentally mobile elements, which may be required to generate the elastic properties of the spectrin family of proteins. Again like spectrin, the α-actinin fragment contains multiple binding sites for long-chain fatty acids, as revealed by quenching of tryptophan fluorescence by 2-bromostearate (though not by 9(10)-bromostearate). The results point to extensive structural and functional similarities between the repeating units of all the proteins of the spectrin family.
    Additional Material: 4 Ill.
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    URL: http://dx.doi.org/10.1002/cm.970200307
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    Conserved β-tubulin binding domain for the microtubule-associated motors underlying sperm motility and fast axonal transport (1991)
    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 20 (1991), S. 249-262 
    Details
    ISSN: 0886-1544
    Keywords: microtubule-based motility ; dynein ; kinesin ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: An antiserum against tubulin, NS20, has been previously shown to inhibit anterograde and retrograde axonal transport by 50% in vivo and in vitro. We report here that Protein A purified NS20 antibodies also attenuate sperm motility by 50% in demembranated sea urchin sperm. This inhibition is absorbed out by preincubating the NS20 antibodies with a biochemically purified porcine microtubule preparation, with recombinant Trypanosoma β- (but not α-) tubulin and most specifically, with a 37 amino acid (a.a.) synthetic peptide corresponding to a domain near (but not including) the porcine β-tubulin C terminus. Furthermore, addition of this β-tubulin peptide alone is sufficient to attenuate motility by 50% in demembranated sperm, indicating that this critical 37a.a. NS20 antigen is a motor binding domain. Together, the results suggest that at least two phenotypically distinct forms of microtubule-based motility, axonal transport and flagellar beating, are homologous at the fundamental level of the microtubule domains (the β-tubulin peptide and we suggest a distinct but similarly located α-tubulin domain) mediating the attachment of tubulin-associated motors.
    Additional Material: 9 Ill.
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    URL: http://dx.doi.org/10.1002/cm.970200308
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    Myosin IB null mutants of Dictyostelium exhibit abnormalities in motility (1991)
    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 20 (1991), S. 301-315 
    Details
    ISSN: 0886-1544
    Keywords: DMIB- cells ; F-actin ; cAMP ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: Cellular and intracellular motility are compared between normal Dictyostelium amoebae and amoebae lacking myosin IB (DMIB-). DMIB- cells generate elongated cell shapes, form particulate-free pseudopodia filled with F-actin, and exhibit an anterior bias in pseudopod extension in a fashion similar to normal amoebae. DMIB- cells also exhibit a normal response to the addition of the chemoattractant cAMP, including a depression in cellular and intracellular particle velocity, depolymerization of F-actin in pseudopodia, and a concomitant increase in cortical F-actin. DMIB- cells do, however, form lateral pseudopodia roughly three times as frequently as normal cells, turn more often, and exhibit depressed average instantaneous cell velocity. DMIB- cells also exhibit a decrease in the average instantaneous velocity of intracellular particle movement and an increase in the degree of randomness in particle direction. These findings indicate that if there is functional substitution for myosin IB by other myosin I isoforms, it is at best only partial, with myosin IB being necessary for maintenance of the normal rate and persistence of cellular translocation, suppression of lateral pseudopod formation and subsequent turning, rapid intracellular particle motility, and the normal anterograde bias of intracellular particle movement. Furthermore, it is likely that the behavioral abnormalities observed here for DMIB- cells underlie the delay in the onset of chemotactic aggregation, the increase in the time required to complete streaming, and the abnormalities in morphogenesis exhibited by DMIB- cells.
    Additional Material: 9 Ill.
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    URL: http://dx.doi.org/10.1002/cm.970200406
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    Disruption of the golgi apparatus with brefeldin a does not destabilize the associated detyrosinated microtubule network (1991)
    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 20 (1991), S. 289-300 
    Details
    ISSN: 0886-1544
    Keywords: stable microtubules ; detyrosinated α-tubulin ; microtubule organizing center ; trans Golgi network ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: Stable subsets of microtubules (MTs) are often enriched in detyrosinated α-tubulin. Recently it has been found that the Golgi apparatus is associated with a subset of relatively stable MTs and that detyrosinated MTs colocalize spatially and temporally with the Golgi apparatus in several cell lines. To determine whether the Golgi apparatus actively stabilizes associated MTs and thus allows their time-dependent detyrosination, we have used the drug brefeldin A (BFA) to disrupt the Golgi apparatus and have monitored changes in the Golgi apparatus and MT populations using simultaneous immunofluorescence and fluorescent lectin microscopy. We found that although BFA caused the Golgi apparatus to completely redistribute to the endoplasmic reticulum (ER), the detyrosinated MTs were not disrupted and remained in a juxtanuclear region. By Western blot analysis we found that even after 6 h of continuous exposure of cells to BFA, there was no detectable reduction in the level of detyrosinated α-tubulin. Simultaneous treatment with nocodazole and BFA led to a complete disruption of all MTs and normal Golgi structure/organization. Upon removal of nocodazole in the continued presence of BFA, we found that the detyrosinated MTs reformed in a compact juxtanuclear location in the absence of an intact Golgi complex. Finally, we found that the detyrosinated MTs colocalized precisely with a BFA-resistant structure that binds to the lectin, wheat germ agglutinin. We conclude that the juxtanuclear detyrosinated MTs are not actively stabilized by association with BFA-sensitive Golgi membranes. However, another closely associated structure which binds wheat germ agglutinin may serve to stabilize the juxtanuclear MTs. Alternatively, the MT organizing center (MTOC) and/or MT-associated proteins (MAPs) may organize and stabilize the juxtanuclear detyrosinated MTs.
    Additional Material: 5 Ill.
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    URL: http://dx.doi.org/10.1002/cm.970200405
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    Examination of the calcium-modulated protein S100α and its target proteins in adult and developing skeletal muscle (1991)
    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 20 (1991), S. 325-337 
    Details
    ISSN: 0886-1544
    Keywords: fiber type ; immunohistochemistry ; myofibril ; Northern blot analysis ; radioimmunoassay ; sarcoplasmic reticulum ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: In this study radioimmunoassay, immunohistochemistry, Northern blot analysis, and a gel overlay technique have been used to examine the level, subcellular distribution, and potential target proteins of the S100 family of calcium-modulated proteins in adult and developing rat skeletal muscles. Adult rat muscles contained high levels of S100 proteins but the particular form present was dependent on the muscle type: cardiac muscle contained exclusively S100α, slow-twitch skeletal muscle fibers contained predominantly S100α, vascular smooth muscle contained both S100α and S100β, and fast-twitch skeletal muscle fibers contained low but detectable levels of S100α and S100β. While the distribution of S100 mRNAs paralled the protein distribution in all muscles there was no direct correlation between the mRNA and protein levels in different muscle types, suggesting that S100 protein expression is differentially regulated in different muscle types. Immunohistochemical analysis of the cellular distribution of S100 proteins in adult skeletal muscles revealed that S100α staining was associated with muscle cells, while S100β staining was associated with nonmuscle cells. Radioimmunoassays of developing rat skeletal muscles demonstrated that all developing muscles contained low levels of S100α at postnatal day 1 and that as development proceeded the S100α levels increased. In contrast to adult muscle, S100α expression as confined to fast-twitch fibers in developing skeletal muscle until postnatal day 21. At postnatal day 1, developing contractile elements were S100α positive, but no staining periodicity was detectable. At postnatal day 21, S100α exhibited the same subcellular localization as seen in the adult: colocalization with the A-band and/or longitudinal sarcoplasmic reticulum. Comparison of the S100α-binding protein profiles in fast- and slow-twitch fibers of various species revealed few, if any, species- or fiber type-specific S100 binding proteins. Isolated sarcoplasmic reticulum fractions and myo fibrils contained multiple S100α-hinding proteins. The colocalization of S100α and S100α-binding proteins with the contractile apparatus and sarcoplasmic reticulum suggest that S100α may regulate excitation and/or contraction in slow-twitch fibers.
    Additional Material: 8 Ill.
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    URL: http://dx.doi.org/10.1002/cm.970200408
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    Masthead (1991)
    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 18 (1991) 
    Details
    ISSN: 0886-1544
    Keywords: Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/cm.970180401
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    Cell locomotion: New research tests old ldeas on membrane and cytoskeletal flow (1991)
    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 18 (1991), S. 245-257 
    Details
    ISSN: 0886-1544
    Keywords: lipid flow ; cytoskeleton ; actin ; microscopy ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: Recent studies on the mobility of membrane markers on crawling cells indicate that there is no long-range centripetal flow of membrane proteins or lipids during cell locomotion. In this article we reflect on the history of ideas about membrane flow in cells, and we discuss how these new findings will shift the focus of research in cell locomotion away from the cell surface to the molecular interactions and dynamics of the actin cytoskeleton.
    Additional Material: 4 Ill.
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    URL: http://dx.doi.org/10.1002/cm.970180402
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    Localization of the centrin-related 165,000-Mr protein of PtK2 cells during the cell cycle (1991)
    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 18 (1991), S. 1-14 
    Details
    ISSN: 0886-1544
    Keywords: centrin ; centrosome ; pericentriolar lattice ; pericentriolar material ; mitosis ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: In this study, we follow changes in localization of the centrin-related 165,000-Mr protein of PtK2 cells during the cell cycle. This protein is a component of a pericentriolar lattice that consists of pericentriolar satellites, pericentriolar matrix, and basal feet (Baron A.T., and J.L. Salisbury, J. Cell Biol. 107:2669-2678, 1988). By immunofluorescence microscopy, the 165,000-Mr protein is seen as a constellation of pericentrosomal spots. We observe that cells in late G1 and S are characterized by a dense centrosomal focus of spots with additional spots dispersed throughout the cytoplasm. In G2, one bright centrosomal focus of clustered spots is observed. As the cells proceed through prophase this single focus divides, forming two foci that move toward opposite sides of the nucleus. During prometaphase, each polar focus of spots disperses. At metaphase, the spots are distributed throughout each half-cytoplast from the poles to the chromosomes. During anaphase chromosome movement, some spots are seen beside and behind the trailing chromosome arms while others are clustered at the poles. At telo-phase, pericentrosomal spots radiate from the poles to surround each mass of chromatin. In early G1, pericentrosomal spots surround each newly formed nucleus. We conclude that the 165,000-Mr protein is a dynamic component of both the centrosome (pericentriolar matrix) and the mitotic apparatus (spindle matrix).
    Additional Material: 8 Ill.
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    URL: http://dx.doi.org/10.1002/cm.970180102
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    Announcement (1991)
    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 18 (1991), S. 76-76 
    Details
    ISSN: 0886-1544
    Keywords: Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/cm.970180108
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    Chromatin motion in neuronal interphase nuclei: Changes induced by disruption of intermediate filaments (1991)
    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 18 (1991), S. 63-75 
    Details
    ISSN: 0886-1544
    Keywords: nuclear rotation ; nucleus ; nuclear lamina ; acrylamide ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: Motion of nucleoli within interphase nuclei, known as nuclear rotation, may be used as a measure of motion of chromatin domains within the global confines of the nucleus. Mechanisms by which chromatin domains are transposed remain enigmatic. It has been established that nuclei are anchored by a network of intermediate filaments, structural proteins which share epitopes with nuclear lamins and possibly representing a constraint on nuclear rotation. It is postulated that selective removal of this constraint, by acrylamide, would result in increased chromatin motion. Mean rates of nucleolar displacement were quantified in neurons, in vitro. Nuclear rotation increased from a mean control rate of 0.102 ± 0.002 μm/min (n = 52) to a maximum mean rate of 0.207 ± 0.026 μm/min (n = 11), after 23 hr of exposure to 4 mM acrylamide. Despite this significant increase in motion of intranuclear domains, cytoplasmic structures in the immediate juxtanuclear area did not exhibit increases in rates of motion. Immunocy-tochemistry was used to visualize cytoskeletal structures and to assay selective disruption of neurofilaments by acrylamide. Increased rates of chromatin motion coincided with breakdown of the intermediate filament network. Ultrastructural analyses showed that the increase in chromatin motion induced by acrylamide was also associated with a significant (P 〈 0.005) change in the thickness of the nuclear lamina, decreasing from 20.9 ± 5.10 nm (n = 159) in controls to 18.9 ± 3.1 nm (n = 148), to 19.5 ± 3.6 nm (n = 240) and to 16.1 ± 4.4 nm (n = 103) at 4, 8 and 22 hr exposure, respectively. Moreover, the number of mito-chondria per unit area changed significantly (P 〈 0.0001) with exposure to acrylamide, increasing from 9.1 ± 2.2 mitochondrial profiles in controls to 16.5 ± 5.3 profiles after 22 hr exposure to acrylamide. Distribution of other cytoskel-etal components, actin and microtubules, was not altered and does not appear to play a significant role in the observed increase in rates of nuclear rotation. We conclude that the removal of the damping effects on chromatin motion normally imposed by the nuclear lamina and by intermediate filaments results in increased chromatin motion.
    Additional Material: 9 Ill.
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    URL: http://dx.doi.org/10.1002/cm.970180107
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    Production and specificity of monoclonal antibodies against calmodulin from dictyostelium discoideum (1991)
    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 18 (1991), S. 113-122 
    Details
    ISSN: 0886-1544
    Keywords: calcium ; immunoblot ; PVDF membrane ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: Monoclonal antibodies were raised against calmodulin purified from Dictyostelium discoideum. To increase its antigenicity, the calmodulin was conjugated to keyhole limpet hemocyanin; mice were immunized with the conjugate. Hybridomas producing antibodies against calmodulin were identified by screening culture supernatants with calmodulin coupled to bovine serum albumin. The specificity of antibodies from hybridoma culture supernatants was tested by Western blot of Dictyostelium cell lysates. For this purpose, methods were developed that permitted sensitive detection of calmodulin bound to membranes. The key elements of the blotting protocol were use of PVDF membrane, transfer conducted in phosphate buffer, and glutaraldehyde fixation after transfer. These methods permitted detection of as little as 0.1 ng of calmodulin spotted directly onto the membrane, or 10 ng transferred from an SDS polyacrylamide gel. Ten calmodulin-specific antibodies were identified; most of these reacted preferentially with the calcium-containing form of Dictyostelium calmodulin. Several of the monoclonal antibodies cross-reacted with calmodulin from bovine brain.
    Additional Material: 6 Ill.
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    URL: http://dx.doi.org/10.1002/cm.970180206
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    Microtubules in the fission yeast Schizosaccharomyces pombe contain only the tyrosinated form of α-tubulin (1991)
    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 18 (1991), S. 86-93 
    Details
    ISSN: 0886-1544
    Keywords: tubulin ; detyrosination ; cdc mutants ; D2O ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: The state of tubulin tyrosination in the fission yeast Schizosaccharomyces pombe was investigated using a combination of indirect immunofluorescence microscopy and Western blotting. Antibodies specific for the tyrosinated form of α-tubulin stained all microtubule arrays in wild type cells and recognised the two α-tubulin polypeptides in Western blots of cell extracts enriched for tubulin by DEAE-Sephadex chromatography. Antisera that specifically recognised the detyrosinated, glu, form, on the other hand, gave consistently negative results, both in cells undergoing rapid exponential growth and in those allowed to accumulate in stationary phase. Neither the “ageing” of microtubules, by arresting cells at different points (late G1 or G2/M) in the cell division cycle, nor stabilising them, using D2O, lead to any detectable tubulin detyrosination. These results suggest that S. pombe lacks the carboxypeptidase that carries out the tubulin detyrosination reaction. This is the first report of an organism that possesses the correct C-terminal α-tubulin sequence yet fails to carry out this post-translational modification. The implication of this novel finding for the biological role of these events is discussed.
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    URL: http://dx.doi.org/10.1002/cm.970180203
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    Calcium sensors in sea urchin sperm flagella (1991)
    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 18 (1991), S. 123-130 
    Details
    ISSN: 0886-1544
    Keywords: calmodulin ; motility ; spermatozoa ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: The asymmetry of ATP-reactivated flagellar bending waves of Triton-demem-brated sea urchin spermatozoa has been measured over a range of free Ca2+ ion concentrations from 10-9 to 10-4 M. Detailed examination of the gradual response of asymmetry to Ca2+ ion concentration over this wide range indicates the presence of two Ca2+ sensors. A high-affinity sensor operates at Ca2+ concentrations near 10-7.5 M. A lower-affinity sensor operates at Ca2+ concentrations above 10-6 M, in the typical range for calmodulin-mediated responses. Incubation of demembranated sperm flagella at high Ca2+ concentrations to release calmodulin is required to enable these Ca2+ responses to be observed. This treatment also causes a decrease in the apparent affinity of the flagella for cal-modulin, as determined by measuring the increase in asymmetry in response to addition of exogenous calmodulin at low Ca2+ concentration.
    Additional Material: 6 Ill.
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    URL: http://dx.doi.org/10.1002/cm.970180207
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    Chromosome fiber dynamics and congression oscillations in metaphase PtK2 Cells at 23°C (1991)
    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 18 (1991), S. 131-142 
    Details
    ISSN: 0886-1544
    Keywords: mitosis ; microtubules ; tubulin incorporation ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: A bioriented chromosome is tethered to opposite spindle poles during congression by bundles of kinetochore microtubules (kMts). At room temperature, kinetochore fibers are a dominant component of mitotic spindles of PtK2 cells. PtK2 cells at room temperature were injected with purified tubulin covalently bound to DTAF and congression movements of individual chromosomes were recorded in time lapse. Congression movements of bioriented chromosomes between the poles occur over distances of 4.5 μm or greater. DTAF-tubulin injection had no effect on either the velocity or extent of these movements. Other cells were lysed, fixed, and the location of DTAF-tubulin incorporation was detected from digitally processed images of indirect immunofluorescence of an antibody to DTAF. Microtubules were labeled with an anti-beta tubulin antibody. At 2-5 minutes after injection, concentrated DTAF-tubulin staining was seen in the kinetochore fibers proximal to the kinetochores; a low concentration of DTAF-tubulin staining occurred at various sites through the remaining length of the fibers toward the pole. Kinetochore fibers in the same cell displayed different lengths (0.2 to 4 μm) of concentrated DTAF-tubulin incorporation proximal to the kinetochore, as did sister kinetochore fibers. Ten minutes after injection, the lengths of DTAF-containing chromosomal fibers were greater than expected if incorporation resulted solely from the lengthening of kinetochore microtubules due to congression movements of the chromosomes. Besides incorporation as a result of chromosome movement, two other mechanisms might explain the length of the DTAF-containing segments: (1) a poleward flux of tubulin subunits (Mitchison, 1989) or (2) capture of DTAF-containing nonkinetochore microtubules.
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    Inhibition of spindle elongation by taxol (1991)
    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 20 (1991), S. 136-144 
    Details
    ISSN: 0886-1544
    Keywords: interzonal microtubules ; anaphase B ; PtK1 cells ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: During anaphase B spindle elongation, interzonal microtubules lengthen to accomplish pole-pole separation, while at the same time remaining highly dynamic [Shelden and Wadsworth, J. Cell Sci. 97:273-281, 1990]. To further examine the role of microtubule polymerization and dynamics during spindle elongation, cells have been treated with taxol, which induces microtubule polymerization and stabilizes microtubules. Taxol was added to PtK1 cells 3 minutes after initial chromatid separation, so that the effect on anaphase B could be observed with minimal disruption to anaphase A movement. In 20 μM taxol, the rate and extent of pole-pole separation, measured from time-lapse video records, are reduced to 4% and 9.5% of controls, respectively. The organization of microtbules in taxol treated cells was examined using tubulin immunofluorescence and confocal fluorescence microscopy. Taxol induces a dramatic reorganization of interzonal microtubules resulting in a narrow gap, which is nearly completely lacking in MTs, across the center of the interzone. Furthermore, microtubules in taxol treated cells are resistant to nocodazole induced microtubule disassembly. Our results reveal that taxol rapidly inhibits anaphase B spindle elongation; inhibition is accompanied by a depletion of interdigitated interzonal microtubules and a reduction in microtubule dynamic behavior.
    Additional Material: 5 Ill.
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    URL: http://dx.doi.org/10.1002/cm.970200206
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    Analysis of inducible contractile rings suggests a role for protein kinase C in embryonic cytokinesis and wound healing (1991)
    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 20 (1991), S. 145-157 
    Details
    ISSN: 0886-1544
    Keywords: amphibian ; cleavage regulation ; in vitro ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: A semi-in vitro system derived from Xenopus oocytes which allows induction of contractile ring (CR) formation and closure is described and exploited to elucidate regulatory and structural features of cytokinesis. The inducible CRs (ICRs) are composed of actin filaments and closure is actin filament-dependent as is cytokinesis in vivo. ICR closure in this system is calcium-dependent and pH-sensitive, as is cytokinesis in permeabilized cells (Cande: Journal of Cell Biology 87:326, 1980). Closure of ICRs proceeds at a rate and with a kinetic pattern similar to embryonic cytokinesis. Collectively, these data demonstrate that this system is a faithful mimic of cytokinesis in vivo. ICR formation and closure is protein kinase C (PKC)-dependent and neomycin-sensitive, indicating that the PKC branch of the polyphosphoinositide pathway regulates formation of the actomyosin ring which is the effector of cytokinesis. Kinetic measurements show that the rate of ICR closure reaches a peak of 4-8 μm/sec. Since the maximum measured velocity of actin filament translocation by vertebrate, non-muscle myosins is 0.04 μm/sec, the later observations support a model in which the CR is segmented, containing multiple sites where filaments overlap in a “sliding filament” fashion. Because the rate decreases after reaching a peak, the results also suggest that the number of overlap sites decrease with time.
    Additional Material: 13 Ill.
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    Post-translational incorporation of actin into myofibrils in vitro: Evidence for isoform specificity (1991)
    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 20 (1991), S. 158-168 
    Details
    ISSN: 0886-1544
    Keywords: myofibril assembly ; protein isoforms ; confocal microscopy ; muscle development ; cell-free translation ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: The incorporation of actin into myofibrils has been examined in a cell-free system [Bouché et also Journal of Cell Biology 107:587-596, 1988; Goldfine et all Cellular and Molecular Biology of Muscle Development, 1989]. Actin was translated in a reticulocyte lysate in the presence of 35S-methionine (35S-actin) or purified from muscle and labeled with fluorescein-5-isothiocyanate (FITC-actin). Myofibrils were incubated with either 35S-actin or FITC-actin and then analyzed by gel electrophoresis or fluorescence microscopy. When myofibrils were incubated with FITC-actin monomer in the reticulocyte lysate buffer, strong fluorescent labeling was observed in Z-band regions and less so in I-bands. No fluorescence was detected in non-overlap regions of A-bands. Confocal microscopic analysis of these myofibrils indicated that FITC-actin was distributed evenly across the diameter of the myofibrils. These observations suggest that actin incorporation in the reticulocyte lysate buffer occurred at sites in the sarcomere which contain actin. In contrast, FITC-actin showed a variety of non-physiological incorporation patterns when incubated with myofibrils in the presence of an isotonic buffer (I-buffer). However, when ATP was added to I-buffer, FITC-actin showed a pattern of incorporation into myofibrils similar to that seen in the reticulocyte lysate buffer. Immunoblots indicated that actin of native size was released from myofibrils during incubation in the reticulocyte lysate buffer. No actin release was detected when the myofibrils were incubated in I-buffer lacking ATP. We used this system to compare the incorporation of actin isoforms into myofibrils. Both α- and β-actins exhibited incorporation into the myofibrils but there was a three-fold greater incorporation of the α isoform. We propose that the differential affinities of actin isoforms for myofibrils and other cytoskeletal structures could provide a mechanism for actin isoform targeting within the cytoplasm.
    Additional Material: 7 Ill.
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    URL: http://dx.doi.org/10.1002/cm.970200208
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    Dynamic morphology of metastatic mouse T-lymphoma cells invading through monolayers of 10T½ cells (1991)
    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 20 (1991), S. 203-214 
    Details
    ISSN: 0886-1544
    Keywords: T-cells ; lymphoma ; invasion ; in vitro ; motility ; video microscopy ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: We have used an in vitro model system to analyze cytomechanical aspects of tissue infiltration by T-lymphocytes. The interaction of metastatic T-lymphoma cells with a precultured monolayer of 10T½ fibroblast-like cells was recorded in time-lapse video with alternating phase contrast and reflection interference contrast microscopy. Sectioning of embedded specimens as well as cytoskeletal stainings have been performed on matching cocultures.The lymphoma cells did not strongly attach or spread on the dorsal surface of the monolayer cells. Invasion started with the protrusion of a pseudopodium through a narrow gap, and conspicious constriction of the invading cell's body and nucleus was a consistent feature during the later steps. Overt retraction of the target cells was not seen, but the invading lymphoma cells elevated the fibroblasts over relatively large areas, thereby creating dome-shaped open spaces, allowing for further migration under the monolayer with minimal resistance. Invasion was not unidirectional but was readily reversible at any stage. Due to this wavering character, an invasion event could take more than 1 hour, although the shape alterations involved were fast. Even after the invasion process had been completed, the lymphoma cells could come out from below the monolayer again. Therefore we propose that invasion in this model should be considered as a dynamic equilibrium.Invading T-lymphoma cells displayed diffuse F-actin staining and a well-organized microtubular complex with the centrosomes behind the nucleus in the uropod, which also contained most vesicular organelles.
    Additional Material: 7 Ill.
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    URL: http://dx.doi.org/10.1002/cm.970200304
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    Masthead (1991)
    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 20 (1991) 
    Details
    ISSN: 0886-1544
    Keywords: Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/cm.970200401
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    Kinky microtubules: Bending and breaking induced by fixation in vitro with glutaraldehyde and formaldehyde (1991)
    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 20 (1991), S. 272-278 
    Details
    ISSN: 0886-1544
    Keywords: video-enhanced light microscopy ; microtubules ; glutaraldehyde and formaldehyde fixation ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: We have employed video-enhanced light microscopy to study alterations of the overall shape of microtubules that are produced by the aldehyde fixation methods commonly employed to study them in vitro. Changes brought about by these methods include deformation and breakage. The severity of the effects depends on the fixative employed and increases with its concentration, and with the time of fixation. The changes are observed under a variety of conditions, such as brief exposure to 3.7% formaldehyde, or somewhat longer exposure to glutaraldehyde at concentrations as low as 0.05%. The observed distortion explains why microtubules usually appear curved or sinuous in electron micrographs while appearing relatively rigid and linear in video-enhanced light microscopy. The observed breakage implies that caution must be used in inferring length distributions from measurements of aldehyde-fixed microtubules.
    Additional Material: 5 Ill.
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    URL: http://dx.doi.org/10.1002/cm.970200403
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    Comparative modeling of mammalian aspartate transcarbamylase (1991)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 9 (1991), S. 191-206 
    Details
    ISSN: 0887-3585
    Keywords: CAD ; E. coli ATCase ; energy minimization ; multifunctional proteins ; protein domains ; sequence homology ; evaluation of protein models ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Mammalian aspartate transcarbamylase (ATCase) is part of a 243 kDa multidomain polypeptide, called CAD, that catalyzes the first three steps in de novo pyrimidine biosynthesis. The structural organization of the mammalian enzyme is very different from E. coli ATCase, a dodecameric, monofunctional molecule comprised of six copies of separate catalytic and regulatory chains. Nevertheless, sequence similarities and other properties suggested that the mammalian ATCase domain and the E. coli ATCase catalytic chain have the same tertiary fold. A model of mammalian ATCase was built using the X-ray coordinates of the E. coli catalytic chain as a tertiary template. Five small insertions and deletions could be readily accommodated in the model structure. Following energy minimization the RMS difference in the α carbon positions of the mammalian and bacterial proteins was 0.93 Å. A comparison of the hydrophobic energies, surface accessibility index, and the distribution of hydrophilic and hydrophobic residues of the CAD ATCase structure with correctly and incorrectly folded proteins and with several X-ray structures supported the validity of the model. The mammalian ATCase domain associates to form a compact globular trimer, a prerequisite for catalysis since the active site is comprised of residues from adjacent subunits. Interactions between the clearly defined aspartate and carbamyl phosphate subdomains of the monomer were largely preserved while there was appreciable remodeling of the trimeric interfaces. Several clusters of basic residues are located on the upper surface of the domain which account in part for the elevated isoelectric point (pI = 9.4) and may represent contact regions with other more acidic domains within the chimeric polypeptide. A long interdomain linker connects the monomer at its upper surface to the remainder of the polypeptide. The configuration of active site residues is virtually identical in the mammalian and bacterial enzymes. While the CAD ATCase domain can undergo the local conformational changes that accompany catalysis in the E. coli enzyme, the high activity, closed conformation is probably more stable in the mammalian enzyme.
    Additional Material: 12 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340090305
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    Conformational perturbation of interleukin-2: A strategy for the design of cytokine analogs (1991)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 9 (1991), S. 207-216 
    Details
    ISSN: 0887-3585
    Keywords: interleukin-2 ; lymphokine structure ; α-helical proteins ; circular dichroism ; receptor signaling defect ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Interleukin-2 (IL-2) is a representative of a growing family of small proteins termed lymphokines which are responsible for mediating cell differentiation, growth and function in the immune system. Many of these proteins are being evaluated for their clinical potential. From the perspective of drug development, structure-function analysis of these molecules and their receptors require the use methodologies different than those traditionally employed for small peptides and other natural products. However, similar pharmacologic principles apply and an understanding of ligand-receptor interactions and the asssociated responses is required in order to efficiently pursue agonist and antagonist design.Although IL-2 is a protein of only 133 amino acid residues for which a low resolution X-ray structure does exist, the complexity of its receptor system has provided an added challenge to structure-function studies. Consequently, little is known concerning the receptor contact residues for this protein. We have attempted to utilize established principles of protein and peptide structure to manipulate the conformation of IL-2 in a manner which has provided analogs helpful for receptor interactions studies. These proteins have not only providing useful information on the nature of the IL-2 receptor but have also revealed potential strategies for the design of IL-2 agonists and antagonists.
    Additional Material: 7 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340090306
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    Phospholipase A2 at the bilayer interface (1991)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 9 (1991), S. 229-239 
    Details
    ISSN: 0887-3585
    Keywords: phospholipase A2 ; interfacial catalysis ; interfacial activation ; resonance energy transfer ; lipid-protein interaction ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Interfacial catalysis is a necessary consequence for all enzymes that act on amphipathic substrates with a strong tendency to form aggregates in aqueous dispersions. In such cases the catalytic event occurs at the interface of the aggregated substrate, the overall turnover at the interface is processive, and it is influenced the molecular organization and dynamics of the interface. Such enzymes can access the substrate only at the interface because the concentration of solitary monomers of the substrate in the aqueous phase is very low. Moreover, the microinterface between the bound enzyme and the organized substrate not only facilitates formation of the enzyme-substrate complex, but a longer residence time of the enzyme at the substrate interface also promotes high catalytic processivity.Binding of the enzyme to the substrate interface as an additional step in the overall catalytic turnover permits adaptation of the Michaelis-Menten formalism as a basis to account for the kinetics of interfacial catalysis. As shown for the action of phospholipase A2 on bilayer vesicles, binding equilibrium has two extreme kinetic consequences. During catalysis in the scooting mode the enzyme does not leave the surface of the vesicle to which it is bound. On the other hand, in the hopping mode the absorption and desorption steps are a part of the catalytic turnover.In this minireview we elaborate on the factors that control binding of pig pancreatic phospholipase A2 to the bilayer interface. Binding of PLA2 to the interface occurs through ionic interactions and is further promoted by hydrophobic interactions which probably occur along a face of the enzyme, with a hydrophobic collar and a ring of cationic residues, through which the catalytic site is accessible to substrate molecules in the bilayer. An enzyme molecule binds to the surface occupied by about 35 lipid molecules with an apparent dissociation constant of less than 0.1 pM for the enzyme on anionic vesicles compared to 10 mM on zwitterionic vesicles. Results at hand also show that aggregation or acylation of the protein is not required for the high affinity binding or catalytic interaction at the interface.
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    URL: http://dx.doi.org/10.1002/prot.340090402
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    Masthead (1991)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 10 (1991) 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340100101
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    Comparison of the crystal structure of bacteriophage T4 lysozyme at low, medium, and high ionic strengths (1991)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 10 (1991), S. 10-21 
    Details
    ISSN: 0887-3585
    Keywords: electrostatics ; salt bridge ; thermal factor ; cysteine ; disulfide ; protein crystallography ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Crystals of bacteriophage T4 lysozyme used for structural studies are routinely grown from concentrated phosphate solutions. It has been found that crystals in the same space group can also be grown from solutions containing 0.05 M imidazole chloride, 0.4 M sodium choride, and 30% polyethylene glycol 3500. These crystals, in addition, can also be equilibrated with a similar mother liquor in which the sodium chloride concentration is reduced to 0.025 M. The availability of these three crystal variants has permitted the structure of T4 lysozyme to be compared at low, medium, and high ionic strength. At the same time the X-ray structure of phage T4 lysozyme crystallized from phosphate solutions has been further refined against a new and improved X-ray diffraction data set.The structures of T4 lysozyme in the crystals grown with polyethylene glycol as a precipitant, regardless of the sodium chloride concentration, were very similar to the structure in crystals grown from concentrated phosphate solutions. The main differences are related to the formation of mixed disulfides between cysteine residues 54 and 97 and 2-mercaptoethanol, rather than to the differences in the salt concentration in the crystal mother liquor. Formation of the mixed disulfide at residue 54 resulted in the displacement of Arg-52 and the disruption of the salt bridge between this residue and Glu-62.Other than this change, no obvious alterations in existing salt bridges in T4 lysozyme were observed. Neither did the reduction in the ionic strength of the mother liquor result in the formation of new salt bridge interactions. These results are consistent with the ideas that a crystal structure determined at high salt concentrations is a good representation of the structure at lower ionic strengths, and that models of electrostatic interactions in proteins that are based on crystal structures determined at high salt concentrations are likely to be relevant at physiological ionic strengths.
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    URL: http://dx.doi.org/10.1002/prot.340100103
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    Masthead (1991)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 10 (1991) 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340100201
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    Computational studies of ligand diffusion in globins: I. Leghemoglobin (1991)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 10 (1991), S. 70-80 
    Details
    ISSN: 0887-3585
    Keywords: locally enhanced sampling ; molecular dynamics ; ligand penetration ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The thermally assisted diffusion of a small ligand (carbon monoxide) through a protein matrix (lupine leghemoglobin) is investigated computationally. The diffusion paths are calculated by a varient of the time-dependent Hartree approximation which we call LES (locally enhanced sampling). The variant which was recently introduced by Elber and Karplus1 is based on the classical TD-SCF approximation of Gerber et al.2 The simulation enables more significant search for diffusion pathways than was possible before. This is done by increasing the number of ligand trajectories using a single trajectory for the protein. We compare qualitatively diffusion rates in leghemoglobin and in myoglobin. The calculation shows that the diffusion in leghemoglobin is much faster than the diffusion in myoglobin, in agreement with experiment. The gate in leghemoglobin is opened by fluctuations at a close contact between the B/C and the G helices. The most relevant fluctuation is the rigid shift of the C helix with respect to the G helix. This path is not observed in a comparable calculation for myoglobin.1 This finding is rationalized by the lack of the D helix in leghemoglobin and a significantly more flexible CE loop. Supporting experimental evidence for the importance of the CE loop in leghemoglobin can be found in the kinetics studies of Gibson et al.28
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    URL: http://dx.doi.org/10.1002/prot.340100107
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    The crystal structure of staphylococcal nuclease refined at 1.7 Å resolution (1991)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 10 (1991), S. 92-105 
    Details
    ISSN: 0887-3585
    Keywords: protein structure ; ligand binding ; crystallographic refinement ; phosphodiesterase ; calcium ligands ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The crystal structure of staphylococcal nuclease has been determined to 1.7 Å resolution with a final R-factor of 16.2% using stereochemically restrained Hendrickson-Konnert least-squares refinement. The structure reveals a number of conformational changes relative to the structure of the ternary complex of staphylococcal nuclease1,2 bound with deoxythymidine-3′,5′-diphosphate and Ca2+. Tyr-113 and Tyr-115, which pack against the nucleotide base in the nuclease complex, are rotated outward creating a more open binding pocket in the absence of nucleotide. The side chains of Ca2+ ligands Asp-21 and Asp-40 shift as does Glu-43, the proposed general base in the hydrolysis of the 5′-phosphodiester bond. The significance of some changes in the catalytic site is uncertain due to the intrusion of a symmetry related Lys-70 side chain which hydrogen bonds to both Asp-21 and Glu-43. The position of a flexible loop centered around residue 50 is altered, most likely due to conformational changes propagated from the Ca2+ site. The side chains of Arg-35, Lys-84, Tyr-85, and Arg-87, which hydrogen bond to the 3′- and 5′-phosphates of the nucleotide in the nuclease complex, are unchanged in conformation, with packing interactions with adjacent protein side chains sufficient to fix the geometry in the absence of ligand. The nuclease structure presented here, in combination with the stereochemically restrained refinement of the nuclease complex structure2 at 1.65 Å, provides a wealth of structural information for the increasing number of studies using staphylococal nuclease as a model system of protein structure and function.
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    URL: http://dx.doi.org/10.1002/prot.340100203
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    Modelling the three-dimensional structure and electrostatic potential field of the two Cu,Zn superoxide dismutase variants from xenopus laevis (1991)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 10 (1991), S. 149-155 
    Details
    ISSN: 0887-3585
    Keywords: Cu,Zn superoxide dismutase ; model building ; protein structure-function ; Poisson-Boltzmann ; electrostatic potentials ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The crystallographic structure of bovine superoxide dismutase has been used as a template for the graphic reconstruction of the three-dimensional structures of the two Xenopus laevis variants (Schinina', M. E. et al. Arch. Biochem. Biophys. 272:507-515, 1989). In these models the structure-essential residues maintain their position and their structural role, and the interactions between the subunits and the close packing within the β-barrel are maintained with conservative substitutions and even increased with “aromatic pairs.” Because of the same topological motif and surface location of charges, arising from the model building of the two variants with respect to the bovine enzyme, we have calculated the electrostatic potential fields around the models of the two Xenopus laevis variants by numerically solving the Poisson-Boltzmann equation. We show that conservation of a specific space-relationship of charges maintains the potential field pattern already observed in the bovine enzyme, where a negative potential field surrounds the protein surface and specific positive regions wrap up the copper center active site. This electrostatic potential field distribution supports the idea that electrostatic interactions control, like in the bovine enzyme, the mechanism of enzyme-substrate recognition in the Xenopus laevis Cu,Zn superoxide dismutases, suggesting that coordinated mutation of charged residues has occurred in the evolution of this enzyme.
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    The future at proteins (1991)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 10 (1991), S. i 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340100302
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    On the multiple-minima problem in the conformational analysis of polypeptides. V. Application of the self-consistent electrostatic field and the electrostatically driven monte carlo methods to bovine pancreatic trypsin inhibitor (1991)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 10 (1991), S. 188-198 
    Details
    ISSN: 0887-3585
    Keywords: empirical potentials ; energy calculations ; protein structure prediction ; protein folding ; minimization ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: In connection with the accompanying paper to test various models for the hydration of polypeptides, we have explored a limited portion of the conformational energy hyperspace of the small protein bovine pancreatic trypsin inhibitor (BPTI) with the aid of two search methods developed in this laboratory. A series of low-energy conformations was obtained as a result of this study. These conformations constitute a set of local minima in the conformational energy space of the molecule as described by the ECEPP/2 (Empirical Conformational Energy Program for Peptides) potential energy function, without the inclusion of hydration. Five different initial conformations were used in this exploration: the first corresponds to an energy-refined structure based on the crystallographic coordinates (4PTI) provided by Deisenhofer and Steigemann25 and reported previously by Meirovitch and Scheraga.3 The remaining four initial conformations were obtained by using a Variable-Target-Function procedure, applied to the experimental Cartesian coordinates (5PTI) reported by Wlodawer et al.26The self-consistent electrostatic field (SCEF) and the electrostatically driven Monte Carlo (EDMC) methods were used to search the conformational space. The SCEF and EDMC methodologies assume that a polypeptide or protein molecule is driven toward the native structure mainly by the action of the electrostatic interactions. Application of these methodologies led to a set of conformations (up to 50 kcal/mol lower than the starting ones) with ECEPP/2 energies lower than any of those that we had previously found. Application of both methods to the initial conformation generated from 4PTI led to a series of low-energy conformations exhibiting similar rms deviations with respect to the experimental data (4PTI) as did the starting conformation. However, statistical analysis of the runs that had started from the conformations generated by using the variable-target-function procedure (and applying the EDMC method) indicated that the rms deviations of the atomic positions of the new low-energy conformations tended to increase as the energy improved, when compared with the X-ray data from which the starting conformations had been generated. The structures with the lowest energies also had radii of gyration smaller than the experimentally observed one. These results indicated a need to include hydration in the potential function, and provided the conformations used in the accompanying paper to test various hydration models.
    Additional Material: 6 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340100304
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    Structure of ricin B-chain at 2.5 Å resolution (1991)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 10 (1991), S. 260-269 
    Details
    ISSN: 0887-3585
    Keywords: ricin toxin ; B-chain ; galactose binding ; molecular evolution ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The heterodimeric plant toxin ricin has been refined to 2.5 Å resolution. The B-chain lectin (RTB) is described in detail. The protein has two major domains, each of which has a galactose binding site. RTB has no regular secondary structure but displays several Ω loops. Each RTB domain is made of three copies of a primitive 40 residue folding unit, which pack around a pseudo threefold axis. In each domain, galactose binds in a shallow cleft formed by a three residue peptide kink on the bottom and an aromatic ring on the top. At the back of the cleft, an aspartate forms hydrogen bonds to the C3 and C4 hydroxyls of galactose, whereas a glutamine bonds to the C4 alcohol, helping to define specific epimer binding. In addition to analyzing the sugar binding mechanism, the assembly of subdomain units around the pseudo threefold axis of each domain is described. The subdomains contribute conserved Trp, Leu, and Ile residues to a compact central hydrophobic core. This tight threefold binding probably drives the peptide folding and stabilizes the protein structure.
    Additional Material: 6 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340100310
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  • 88
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    Active site conformation in myoglobin as determined by X-ray absorption spectroscopy (1991)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 10 (1991), S. 279-286 
    Details
    ISSN: 0887-3585
    Keywords: myoglobin ; structure of the active site ; XAFS Debye-Waller factor ; Einstein model ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: X-ray absorption fine structure experiments were performed to study structural and dynamic aspects of the active site of various forms of myoglobin. The structures determined for deoxyMb, MbCO, and MbO2 are consistent with the structure established by X-ray absorption fine structure experiment and X-ray crystallography. The first shell of ferrous MbNO determined contains 5 nitrogens located at 2.02 Å and a short NO bond length of 1.76 Å. This study focuses on the change of the XAFS Debye-Waller factor with temperature, which is a measure of thermal and static disorder. It was found that the changes of Debye-Waller factor with temperature for the Mb proteins, except deoxyMb, are consistent with a simple Einstein model, in which a single frequency was assumed for the bond stretching modes. In contrast, the temperature dependence of deoxyMb cannot be fitted to the Einstein model and a large disorder was found at low temperatures, which indicates the existence of conformational substates of the active site.
    Additional Material: 7 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340100402
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    Relaxation data in NMR structure determination: Model calculations for the lysozyme-Gd3+ complex (1991)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 10 (1991), S. 117-129 
    Details
    ISSN: 0887-3585
    Keywords: protein NMR ; distance restraints ; paramagnetic relaxation ; protein structure determination ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The effect of including paramagnetic relaxation data as additional restraints in the determination of protein tertiary structures from NMR data has been explored by a systematic series of model calculations. The system used for testing the method was the 2.0 Å resolution tetragonal crystal structure of hen egg white lysozyme (129 amino acid residues) and structures were generated using a version of the hybrid “distance geometry-dynamic simulated annealing” procedure. A limited set of 769 NOEs was used as restraints in all the calculations; the strengths of these were categorized into three classes on the basis of distances observed in the crystal structure. The values of 50 φ angles were also restrained on the basis of amide-alpha coupling constants calculated from the X-ray structure. Five sets of 12 structures were determined using differing sets of paramagnetic relaxation data as restraints additional to those involving the NOE and coupling constant data. The paramagnetic relaxation data were modeled on the basis of the distances of defined protons from the crystallographic binding site of Gd3+ in lysozyme. Analysis of the results showed that the relaxation data significantly improved the correspondence between the set of generated structures and the crystal structure, and that the more well defined the relaxation data, the more significant the improvement in the quality of the structures. The results suggest that the inclusion of paramagnetic relaxation restraints could be of significant value for the experimental determination of protein structures from NMR data.
    Additional Material: 7 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340100205
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    Side chain-backbone hydrogen bonding contributes to helix stability in peptides derived from an α-helical region of carboxypeptidase A (1991)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 10 (1991), S. 130-139 
    Details
    ISSN: 0887-3585
    Keywords: α-helix ; side chain-backbone hydrogen bonding ; helix dipole ; circular dichroism ; carboxypeptidase A ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Recently, Presta and Rose proposed1 that a necessary condition for helix formation is the presence of residues at the N-and C-termini (called NTBs and CTBs) whose side chains can form hydrogen bonds with the initial four amides and the last four carbonyls of the helix, which otherwise lack intrahelical hydrogen bonding partners. We have tested this hypothesis by conformational analysis by circular dichroism (CD) of a synthetic peptide corresponding to a region (171-188) of the protein carboxypeptidase A; in the protein, residues 174 to 186 are helical and are flanked by NTBs and CTBs. Since helix formation in this peptide may also be stabilized by electrostatic interactions, we have compared the helical content of the native peptide with that of several modified peptides designed to enable dissection of different contributions to helix stability. As expected, helix dipole interactions appear to contribute substantially, but we conclude that hydrogen bonding interactions as proposed by Presta and Rose also stabilize helix formation. To assist in comparison of different peptides, we have introduced two concentration-independent CD parameters which are sensitive probes of helix formation.
    Additional Material: 7 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340100206
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  • 91
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    Free energy calculations on binding and catalysis by α-lytic protease: The role of substrate size in the P1 pocket (1991)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 10 (1991), S. 140-148 
    Details
    ISSN: 0887-3585
    Keywords: α-lytic protease ; free energy perturbation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We present free energy calculations using molecular dynamics on different substrates of α-lytic protease in the gas phase, in solution, while forming a noncovalent Michaelis complex with the enzyme, and in a tetrahedral structure representing a transition state/intermediate for acylation by the enzyme. Various P1 substrates were studied, with P1 = Gly, Ala, Val, and Leu. In qualitative agreement with experiment, the enzyme was calculated to bind and catalyze most effectively substrates with P1 = Ala over those with P1 = Gly, Val or Leu. Also, the calculated relative solvation free energies of Gly → Ala and Ala → Val were in qualitative agreement with experimental values in corresponding model systems. However, the level of quantitative agreement with experiment achieved in our earlier study of relative binding and catalysis of native subtilisin and an Asn-155 → Ala mutant was not achieved. We surmise that this is due to the greater difficulty in quantitatively simulating effects that are predominantly van der Waals and hydrophobic compared to those that are hydrogen bonding/electrostatic.
    Additional Material: 7 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340100207
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  • 92
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    Modeling conformational change in macromolecules as an elastic deformation (1991)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 10 (1991), S. 162-170 
    Details
    ISSN: 0887-3585
    Keywords: conformation difference ; strain ; elasticity ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Macromolecules are elastic bodies. Atomic strucutres are available for nucleic acids and proteins in two or more different conformations. It is a common practice to compare two structures by finding the best rigid body superposition of the molecules. This ignores possible deformations. There is useful information in the deviations from the rigid body superposition. If the deviations are considered to be elastic deformations of a common structure than it is possible to extract this information. Results are shown for comparisons of deoxyhemoglobin versus carbonmonoxyhemoglobin and for two different conformations of catabolite gene activator protein.
    Additional Material: 6 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340100210
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    Addendum (1991)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 10 (1991), S. 359-359 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340100408
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  • 94
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    The electrostatic potential of Escherichia coli dihydrofolate reductase (1991)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 11 (1991), S. 1-12 
    Details
    ISSN: 0887-3585
    Keywords: electrostatics ; enzyme-substrate interaction ; solvent screening ; active site potential ; structure-function relationship ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Escherichia coli dihydrofolate reductase (DHFR) carries a net charge of -10 electrons yet it binds ligands with net charges of -4 (NADPH) and -2 (folate or dihydrofolate). Evaluation and analysis of the electrostatic potential of the enzyme give insight as to how this is accomplished. The results show that the enzyme is covered by an overall negative potential (as expected) except for the ligand binding sites, which are located inside “pockets” of positive potential that enable the enzyme to bind the negatively charged ligands. The electrostatic potential can be related to the asymmetric distribution of charged residues in the enzyme.The asymmetric charge distribution, along with the dielectric boundary that occurs at the solvent-protein interface, is analogous to the situation occurring in superoxide dismutase. Thus DHFR is another case where the shape of the active site focuses electric fields out into solution.The positive electrostatic potential at the entrance of the ligand binding site in E. coli DHFR is shown to be a direct consequence of the presence of three positively charged residues at positions 32, 52, and 57-residues which have also been shown recently to contribute significantly to electronic polarization of the ligand folate. The latter has been postulated to be involved in the catalytic process. A similar structural motif of three positively charged amino acids that gives rise to a positive potential at the entrance to the active site is also found in DHFR from chicken liver, and is suggested to be a common feature in DHFRs from many species. It is noted that, although the net charges of DHFRs from different species vary from +3 to -10, the enzymes are able to bind the same negatively charged ligands, and perform the same catalytic function.
    Additional Material: 6 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340110102
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    Erratum (1991)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 11 (1991), S. 77-77 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340110109
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    Sesam: A relational database for structure and sequence of macromolecules (1991)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 11 (1991), S. 59-76 
    Details
    ISSN: 0887-3585
    Keywords: protein structure ; amino acid sequence ; database ; macromolecules ; molecular modeling ; knowledge base ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A system is described that provides ways of integrating data on protein structure, sequence, and survey results, with molecular graphics and molecular mechanics software. Its major component is the relational database SESAM, presently implemented under the commercial package SYBASE. By desin, the database allows full integration - within the same data organization - of raw data on protein structure, sequence, ligands, and heterogroups, obtained from the Brookhaven Protein Databank, with pure sequence information available from other databanks such as SWISS-PROT. It contains in addition higher level descriptions of structural and topological properties, as well as survey results, obtained by executing specialized computer programs. Aside from the very useful attribute of closely combining structural and nonstructural information, other important features distinguish it from analogous systems developed elsewhere. It includes a molecular dictionary with complete description of geometric properties and energy parameters used in modeling and conformational energy calculations. Using this dictionary, structural data are validated by checking for localized inconsistencies in atomic coordinates, atomic symbols, chirality definitions, and flagging errors and incomplete entries. Because of both the dictionary and the validation procedures, SESAM can be readily interfaced with conventional molecular graphics and mechanics software packages, or with other specialized application programs. With the aid of appropriate interfaces, data access is sufficiently fast for SESAM to be interrogated interactively. Prototypes of user interfaces, as well as an interface with the molecular graphics package BRUGEL, are described and the power of the system is illustrated in applications such as homology-based protein modeling, computer-aided protein design, protein structure predictions, analysis of local structure motifs, and of relationships between protein sequence and structure.
    Additional Material: 5 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340110108
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    Crystallization and preliminary X-ray investigation of a recombinant form of rat catechol O-methyltransferase (1991)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 11 (1991), S. 233-236 
    Details
    ISSN: 0887-3585
    Keywords: protein crystals ; X-ray crystallography ; catechol O-methyltransferase ; protein structure ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Rat catechol O-methyltransferase cDNA was introduced into an E. coli expression vector pKEX14, which utilizes the inducible T7 promoter. Active and soluble recombinant catechol O-methyltransferase was produced in bacteria and purified to electrophoretic homogeneity by chromatographic procedures. The purified enzyme has been crystallized by the method of vapor diffusion using polyethylene glycol as precipitant. The space group is P3121 or P3221 with a = b = 51.3 Å and c = 168.5 Å and one molecule in the asymmetric unit. The crystals diffract beyond 3.2 Å and are suitable for three-dimensional X-ray structure determination.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340110309
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    FASTRUN: A special purpose, hardwired computer for molecular simulation (1991)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 11 (1991), S. 242-253 
    Details
    ISSN: 0887-3585
    Keywords: FASTRUN ; special purpose processors ; computer hardware ; molecular mechanics ; supercomputing ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We describe the design, construction, and performance of a special purpose, hardwired accelerator for molecular mechanical calculations called FASTRUN. The processor was designed at Columbia University in 1984, constructed in the Instrumentation Division of Brookhaven National Laboratory, and delivered to Columbia in final form in 1989. It was rendered functional for molecular mechanics in early 1990. Together with its host Star array processor, FASTRUN has a measured performance for molecular dynamics simulations which compares favorably with present day supercomputers. The hardware replication cost of FASTRUN is on the order of $100,000.00
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340110403
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  • 99
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    1.59 Å structure of trypsin at 120 K: Comparison of low temperature and room temperature structures (1991)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 10 (1991), S. 171-187 
    Details
    ISSN: 0887-3585
    Keywords: cryocrystallography ; temperature factor ; serine protease structure ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The structure of a rat trypsin mutant [S195C] at a temperature of 120 K has been refined to a crystallographic R factor of 17.4% between 12.0 and 1.59 Å and is compared with the structure of the D102N mutant at 295 K. A reduction in the unit cell dimensions in going from room temperature to low temperature is accompanied by a decrease in molecular surface area and radius of gyration. The overall structure remains similar to that at room temperature. The attainable resolution appears to be improved due to the decrease in the fall off of intensities with resolution [reduction of the temperature factor]. This decreases the uncertainty in the atomic positions and allows the localization of more protein atoms and solvent molecules in the low temperature map. The largest differences between the two models occur at residues with higher than average temperature factors. Several features can be localized in the solvent region of the 120 K map that are not seen in the 295 K map. These include several more water molecules as well as an interstitial sulfate ion and two interstitial benzamidine molecules.
    Additional Material: 14 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340100303
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    Crystal parameters and molecular replacement of an anticholera toxin peptide complex (1991)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 11 (1991), S. 218-222 
    Details
    ISSN: 0887-3585
    Keywords: antibody ; Fab ; antigen ; crystallization ; x-ray crystallography ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: TE33 is an Fab fragment of a monoclonal antibody raised against a 15-residue long peptide (CTP3), corresponding in sequence to residues 50-64 of the cholera toxin B subunit. Crystals of the complex between TE33 and CTP3 have been grown from 20% (w/v) polyethylene glycol-8000 at pH 4.0. The crystals are orthorhombic, space group P21212, with unit cell dimensions a = 104.15, b = 110.61, and c = 40.68 Å. X-Ray data have been collected to a resolution of 2.3 Å. The asymmetric unit contains one molecule of Fab and one molecule of CTP3. The presence of CTP3 has been demonstrated by fluorescence quenching of the dissolved crystal after X-ray data collection. A molecular replacement solution was found based on the coordinates of DB3, an antiprogesterone Fab fragment.
    Additional Material: 1 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340110306
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