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  • 2010-2014
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  • 1990-1994  (2,697)
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  • 101
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 15 (1990), S. 88-98 
    ISSN: 0886-1544
    Keywords: tau ; MAP2 ; dynamic instability ; microtubule nucleation ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: In this paper, we report on the effect of brain microtubule-associated proteins (MAPs) on the dynamic instability of microtubules as well as on the nucleation activity of purified centrosomes. Under our experimental conditions, tau and MAP2 have similar effects on microtubule nucleation and dynamic instability. Tau increases the apparent elongation rate of microtubules in proportion to its molar ratio to tubulin, and we present evidence indicating that this is due to a reduction of microtubule instability rather than to an increase of the on rate of tubulin subunits at the end of growing microtubules. Increasing the molar ratio of tau over tubulin leads also to an increase in the average number of microtubules nucleated percentrosome. This number remains constant with time. This suggests that the number of centrosome-nucleated microtubules at steady state can be determined by factors that are not necessarily irreversibly bound to centrosomes but, rather, affect the dynamic properties of microtubules.
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  • 102
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 15 (1990), S. 76-87 
    ISSN: 0886-1544
    Keywords: antiactin ; cytochalasin B ; plant cytoskeleton ; tubulin ; oryzalin ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: Following our recent description [McCurdy et al.: Protoplasma. 147:204-206, 1988] of arrays of transverse cortical microfilaments (MFs) in preprophase roottip cells of wheat (Triticum aestivum L. cv. Kite), we have performed double label immunofluorescence microscopy to correlate the formation of these arrays with the known rearrangement of cortical microtubules (MTs) that occurs during preprophase. At early preprophase, indicated by a broad (i.e., young) preprophase band (PPB) of MTs, actin MFs are transverse only in the central region of the cell cortex. By late preprophase, however, cells that possess a mature (i.e., narrow) PPB of MTs have arrays of transverse MFs that occupy the entire cortical surface of the cell. Thus, apart from the PPB zone, the transverse MFs in these arrays do not colocalize with transverse cortical MTs. Depolymerization of MTs using the herbicide oryzalin does not effect the arrays of cortical MFs; however, experiments using cytochalasin B in combination with oryzalin indicate that cellular MTs are necessary for the formation of the arrays of transverse cortical MFs. The arrays of cortical MFs disintegrate during prophase into short fragments of random, filamentous actin. This situation persists until the completion of cytokinesis. The absence of MFs during mitosis in densely-cytoplasmic meristematic cells of wheat root tips indicates that filamentous actin may not have a universal function in plant cell division. The possible function of the arrays of cortical MFs in preprophase cells is discussed.
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  • 103
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 15 (1990) 
    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
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  • 104
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 16 (1990), S. 22-32 
    ISSN: 0886-1544
    Keywords: image analysis ; sperm cell ; tracking ; motility ; velocity ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: The effect of increasing temperature from 22-25°C to 37°C on various motion characteristics of individual normal human spermatozoa and spermatozoa lacking the outer dynein arms (LODA) was studied by using a new automatic microscopic tracking method. It was found that: (1) The curvilinear velocity (Vc, measured between 1-3 sec) of both normal and LODA spermatozoia, fluctuated more or less intensely between spermatozoa; this fluctuation was not thermodependent. (2) The average Vc in the two groups of spermatozoa increased with the rise in temperature at a similar rate (1μm/sec/°C), but LODA spermatozoa had an initial Vc lower than that of normal spermatozoa (12.5 ± 5.3 μm/sec and 34.2 ± 8.2 μm/sec, respectively). (3) The profile of the Vc increase associated with the temperature rise was different for the two groups of spermatozoa: for LODA spermatozoa it was linear between 25-37°C, whereas for normal spermatozoa a plateau was reached at about 31°C. (4) Various patterns of trajectory were found for both normal and LODA spermatozoa; these patterns were unrelated to temperature. However, LODA spermatozoa had more linear trajectories than normal spermatozoa. (5) Plots derived from reaction rate theory showed that the activation enthalpy, δH
    Additional Material: 9 Ill.
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  • 105
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    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 16 (1990), S. 88-88 
    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
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  • 106
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    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 16 (1990), S. 146-154 
    ISSN: 0886-1544
    Keywords: sea urchin ; centrosome ; immunofluorescence microscopy ; barrel-shaped spindle ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: T-1 induces modifications in the shape of the centrosome at division in fertilized eggs of the North American sea urchin, Lytechinus pictus. Phase contrast microscopy observations of mitotic apparatus isolated from T-1treated (1.7-8.5μM) eggs at first division shows that the centrosomes already begin to spread or to separate by prophase and that the mitotic spindle is barrel-shaped. When eggs are fertilized with sperm that have been pretreated with T-1, the centrosomes become flattened; the spindles are of normal length. Immunofluorescence microscopy using an anti-centrosomal monoclonal antibody reveals that T-l modifies the structure of the centrosome so that barrel-shaped spindles with broad centrosomes are observed at metaphase, rather than the expected focused poles and fusiform spindle. Higher concentrations of T-l induce fragmentation of centrosomes, causing abnormal accumulation of microtubules in polar regions. These results indicate that T-l directly alters centrosomal configuration from a compact structure to a flattened or a spread structure. T-l can be classified as a new category of mitotic drugs that may prove valuable in dissecting the molecular nature of centrosomes.
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  • 107
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    Electronic Resource
    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 16 (1990) 
    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
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  • 108
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    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 16 (1990), S. 164-166 
    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
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  • 109
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 17 (1990), S. 46-58 
    ISSN: 0886-1544
    Keywords: circumferential microfilament bundles ; intercellular adhesion ; cytoskeleton ; junctional complex ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: The junctional complexes in chick retinal pigment epithelial (RPE) cells in situ contain unusually large zonulae adhaerentes (ZAs) composed of subunits termed zonula adhaerens complexes (ZACs). To determine whether the properties of the ZAs differ between RPE cells which contain ZACs, and MDCK cells which lack ZACs, we investi-gated the effects of treatment with trypsin and/or low Ca2+ by transmission electron microscopy and staining for F-actin. Treatment of RPE cells for 1 h with trypsin alone has no apparent effect on the morphology of the ZA in either MDCK or RPE cells. In contrast to the ZAs in MDCK cells, which split after 3 min in low Ca2+, the ZAs in chick RPE cells stay intact even after 2 h, although the intermembrane discs, i.e., the extracellular components of the ZACs, are no longer visible. After 30 min of treatment with trypsin and low Ca2+, the ZAs split in both cell types. The CMBs start to contract, translocate toward the cell interior, and eventually disappear. This process continues even when the RPE cells are returned to normal medium. New ZAs, composed of ZACs, form between RPE cells 3 h after return to normal medium. These findings suggest that the ZACs in the ZAs of RPE cells are not directly responsible for the increase in resistance to low Ca2+. They also show that the ZA-junctions in RPE cells are not only structurally different from those previously examined, but also behave differently in response to experimental manipulation.
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  • 110
    Electronic Resource
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    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 17 (1990), S. 187-196 
    ISSN: 0886-1544
    Keywords: axonemal shape changes ; Ca/Ba/Sr ; macrocilia ; Beroë ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: Macrocilia of the ctenophore Beroë undergo Ca/Ba/Sr-dependent activation of ciliary beating and microtubule sliding disintegration [Tamm, J. Comp. Physiol. A163:23-31. 1988a: Tamm, Cell Motil. Cytoskeleton 11:126-138, 1988b; Tamm, Cell Motil. Cytoskeleton 12:104-112, 1989: Tamm and Tamm, Proc. Natl. Acad. Sci. U.S.A. 86:6987-6991, 1989]. Here we report that detergent-extracted macrocilia show an ATP-independent conformational change in response to high concentrations of Ca. Ba. or Sr ions. When applied locally by iontophoresis, these ions induce a rapid planar curvature of the distal end of the macrociliary shaft, followed by a slower relaxation to the rest position. Tip curling occurs in a direction opposite to the physiological Ca/Ba/Sr response. When applied uniformly in the bath, a threshold concentration of 10-1 M Sr is required to induce curling of the tip, and the distal ends remain curved. Calmodulin antagonists do not inhibit the tip curling response.Previous workers found that Ca induces changes in the helical shape of isolated doublet microtubules [Miki-Noumura and Kamiya, Exp. Cell Res. 97:451-453, 1976: Miki-Noumura and Kamiya. J. Cell Biol. 81:355-360, 1979; Takasaki and Miki-Noumura. J. Mol. Biol. 158:317-324, 1982] and sperm axonemes [Okuno and Brokaw, Cell Motil. 1:349-362. 1981] and suggested that conformational changes in microtubules may play a role in Ca regulation of ciliary motility. We propose that the Ca/Ba/Sr-induced curling of the macrociliary tip is due to similar helical changes of doublet microtubules, some of which in macrocilia are prevented from sliding by permanent connections (compartmenting lamellae) between adjacent axonemes within the shaft. Although the tip curling response does not appear to be directly relevant to the physiological Ca response of macrocilia, it provides a novel system for investigating Ca-induced conformational changes of microtubules independent of dynein-powered active sliding.
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  • 111
    ISSN: 0886-1544
    Keywords: yeast ; myosin ; budding ; cell wall ; cytoskeleton ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: Recent studies with myosin heavy chain mutants in the slime mold Dictyostelium discoideum and the yeast Saccharoymyces cerevisiae indicate that the myosin heavy chain gene is not essential for cell survival under laboratory growth conditions. However, cells lacking a normal myosin heavy chain gene demonstrate substantial alterations in growth and cell division. In this study, we report that a disruption mutant in the rod portion of the yeast myosin heavy chain gene, MYOl, produces abnormal chitin distribution and cell wall organization at the mother-bud neck in a high proportion of dividing cells. It is suggested that this phenotype is the cause of the cell division defect and the osmotic sensitivity of yeast MYOl mutants. In the absence of a normal MYOl polypeptide, yeast cells alter their cell type specific budding pattern. It is concluded that an intact myosin heavy chain gene is required to maintain the cell type specific budding pattern and the correct localization and deposition of chitin and cell wall components during cell growth and division.
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  • 112
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    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 17 (1990), S. 356-372 
    ISSN: 0886-1544
    Keywords: Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
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  • 113
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    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 17 (1990), S. 329-344 
    ISSN: 0886-1544
    Keywords: cytoskeleton ; glycoconjugates ; axoneme ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: The photoreceptor connecting cilium bears a unique transmembrane assemblage which stably links cell surface glycoconjugates with the underlying axonemal cytoskeleton. Structural similarities between the photoreceptor connecting cilium and the transition zone of motile cilia suggests that this assemblage may also be present in motile cilia. Using a subcellular fraction enriched in detergent-extracted photoreceptor axonemes, three high molecular mass glycoconjugates (425, 600, and 700 kD) were previously identified as potential components of the assemblage. Through oligosaccharide characterization and binding of a specific monoclonal antibody, we have verified the localization of the 425 kD glycoconjugate to the transmembrane assemblage. Binding of the lectin peanut agglutinin (PNA) to the 425 kD glycoconjugate on nitrocellulose blots, and to isolated detergentextracted axonemes, was assessed following treatment with the enzymes neuraminidase and O-glycanase. Changes in binding to the 425 kD glycoconjugate precisely paralleled changes in binding to intact axonemes, supporting the hypothesis that the 425 kD glycoconjugate is a component of the transmembrane assemblage. Furthermore, the results suggest that the 425 kD glycoconjugate contains sialated galactose-N-acetylgalactosamine oligosaccharides which are Olinked to the protein backbone. To directly assess the distribution of the 425 kD glycoconjugate, we produced a monoclonal antibody directed against this glycoconjugate. The antibody, K26, recognizes only the 425 kD on transblots of the axoneme fraction. K26 immunoreactivity of intact axonemes is identical to that seen by PNA staining. K26 staining of isolated photoreceptors and whole retina is uniquely localized to the region of the connecting cilium. Thus, in the photoreceptor, the 425 kD is not only a component of the transmembrane assemblage but is also completely restricted to the connecting cilium.Based on morphological similarities, the photoreceptor connecting cilium is thought to be homologous to the transition zone of the motile cilium. As such, we have stained oviduct epithelium with the K26 monoclonal antibody. Immunoreactivity is restricted to the region of the transition zone at the base of motile cilia. This demonstrates that the photoreceptor connecting cilium and motile cilium transition zone are immunologically related.
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  • 114
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    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 17 (1990), S. 345-355 
    ISSN: 0886-1544
    Keywords: cell fusion ; polykaryon ; cytoskeleton ; F-actin ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: To study the involvement of the cytoskeletal system in the fusion of animal cells, we examined the dynamic changes of cytoskeletal proteins during the various stages of cell fusion. CV-l cells were fused by applying a radio-frequency electrical pulse. Structural changes of microtubules (MTs) and F-actin were monitored simultaneously by double-label fluorescence microscopy. It was observed that in a few minutes after the initiation of cell fusion, MT bundles began to extend into the cytoplasmic bridges which were formed by fusing the membranes of neighboring cells. Later, a network of parallel MT bundles appeared between the adjacent nuclei of the fusing cells; such MT bundles may provide the mechanical links that are responsible for nuclear aggregation. The structural changes of Factin during cell fusion were more complicated. We observed many different patterns of actin distribution in the fusing cells, including some giant, ring-shaped structures. Reorganization of actin is unlikely to be involved in the nuclear aggregation process. Instead, actin bundles condensed at the cell edges may help to widen the cytoplasmic bridges to allow merging of cellular contents between the fusing cells.
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  • 115
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    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 16 (1990), S. 133-145 
    ISSN: 0886-1544
    Keywords: marsupials ; mammals ; primitive erythrocytes ; nucleated erythrocytes ; marginal bands ; microtubules ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: Seeking to resolve conflicting literature on cytoskeletal structure in mammalian “primitive” generation erythrocytes, we have utilized the circulating blood of developing marsupials. In young of the Tammar Wallaby (Macropus eugenii) and the Gray Short-tailed Opossum (Monodelphis domestica), relatively large, nucleated primitive erythrocytes constituted nearly 100% of the circulating population of birth (= day 0) and in fetuses (Tammar) several days before birth. These cells were discoidal or elliptical, and flattened except for a nuclear bulge. Their cytoskeletal system, consisting of a marginal band of microtubules enclosed within a cell surface-associated network (membrane skeleton), closely resembled that of non-mammalian vertebrate erythocytes. By day 2 or 3, much smaller anucleate erythrocytes of “definitive” morphology, lacking marginal bands, appeared in abundance. These accounted for 〉90% of the circulating population of both species by day 6-8. Non-nucleated erythrocytes of a different type, constituting 1-6% of the cells in most blood samples up to day 7, were identified as anucleate primitives on the basis of size, shape, and presence of a marginal band. Thus, loss of erythrocyte nuclei in mammals appears to begin earlier than generally recognized, i.e., in the primitive generation. Counts of these anucleate primitives in young of various ages implicated nucleated primitives as their probable source. Pointed erythrocytes, occasionally found in younger neonates of both species, occurred in greatest number in fetuses (Tammar) prior to birth. This is in accord with previous work on non-mammalian vertebrates suggesting that such cells are morphogenetic intermediates. The results confirm the long-suspected similarity between mammalian primitive erythrocytes and the nucleated erythrocytes of all non-mammalian vertebrates.
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  • 116
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    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 16 (1990), S. 155-155 
    ISSN: 0886-1544
    Keywords: Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
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  • 117
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    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 16 (1990), S. 159-163 
    ISSN: 0886-1544
    Keywords: Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
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  • 118
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    Cell Motility and the Cytoskeleton 16 (1990), S. 167-181 
    ISSN: 0886-1544
    Keywords: metachronal wavelength ; metachronal wave direction ; asymmetry of beating ; ciliary beating ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: A mathematical model is proposed to explain the dependence of the direction and the length of the metachronal wave on parameters that characterize the ciliary beat, the dimensions of the cilia, and the geometry of their arrangement on the ciliated surface. The metach/onal wave is decomposed into two mutually perpendicular components, which are chosen in such a way that the direction of one of them is in the direction of the effective stroke. The magnitudes of the two components are determined by using the concept of the time of delay between adjacent cilia. The properties of the metachronal wave are then calculated as a function of the ciliary parameters.The results obtained with the present model predict that the direction of the wave propagation is strongly dependent on the type of metachronism in the direction of the effective stroke and the polarization in time and in space of the ciliary beat. The metachronal wavelength is found to depend on four parameters: the ciliary length, the angle of the arc projected on the cell surface by the ciliary tip during the recovery stroke, the degree of asymmetry of ciliary beat, and the portion of the cycle occupied by the pause. The metachronal wavelength is also found to be only weakly dependent on the ciliary frequency.At this stage there exists relatively little experimental information with which t o characterize fully the metachronal properties of ciliary systems. Even when only partial information exists, the model allows prediction, to within a certain range, of the direction of the wave propagation. It also suggests a possible mechanism for the influence of changes in environmental conditions on wave direction and wavelength. In severalcases in which full information does exist, good agreement between the experimental findings and the predictions of the model is found. According to this model it will be worthwhile to invest more effort in measuring the time and space polarization of ciliary beating and the times of delay between cilia.
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  • 119
    ISSN: 0886-1544
    Keywords: Cell motility ; chemotaxis ; mathematical model ; alveolar macrophages ; C5a ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: Phenomenological parameters from a mathematical model of cell motility [1] are used to quantitatively characterize chemosensory migration responses of rat alveolar macrophages migrating to C5a in the linear under-agarose assay, simultaneously at the levels of both single cells and cell populations. This model provides theoretical relationships between single-cell and cell-population motility parameters. Our experiments offer a critical test of these theoretical linking relationships, by comparison of results obtained at the cell population level to results obtained at the single-cell level.Random motility of a cell population is characterized by the random motility coefficient, μ (analogous to a particle diffusion coefficient), whereas single-cell random motility is described by cell speed, s, and persistence time, P (related to the period of time that a cell moves in one direction before changing direction). Population chemotaxis is quantified by the chemotactic sensitivity, χo, which provides a measure of the minimum attractant gradient necessary to elicit a specified chemotactic response. Single-cell chemotaxis is characterized by the chemotactic index, CI, which ranges from 0 for purely random motility to 1 for perfectly directed motility. Measurements of cell number versus migration distance were analyzed in conjunction with the phenomenological model to determine the population parameters while paths of individual cells in the same experiment were analyzed in order to determine the single-cell parameters.The parameter μ shows a biphasic dependence on C5a concentration with a maximum of 1.9 × 10-8 cm2/sec at 10-11 M C5a and relative minima of 0.86 × 10-8 cm2/sec at 10-7 M C5a and 1.1 × 10-8 cm2/sec in the absence of C5a; s and P remain fairly constant with C5a concentration, with s ranging from 2.1 to 2.5 μm/min and P varying from 22 to 32 min. χo is equal to 1.0 × 10-6 cm/receptor for all C5a concentrations tested, corresponding to 60% correct orientation for a difference of 500 bound C5a receptors across a 20 μm cell length. The maximum CI measured was 0.2.Values for the population parameters μ and χo were calculated from single-cell parameter values using the aforementioned theoretical linking relationships. The values of μ and χo calculated from single-cell parameters agreed with values of μ and χo determined independently from population migrations, over the full range of C5a concentrations, confirming the validity of the linking equations. Experimental confirmation of such relationships between single-cell and cell-population parameters has not previously been reported.
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  • 120
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    Cell Motility and the Cytoskeleton 17 (1990), S. 174-186 
    ISSN: 0886-1544
    Keywords: MAPs ; cold-stable microtubules ; microtubule assembly ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: Microtubules and presumptive microtubule-associated proteins (MAPs) were isolated from the brain tissues of four Antarctic fishes (Notothenia gibberifrons, N. coriiceps neglecta, Chaenocephalus aceratus, and a Chionodraco sp.) by means of a taxol-dependent, microtubule-affinity procedure (cf. Vallee: Journal of Cell Biology 92:435-442, 1982). MAPs from these fishes were similar to each other in electrophoretic pattern. Prominent in each preparation were proteins in the molecular weight ranges 410,000-430,000, 220,000-280,000, 140,000-155,000, 85,000-95,000, 40,000-45,000, and 32,000-34,000. The surfaces of MAP-rich microtubules were decorated by numerous filamentous projections. Exposure to elevated ionic strength released the MAPs from the microtubules and also removed the filamentous projections. Addition of fish MAPs to subcritical concentrations of fish tubulins at 0-5°C, induced the assembly of microtubules. Both the rate and the extent of this assembly increased with increasing concentrations of the MAPs. Sedimentation revealed that approximately six proteins, with apparent molecular weights between 60,000 and 300,000, became incorporated into the microtubule polymer. Bovine MAPs promoted microtubule formation by fish tubulin at 2-5°C, and proteins corresponding to MAPs 1 and 2 co-sedimented with the polymer. MAPs from C. aceratus also enhanced the polymerization of bovine tubulin at 33°C, but the microtubules depolymerized at 0°C, We conclude that MAPs are part of the microtubules of Antarctic fishes, that these proteins promote microtubule assembly in much the same way as mammalian MAPs, and that they do not possess special capacities to promote microtubule assembly at low temperatures or to prevent cold-induced microtubule depolymerization.
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  • 121
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    Cell Motility and the Cytoskeleton 17 (1990), S. 214-226 
    ISSN: 0886-1544
    Keywords: actin ; cytoskeleton ; dynamic instability ; protozoa ; video microscopy ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: Microtubule dynamics has been studied extensively in vitro, but comparatively little information is available on the in vivo behavior of microtubules. Here we report on the assembly, disassembly, and sliding of microtubules in the giant freshwater amoeba, Reticulomyxa. We have found that treating the cell with 0.25% trypsin induces the rapid formation of exceedingly flat areas within the reticulopodial network, allowing for the direct observation of microtubule behavior by DIC optics and computer-enhanced video microscopy. In flattened areas, microtubule sliding occurs at rates of between 1 and 6.5 μm/sec. The average rate of microtubule assembly is 1.6 μm/sec, while microtubule disassembly takes place at about 4 μm/sec and can reach up to 19.5 μm/sec. We also observed many cases where a microtubule forms a hairpin loop and eventually breaks, resulting in bidirectional disassembly from the point of breakage. Our observations demonstrate sliding of cytoplasmic microtubules in vivo. The high rates of microtubule assembly/disassembly in this cell type are difficult to reconcile with conventional views of association and dissociation processes at microtubule ends and suggest unconventional mechanisms for the growth and shrinkage of microtubules.
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  • 122
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    Cell Motility and the Cytoskeleton 17 (1990), S. 227-235 
    ISSN: 0886-1544
    Keywords: mitosis ; kinetochores ; cell division cycle ; protein phosphorylation ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: Antibodies to both the C-terminal and the N-terminal regions of the 34 kd serinethreonine specific protein kinase, p34cdc2, were used to study the distribution of this protein in dividing cells and isolated chromosomes of the Indian muntjac. p34cdc2 was found to be present throughout the cytoplasm of dividing cells. In addition, a portion of cellular p34cdc2 was localized to the centrosome, kinetochore, and intercellular bridge and along kinetochore-to-pole microtubules during cell division. Tubulin-denuded metaphase kinetochores retained their association with p34cdc2. The detection of p34cdc2 within a variety of domains of the mitotic apparatus, in addition to the previous reported association with the centrosome [Bailly et al., EMBO J. 8:3985-3995, 1989; Raibowol et al., Cell 57:393-401, 1989] suggests that p34cdc2 may play a role in events associated with anaphases A and B as well as with the transition between interphase and mitosis.
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  • 123
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    Cell Motility and the Cytoskeleton 17 (1990), S. 236-249 
    ISSN: 0886-1544
    Keywords: bundles ; cytomechanics ; photobleaching ; rheology ; viscoelasticity ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: We have previously established [Cortese and Frieden, J. Cell Biol. 107:1477-1487, 1988] that actin gels formed under shear are microheterogeneous. In this study, the effect of cross-linking (by chicken gizzard filamin), severing (by plasma gelsolin), and shear on actin microheterogeneity are investigated using fluorescence photobleaching recovery and video microscopy. We find that filamin and shear form microheterogeneous F-actin:gelsolin gels by different mechanisms. Bundling of actin:gelsolin filaments by filamin can be explained by an increase in the apparent length of the filaments due to interfilament binding, resulting in a decrease of the polymer number concentration at which filaments organize into anisotropic phases. Some intrafilament binding of filamin to actin filaments may also be present, and those filaments coated with filamin immobilize more slowly than actin under the same polymerization conditions. The length of F-actin/gelsolin filaments seems to be a major factor in controlling the extent of bundling relative to network formation. In contrast, the effect of shear on the microheterogeneity of actin:gelsolin filaments is consistent with our previous proposal that shear aligns actin filaments, allowing filament-filament interactions and phase formation to occur. Short filaments are unable to organize into branched actin networks, but they can create large aggregates under low shear. Longer actin filaments will exist as networks with variable levels of branching and are less sensitive to shear. The effect of the intensity of a shear field on the spatial distribution of actin may involve a progressively more random orientation of actin molecules and bundles. A regular pattern develops across the sample at low shear rates (0.04-1.39 s-1), and becomes very irregular at higher shear rates (〉 10 s-1). We suggest here that actin-binding proteins and shear can control the transition between isotropic networks and anisotropic phases by their effect on apparent length and local filament concentration, and also that this transition can have substantial effects on the resistance of cells to mechanical stress.
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  • 124
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    Cell Motility and the Cytoskeleton 17 (1990), S. 291-300 
    ISSN: 0886-1544
    Keywords: PtK1 keratin filaments ; electrophoresis ; autoradiography ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: Treatment of PtK1 cells with 5 mM acrylamide for 4 hr induces reversible de-phosphorylation of keratin in concert with reversible aggregation of intermediate filaments (Eckert and Yeagle, Cell Motil. Cytoskeleton 11:24-30, 1988). We have examined this phenomenon by 1) in vitro phosphorylation of isolated PtK1 keratin filaments and 2) combined treatments of PtK1 cells with both acrylamide and agents which elevate intracellular cAMP levels. PtK1 keratins were incubated in gamma-32P-ATP in the presence or absence of cAMP-dependent kinase (A-kinase) and cAMP. Levels of phosphorylation were analyzed by electrophoresis and autoradiography. Phosphorylation of keratin polypeptides (56 kD, 53 kD, 45 kD, 40 kD) occurred without added kinase, suggesting the presence of an endogenous kinase which remains with intermediate filaments in residues of Triton X-100 extracted cells. Phosphorylation levels were increased by A-kinase but not by cAMP alone, indicating the presence of cAMP-dependent phosphorylation sites in addition to sites phosphorylated by the endogenous kinase. To study the possible role of cAMP-dependent phosphorylation in acrylamide-induced aggregation of keratin filaments, we treated cells with acrylamide in the presence of 8-bromo-cAMP (brcAMP), pertussis toxin (PT), isobutylmethylxanthine (IBMX), or forskolin, which increase intracellular cAMP levels. The distribution and phosphorylation levels of keratin filaments, as well as intracellular cAMP levels, were determined for each of these treatments. In addition to aggregation and dephosphorylation of keratin filaments reported previously, treatment of cells with acrylamide alone also results in reduced levels of intracellular cAMP. 8-bromo-cAMP, IBMX, and forskolin prevent acrylamide-induced aggregation of keratin filaments and result in both normal levels of keratin phosphorylation and normal intracellular cAMP levels. PT was apparently ineffective. These observations suggest that 1) PtK1 keratins are phosphorylated by cAMP-dependent kinase and an endogenous, cAMP-independent kinase and 2) alteration of levels of cAMP-dependent phosphorylation may be involved in aggregation of keratin filaments in response to acrylamide.
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  • 125
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    Proteins: Structure, Function, and Genetics 7 (1990) 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
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  • 126
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    Proteins: Structure, Function, and Genetics 7 (1990), S. 16-31 
    ISSN: 0887-3585
    Keywords: BPTI ; dithiothreitol ; DTT-sensitive mutants ; protein folding ; random mutagenesis ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A genetic screening procedure has been developed to identify mutant forms of bovine pancreatic trypsin inhibitor (BPTI) that can fold to an active conformation but are inactivated more rapidly than the wild type protein. Small cultures of Escherichia coli containing plasmids with mutagenized BPTI genes were grown in microtiter plates, lysed, and treated with dithiothreitol (DTT). Under these conditions, unfolding and inactivation of wild-type protein has a half-time of about 10 hours. Variants of BPTI that are inactivated within 1 hour were identified by adding trypsin and a chromogenic substrate. Approximately 11,000 mutagenized clones were screened in this way and 75 clones that produce proteins that can fold but are inactivated by DTT were isolated. The genes coding for 68 “DTT-sensitive” mutant proteins were sequenced, and 25 different single amino acid substitutions at 15 of the 58 residues of the protein were identified. Most of the altered residues are largely buried in the core of the naive wild-type structure and are highly conserved among proteins homologous to BPTI. These results indicate that a large fraction of the sequence of the protein contributes to the kinetic stability of the active conformation, but it also appears that substitutions can be tolerated a most sites without completely preventing folding Because this genetics, further studies of the isolated mutants are expected to provide information about the roles of the altered residues in folding and unfolding.
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  • 127
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    Proteins: Structure, Function, and Genetics 7 (1990) 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
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  • 128
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    Proteins: Structure, Function, and Genetics 7 (1990), S. 74-92 
    ISSN: 0887-3585
    Keywords: thermostability ; bacterial lactate dehydrogenase ; allosteric regulations ; crystallography ; molecular replacement ; coenzyme binding ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Structures have been determined of Bacillus stearothermophilus “apo” and holo lactate dehydrogenase. The holo-enzyme had been co-crystallized with the activator fructose 1,6-biosphosphate. The “apo” lactate dehydrogenase structure was solved by use of the known apo-M4 dogfish lactate dehydrogenase molecule as a starting model. Phases were refined and extended from 4 Å resolution by means of the noncrystallographic molecular 222 symmetry. The R-factor was reduced to 28.7%, using 2.8 Å resolution data, in a restrained least-squares refnement in which the molecula rsymmetry was imposed as a constraint. A low occupancy of coenzyme was found in each of the four subunits of the “apo” enzyme.Further refinement proceeded with the isomorphous holo-enzyume from Bacillus Stearothermophilus. After removing the noncrystallographic constraints, the R-factor dropped from 30.3% to a final value of 26.0% with a 0.019 Å and 1.7° r.m.s. deviation from idealized bond length and angles, respectively.Two sulfate ions per subunit were included in the final model of the “apo” -from-one at the substrate binding site and one close to the molecular P -axis near the location of the fructose 1,6-bisphosphate activator. The final model of the holo-enzyme incorporated two sulfate ions per subunit, one at the substrate binding site and another close to the R-axis. One nicotinamide adenine dinucleotide coenzyme molecule per subunit and two fructose 1,6-bisphosphate molecules per tetramer were also included. The phosphate positions of fructose 1,6-bisphosphate are close to the sulfate ion near the P-axis in the “apo” model.This structure represents the first reported refined model of an allosteric activated lactate dehydrogenase. The structure of the activated holo-enzyme showed far greater similarity to the ternary complex of dogfish M4 lactate dehydrogenase with incotinamide adenine dinucleotide and oxamate than to apo-M4 dogfish lactate dehydrogenase. The conformations of nicotinamide adenine dinucleotide and fructose, 1,6-bisphosphate were also analyzed.
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  • 129
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    Proteins: Structure, Function, and Genetics 7 (1990), S. 185-197 
    ISSN: 0887-3585
    Keywords: restriction enzyme ; DNA-protein interactions ; DNA recognition ; enzyme-substrate interaction ; active site ; site-directed mutagenesis ; protein structure-function ; DNA double-strand breaks ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The EcoRI restriction endonuclease is one of the most widely used tools for recombinant DNA manipulations. Because the EcoRI enzyme has been extremely well characterized biochemically and its structure is known at 3 Å resolution as an enzyme-DNA complex, EcoRI also serves as an important model of DNA-protein interactions. To facilitate a genetic analysis of the EcoRI enzyme, we devised an in vivo DNA scission assay based on our finding that DNA double-strand breaks induce the Escherichia coli SOS response and thereby increase β-galactosidase expression from SOS::lacZ gene fusions. By site-directed mutagenesis, 50 of 60 possible point mutations were generated at three amino acids (E144, R145, and R200) implicated in substrate recognition by the crystal structure. Although several of these mutant enzymes retain partial endonuclease activity, none are altered in substrate specificity in vivo or in vitro. These findings argue that, in addition to the hydrogen bond interactions revealed by the crystal structure, the EcoRI enzyme must make additional contacts to recognize its substrate.
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  • 130
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    Proteins: Structure, Function, and Genetics 7 (1990), S. 234-248 
    ISSN: 0887-3585
    Keywords: computer modelling ; Ca2+-binding proteins ; hydrophobic binding interactions ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Crystals of troponin are stabilized by an intermolecular interaction that involves the packing of helix A from the N-terminal domain of one molecule onto the exposed hydrophobic cleft of the C-terminal domain of a symmetry related molecules. Analysis of this molecular recognition interaction in troponin C suggests a possible mode for the binding of amphiphilic helical molecules to troponin C and to calmodulin. From the template provided by this troponin C packing, it has been possible to build a model of the contact region of mastoporan as it might be bound to the two Ca2+ binding proteins. A possible binding mode of melittin to calmodulin is also proposed. Although some of the characteristics of binding are similar for the two amphiphilic peptides, the increased length of melittin requires a significant bend in the calmodulin central helix similar to that suggested recently for the myosin light chain kinase calmodulin binding peptide (Persechini and Kretsinger: Journal of Cardiovascular Pharmacology 12:501-512, 1988). Not only are the hydrophobic interactions important in this model, but there are several favorable electrostatic interactions that are predicted as a result of the molecular modeling. The regions of troponin-C and calmodulin to which amphiphilic helices bind are similar to the regions to which the neuroleptic drugs such as trifluoperazine have been predicted to bind (Strynadka and James: Proteins 3:1-17, 1988).
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  • 131
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    Proteins: Structure, Function, and Genetics 7 (1990), S. 249-256 
    ISSN: 0887-3585
    Keywords: β-barrels ; β-strand ; scaffold design ; molecular modeling ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The 8-old parallel α/β-barrel topology is encountered in proteins that display an impressive variety of functions, suggesting that this topology may be a rather nonspecific and stable folding motif. Consequently, this motif can be considered as an interesting framework to design novel proteins. It has been shown that the shape of the β-sheet portion of the barrel can be approximated by a hyperboloid. This geometric object may therefore be used as a scaffold to construct an idealized eight-standard β-barrel. To facilitate the de novo design of such structures, a collection of modelling tools has been developed allowing secondary structure elements to be mapped onto the scaffold surface and rotation and translation operations to be performed about user defined axes while evaluating their contribution to the conformational energy of the system. These tools have been applied in a systematic study assessing the φ, ψ requirements to design symmetric eight standard β barrels with optimal hydrogen bonding between adjacent β-strands. It is observed that: (a) the β-sheet structure can be closed without introducing irregular stagger between β-strands and (b) the region of φ, ψ dihedral angle space compatible with the formation of regular symmetric eight standard β-barrels coincides with the φ, ψ region corresponding to average β-strands in known protein structures, suggesting that barrel closure does not impose gross constraints on β-strand geometry.
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  • 132
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    Proteins: Structure, Function, and Genetics 7 (1990), S. 280-290 
    ISSN: 0887-3585
    Keywords: proteases ; protein turnover ; post-translational processing ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A system has been developed or the expression in E. coli of 12 of the 14 expressed mouse submandibular gland kallikreins as cassettes subcloned directly from cDNA. Using the epidermal growth factor binding protein (mGK-9) and the γ-subunit of nerve growth factor (nGK)-3, as test cases, mature processed forms, obtained as functionally active proteins, as well as various precursor forms, were isolated. The expression system described allows rapid isolation of kallikrein protein from corresponding cDNA with yields of approximately 1.0 mg of purified protein from 10 g of initial cell paste. This expression system will facilitate structure/function studies of the mouse glandular kallikrein gene family and help elucidate the regions of the mature proteins responsible for the diverse catalytic behavior and growth factors interactions observed in this family of proteins.
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  • 133
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    Proteins: Structure, Function, and Genetics 8 (1990), S. 203-212 
    ISSN: 0887-3585
    Keywords: hydrogen bonding diagram ; motifs ; helical wheel ; helical net ; protein structure ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A program is described which generates hydrogen bonding diagrams of protein structures and optionally helical wheels and helical nets. The program can also be used simply to calculate the connectivities of β-strands and to automatically extract simple structural motifs such as hairpins or Greek keys. The program greatly reduces the effort required to produce these diagrams and offers considerable flexibility in the information which can be represented. The usefulness of the program is illustrated by several examples including comparing homologous families, correlating protein structure with attributes of individual residues, and extracting all examples of the ψ-loop motif from the Brookhaven Data Bank.
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  • 134
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    Proteins: Structure, Function, and Genetics 8 (1990), S. 251-257 
    ISSN: 0887-3585
    Keywords: peroxidase ; active site ; structure conservation ; hydrophobic cluster analysis ; sequence comparison ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A number of peroxidase amino acid sequences show limited homology to short regions comprising the known active site cleft of yeast cytochrome c peroxidase. Otherwise no clear homology is visible in linear alignments between this enzyme and other peroxidases. We have subjected eight peroxidase sequences to hydrophobic cluster analysis. Our results suggest that these peroxidases are evolutionary related and that they share many folding characteristics.
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  • 135
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    Proteins: Structure, Function, and Genetics 7 (1990), S. 257-264 
    ISSN: 0887-3585
    Keywords: protein families ; structure prediction ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Hydrophobic side chains often are buried in the interior of a protein, and evolutionarily related proteins usually maintain the hydrophobic character of buried position. In this paper we shown that a pattern of hydrophobicity values derived from a set of related protein sequences is well correlated with the linear pattern of side-chain solvent accessibility values, calculated from a known protein structure representative of the sequences. In several cases, information from aligned sequences can be used to select the correct tertiary fold from a large database of protein structures.
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  • 136
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    Proteins: Structure, Function, and Genetics 7 (1990), S. 291-295 
    ISSN: 0887-3585
    Keywords: full screen editor ; consensus calculation ; secondary structure ; automatic alignment ; alignment merging ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A dedicated sequence editor ALMA, was developed for aligning many sequences of proteins or RNA molecules or longer DNA fragments. Like previously published editors, ALMA is menu directed, screen oriented, and offers similarity and consensus display. ALMA has the additional features of collective movement of sequences, acceptance of input from many sources including structure files and databases, secondary structure display, and easy merging of alignments. In order to maintain sequence integrity and save disk space, gaps and sequences are stored separately. Automatic recovery of a session is possible. Finally, The program allows interaction between manual and automatic alignment.
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  • 137
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    Proteins: Structure, Function, and Genetics 7 (1990), S. 317-334 
    ISSN: 0887-3585
    Keywords: protein structure ; computer modeling ; structure prediction ; sequence homology ; structure homology ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Comparative modeling methods are described that can be used to construct a three-dimensional model structure of a new protein from knowledge of its sequence and of the experimental structure and sequences of other members of its homology family. The methods are illustrated with the mammalian serine protease family, for which seven experimental structures have been reported in the literature, and the sequence for over 35 different protein members of the family are available. The strategy for modeling these proteins is presented, and criteria are developed for determining and assigning the reliability of the modeled structure. Criteria are described that are specially designed to help detect cases in which it is likely that the local structure diverges significantly from the usual conformation of the family.
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  • 138
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    Proteins: Structure, Function, and Genetics 7 (1990), S. 366-377 
    ISSN: 0887-3585
    Keywords: computer modeling ; protein ; structure ; α-carbons ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A procedure for the construction of complete protein structures from only αcarbon coordinates is described. This involves building the backbone by sequential addition of Pro, Gly, or Ala residues. This main chain structure is then refined using molecular dynamics. Side chains are constructed by sequential addition of atoms with intermediate molecular dynamics refinement. For α lytic protease (a structure that is mostly β sheet) a backbone root mean square deviation (RMSD) of 0.19 Å and an overall RMSD of 1.24 Å from the crystallographic coordinates are attained. For troponin C (67% β-helix), where the coordinates are available only for the α-carbons, a backbone RMSD of 0.41 Å and an overall RMSD of 1.68 Å are attained (fits kindly provided by Dr. Michael James and Natalie Strynadka). For flavodoxin a backbone RMSD of 0.49 Å and an overall RMSD of 1.64 Å were attained.
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  • 139
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    Proteins: Structure, Function, and Genetics 7 (1990), S. 378-402 
    ISSN: 0887-3585
    Keywords: conformational distance ; conformational comparison ; generalized bond matrix representation ; structure space ; evolution ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We address herein the problem of delineating the relationships between the known protein structures. In order to study this problem, methods have been developed to represent arbitrarily sized fragments of biopolymer backbone, and to compare distributions of such fragments. These methods are applied to a classification of 123 structures representing the entire set of known x-ray structures. The resulting data are analyzed (on the four-Cα length scale) to determine both the large-scale organization of the set of known structures (i.e., the relationships between large groups of structures, each comprised of proteins that are structurally related) and its local structure (i.e., the quantitative degree of similarity between any two specific structures). It is shown that the set of structures from a continuum of structural types, ranging from allhelical to all-sheet/barrel proteins. It is further demonstrated that the density of protein structures is not uniform across this continuum, but rather that structures cluster in certain regions, separated by regions of lower population. The properties of the various regions of the structural space are determined. The existence is demonstrated of strong quantitative correlations between the contents of different types of four-Cα fragments within protein structures, which imply significant constraints on the types of architecture that can occur in proteins. Analysis of the distribution of structures demonstrates some hitherto unsuspected similarities and suggests that, in some circumstances, neither structural similarity no sequence homology may be necessary conditions for evolutionary relationship between proteins. It is also suggested that these unsuspected similarities may imply similar folding mechanisms for structures of apparently different global architecture. Cases are also noted in which apparently similar structures may fold by different mechanisms. The connection between structure and dynamic properties is discussed, and a possible role of dynamics in the evolution of protein structures is suggested. The sensitivity of the methods presented herein to anomalies of structure refinement is demonstrated. It is suggested that present results provide a frame-work for analyzing experimental results on structural similarity obtained using vibrational circular dichroism spectra, which are sensitive to local backbone structure.
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    Proteins: Structure, Function, and Genetics 8 (1990), S. 173-178 
    ISSN: 0887-3585
    Keywords: mitochondria ; amino acid composition ; hydrophobicity ; composition space ; membrane protein ; transmembrane region ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A compact mitochondrial gene contains all essential information about the synthesis of mitochondrial proteins which play their roles in a small compartment of the mitochondrium. Almost no noncoding regions have been found through the gene, but a necessary set of tRNAs for the 20 amino acids is provided for biosynthesis, some of them coding different amino acids from those in a usual cell. Since the gene is so compact that the produced proteins would have some characteristic aspects for the mitrochondrium, amino acid compositions of mitochondrial proteins (mt-proteins) were examined in the 20-dimensional composition space. The results show that compositions of proteins translated from the mitochondrial genes have a distinct character having more hydrophobic content than others, which is illustrated by a clustered distribution in the multidimensional composition space. The cluster is located at the tail edge of the global distribution pattern of a Gaussian shape for other various kinds of proteins in the space. The mt-proteins are rich in hydrophobic amino acids as is a membrane protein, but are different from other membrane proteins in a lesser content of Val. A good correlation found between the base and amino acid compositions for the mitochondria was examined in comparison to those of organisms such as thermophilic bacterium having an extreme G-C-rich base composition.
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    Proteins: Structure, Function, and Genetics 8 (1990), S. 213-225 
    ISSN: 0887-3585
    Keywords: molecular modeling ; energy calculations ; δ-hemolysin ; melittin ; crystal packing ; raft ; bilayer ; membrane insertion ; channel formation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Molecular modeling and energy calculations have been used to study how δ-hemolysin and melittin helices may aggregate on membrane surfaces and insert through membranes to form channels. In these models adjacent antiparallel amphipathic helices form planar “raft” structures, in which one surface is hydrophobic and the other hydrophilic. Models of δ-hemolysin crystal structure were developed using these “rafts.” These models are based on the unit cell constants and the crystal symmetry obtained from the preliminary crystal data. Energy calculations favor channel models of δ-hemolysin with six or eight monomers per channel.
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  • 142
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    Proteins: Structure, Function, and Genetics 8 (1990), S. 280-286 
    ISSN: 0887-3585
    Keywords: circular dichroism ; secondary structure ; insulin ; insulin analogs ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Vacuum UV circular dichroism spectra measured down to 178 nm for hexameric 2-zinc human insulin, zinc-free human insulin, and the two engineered and biologically active monomeric mutants, [B/S9D] and [BS9D, T27E] human insulin, show significant differences. The secondary structure analysis of the 2-zinc human insulin (T6) in neutral solution was determined: 57% helix, 1% β-strand, 18% turn, and 24% random coil. This is very close to the corresponding crystal structure showing that the solution and solid structures are similar. The secondary structure of the monomer shows a 10-15% increase in antiparallel β-structure and a corresponding reduction in random coil structure. These structural changes are consistent with an independent analysis of the corresponding difference spectra. The advantage of secondary structure analyses of difference spectra is that the contribution of odd spectral features stemming mainly from side chain chromophores is minimized and the sensitivity of the analyses improved. Analysis of the CD spectra of T6 2-zinc, zinc-free human insulin and monomeric mutant insulin by singular value decomposition indicates that the secondary structure changes following the dissociation of hexamers into dimers and monomers are two-state processes.
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    Proteins: Structure, Function, and Genetics 8 (1990), S. 334-340 
    ISSN: 0887-3585
    Keywords: protein structure ; structural comparison ; α-β barrels ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: By exhaustive structural comparisons, we have found that about one-third of the α-helix-turn-β-strand polypeptides in α-β barrel domains share a common structural motif. The chief characteristics of this motif are that first, the geometry of the turn between the α-helix and the β-strand is somewhat constrained, and second, the β-strand contains a hydrophobic patch that fits into a hydrophobic pocket on the α-helix. The geometry of the turn does not seem to be a major determinant of the α-β unit, because the turns vary in length from four to six residues. However, the motif does not occur when there are few constraints on the geometry of the turn-for instance, when the turns between the α-helix and the β-strands are very long. It also occurs much less frequently in flat-sheet α-β proteins, where the topology is much less regular and the amount of twist on the sheet varies considerably more than in the barrel proteins. The motif may be one of the basic building blocks from which α-β barrels are constructed.
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  • 144
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    Proteins: Structure, Function, and Genetics 8 (1990), S. 341-351 
    ISSN: 0887-3585
    Keywords: conserved sequence ; diagnostic peptide ; superfamily classificaiton ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: From protein sequence comparison data found in the literature, a library was organized using peptide fragment sequences which are common to related proteins. Each of the fragments was then examined for its occurrence in all the protein superfamilies defined by the NBRF-PIR data base. We have selected those fragment peptides that appear exclusively in one or a few superfamilies, and thus made a library of fragment peptides that characterize specific superfamilies. Such characteristic peptides are, in general, five to seven residues long and contain unusually high proportions of glycine and cysteine. This collection is a useful resource for the classification and functional prediction of protein molecules.
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  • 145
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    Proteins: Structure, Function, and Genetics 8 (1990), S. 352-364 
    ISSN: 0887-3585
    Keywords: crystallography ; refinement ; structure comparison ; molecular replacement ; precision ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The structure of a small rubredoxin from the bacterium Desulfovibrio desulfuricans has been determined and refined at 1.5 Å resolution. The hairpin loop containing seven residues in other rubredoxins is missing in this 45 residue molecule, and once that fact was determined by amino acid sequencing studies, refinement progressed smoothly to an R value of 0.093 for all reflections from 5 to 1.5 Å resolution. Nearly all of the water molecules in the well-ordered triclinic unit cell have been added to the crystallographic model. As in the other refined rubredoxin models, the Fe-S4 complex is slightly distorted from ideal tetrahedral coordination.
    Additional Material: 11 Ill.
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  • 146
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    Proteins: Structure, Function, and Genetics 7 (1990), S. 1-15 
    ISSN: 0887-3585
    Keywords: α-fibrous proteins ; 4-α-helix bundle ; membrane-spanning proteins ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Additional Material: 5 Ill.
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  • 147
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    Proteins: Structure, Function, and Genetics 7 (1990), S. 52-61 
    ISSN: 0887-3585
    Keywords: molecular dynamics ; protein simulations ; dihydrofolate reductase ; trimethoprim ; drug binding ; solvation ; binding free energies ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Structural and thermodynamic interactions for the binding of trimethoprim and related congeners to the binary complex of diphydrofolate reductase (from chicken) and NADPH are explored using free energy simulation methods. Good agreement between structures from experimental X-ray refinement and molecular dynamics simulations is found for the complexes. Agreement with thermodyanmic measurements is found as well. Our thermodynamic calculations suggest that entropic contributions and desolvation thermodynamics can play a crucial role in overall bindings, and that extreme care must be taken in the use of simple model building to rationalize or predict protein-drug binding.
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  • 148
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    Proteins: Structure, Function, and Genetics 7 (1990), S. 172-184 
    ISSN: 0887-3585
    Keywords: aspartic proteases ; retroviral proteases ; sequence homology ; related structures ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The model of human immuno-deficiency virus (HIV-1) protease which was based on the crystal structure of Rous sarcoma virus (RSV) protease has been compared to the recently determined crystal structure of chemically synthesized HIV-1 protease. The overall difference between the model and crystal structure was 1.4 Å root mean square (rms) deviation for 86 superimposed Cα atoms. The position of the flexible flap differs in the model and six residues at the amino terminus were incorrectly placed. With these exceptions, all atoms of the model and crystal structure agree to 2.11 Å runs deviation. The conformation of some surface bends in the model agrees less well with the crystal structure. Identical amino acids in RSV and HIV proteases were modeled more reliably than different types of amino acids. The amino acids which form the substrate binding site were modeled most accurately to 1.2 Å rms deviation for all atoms compared to the crystal structure. This suggests that functionally significant regions of related proteins can be modeled with high accuracy. The model gave correct predictions for residues making interactions with the substrate, and thereof could be used to design inhibitors, The model based on the RSV protease structure is more similar to the experimental structure than are previous models based on the structures of non-viral aspartic proteases.
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  • 149
    ISSN: 0887-3585
    Keywords: phosphorylation ; tyrosine ; cis-peptide ; exocytosis ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Seven proteins each contain 8 to 52 tandem repeats of a unique class of oligopeptide. The consensus peptide for each is rhodopsin Tyr Pro Pro Gln Glysynapto-physin Tyr Gly Pro Gln Glysynexin Tyr Pro Pro Pro Pro Glygliadin Tyr Pro Pro Pro Gln ProRNA polymerase II Tyr Ser Pro Thr Ser Pro Serhordein Phe Pro Gln Gln Pro Gln Gln Progluten Tyr Pro Thr Ser Pro Gln Gn Gly TyrAlthough there is obvious variations of sequence and of length, the penta-to nonapeptides share an initial Tyr(or Phe) and have high Pro contents and abundant Gly, Gln, and Ser. We have evaluated helical models that both recognize the uniqueness of these sequence repeats and accommodate variations on the basic theme.We have developed a group of related heical model for these proteins with about three oligopeptide repeats per turn of 10-20 Å. These models share several common features: Most of the φ dihedral angels are -54°, to accommodate Pro at all positions expect the first (Tyr). Except for the β-turns, most ψ dihedral angles are near +140° as found in polyproline. Each oligopeptide has at least one β-turn; several have two. Some contains a cis-Tyr, Pro peptide bond; a few have a cis-bond plus one β-turn. Tyr side chains vary from totally exposed to buried within the helices and could mode to accommodate either external hydrophobic interactions or phosphorylation. The several related structures seem to be readily interconverted without major change in the overall helical parameters, and therein may lie the key to their functions.
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  • 150
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    Proteins: Structure, Function, and Genetics 7 (1990), S. 156-171 
    ISSN: 0887-3585
    Keywords: β-lactamase ; penicillinase ; penicillin-binding protein ; penicillin antibiotics ; X-ray diffraction ; protein structure prediction ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Two crystal (A and B) of the 29,500 Da Class A β-lactamase (penicillinase) from Bacillus licheniformis 749/C have been examined crystallographically. The structure of B-form crystals has been solved to 2 Å resolution, the starting model for which was a 3.5 Å structure obtained from A-form crystals. The β-lactamase has an α + β structure with 11 helices and 5 β-strands seen also in a peinicilin target DD-peptidase of Streptomyces R61.1 Atomic parameters of the two molecules in the asymmetric unit were refined by simulated annealing at 2.0 Å resolution. The R factor is 0.208 for the 27,330 data greater than 3 (F), with water molecules excluded from the model. The catalytic Ser-70 is at the N-terminus of a helix and is within hydrogen bonding distance of conversed Lys-73. Also interacting with the Lys-73 are Asn-132 and the conserved Glu-166, which is on a potentially flexible helix-containing loop. The structure suggests the binding of β-lactam substrates is facilitated by interactions with Lys-234, Tyhr-235, and Ala-237 in a conserved β-strand peptide, which is antiparallel to the β-lactam's acylamido linkage; an exposed cavity near Asn-170 exits for acylamido Substituent. The reactive double bond of clavulanate-type inhibitors may interact with Arg-244 on the fourth β-strand. A very similar binding site architecture is seen in the DD-peptidase.
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  • 151
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    Proteins: Structure, Function, and Genetics 7 (1990), S. 198-204 
    ISSN: 0887-3585
    Keywords: protein stability ; protein design ; strain ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: An attempt has been made to identify residues in T4 phage lyoszyme that may have strained conformations and, by appropriate site-directed replacements, to reduce this strain and thus increase the thermostability of the protein. Valine 131, within α-helix 126-134, was identified as a potential candidate. Its side-chain rotational as a potential candidate. Its side-chain rotation angle, χ1, differs by approximately 18° from the low-energy trans configuration. In addition, it is largely solvent exposed, yet is held in a rigid conformation. The mutant protein with Val 131 replaced by alanine temperature 0.9°C higher than that of wildtype lyoszyme at pH 2.8. As a control, The mutant Val 131 → Thr was also constructed and its melting temperature was found to be marginally lower than wild type. Higher-resolution crystal structure determination of the mutant lysozymes show that their structure are virtually identical with that of wild-type lyoszyme, except for the Val → Ala or Val → Thr replacement. Analysis of the different structures suggests that the design of the Val→Ala substitution was, in principle, successful, although the apparent gain in stability caused by reduction in strain is modest and is somewhat offset by the loss of hydrophobic interactions and by entrophic effects. The results also help to provide a structural retionalization that alanine has a higher helix propensity than valine or theronine.
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  • 152
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    Proteins: Structure, Function, and Genetics 7 (1990), S. 265-279 
    ISSN: 0887-3585
    Keywords: potential of means force ; motions of helices ; correlated fluctuations ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The concept of secondary structure motions is examined in a molecular dynamics simulation of the protein myohemerythrin. We extracted from the simulation a corresponding trajectory of helices and demonstrated that the fluctuations of the protein are dominated by a rigid shift of these secondary structure elements. The relative motions of the helices are regular, with no clear periodicity. They are bounded by ∼2 for the center of mass motions and by 20° for the relative orientations. The potential of mean force for the interactions of the helices was calculated, and the correlations between the different extended motions were investigated. It shown that the one-dimensional mean force potentials are close to quadratic for most of the helices coordinates. The anharmonicity is reflected by changes in the direction of the normal modes as a function of the energy and by the existence of multiple free energy minima for the helices packing. The multiple conformations are associated with a single type of secondary structure coordinate: the angle that describes the relative orientation of the helices in a plane perpendicular to the line connecting their center of mass.
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  • 153
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    Proteins: Structure, Function, and Genetics 7 (1990), S. 299-305 
    ISSN: 0887-3585
    Keywords: protein stability ; guanidine hydrochloride denaturation ; conformational changes ; polypeptide backbone ; alanine insertion ; glycine insertion ; circular dichroism spectra ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Single alanine and glycine insertions were introduced at 20 randomly selected positions in staphylococcal nuclease. The resulting changes in catalytic activity and in stability to guanidine hydrochloride denaturation indicate that the native state structure is frequently able to accommodate the extra residue without great difficulty, even insertions within secondary structural elements such as alpha helices and beta sheets. On average, an inserted residue reduces the free energy of denaturation (ΔGH2O) by an amount roughly comparable to an alanine or glycine substitution for one of the residues flanking the site of insertion. Several positions outside of the enzyme active site were found where insertions, but not substitutions, lead to structural changes that modify catalytic activity and the circular dichroism spectrum. Amino acid insertions represent a virtually unexplored class of genetic mutation that may prove complementary to amino acid substitutions for engineering proteins with altered functional and structural properties.
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  • 154
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    Proteins: Structure, Function, and Genetics 7 (1990), S. 358-365 
    ISSN: 0887-3585
    Keywords: synthetic myoglobins ; X-ray crystallography ; protein engineering ; heme proteins ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Crystal have been grown of myoglobin produced in Escherichia coli from a synthetic gene, and the structure has been solved to 1.9 Å resolution. The space group of the crystals is P6, which is different from previously solved myoglobin crystal forms. The synthetic myoglobin is essentially identical to myoglobin isolated from sperm whale tissue, except for the retention of the initiator methionine at the N-terminus and the substitution of asparagine for aspartic acid at position 122. Superposition of the coordinates of native and synthetic sperm whale myoglobins reveals only minor changes in the positions of main chain atoms and roeientation of some surface side chains. Crystals of variant of the “synthetic” myoglobin have also been grown for structural analysis of the role of key amino acid residues in ligand and specificity.
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  • 155
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    Proteins: Structure, Function, and Genetics 8 (1990), S. i 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
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  • 156
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    Proteins: Structure, Function, and Genetics 8 (1990), S. 14-22 
    ISSN: 0887-3585
    Keywords: computation ; conformational energy ; interactions in proteins ; protein folding ; twisted β-sheets ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The preferred structural pattern of antiparallel β-barrels in proteins, described as the right-handed tilting of the peptide strands with respect to the axis of the barrel, is accounted for in terms of intra- and interchain interaction energies. It is related to the preference of β-sheets for right-handed twisting. Conformational energy computations have been carried out on three eight-stranded antiparallel β-barrels composed of six-residue strands, in which L-Val and Gly alternate, and having a right-handed, a left-handed, or no tilt. After energy minimization, the relative energies of these structures were 0.0, 8.6, and 46.1 kcal/mol, respectively; i.e., the right-tilted β-barrel is favored energetically, in agreement with anti-parallel β-barrels observed in proteins. Tilting of the barrel is favored, relative to the nontilted structure, by both intra- and interstrand interactions, because tilting allows better packing of the bulky side chains. On the other hand, the energy difference between the left- and right-tilted barrels arises essentially from intrachain interactions. This is a consequence of the preference of β-sheets for a right-handed twist. Space limitations inside the barrel are satisfied if there is an alternation of bulky residues and residues with small or no side chain (preferably Gly) in neighboring positions on adjacent strands. Such a pattern is seen frequently in antiparallel β-barrels of globular proteins. The computations indicate that a structure with Val…Gly pairs can be accommodated in a β-barrel with no distortion.
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  • 157
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    Proteins: Structure, Function, and Genetics 8 (1990) 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
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  • 158
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    Proteins: Structure, Function, and Genetics 8 (1990), S. 133-155 
    ISSN: 0887-3585
    Keywords: evolution ; alignment ; globins ; phycocyanin ; helix interfaces ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Globins and phycocyanins are two classes of proteins with different function, different ligands, and no substantial sequence similarity, yet the conformations of their polypeptide chains show very similar folding patterns. Does this arise from a genuine, albeit very distant, evolutionary relationship, or does it represent a common solution of a structural problem? We address this question by a very detailed comparison of the structures of the two protein families. An analysis of the helices and their interactions shows many features common to globins and phycocyanins, including some exceptional features of the globins such as a 3-10 C helix and the unusual “crossed-ridge” packing pattern at the B/E helix interfaces. We conclude that the evidence supports the hypothesis of distant evolutionary relationship between globins and phycocyanins.
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  • 159
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    Cell Motility and the Cytoskeleton 15 (1990), S. 23-33 
    ISSN: 0886-1544
    Keywords: centrosome ; cytaster ; MTOG ; pericentriolar material ; 51 kD protein ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: Miniasters formed in mitotic sea urchin egg after treatment with 5% hexylene-glycol were investigated with the combined techniques of indirect immunofluo-rescence using anti-tubulin and anti-51 kD protein antibodies and electron microscopy.The formation of miniasters was dependent on the mitotic cycle. In the cytoplasm of eggs treated with hexyleneglycol at early prometaphase, a small number of microtubule fragments was observed, whereas in those treated at pro-metaphase, many miniasters and microtubule fragments were seen. When treated at metaphase, we found a great number of miniasters: 250-350 in one egg. In contrast, no miniasters were seen in eggs treated at anaphase, although many long microtubules that spread throughout the cytoplasm were observed. In the eggs treated at telophase, we scarcely noticed microtubule structures in the cytoplasm. In the center of miniasters, granules were found, showing the same size and electron density as those of the microtubule-organizing granules (MTOGs). Furthermore, the 51 kD protein, a component of the centrosome and mitotic spindle, was observed to be localized in the region of miniasters.
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  • 160
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    Cell Motility and the Cytoskeleton 15 (1990), S. 71-75 
    ISSN: 0886-1544
    Keywords: Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
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  • 161
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    Cell Motility and the Cytoskeleton 15 (1990), S. 67-70 
    ISSN: 0886-1544
    Keywords: Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
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  • 162
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    Cell Motility and the Cytoskeleton 15 (1990), S. 99-110 
    ISSN: 0886-1544
    Keywords: ascaris ; nematode ; nematoda ; sperm ; amoeboid motility ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: In a highly synchronous process, the immotile spermatids of Ascaris suum extend pseudopods and become rapidly crawling sperm when treated with an extract from the glandular vas deferens of the male under strict anaerobic conditions. Within 9-12. min, a pseudopod develops, elongates rapidly, and exhibits a continuous flow of membrane specializations, the villipodia, from tip toward base. When attached to acid-washed glass, the pseudopod pulls the cell body along at speeds exceeding 70 μm/min. The pseudopod length remains constant while retrograde flow of villipodia proceeds at the same rate as the sperm's forward movement. Cohorts of about 15 villipodia form at the leading edge, move reaward together, and disappear at the junction of pseudopod and cell body. These are the termination of branched, refringent fibers, which extend the length of the pseudopod. The latter are the fiber complexes that form its cytoskeleton (Sepsenwol et al.: Journal of Cell Biology 108:55-66, 1989). Locomoting cells sometimes change direction when another crawls by and follow each other. When cells are exposed to air, forward movement ceases in a predictable pattern: the forward extension of the leading edge ceases, the pseudopod shortens from the base, and the cell body continues to be pulled forward. These data contribute to a model for Ascaris sperm amoeboid motility in which independent processes of continuous extension at the leading edge and continuous shortening at the base of the pseudopod act to propel the cell forward.
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  • 163
    ISSN: 0886-1544
    Keywords: organelle translocation ; translocator ; actin-dependent ATPase ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: The dispersion of carotenoid droplets in permeabilized goldfish xanthophores is dependent on ATP, F-actin, and cytosol. We report here that the motor (ATPase, translocator) resides with the permeabilized cell remnants and not in the cytosol. We also report that the carotenoid droplets have an ATPase that is not conventional myosin, dynein, or an ion pump. Its activity appears to correlate with the actin content of the carotenoid droplet preparation. A carotenoid droplet protein of Mr 72,000 (p72) is shown to be labeled by irradiation with 8-azido-ATP with concomitant loss of ATPase activity of the carotenoid droplets. We propose that this protein may be the ATPase responsible for carotenoid droplet dispersion.
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  • 164
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    Cell Motility and the Cytoskeleton 15 (1990), S. 139-146 
    ISSN: 0886-1544
    Keywords: organelle translocation ; cytosolic factor ; secretion ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: Organelle translocations are essential cellular processes. Although much progress has been made with regards to microtubule-dependent organelle translocations, little is known about actin-dependent organelle translocation(s) except cytoplasmic streaming in Nitella. On the other hand, there is indirect evidence that actindependent organelle translocation may be involved in secretion. We now present evidence that the dispersion of the pigment organelles carotenoid droplets in goldfish xanthophores is apparently actin dependent and that this process may be related to secretory processes. We show that, in digitonin-permeabilized goldfish xanthophores, the pigment organelles can be induced to disperse by a combination of cAMP, ATP, and xanthophore cytosol. This induced dispersion is inhibited by DNase I, phalloidin, or anti-actin, but not by anti-tubulin or anti-intermediate filament proteins, suggesting a dependence on F-actin. Since the dispersion of carotenoid droplets and secretion both involve outward translocation of organelles, we tested the possibility that cytosols of secretory tissues have similar activity. Such activity was indeed found in different tissues, apparently in parallel with the secretory activity of the tissues, suggesting that pigment dispersion in xanthophores and some secretory processes may share a common component.
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  • 165
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    Cell Motility and the Cytoskeleton 15 (1990), S. 156-161 
    ISSN: 0886-1544
    Keywords: microtubule structure ; microtubule assembly ; electron microscopy of microtubules ; polymer stabilization ; microtubule-capping structures ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: Microtubules contain in their lumens distinct structures (plugs) that influence their dynamic behavior in vitro. As observed by electron microscopy, plugs are stainoccluding structures 10-30 nm in length that occur along the lengths and at the ends of microtubules. Plugs occur at a frequency of 20-40% at the ends of microtubules assembled from cycled microtubule protein containing MAPs. While the composition of plugs is not known, preliminary evidence suggests that they are accretions of tubulin, that they are labile, and that they are more common in preparations containing MAPs. When polymers are induced to depolymerize by endwise subuit dissociation, the frequency of plugged microtubule ends increases transiently, suggesting that plugs temporarily stabilize microtubules. The functional significance of plugs may be that they prevent the sudden complete loss of microtubules through catastrophic disassembly. It is possible that plugs, by slowing the rate of disassembly, enable a polymer to add GTP-tubulin subunits, thereby forming a stabilizing GTP-cap. These observations suggest that plugs may stabilize polymers and account for the frequent transitions from shortening to growing phases that characterize dynamic instability.
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  • 166
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    Cell Motility and the Cytoskeleton 17 (1990), S. 95-105 
    ISSN: 0886-1544
    Keywords: colchicine-tubulin ; neurite growth ; process extension ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: We have injected process-bearing PC12 cells with colchicine-tubulin mixed with either fluorescein-dextran or a rhodamine-labelled tubulin analogue to determine the role of microtubule polymerization in neurite elongation. Colchicine-tubulin is a specific, substoichiometric poison of microtubule assembly. We have shown that colchicine-tubulin does not cause existing PC12 microtubules to disassemble, and yet can inhibit the assembly of rhodamine-tubulin injected along with it. In population s'udies of neurite outgrowth in injected and uninjected cells, we find that colchicine-tubulin substantially inhibits neurite extension from injected cells over a wide variety of concentrations. In acute time-course studies of injected cells, we find that colchicine-tubulin does not block neurite outgrowth until the injectate reaches the neurite tip. Thereafter, however, it blocks process elongation completely. Thus we can conclude that microtubule polymerization in the region of the growth cone is an important element in neurite elongation. While polymerization at the cell body may be important in supplying subunits to the distal neurite, it does not play a direct role in process extension.
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  • 167
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    Cell Motility and the Cytoskeleton 16 (1990), S. 182-189 
    ISSN: 0886-1544
    Keywords: cell division ; receptors ; neurotransmitter ; micronlaments ; mitosis ; cytokinesis ; sea urchin eggs ; microtubules ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: Propranolol, a β-adrenergic receptor blocker, blocks the formation of the cleavage furrow, while karyokinesis is unaffected during first division in the sea urchins Paracentrotus lividus or Lytcchinus pictus. This effect is reversed by adrenalin, indicating that it is mediated by an adrenergic mechanism. The staining of F-actin microfilaments by rhodamine phalloidin in eggs in which the cleavage is blocked by the drug has revealed that propranolol affects both the distribution and the organization of actin microfilaments. A low-voltage scanning electron microscopy (LVSEM) study of microvilli in these eggs shows an extensive rearrangement of the egg surface. Anti-tubulin immunofluorescence microscopy of eggs treated with propranolol shows that they form normal mitotic asters. This indicates that while cleavage is affected, mitotic spindle formation is not. These results suggest that neurotransmitter monoamines known to be present in the sea urchin egg might be involved in the reorganization of the actin cytoskeleton underlying the formation of the cleavage furrow.
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  • 168
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    Cell Motility and the Cytoskeleton 17 (1990), S. 59-67 
    ISSN: 0886-1544
    Keywords: Polytoma papillatum ; Megaselia scalaris ; protofilament ; mitosis ; meiosis ; spindle ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: The association of incomplete microtubule assemblies with either another incom-plete structure or complete microtubules was studied in two organisms, the phytoflag-ellate Polytoma papillatum and the phorid fly Megaselia scalaris, using transmission electron microscopy. In the alga, hook-shaped appendages on cytoplasmic and spindle microtubules were detected. These resulted from the lateral association of a curved ribbon of protofilaments with the surface of a complete microtubular wall. In the fly, an S-shaped protofilament sheet was found embedded in the kinetochore plate of a prometaphase I spematocyte. Tracing of the S-shaped element towards the spindle pole revealed that it was formed by the lateral junction of two curved protofilament sheets. In all cases, the C-shaped protofilament sheets represented the endings of complete micro-tubules. Incomplete microtubules are generally considered as representing intermediates of microtubule assembly and disassembly. Since high molecular weight proteins are believed to be responsible for maintaining microtubule-microtubule spacing, it is hypo-thesized that the endings of growing and shrinking microtubules are sparsely studded with these proteins; their depletion allows lateral microtubule contacts. In addition, the microtubule-microtubule contacts may be rendered possible by the flexibility of the slender elongated microtubule-associated molecules. Relatively long C-shaped proto-filament appendages (0.6-1.4 μm) were detected in this study. Therefore, it is plausible to assume that the protofilament sheets are stabilized by contact with one another or with an intact tubule wall.
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  • 169
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    Cell Motility and the Cytoskeleton 16 (1990) 
    ISSN: 0886-1544
    Keywords: Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
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  • 170
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    Cell Motility and the Cytoskeleton 16 (1990), S. 121-132 
    ISSN: 0886-1544
    Keywords: microfilaments ; cytochalasin ; cell shape ; integrins ; intermediate filaments ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: Modulation of the synthesis and secretion of extracellular matrix proteins and matrix-degrading metalloproteases by rabbit synovial fibroblasts in an important model system for studying the control of tissue-specific gene expression. Induction of collagenase expression is correlated with changes in cell shape and actin filament distribution, but the role of the cellular cytoskeleton in the sustained synthesis and secretion of metalloproteases has not been closely examined. When cells were allowed to respread after rounding by trypsin or cytochalasin, two known metalloprotease inducers, reformation of stress fibers was observed within 2 h in the presence of serum. In the absence of serum, trypsin-treated cells did not respread substantially, even after 24 h in culture. In contrast, cytochalasin-treated cells recovered almost as rapidly in the absence as in the presence of serum, showing reformation of well-formed microfilament bundles within 30 min of drug removal, especially at the spreading cell edges. High resolution electron-microscopic views of detergent-extracted cytoskeletons confirmed the rapid rebundling of peripheral microfilaments. Acrylamide-treated cells fell between these two extremes, spreading slowly in the absence of serum, but almost as rapidly as cytochalasin-treated cells in its presence. Reestablishment of normal intermediate filament distribution generally lagged slightly behind actin for all treatments, and intermediate filaments always appeared to spread back into the cellular cytoplasm within the confines of the reforming peripheral microfilament bundles. No obvious interaction between these two cytoskeletal elements was observed after any treatment, and no specific role for intermediate filaments in modulating gene expression in these cells is suggested by these results. The serum dependence displayed after trypsin or acrylamide treatment may be due to the disturbances in fibronectin synthesis observed in these cells and is consistent with evidence that both induction and sustained expression of matrix-degrading metalloprotease may involve signals transduced through plasma membrane matrix receptors (integrins).
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  • 171
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    Cell Motility and the Cytoskeleton 16 (1990), S. 204-213 
    ISSN: 0886-1544
    Keywords: kinesin ; molecular structure ; immunoaffinity purification ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: Previous studies with monoclonal antibodies indicate that sea urchin kinesin contains two heavy chains arranged in parallel such that their N-terminal ends fold into globular mechanochemical heads attached to a thin stalk ending in a bipartitetail [Scholey et al. 1989]. In the present, complementary study, we have used the monoclonal antikinesin. SUK4, to probe the quaternary structure of sea urchin (Strongylocentrotus purpuratus) kinesin. Kinesin prepared from sea urchin cyto-sol sedimented at 9.6 S on sucrose density gradients and consisted of 130-kd heavy chains plus an 84-kd/78 kd doublet (1 mol heavy chain: 1 mol doublet determined by gel densitomctry). Low levels of 110-kd and 90-kd polypeptides were sometimes present as well. The 84-kd/78 kd polypeptides are thought to be light chains because they were precipitated from the kinesin preparation at a stoichiometry of one mol doublet per 1 mol heavy chain using SUK4-Sepharose immunoaffinity resins. The 110-kd and 90-kd peptides, by contrast, were removed using this immunoadsorption method. SUK4-Sepharose immunoaffinity chromatography was also used to purify the 130-kd heavy chain and 84-kd/78-kd doublet (1 mol heavy chain: 1 mol doublet) directly from sea urchin egg cytosolic extracts, and from a MAP (microtubule-associated protein) fraction eluted by ATP from microtubules prepared in the presence of AMPPNP but not from microtubules prepared in ATP. The finding that sea urchin kinesin contains equi-molar quantities of heavy und light chains, together with the aforementioned data on kinesin morphology, suggests that native sea urchin kinesin is a tetramer assembled from two light chains and two heavy chains.
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  • 172
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    Cell Motility and the Cytoskeleton 16 (1990) 
    ISSN: 0886-1544
    Keywords: Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
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  • 173
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    Cell Motility and the Cytoskeleton 17 (1990) 
    ISSN: 0886-1544
    Keywords: Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
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  • 174
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    Cell Motility and the Cytoskeleton 16 (1990), S. 251-265 
    ISSN: 0886-1544
    Keywords: Ciliary motility ; inclination ; polarity of beating ; active sliding velocity ; sliding translocation rate ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: Depolarization-induced cycles of a frontal cirrus of Stylonychia were investigated by applying methods of axial-view analysis of the cilia, high-speed microcinématography, and step voltage-clamp. Rising depolarization (from 3 mV to 7ge; 30mV) increased the rate of beating from zero to maximally 58 Hz. During cyclic activity, the axis of the beat cone of a proximal segment of the cirrus was inclined by 60° (0° = perpendicular to cell surface), and was always oriented 90° counterclockwise to the power stroke. With the stimulus amplitude rising, the orientations of the power stroke and inclination were increasingly shifted in more counterclockwise directions by up to 80° After correction for inclination ( = normalization), and following planification of the track of the segment, we determined the following properties of the cycle during depolarization: The course of the cycle tended to be rounded, i.e., the ratio of major over minor amplitudes (= spatial polarity) approximated a value of 1.6 which is only two thirds of maximal spatial polarity observed during hyperpolarization. The angular velocity generally increased with rising steps of depolarization; up to +5 mV (and comparable to hyperpolarization-induced responses), the velocity maximum occurred during the return stroke. With depolarizations ≥7 mV the angular velocity maximum shifted to the power stroke so that the temporal polarity (rates of power stroke over rates of return stroke) increased from 0.4 to 1.6. Calculations of the angular velocity as referred to the proximal ciliary segment level suggest active sliding rates (between 5 and 30 nm/ms) of identified pairs of doublet microtubules. Ciliary frequency is a function of the rate of reorientation of the cyclic track; this parameter, which corresponds to the rate of translocation of active sliding between pairs of doublets, grew with the amplitude of depolarization. Translocation rates were high during transitions between the beat phases (power stroke, return stroke), and were reduced during these phases. Orientational polarograms of the mean rates of both active sliding and sliding translocation show properties of discreteness as well as continuity. The depolarization-induced changes in inclination, and the inferred patterns of sliding rate and sliding translocation rate, are compared with previous results from hyperpolarization-dependent activation of the same motor organelle.
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  • 175
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    Proteins: Structure, Function, and Genetics 7 (1990), S. 41-51 
    ISSN: 0887-3585
    Keywords: DNA binding proteins ; maximum likelihood ; CRP ; finite mixtures ; transcription regulation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Statistical methodology for the identification and characterization of protein binding sites in a set of unaligned DNA fragments is presented. Each sequence must contain at least one common site. No alignment of the sites is required. Instead, the uncertainty in the location of the sites is handled by employing the missing information principle to develop an “expectation maximization” (EM) algorithm. This approach allows for the simultaneous identification of the sites and characterization of the binding motifs. The reliability of the algorithm increases with the number of fragments, but the computations increase only linearly. The method is illustrated with an example, using known cyclic adenosine monophophate receptor protein (CRP) binding sites. The final motif is utilized in a search for undiscovered CRP binding sites.
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  • 176
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    Proteins: Structure, Function, and Genetics 7 (1990), S. 99-111 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Additional Material: 7 Ill.
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  • 177
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    Proteins: Structure, Function, and Genetics 7 (1990), S. 205-214 
    ISSN: 0887-3585
    Keywords: protein secondary structures ; circular dichroism ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Additional Material: 8 Ill.
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  • 178
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    Proteins: Structure, Function, and Genetics 7 (1990), S. 227-233 
    ISSN: 0887-3585
    Keywords: rhinovirus receptor ; ICAM-1 ; structure prediction ; immunoglobulin superfamily ; docking receptor to virus ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A model has been built of the amino-terminal domain of the intercellular adhesion molecule-1 (ICAM-1), the receptor for most human rhinovirus serotypes. The model was based on sequence and presumed structural homology to immunoglobulin constant domains. It fits well into the putative receptors attachment site, the canyon, on the human rhinovirus-14 (HRV14) surface in a manner consistent with most of the mutational data for ICMA-1 (Staunton, D. E., Dustin, M. L., Erickson, H. P., Springer, T. A. Cell, in press, 1989) and HRV14 (Colonno, R. J., Condra, J. H., Mizutani, S., Callahan, P. L., Davies, M. E., Murcko, M. A. Proc. Natl. Acad. Sci. U.S.A. 85: 5449-5453, 1988).
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  • 179
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    Proteins: Structure, Function, and Genetics 8 (1990), S. 30-43 
    ISSN: 0887-3585
    Keywords: molecular mechanics ; solvation energy ; trypsin ; energy minimization ; side chains ; protein crystallography ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A “knowledge-based” method of predicting the unknown structure of a protein from a homologous known structure using energetics to determine a sidechain conformation is proposed. The method consists of exchangin the residues in the known structure for the sequence of the unknown protein. Then a conformational search with molecular mechanics energy minimization is done on the exchanged residues. The lowest energy conformer is the one picked to be the predicted structure. In the structure of bovine trypsin, the importance of including a solvation energy term in the search is demonstrated for solvent accessible residues, while molecular mechanics alone is enough to correctly predict the conformation of internal residues. The correctness of the model is assessed by a volume error overlap of the predicted structure compared to the crystal structure. Finally, the structure of rat trypsin is predicted from the crystal structure of bovine trypsin. The sequences of these two proteins are 74% identical and all of the significant changes between them are on external residues. Thus, the inclusion of solvation energy in the conformational search is necessary to accurately predict the structure of the exchanged residues.
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  • 180
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    Proteins: Structure, Function, and Genetics 8 (1990), S. 386-397 
    ISSN: 0887-3585
    Keywords: LGIC superfamily ; proto-binding site ; cys-loop motif ; docking model ; anionic site ; specificity residue ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A generalized model is presented of agonist binding to ligand-gated ion channels (LGICs). Broad similarity in the structure of agonists suggests that the binding sites of LGICs may have evolved from a protobinding site. Aligned sequence data identified as a candidate for such a site a highly conserved 15 residue stretch of primary structure in the N-terminal extracellular region of all known LGIC subunits. We modeled this subregion, termed the cys-loop, as a rigid, amphiphilic β-hairpin and propose that it may form a major determinant of a conserved structural binding cleft.In the model of the binding complex (1) an invariant aspartate residue at position 11 of the cys-loop is the anionic site interacting with the positively charged amine group of agonists, (2) a local dipole within the π-electron system of agonists is favorably oriented in the electrostatic field of the invariant aspartate, (3) the ε ring-proton of a conserved aromatic residue at the turn of the cys-loop interacts orthogonally with the agonist α-electron density at its electronegative center, and (4) selective recognition is partly a result of the type of amino acid residue at position 6 of the cys-loop. Additionally, the formation of a hydrogen bond between the electronegative atom of the π-electron system of agonist and a complementary group in the receptor may be important in the high-affinity binding of agonists.
    Additional Material: 5 Ill.
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  • 181
    ISSN: 0887-3585
    Keywords: gonadotropin-releasing hormone ; molecular dynamics ; nuclear magnetic resonance ; antagonist design ; conformation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The introduction of conformational constraints into a flexible peptide hormone can be exploited to develop models for the conformation required for receptor binding and activity. In this review, we illustrate this approach to analog design using our work on antagonists of gonadotropin-releasing hormone (GnRH). Design of a conformationally constrained, competitive antagonist of GnRH, cyclo[Δ3,4 Pro-D4ClPhe-DTrp-Ser-Tyr-DTrp-NMeLeu-Arg-Pro-βAla], led to the prediction of its bioactive conformation. Template forcing experiments show that this conformation is accessible to other active GnRH analogs. Two-dimensional NMR studies verified the predicted conformation in solution. The predicted binding conformation has recently been used to design two new analogs incorporating side chain-side chain linkages suggested by the conformational model: These analogs were synthesized and the one predicted to be most similar to the parent conformation had equivalent potency while the second, designed to refine the conformational hypothesis, was found to exhibit enhanced potency, thus confirming the original binding conformation hypothesis. These compounds and their derivatives now provide a new class of GnRH antagonists possessing both high biological potency and limited conformational flexibility, thus making them ideal for both biophysical and structure-activity studies.
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  • 182
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    Proteins: Structure, Function, and Genetics 8 (1990), S. 195-202 
    ISSN: 0887-3585
    Keywords: simulated annealing ; computer-aided drug design ; substrate docking ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The Metropolis technique of conformation searching is combined with rapid energy evaluation using molecular affinity potentials to give an efficient procedure for docking substrates to macromolecules of known structure. The procedure works well on a number of crystallographic test systems, functionally reproducing the observed binding modes of several substrates.
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  • 183
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    Proteins: Structure, Function, and Genetics 8 (1990), S. 226-236 
    ISSN: 0887-3585
    Keywords: protein structure ; ionic pores ; neural membranes ; protein design ; energy minimization ; molecular dynamics ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Channel proteins are transmembrane symmetric (or pseudosymmetric) oligomers organized around a central ionic pore. We present here a molecular model of the pore forming structures of two channel proteins with different primary structures and oligomeric size: the voltage-sensitive sodium channel and the nicotinic cholinergic receptor. We report low-energy arrangements of α-helical bundles calculated by semiempiricial potential energy functions and optimization routines and further refined using molecular dynamics. The ion-conducting pore is considered to be a symmetric or pseudosymmetric homooligomer of 3-5 amphipathic α-helices arranged such that the polar residues line a central hydrophilic pathway and the apolar residues face the hydrophobic bilayer interior. The channel lining exposes either charged (Asp, Glu, Arg, Lys) or polar-neutral (Ser, Thr) residues. A bundle of four parallel helices constrained to C4 symmetry, the helix axis aligned with the symmetry axis, and the helices constrained to idealized dihedral angles, produces a structure with a pore of the size inferred for the sodium channel protein (area ∼ 16 Å2). Similarly, a pentameric array optimized with constraints to maintain C5 symmetry and backbone torsions characteristic of α-helices adopts a structure that appears well suited to form the lining of the nicotinic cholinergic receptor (pore area ∼ 46 Å2). Thus, bundles of amphipathic α-helices satisfy the structural, energetic, and dynamic requirements to be the molecular structural motif underlying the function of ionic channels.
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  • 184
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    Proteins: Structure, Function, and Genetics 8 (1990) 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
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  • 185
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    Proteins: Structure, Function, and Genetics 8 (1990), S. 377-385 
    ISSN: 0887-3585
    Keywords: structure deteremination ; two-dimensional NMR ; molecular mechanics ; molecular dynamics ; conformational equilibrium ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Structure determination of small proteins using NMR data is most commonly pursued by combining NOE derived distance constraints with inherent constraints based on chemical bonding. Ideally, one would make use of a variety of experimental observation, not just distance constraints. Here, coupling constant constraints have been added to molecular mechanics and molecular dynamics protocols for structure determination in the form of a psuedoenergy function that is minimized in a search for an optimum molecular conformation. Application is made to refinement of a structure for a 77 amino acid protein involved in fatty acid synthesis, Escherichia coli acyl carrier protein (ACP). 54 3JHNα coupling constants, 12 coupling constants for stereospecifically assigned side chain protons, and 450 NOE distance contraints were used to calculate the 3-D structure of ACP. A three-step protocol for a molecular dynamics calculation is described, in analogy to the protocol previously used in molecular mechanics calculations. The structures calculated with the molecular mechanics approach and the molecular dynamics apporach using a rigid model for the protein show similar molecular energies and similar agreement with experimental distance and coupling constant constraints. The molecular dynamics approach shows some advantage in overcoming local minimum problems, but only when a two-state averaging model for the protein was used, did molecular energies drop significantly.
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  • 186
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    Proteins: Structure, Function, and Genetics 7 (1990), S. 93-98 
    ISSN: 0887-3585
    Keywords: protein conformation ; CONGEN ; immunoglobulin ; hydrogen bond ; digoxin ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The mouse hybridoma cell line 40-150 scretes antibodies with high affinity towards the cardiac glycosides digoxin and digitoxin. A spontaneous mutant, 40-150 A2.4, produces and antibody which carries a single residue mutation, Ser → Arg, in its heavy chain (H94) and has an altered specificity. A second order mutant 40-150 A2.4 P.10, produces two antibody molecules, one the same as 40-150 A2.4, the other lacking two residues at the N-terminus of its H chain, and having a specificity profile approaching that of 40-150 antibody. 1 The N-terminus and the position H94 are distant from the antigen-binding site of the antibody; thus, the structural basic of the specificity changes was not immediately clear. Approximate structures of the 40-150 antibody and its mutants were constructed in the computer, based on atomic coordinates of the homologous mouse antibody McPC 603. Using the program OCNGEN, the torsional space of the polypeptide backbone and side chains around position H94 was uniformly sampled, and the lowest energy conformations were analyzed in detail. The results indicate that when Arg-H94 is substituted for Ser. Agr-H94 can hydrogen bond to side chains of Asp-H101, Arg-L46, and Asp-L55. The results in a change in the surface of the combining site which may account for the affinity changes. Deletion of the two N-terminal residues increases solvent accessibility of Arg-H94. The solvation may cause a hydrogen bond between Arg-H94 and Asp-H101 to be lost, restoring the structure to one similar to that of 40-150.
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  • 187
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    Cell Motility and the Cytoskeleton 15 (1990), S. 168-180 
    ISSN: 0886-1544
    Keywords: microtubule-associated proteins (MAPs) ; taxol ; oocyte maturation ; fertilization ; cell division ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: A microtubule-binding protein was purified from eggs of the starfish, Asterias amurensis, through several steps of purification including the taxol-dependent procedure [Vallee, 1982, J. Cell Biol. 92:435-442]. This protein consists of a single polypeptide chain having an apparent molecular mass of 70 kD determined by SDS-PAGE. The 70 kD protein was identified as a unique microtubulebinding protein, judging from electrophoretic mobility, cleavage pattern by limited proteolysis, heat stability, and immunocrossreactivity. The 70 kD protein binds to brain and egg microtubules. It does not promote assembly of brain tubulin, but promotes that of egg tubulin in vitro in a concentration-dependent manner.Using indirect immunofluorescence and immunoelectron microscopy with the anti-70 kD protein antibody, we analyzed the cellular localization of the 70 kD protein in starfish oocytes and eggs during both meiotic maturation (meicsis) and first cleavage (mitosis). Immunofluorescence studies showed that the 70 kD protein localized on microtubule structures spread widely throughout the cytoplasm, the sperm aster, and the microtubules making up the mitotic apparatus through both meiosis and mitosis. The antibody, however, did not recognize sperm axonemes. These results were confirmed by immunoelectron microscopy. Using a colloidal gold technique, the 70 kD protein was localized along the microtubules in vivo.This 70 kD protein is the first microtubule-binding protein that has been shown to localize along the microtubules in oocytes and eggs throughout meiosis and mitosis and to promote microtubule assembly. The 70 kD protein may be involved in the dynamic changes of microtubule structures occurring within oocytes and eggs.
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  • 188
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    Cell Motility and the Cytoskeleton 15 (1990), S. 204-209 
    ISSN: 0886-1544
    Keywords: Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Additional Material: 2 Ill.
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  • 189
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    Cell Motility and the Cytoskeleton 15 (1990), S. 210-219 
    ISSN: 0886-1544
    Keywords: organelle motors ; nucleoside triphosphates ; fast axonal transport ; video microscopy ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: Video microscopy of isolated axoplasm from the squid giant axon permits correlated quantitative analyses of membrane-bounded organelle transport both in the intact axoplasm and along individual microtubules. As a result, the effects of experimental manipulations on both anterograde and retrograde movements of membrane-bounded organelles can be evaluated under nearly physiological conditions. Since anterograde and retrograde fast axonal transport are similar but distinct cellular processes, a systematic biochemical analysis is important for a further understanding of the molecular mechanisms for each. In this series of experiments, we employed isolated axoplasm of the squid to define the nucleoside triphosphate specificity for bidirectional organelle motility in the axon. Perfusion of axoplasm with 2-20 mM ATP preserved optimal vesicle velocities in both the anterograde and retrograde directions. Organelle velocities decreased to 〈50% of optimal values when the axoplasm was perfused with 10-20 mM UTP, GTP, ITP, or CTP with simultaneous depletion of endogenous ATP with hexokinase. Under the same conditions, TTP and ATP-γ-S were unable to support significant levels of transport. None of the NTPs tested had a differential effect on anterograde vs. retrograde movement of vesicles. Surprisingly, several inconsistencies were revealed when a comparison was made between these results and nucleoside triphosphate specificities that have been reported for putative organelle motors by using in vitro assays. These data may be used in conjunction with data from well-defined in vitro assays to develop models for the molecular mechanisms of axonal transport.
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  • 190
    ISSN: 0886-1544
    Keywords: polycentric chromosome ; light microscopy ; electron microscopy ; high-pressure freezing ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: Mitosis in the hemipteran Agallia constricta (leafhopper) cell line AC-20 was examined by light microscopy of living and fixed cells. During early prometaphase the numerous small (0.30-3.0-μm) chromosomes appear as discrete units that lack a primary constriction. However, by late prometaphase the chromosomes are tightly packed at the spindle equator and are no longer clearly resolvable as individuals. When viewed from the side the metaphase chromatin appears as a 2-3-μm wide band that spans the width of the spindle; when viewed from the pole it appears as a fenestrated disk. The metaphase chromatin splits at anaphase into two sister chromatin plates, each of which exhibits holokinetic poleward movement, i.e., all parts of each plate move as a single unit with the same velocity. In many early-to-mid anaphase cells the separating sister plates are connected by chromatin-containing bridges that break as anaphase progresses. Ultrastructural analyses of serial thick and thin sections from cells fixed by conventional, OsO4/KFeCN, or high pressure rapid freezing methods, reveal that by metaphase all of the chromosomes are interconnected to form a large, irregularly shaped fenestrated disk of chromatin. Similar analyses reveal that adjacent chromatids remain interconnected throughout anaphase. Each disk of metaphase and anaphase chromatin contains numerous kinetochores recessed within its polefacing surface. Kinetochores consist of a fine, faintly staining fibrillar material arranged along the chromatin surface as thin (0.1-0.3 μm dia.) rods varying considerably (0.15-2.3 μm) in length. From these observations we conclude that the polycentric metaphase chromatin of A. constricta, and its holokinetic behavior during anaphase, arises from the aggregation or cohesion of smaller prometaphase chromosomes, each of which contains a single, diffuse kinetochore.
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    Cell Motility and the Cytoskeleton 15 (1990), S. 271-272 
    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
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  • 192
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    Cell Motility and the Cytoskeleton 16 (1990), S. 1-6 
    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
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  • 193
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    Cell Motility and the Cytoskeleton 15 (1990), S. 260-270 
    ISSN: 0886-1544
    Keywords: Fc-receptors ; antibodies ; “frustrated” phagocytosis ; leucocytes ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: When phagocytes spread on surfaces coated with ligands such as IgG, they form a tight seal with the substrate. This seal excludes soluble macromolecules in the medium from the interface between the cell and substrate. In contrast, when cells spread on control surfaces that are not coated with ligands, the underside of the cell remains freely accessible to soluble proteins (Wright and Silverstein: Nature 309:359, 1984). We employed reflection-interference microscopy (RIM) to determine where the seal forms during interaction with ligand (IgG) -coated surfaces. Human monocyte-derived macrophages (MO) were plated at 37°C on dinitrophenylated (DNP)-glass coverslips (control substrate), IgM anti-DNP-DNP-coated glass (control substrate), or on IgG anti-DNP-DNP-coated glass (phagocytosis-promoting substrate). Live or fixed cells were examined by RIM. Spreading on control surfaces at 37°C was complete in 25 minutes, whereas spreading on IgG-coated surfaces was maximal within 15 minutes and resulted in cell-substrate contact area 1.6 × that of control cells. Within 1 h at 37°C, 90% of MO that spread on IgG-coated substrates, but not on control substrates, excluded macromolecules from their underside. A minor population of cells (19%) exhibited a uniform iron gray RIM appearance indicating an even, close approach to the substrate. These cells may represent early stages of frustrated phagocytosis. In contrast to cells on control substrates, 70% of cells on IgG-coated substrates developed continuous peripheral dark rings in RIM indicative of close association with the substrate. Essentially all cells with peripheral dark rings in RIM excluded macromolecules from their underside. Enclosed within this ring was an area of greater separation between the cell membrane and the substrate, as indicated by the lighter grey of this region in RIM and by the accessibility of substrate to anti-substrate antibody when breaks in the dark ring occur. Thus, MO can create a closed compartment between plasma membrane and substrate that excludes proteins in the surrounding medium, thereby protecting substances secreted into this space from potentially inhibitory substances in the medium.
    Additional Material: 6 Ill.
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  • 194
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    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 16 (1990), S. 47-57 
    ISSN: 0886-1544
    Keywords: endothelium ; wound repair ; inhibitors ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: The role of microfilaments and microtubules during injury-induced cell migration of corneal endothelial cells in situ along their natural basement membrane has been investigated using organ culture. In the noninjured tissue, actin is localized at or near the plasma membrane, whereas tubulin is observed as a delicate lattice pattern throughout the cytoplasm. Twenty-four hours after a circular freeze injury, cells surrounding the wound area extend processes into this region. Fluorescent microscopy using phallotoxins and anti-tubulin antibodies demonstrated the presence of stress fibers and microtubule reorganization within these cells. Between 24 and 48 h post-injury endothelial cells move into the wound region, and by 48 h, the injury zone is repopulated and the monolayer is becoming resstablished. When injured corneas are placed in media containing 5 × 10-7 M cytochalasin B, endothelial cell migration occurs: but it is slow, and wound closure is not complete even by 72 h. In contrast, when tissues are cultured in the presence of 10-8 M colchicine, cell movement is greatly reduced, complete wound closure does not occur, and endothelial cells at the wound edge fail to display extensions typical of migrating cells. Furthermore, when injured endothelia are exposed to 0.05 μg/ml of actinomycin D for 15 min within the first hour after injury and transferred back into culture media lacking the drug for the duration of the experiment, migration does not occur and the wound persists. These actinomycin D treated cells remain viable as shown by their ability to incorporate 3H-uridine and 3H-thymidine. Fluorescence microscopy of actinomycin D treated tissues revealed the presence of stress filaments but disorganized microtubule patterns. Interestingly, 24 h after injury, if the tissue is exposed to actinomycin D, even for periods of up to 1 h, migration is not inhibited. Our results indicate that injury-induced endothelial cell movement appears to be more dependent on microtubule than microfilament reorganization and may require a critical timing of macromolecular synthesis.
    Additional Material: 26 Ill.
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  • 195
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    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 16 (1990) 
    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
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  • 196
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    Cell Motility and the Cytoskeleton 16 (1990), S. 225-228 
    ISSN: 0886-1544
    Keywords: Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Additional Material: 1 Ill.
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  • 197
    ISSN: 0886-1544
    Keywords: Aspergillus ; benomyl ; chimeric gene ; tubulin mutants ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: We have constructed a chimeric β-tubulin gene that places the structural gene for the tubC β-tubulin of Axpergillus nidulans under the control of the benA β-tubulin promoter. Introduction of cither this chimeric gene or a second wild-type ben.A gene into a benomyl-resistant benA22 strain causes it to become benomyl sensitive, indicating that the introduced genes are functional. Analysis of the tubulin proteins synthesized in benA22 strains into which a second wild-type benA β-tubulin gene was transformed showed that the total amount of β-tubulin protein was the same as in the parental strain with a single benA gene. Thus the level of β-tubulin must be regulated. This was also true of transformants carrying an extra copy of the chimeric β-tubulin gene. The total amount of β-tubulin was the same as in the parental strain. Two-dimensional gel analysis showed that the endoge-nous benA22 and the introduced chimeric tubC gene contributed equally to the total β-tubulin pool. Th; fact that one-half of the benA β-tubulin could be replaced by tubC β-tubulin with no effect on the growth of the cells suggests that the benA and tubC β-tubulins are functionally interchangeable.
    Additional Material: 4 Ill.
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  • 198
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    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 15 (1990) 
    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
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  • 199
    ISSN: 0886-1544
    Keywords: tubulin heterogeneity ; neural differentiation ; neuronal microtubules ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: Five β-tubulin isotypes are expressed differentially during chicken brain development. One of these isotypes is encoded by the gene cβ4 and has been assigned to an isotypic family designated as Class III (βIII). In the nervous system of higher vertebrates, βIII is synthesized exclusively by neurons. A βIII-specific monoclonal antibody was used to determine when during chick embryogenesis cβ4 is expressed, the cellular localization of βIII, and the number of charge variants (isoforms) into which βIII can be resolved by isoelectric focusing. On Western blots, βIII is first detectable at stages 12-13. Thereafter, the relative abundance of βIII in brain increases steadily, apparently in conjunction with the rate of neural differentiation. The isotype was not detectable in non-neural tissue extracts from older embryos (days 10-14) and hatchlings. Western blots of protein separated by two-dimensional gel electrophoresis (2D-PAGE) reveal that the number of βIII isoforms increases from one to three during neural development. This evidence indicates that βIII is a substrate for developmentally regulated, multiple-site posttranslational modification. Immunocytochemical studies reveal that while cβ4 expression is restricted predominantly to the nervous system, it is transiently expressed in some embryonic structures. More importantly, in the nervous system, immunoreactive cells were located primarily in the non-proliferative marginal zone of the neural epithelia. Regions containing primarily mitotic neuroblasts were virtually unstained. This localization pattern indicates that cβ4 expression occurs either during or immediately following terminal mitosis, and suggests that βIII may have a unique role during early neuronal differentiation and neurite outgrowth.
    Additional Material: 10 Ill.
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  • 200
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    Cell Motility and the Cytoskeleton 15 (1990), S. 51-62 
    ISSN: 0886-1544
    Keywords: microtubule-associated proteins ; intracellular motility ; CTPase ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: A high molecular weight microtubule binding protein has been isolated from homogenates of Dictyostelium. Because of its sedimentation velocity (20s), ATP-sensitive binding to microtubules. UV-vanadate-ATP mediated fragmentation, prominent CTPase activity, and its ability to produce limited microtubule movement in vitro, we consider this protein to be a form of cytoplasmic dynein. A polyclonal antibody monospecific to this protein was produced, and dynein's intracellular distribution in ameboid cells was examined by immunofluorescence. The antibody labels a punctate cytoplasmic pattern, localizes to a spherical region adjacent to the nucleus, and also appears to label the nuclei. The punctate staining pattern is consistent with cytoplasmic dynein's proposed function in organelle transport. The spherical juxtanuclear object stained is coincident with this cell's microtubule organizing center, an obvious termination point for minus-end directed microtubule motors. By immunofluorescence, there does not appear to be a substantial amount of dynein in the intranuclear mitotic spindles of Dictyostelium, These data provide evidence for localization of cytoplasmic dynein in cells, and suggest that Dictyostelium will be a useful system in which to study the molecular biology of microtubule-associated motor enzymes.
    Additional Material: 7 Ill.
    Type of Medium: Electronic Resource
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