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  • 1990-1994  (4,214)
  • 1965-1969  (424)
  • 1920-1924
  • 1910-1914
  • 1880-1889
  • Biochemistry and Biotechnology  (4,471)
  • Bone
  • Psychopharmacology
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  • 1
    Electronic Resource
    Electronic Resource
    The biochemistry of ancient DNA in bone (1994)
    Springer
    Cellular and molecular life sciences 50 (1994), S. 530-535 
    Details
    ISSN: 1420-9071
    Keywords: Bone ; collagen ; fulvic acids ; DNA ; ancient DNA
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract The amount of DNA in ancient bone was determined by ethidium bromide staining after the removal of the potent Taq inhibitor, fulvic acid. A complete decalcification and a perfusion protocol were used to recover DNA from bone. A variety of purification techniques including molecular sieve, hydroxyapatite binding and ‘Magic’ preparations yielded DNA that spanned from 3.4μg/g of bone to below detectable limits. Fulvic acid was shown to interfere with the quantification of DNA derived from ancient human skeletal material one hundred to over seven thousand years old. Scanning UV in the 300 to 230 nm range is a simple and sensitive technique for documenting fulvic acid contamination in ancient bone extracts.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01921721
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  • 2
    Electronic Resource
    Electronic Resource
    The effect of homocysteine thiolactone and its alpha methylated derivative on bone matrix in the mouse (1994)
    Springer
    Amino acids 6 (1994), S. 199-203 
    Details
    ISSN: 1438-2199
    Keywords: Amino acids ; Homocysteine thiolactone ; Alpha-homocysteine thiolactone ; Bone ; Glycosaminoglycans
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Summary Homocysteine (HC) is a radiation protector but toxic to bone. Its derivative homocysteine thiolactone (HCTL) and the alpha-alkylated analogue (A-methyl-HCTL) was fed to mice for a period of six weeks in a daily dose of 50 mg/kg body weight. Parameters for bone matrix as collagen content, acid solubility of bone collagen, urinary bone collagen cross links (pyridinolines) and urinary acid glycosaminoglycans were determined. Urinary acid glycosaminoglycans were significantly reduced in the HCTL treated group but not in the alpha-methyl-homocysteine thiolactone (A-methyl-HCTL) group (controls: 45 ± 7 mg/mmol creatinine, homocysteine thiolactone 38 ± 5 mg/mmol creatinine, A-methyl HCTL 45 ± 6 mg/mmol creatinine). No differences were found for the parameters of bone collagen between the groups. The potent radiation protecting methylated derivative therefore did not change bone matrix and should be a candidate for further toxicological studies.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00805847
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  • 3
    Electronic Resource
    Electronic Resource
    The time course of renal function and bone turnover in parathyroid crisis due to intratumoral hemorrhage (1994)
    Springer
    Journal of molecular medicine 72 (1994), S. 448-450 
    Details
    ISSN: 1432-1440
    Keywords: Parathyroid ; Crisis ; Kidney ; Bone ; Turnover
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract Parathyroid crisis occurring in primary hyperparathyroidism is characteized by extremely high circulating levels of parathyroid hormone and acute onset of severe hypercalcemia. We describe a 62-year-old woman with parathyroid crisis probably due to an intraturnoral hemorrhage. Renal dysfunction reduced the effectiveness of preoperative management and continued to deteriorate for 5 days after parathyroidectomy. The normalization of serum calcium after parathyroidectomy delayed and it took 6 days. Maintenance of renal function is important for pre- and postoperative courses of the present case. The rapid decrease in serum parathyroid hormone after parathyroidectomy was followed by a rapid and transient (about fivefold) increase in serum alkaline phosphatase with peak value on the 10th postoperative day. This indicated that reversal phase from bone resorption (accelerated by parathyroid hormone) to bone formation lasted about 10 days under the conditions of the present case.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00180519
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  • 4
    Electronic Resource
    Electronic Resource
    Comparison of DNA extraction and amplification from ancient human bone and mummified soft tissue (1994)
    Springer
    International journal of legal medicine 107 (1994), S. 152-155 
    Details
    ISSN: 1437-1596
    Keywords: Ancient DNA ; Bone ; Soft tissue ; Automated DNA extraction ; PCR ; Sex determination ; alte DNA ; Knochen ; Weichgewebe automatisierte ; DNA-Extraktion ; PCR Geschlechtsbestimmung
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine , Law
    Description / Table of Contents: Zusammenfassung Für eine vergleichende Untersuchung von Knochen und Weichgewebe als Quellenmaterial für DNA-Analysen wurden südamerikanische, präkolumbische, männliche Mumien verwendet. Die Eignung der DNA-Extrakte beider Quellen wurde über ihre Effektivität als Ziel-DNA in PCR-Amplifikationen bewertet. Die Ergebnisse zeigen, daß bei Verwendung stark degradierten Materials Knochen den Weichgeweben für PCR-Analysen vorzuziehen sind. Dies scheint unabhängig von der spezifischen anatomischen Herkunft der Proben zu sein.
    Notes: Abstract South american precolumbian male mummies were employed as source material for a comparative investigation of bone and soft tissues by DNA analysis. The suitability of the DNA extracts from both sources was tested and evaluated by their effectiveness as target DNA in PCR amplifications. The results suggest that skeletal material should be given preference over soft tissues for PCR analysis if the material is severely degraded. This seems to be independent of the specific anatomical origin of the samples.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01225603
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  • 5
    Electronic Resource
    Electronic Resource
    Purification of mineralized tissue-associated osteopontin (1994)
    Springer
    Methods in cell science 16 (1994), S. 211-215 
    Details
    ISSN: 1573-0603
    Keywords: Bone ; Bone sialoprotein ; Osteopontin ; Protein purification
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary A protocol to extract and purify osteopontin, a protein with cell adhesion and mineral-crystal binding properties, from mineral-associated tissues is described. This procedure provides for the complete separation of osteopontin from bone sialoprotein, a mineralized tissue-specific protein with similar properties to that of osteopontin.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01540653
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  • 6
    Electronic Resource
    Electronic Resource
    Three-dimensional photographic study of cancellous bone in human fourth lumbar vertebral bodies (1994)
    Springer
    Anatomy and embryology 189 (1994), S. 259-274 
    Details
    ISSN: 1432-0568
    Keywords: Bone ; Cancellous ; Trabecular ; Age ; Osteoporosis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract In an analysis of the 3D architecture of cancellous bone, two-dimensional techniques are of limited value. A simple technique employing stereophotographs of whole sections of lumbar vertebrate made possible a detailed description of the 3D structure of the normal fourth lumbar vertebral body and its changes with ageing and osteoporosis. Parallax measurements were used to calculate the real lengths of horizontal trabeculae. The bone presented a continuous spectrum of microstructure, from a honeycomb of tubes, to plates and braces and, finally, fragile rods. A distinct pattern was produced in osteoporotic samples by the removal of horizontal and selected vertical trabeculae followed by a thickening of the remaining vertical trabeculae in the peripheral regions. Very long, thin horizontal trabeculae were formed in all three zones (superior, middle and inferior) during this process. The observation of porotic architecture in intact specimens points to the inadequacy of the clinical criterion of the occurrence of a fracture in judging the osteoporotic state.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00239013
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  • 7
    Electronic Resource
    Electronic Resource
    Simulation of bone resorption-repair coupling in vitro (1994)
    Springer
    Anatomy and embryology 190 (1994), S. 339-349 
    Details
    ISSN: 1432-0568
    Keywords: Osteoclasts ; Osteoblasts ; Resorption ; Remodelling ; Dentine ; Bone
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract In the normal adult human skeleton, new bone formation by osteoblasts restores the contours of bone surfaces following osteoclastic bone resorption, but the evidence for resorption-repair coupling remains circumstantial. To investigate whether sites of prior resorption, more than the surrounding unresorbed surface, attract osteoblasts or stimulate them to proliferate or make new matrix, we developed a simple in vitro system in which resorption-repair coupling occurs. Resorption pits were produced in mammalian dentine or bone slabs by culturing chick bone-derived cells on them for 2–3 days. The chick cells were swept off and the substrata reseeded with rat calvarial osteoblastic cells, which make bone nodules in vitro, for periods of up to 8 weeks. Cell positions and new bone formation were investigated by ordinary light microscopy, fluorescence and reflection confocal laser microscopy, and SEM, in stained and unstained samples. There was no evidence that the osteoblasts were especially attracted to, or influenced by, the sites of resorption in dentine or bone before cell confluence was reached. Bone formation was identified by light microscopy by the accumulation of matrix, staining with alizarin and calcein and by von Kossa's method, and confirmed by scanning electron microscopy (SEM) by using backscattered electron (BSE) and transmitted electron imaging of unembedded samples and BSE imaging of micro-milled embedded material. These new bone patches were located initially in the resorption pits. The model in vitro system may throw new light on the factors that control resorption-repair coupling in the mineralised tissues in vivo.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00187292
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  • 8
    Electronic Resource
    Electronic Resource
    Ectopic ossicles associated with metacercariae of Apophallus brevis (Trematoda) in yellow perch, Perca ftavescens (Teleostei): development and identification of hone and chondroid bone (1994)
    Springer
    Anatomy and embryology 190 (1994), S. 29-46 
    Details
    ISSN: 1432-0568
    Keywords: Ectopic ossification ; Ossicles ; parasite infection ; Chondroid bone ; Bone
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract This paper describes the development and tissues in mineralized ossicles in the musculature of Perca flavescens infected with metacercariae of the trematode Apophallus brevis. Analysis involved light microscopy, transmission and scanning electron microscopy, X-ray scanning electron microprobe analysis, and tetracycline labelling. Two to 14 days post-infection, fibroblast-like host cells stream towards the parasite cyst forming a fusiform cellular capsule. By 14 days post-infection the capsule differentiates into an inner hypertrophied layer, an extensive middle layer of fibroblast-like cells, and a thin outer layer of flattened fibroblast-like cells forming a fibrous sheath at the capsule/muscle interface. From 21–35 days post-infection, a bony tissue is deposited periosteally in an equatorial ring around the cyst. With time, additional tissue is secreted over the ring increasing its thickness and advancing the matrix front towards the poles of the ossicle. Plump osteoblast-like cells cover the developing ossicle and may become trapped within the matrix in lacunae encapsulated by collagen. By 63 days post-infection, medium-sized ossicles are morphologically similar to large cysts from perch captured in the wild; ovoid with two polarized canals, but lacking acellular or lamellar bone-like tissue. Mineralized ossicles contain calcium, phosphorus and oxygen. Large ossicles retrieved from perch given multiple doses of tetracycline revealed discrete fluorescent bands, indicative of incremental growth. Fully developed ossicles are composed of two skeletal tissues, an inner region of chondroid bone and an outer region of acellular, lamellar bone.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00185844
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  • 9
    Electronic Resource
    Electronic Resource
    A study of the nutrient foramina of lower limb long bones (1994)
    Springer
    Surgical and radiologic anatomy 16 (1994), S. 409-412 
    Details
    ISSN: 1279-8517
    Keywords: Nutrient foramina ; Bone ; Lower limb
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Description / Table of Contents: Résumé Les foramens nourriciers de 269 os longs de membres inférieurs d'adultes ont été étudiés afin d'en préciser le nombre et le siège. L'index foraminal moyen était de 48,82 pour le fémur, 33,17 pour le tibia, 47,82 pour la fibula. Sur le fémur, les foramens sont le plus souvent doubles, situés au tiers moyen de la ligne âpre. Sur le tibia, le foramen est le plus souvent au tiers supérieur de la face postérieure. Enfin sur la fibula, il se situe en général au tiers moyen de face postérieure.
    Notes: Summary In this study a total of 269 adult lower limb long bones were examined to determine the number and location of the nutrient foramina in the shafts of bones. The mean of foraminal index was 48.82 for femur, 33.17 for tibia, and 47.82 for fibula. The number of foramina noted were: two on the linea aspera in the middle third of the femur, one on the posterior surface of the upper third of the tibia, and one on the posterior surface of the middle third of the fibula.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01627662
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  • 10
    Electronic Resource
    Electronic Resource
    Effects of magnesium deficiency on strength, mass, and composition of rat femur (1994)
    Springer
    Calcified tissue international 54 (1994), S. 44-49 
    Details
    ISSN: 1432-0827
    Keywords: Bone ; Stress ; Elasticity ; Mechanical properties ; Calcium
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine , Physics
    Notes: Abstract Magnesium (Mg) participates in the normal formation and remodeling of bone. However, little is known about effects of Mg status on the biomechanical function of bone. We examined gross morphometry and composition as well as biomechanical properties of the femurs of male rats fed diets adequate or deficient in Mg. Comparison of deficient animals and controls yielded a number of differences (all significant at P〈0.05). Mg-depleted animals exhibited slow growth, inefficient food utilization, and greatly reduced concentrations of Mg in both serum and femur ash. Compared with controls, femurs from depleted animals were shorter, but wet weights, diameters, and midfemoral cross-sectional areas showed no differences. Bone length was reduced to a greater degree than could be accounted for by differences in body weights between the groups. Bones of Mg-deficient rats contained less dry matter and less ash (which contained more Ca/g) than those of controls, along with a higher percentage of moisture. Significantly reduced bone strength in depleted animals was evident from the lighter loads supported at the elastic limit (yield point) and at fracture and from decreased stresses accompanying those loads. Modulus of elasticity, however, was not affected by Mg depletion. Different yield and breaking loads were related to different body weights of groups, but stresses were reduced for deficient bones even after adjusting for body size. Our data establish abnormal biomechanical behavior of cortical bone in Mg-deficient animals and emphasize the importance of measuring such functional properties of bone in the assessment of responses to altered metabolic conditions under experimental conditions.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00316289
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  • 11
    Electronic Resource
    Electronic Resource
    Broadband ultrasonic attenuation imaging: A new imaging technique of the os calcis (1994)
    Springer
    Calcified tissue international 54 (1994), S. 83-86 
    Details
    ISSN: 1432-0827
    Keywords: Ultrasound attenuation ; Bone ; Osteoporosis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine , Physics
    Notes: Abstract Ultrasound transmission measurement through the os calcis is an emerging technique and a promising clinical tool for early assessment of osteoporosis. However, several previous studies showed that broadband ultrasonic attenuation (BUA) is sensitive to small variations in bone mass or structure. The os calcis is an inhomogeneous bone and therefore, the attenuation depends on the location in the os calcis. BUA distribution within the os calcis can be measured by rectilinear scanning over the entire bone. We used a mechanical scanning device with both unfocused and focused transducers. The spatial resolution of these was about 25 mm and 4 mm, respectively. There was good agreement (r=0.97) between the results with unfocused and focused transducers. In addition, imaging the variations of BUA is possible with the focused transducers, and high quality images are obtained. These images permit the selection of optimal regions of interest for ultrasound attenuation measurement.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00296055
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  • 12
    Electronic Resource
    Electronic Resource
    Age-dependence of bone material quality shown by the measurement of frequency of resonance in the ulna (1994)
    Springer
    Calcified tissue international 54 (1994), S. 96-100 
    Details
    ISSN: 1432-0827
    Keywords: Bone ; Material quality ; Sound transmission ; Frequency of resonance ; Age ; Bone width
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine , Physics
    Notes: Abstract In women before and after the age of peak bone mass, identical values of bone mineral density (BMD) can be obtained. However, there is a much higher incidence of osteoporotic fractures in older women. We investigated whether a deterioration of bone material quality with increasing age might contribute to this phenomenon. Material properties of bone tissue can be characterized by the modulus of elasticity, which is correlated to the square of sound transmission velocity. In this study, sound transmission velocity was determined in cortical bone by measuring the frequency of resonance in the ulna in the direction of the bone's longitudinal axis and correcting the values by multiplying by ulna length. Validation of this method indicated acceptable reproducibility: interobserver variability determined as the mean coefficient of variation was 1.82%. In a clinical study, 21 young women (22.5±1.2 years old) were compared with 21 middle-aged women (52.9±2.7 years old). Pairs were matched that had identical values of BMD in the nondominant forearm at a location representing mainly cortical bone (SPA). The product of ulna length and frequency of resonance in the ulna in the younger women was found to be 61.4±5.8 m/second, and in the middle-aged women 55.7±4.5 m/second. The difference was highly significant with P〈0.005. Our results confirm recent findings indicating a deterioration of bone material quality independent of BMD with increasing age. As shown by comparing ulna width at the site of measurement of bone mineral density between both groups of women, the deterioration of bone material quality in ulnar cortical bone with increasing age might at least in part be functionally compensated by an increase of the moment of inertia due to greater bone width [8, 10].
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00296058
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  • 13
    Electronic Resource
    Electronic Resource
    Helodermin, helospectin, and PACAP stimulate cyclic AMP formation in intact bone, isolated osteoblasts, and osteoblastic cell lines (1994)
    Springer
    Calcified tissue international 54 (1994), S. 284-289 
    Details
    ISSN: 1432-0827
    Keywords: Helodermin ; Bone ; Cyclic AMP
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine , Physics
    Notes: Abstract Helodermin and helospectin are peptides structurally similar to vasoactive intestinal polypeptide (VIP) which were recently isolated from the salivary gland venom of the lizard Heloderma suspectum. Pituitary adenylate cyclaseactivating polypeptide (PACAP) has been isolated from ovine hypothalamus and also shows sequence homology to VIP. A helodermin-like peptide has been detected by combined immunohistochemical and immunochemical techniques in the thyroid C-cells. In the present study, lizard helodermin was found to cause a time- and dose-dependent stimulation of cyclic AMP (cAMP) formation in neonatal mouse calvarial bones. Also, helospectin I, PACAP 27, and the C-terminally extended PACAP 38 stimulated cAMP accumulation in the mouse calvariae. The cAMP rise in response to helodermin was comparable to that induced by VIP, both in terms of potency and magnitude of the response. Helodermin, helospectin I, PACAP 27, and PACAP 38, at concentrations of 1 μmol/liter, stimulated cAMP accumulation in enzymatically isolated mouse calvarial bone cells. A significant response to all peptides was observed in both early and late released bone cells isolated from the calvariae, with low and high alkaline phosphatase activity, respectively. Helodermin and VIP stimulated cAMP accumulation in the cloned mouse calvarial osteoblastic cell line MC3T3-E1, in rat (UMR 106-01), and human (Saos-2) osteoblastic osteosarcoma cell lines, but not in the rat osteosarcoma cell line ROS 17/2.8. The effect of helodermin was synergistically and dose-dependently enhanced by forskolin (0.1 and 1 μmol/liter). These data show that bone cells, including osteoblasts, respond to several peptides of the VIP family, including helodermin, helospectin I, PACAP 27, and PACAP 38. Whether the responses are mediated via one or several receptor populations remains to be established. The finding that VIP and helodermin, at maximally effective concentrations, did not cause additive effect on cAMP formation in intact mouse calvariae suggests that these two agonists may use a common receptor.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00295952
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  • 14
    Electronic Resource
    Electronic Resource
    Human recombinant interleukin-1 receptor antagonist blocks bone resorption induced by interleukin-1β but not interleukin-1α (1994)
    Springer
    Calcified tissue international 55 (1994), S. 12-15 
    Details
    ISSN: 1432-0827
    Keywords: IL-1α ; IL-1β ; IL-1 receptor antagonist ; Bone ; Calcium ; Parathyroid hormone
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine , Physics
    Notes: Abstract Both interleukin-1α (IL-1α) and interleukin-1β (IL-1β) are powerful stimulators of bone resorption in vivo and in vitro. Interleukin-1 receptor antagonist (IL-1ra) binds to many interleukin-1 receptors. It does not activate the receptor and effectively blocks the action of IL-1α and IL-1β. In this study, human recombinant IL-1ra, at 100-fold excess, was found to block bone resorption in cultured mouse calvaria due to IL-1β but not IL-1α. These observations may be explained by differential affinities of receptors for IL-1α, IL-1β and rhIL-1ra on target bone cells.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00310162
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  • 15
    Electronic Resource
    Electronic Resource
    Combined magnetic fields increased net calcium flux in bone cells (1994)
    Springer
    Calcified tissue international 55 (1994), S. 376-380 
    Details
    ISSN: 1432-0827
    Keywords: Electromagnetic ; Bone ; Calcium ; Osteoblast
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine , Physics
    Notes: Abstract Low energy electromagnetic fields (EMF) exhibit a large number of biological effects. A major issue to be determined is “What is the lowest threshold of detection in which cells can respond to an EMF?” In these studies we demonstrate that a low-amplitude combined magnetic field (CMF) which induces a maximum potential gradient of 10-5 V/m is capable of increasing net calcium flux in human osteoblast-like cells. The increase in net calcium flux was frequency dependent, with a peak in the 15.3–16.3 Hz range with an apparent bandwidth of approximately 1 Hz. A model that characterizes the thermal noise limit indicates that nonspherical cell shape, resonant type dynamics, and signal averaging may all play a role in the transduction of lowamplitude EMF effects in biological systems.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00299318
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  • 16
    Electronic Resource
    Electronic Resource
    Contribution of collagen and mineral to the elastic anisotropy of bone (1994)
    Springer
    Calcified tissue international 55 (1994), S. 381-386 
    Details
    ISSN: 1432-0827
    Keywords: Acoustic microscopy ; Bone ; Collagen fiber ; Elastic anisotropy ; Mineral crystal
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine , Physics
    Notes: Abstract It has long been thought that collagen fibers within the bone matrix are deposited in an aligned pattern that channels mineral growth. If this model of bone structure is correct, both organic and inorganic phases of bone should have similar elastic anisotropy. Using an acoustic microscope, we measured longitudinal and transverse acoustic velocities of cortical specimens taken from 10 dog femurs before and after removal of either the mineral (using 10% EDTA) or collagen phases (using 7% sodium hypochlorite) and calculated longitudinal (CL) and transverse (CT) elastic coefficients. The anisotropy ratio (CL/CT) decreased significantly after demineralization (1.61 before versus 1.06 after, P〈0.0001, paired t-test). However, there was no significant change after decollagenization (1.51 before versus 1.48 after, P=0.617, paired t-test). We conclude that the orientation of mineral crystals is the primary determinant of bone anisotropy, and the collagen matrix within osteonal bone has little directional orientation.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00299319
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  • 17
    Electronic Resource
    Electronic Resource
    Magnesium distribution in human bone (1994)
    Springer
    Calcified tissue international 54 (1994), S. 34-37 
    Details
    ISSN: 1432-0827
    Keywords: Magnesium ; Bone ; Aging ; Human
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine , Physics
    Notes: Abstract The present study was undertaken to reveal the magnesium distribution in human bone. Sixty human ribs, obtained from subjects aged 10–80 years of age, were used. Transverse sections were prepared from the middle region of the human ribs. Adjacent sections were ground to a thickness of about 1000 μm. One section was used for magnesium determination by atomic absorption spectrophotometry, and the other was used for analysis with X-ray microanalysis. Thirty micron thick samples were abraded continuously from the periosteal and the endosteal surfaces by abrasive microsampling, as previously described by Weatherell et al. [3]. Results showed that magnesium concentrations were higher in both the periosteal and endosteal surfaces and did not change with age in general, although it tended to be higher among teenagers and lower over 80 years old.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00316287
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  • 18
    Electronic Resource
    Electronic Resource
    Antiresorptive drugs and trabecular bone turnover: Validation and testing of a computer model (1994)
    Springer
    Calcified tissue international 54 (1994), S. 179-185 
    Details
    ISSN: 1432-0827
    Keywords: Bone ; Drugs ; Trabecular ; Turnover ; Computer ; Model ; Sensitivity ; Activation frequency
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine , Physics
    Notes: Abstract A computer model of trabecular bone turnover has been developed, based on concepts of Jonathan Reeve [1]. This model predicts changes in bone volume by summing bone resorption and formation over a large number of remodeling sites. Clinical data [histomorphometry and bone mineral content (BMC)] from two clinical studies using an antiresorptive drug (etidronate disodium, EHDP) in post-menopausal osteoporosis were used to test the model. The results for BMC obtained from the EHDP and placebo groups in each study at 60 and 120 weeks were correctly predicted by the model from the histomorphometric data obtained from baseline and week 60 biopsies. The parameter in this model having the greatest influence on predicted changes in bone volume was found by sensitivity analysis to be activation frequency. These results suggest that the contribution of bone turnover to BMC can be predicted solely by considering the cell kinetics of the basic multicellular unit (BMU), and that, in the case of antiresorptive drugs, maximal effects on bone volume may be achieved by pharmacological reduction of activation frequency. The results also suggest that the present model may be useful in predicting in clinical studies the effects of EHDP and similar drugs on bone turnover.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00301675
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  • 19
    Electronic Resource
    Electronic Resource
    Intact serum parathyroid hormone levels increase during running exercise in well-trained men (1994)
    Springer
    Calcified tissue international 54 (1994), S. 256-261 
    Details
    ISSN: 1432-0827
    Keywords: Calcium ; Lactate ; Acidosis ; Treadmill ; Bone
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine , Physics
    Notes: Abstract The purpose of this study was to examine the influence of exercise on the serum concentrations of intact parathyroid hormone (PTH). Serum PTH and plasma lactate were measured in 15 well-trained men, 9 long-distance runners and 6 fire-fighters, during two running exercises. Test one consisted of 40-minute treadmill running with a stepwise increased load and test two consisted of 50-minute treadmill running with a constant velocity. When the load was step-wise increased, the PTH concentrations increased moderately at the slower running paces but reached a final value that was about 50% higher than the starting value. This rise occurred despite a concomitant increase of total serum calcium from 2.38±0.06 to 2.49±0.05 mmol/liter (P〈0.01). During the constant running exercise, the long-distance runners, but not the fire-fighters, displayed a significant increase in PTH concentrations although the rise in total serum calcium was similar in both groups. There was a weak correlation between the changes in PTH and lactate in both exercises. The findings demonstrate that both high and low intensity exercise enhance release of PTH in long-distance runners through a mechanism that does not involve serum calcium. This relationship might be of importance for bone mass in men performing long-distance training.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00295947
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  • 20
    Electronic Resource
    Electronic Resource
    Lower extremity stress fractures during intermittent cyclical etidronate treatment for osteoporosis (1994)
    Springer
    Calcified tissue international 54 (1994), S. 431-434 
    Details
    ISSN: 1432-0827
    Keywords: Bone ; Diphosphonate ; Osteoporosis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine , Physics
    Notes: Abstract During intermittent cyclical etidronate treatment, a lower extremity pain syndrome associated with stress fractures was observed in three osteoporotic patients. This report describes the development of stress fractures during initial cycles of treatment, with recurrence of symptoms in two patients when etidronate therapy was resumed. Further studies are needed to confirm whether stress fractures are associated with cyclic etidronate treatment and if so, the incidence and pathophysiology need to be determined.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00305532
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  • 21
    Electronic Resource
    Electronic Resource
    The modulatory effect of endogenous parathyroid hormone on the action of hydrochlorothiazide in pseudohypoparathyroidism type I (1994)
    Springer
    Calcified tissue international 54 (1994), S. 473-476 
    Details
    ISSN: 1432-0827
    Keywords: Pseudohypoparathyroidism ; Thiazide ; Kidney ; Bone ; Parathyroid hormone
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine , Physics
    Notes: Abstract We compared the effect of orally administered 100 mg of hydrochlorothiazide (HCTZ) among eight patients with pseudohypoparathyroidism (PHP) type I, 11 patients with idiopathic hypoparathyroidism (IHP), and 12 patients with primary hyperparathyroidism (1oHPT). Patients with PHP type I or with IHP were studied during the treatment with 1α-hydroxylated metabolites of vitamin D3. HCTZ raised serum levels of calcium (Ca) in 1oHPT (P〈0.001) and PHP type I (P〈0.01) but did not increase urinary excretion of Ca. Serum parathyroid hormone (PTH) in PHP type I decreased (P〈0.02) after HCTZ administration in response to the increase in serum Ca. HCTZ did not raise serum levels of Ca in IHP but increased urinary excretion of Ca in this group (P〈0.01). HCTZ suppressed tubular reabsorption of phosphate (P) in IHP (P〈0.01) and 1oHPT (P〈0.05) but not in PHP type I. Urinary excretion of cAMP did not change after HCTZ administration in PHP type I, IHP, or 1oHPT. Endogenous PTH modulated the effects of HCTZ on Ca mobilization from bone and renal reabsorption of Ca in PHP type I with normal or high serum levels of PTH and in 1oHPT with high serum levels of PTH. The inhibitory effect of HCTZ on renal tubular reabsorption of P (probably from proximal tubules) was independent of PTH. The resistance to this inhibitory effect of HCTZ on P reabsorption in PHP type I suggested a proximal tubular dysfunction in this disorder.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00334326
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  • 22
    Electronic Resource
    Electronic Resource
    Selective extractability of noncollagenous proteins from chicken bone (1994)
    Springer
    Calcified tissue international 55 (1994), S. 230-235 
    Details
    ISSN: 1432-0827
    Keywords: Noncollagenous ; Proteins ; Bone ; Sialo-protein ; Osteopontin ; Osteocalcin
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine , Physics
    Notes: Abstract Quantitative analyses of a wide variety of different solvents used for the extraction of several of the noncollagenous proteins of fully mineralized chicken bone powder were carried out to compare both the effectiveness of various procedures and the distribution of specific proteins which were solubilized. Extraction procedures included solutions of 6 M guanidine-HCl, pH 7.0, 0.5 M EDTA, pH 7.4, 0.3 N citric acid, 0.3 N HCl, 0.3 N formic acid, and 0.3 N acetic acid. Chelation of calcium ions by EDTA and dissolution of the mineral phase by acid extraction released 95% or more of the total calcium content of the bone powder by 48 hours, guanidine-HCl released less than 20% or less of the total calcium content even when extraction was carried out by 168 hours. Moreover, although guanidine-HCl solubilized a significant amount of collagen as gelatin, essentially none of the phosphoproteins, osteocalcin, or the proteoglycan decorin were solubilized, as detected by immunological techniques. In contrast, extraction of the mineralized bone powder by HCl and formic acid was very efficient in selectively solubilizing osteocalcin and osteopontin, while bone sialoprotein was selectively released by EDTA, and solubilized to a lesser extent by formic acid. Similarly, EDTA selectively removed decorin compared with HCl, formic, acetic, or citric acids. Only small amounts of osteopontin and osteocalcin were detected in the acetic acid extracts. These results provide methods for the selective solubilization of several different major, noncollagenous proteins from mineralized bone which should significantly aid in maximizing the amount of the specific protein recovered, and the ease with which the various proteins can be purified. The data also provide some insight into the intrinsic solubility characteristics of collaten, the specific noncollagenous proteins, and their potential association with each other and the mineral phase.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00425880
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  • 23
    Electronic Resource
    Electronic Resource
    Effects of infusion of parathyroid hormone and primary hyperparathyroidism on formation and breakdown of type I collagen (1994)
    Springer
    Calcified tissue international 55 (1994), S. 412-416 
    Details
    ISSN: 1432-0827
    Keywords: Bone ; Biochemical markers
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine , Physics
    Notes: Abstract The influence of chronic and acute exposure to parathyroid hormone (PTH) on formation and breakdown of type I collagen, using two recently developed radioimmunoassays for serum PICP (the carboxyterminal propeptide of type I procollagen) and serum ICTP (the carboxyterminal telopeptide of type I collagen), have been evaluated. Fasting morning values were obtained from 18 women with primary hyperparathyroidism (HPT) and an equal number of age-matched, healthy controls. A 24-hour infusion of synthetic human parathyroid hormone (PTH 1-38) was performed in 14 healthy females. The patients with HPT had higher values for serum ICTP than the controls (6.0±3.0 and 4.1±2.1 μg/liter; P〈0.05), whereas the serum PICP concentrations were not different (170±72 and 151±65 μg/liter; n.s.). During infusion of PTH in healthy subjects, there was an increase of the serum ICTP concentrations (from 3.6±1.3 to 4.4±1.8 μg/liter; P〈0.001) whereas those of serum PICP decreased (from 185±78 to 118±42 μg/liter; P≤0.0001). The increase of serum ICTP during infusion of PTH was positively related to the increase of serum calcium and other indices of bone resorption, i.e., fasting urinary excretions of hydroxyproline and calcium. The decrease of serum PICP was also related to the changes of serum ICTP and hydroxyproline in urine, serum calcium, and alkaline phosphatase but not to osteocalcin, an established marker of osteoblastic activity. The findings support the fact that serum ICTP is a valuable method for evaluating bone resorption and is also easy to perform. Furthermore, the discordant results for the different markers of osteoblastic activity indicat that they reflect different functions of the cell.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00298553
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  • 24
    Electronic Resource
    Electronic Resource
    Dietary variation in arctic foxes (Alopex lagopus)-an analysis of stable carbon isotopes (1994)
    Springer
    Oecologia 99 (1994), S. 226-232 
    Details
    ISSN: 1432-1939
    Keywords: Carbon isotopes ; Arctic fox ; Diet ; Bone ; Collagen
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract We used stable carbon isotopes to analyse individual variation in arctic fox diet. We extracted collagen from bones (the lower jaw), and measured stable carbon isotopes. The foxes came from three different localities: Iceland, where both microtines and reindeer are rare; west Greenland, where microtines are absent; and Sweden, where scat analyses showed the primary food to be microtine rodents and reindeer. The Icelandic samples included foxes from both coastal and inland habitats, the Swedish sample came from an inland area, and the Greenland sample from coastal sites. The spatial variation in the isotopic pattern followed a basic division between marine and terrestrial sources of protein. Arctic foxes from inland sites had δ13C values of −21.4 (Iceland) and −20.4‰ (Sweden), showing typical terrestrial values. Coastal foxes from Greenland had typical marine values of −14.9‰, whereas coastal foxes from Iceland had intermediate values of −17.7‰. However, there was individual variation within each sample, probably caused by habitat heterogeneity and territoriality among foxes. The variation on a larger scale was related to the availability of different food items. These results were in accordance with other dietary analyses based on scat analyses. This is the first time that stable isotopes have been used to reveal individual dietary patterns. Our study also indicated that isotopic values can be used on a global scale.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00627734
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  • 25
    Electronic Resource
    Electronic Resource
    Présentation de la série du GECO de métastases osseuses des membres : 90 cas (1994)
    Springer
    European journal of orthopaedic surgery & traumatology 4 (1994), S. 21-21 
    Details
    ISSN: 1432-1068
    Keywords: Metastases ; Bone ; Métastases osseuses
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Description / Table of Contents: Résumé Dans cette série de cas, vus par des chirurgiens, une métastase sur deux est traitée au stade de fracture. Une fracture sur deux est survenue en l'absence de toute symptomatologie évocatrice.
    Notes: Abstract This series of surgical patients shows that 50% of bony metastases are complicated by a fracture. Of these, 50% occurred without any preceding symptoms or signs.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01806724
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  • 26
    Electronic Resource
    Electronic Resource
    Ostéolyse tumorale maligne métastatique Données actuelles sur la physiopathologie et le traitement (1994)
    Springer
    European journal of orthopaedic surgery & traumatology 4 (1994), S. 5-8 
    Details
    ISSN: 1432-1068
    Keywords: Bone ; Metastases ; Osteoclast ; Cytokines ; Métastases osseuses ; Ostéoclaste ; Cytokines
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Description / Table of Contents: Résumé Les métastases ostéolytiques des cancers sont à l'origine de douleurs et de fractures pathologiques responsables d'une importante invalidité altérant la qualité de survie des patients. Ces destructions osseuses sont dues à une augmentation de la résorption osseuse, liée à la stimulation des ostéoclastes par des médiateurs sécrétés localement par les cellules tumorales et médullaires. Les bisphosphonates, puissants agents anti-ostéoclastiques, ont une bonne efficacité sur les douleurs osseuses, la prévention des fractures et des épisodes hypercalcémiques.
    Notes: Abstract Osteolytic metastases are the cause of pain and pathological fractures with marked disability affecting the patient's quality of life. The bone destruction is due to an increase of bone resorption, linked to stimulation of osteoclasts by mediators secreted locally by tumour and medullary cells. Bisphosphonates, strong anti-osteoclastic agents, are effective for bone pain, prevention of fractures and the treatment of hypercalcaemic episodes.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01806718
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  • 27
    Electronic Resource
    Electronic Resource
    Evolution du traitement des métastases osseuses (1994)
    Springer
    European journal of orthopaedic surgery & traumatology 4 (1994), S. 3-4 
    Details
    ISSN: 1432-1068
    Keywords: Metastases ; Bone ; Métastases osseuses
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Description / Table of Contents: Résumé Le traitement des métastases osseuses a vu ses modalités évoluer en fonction d'améliorations obtenues dans la prise en charge du cancer primitif et en raison d'une meilleure compréhension des phénomènes biologiques constatés au niveau de l'os métastatique. Du simple traitement palliatif des douleurs osseuses, la thérapeutique s'est orientée vers la prévention des complications dégradantes que sont les fractures et les paraplégies. Des résultats intéressants sont obtenus actuellement par l'utilisation de traitements chimiques luttant contre l'ostéolyse métastatique.
    Notes: Abstract The treatment of bony metastases has developed due to improvements in the care of the primary cancer and due to a better understanding of the biological phenomenon in the metastasis. From simple palliative treatment of bone pain, treatment is now being directed towards the prevention of the complications of metastasis, such as fractures and paraplegia. Interesting results are currently being obtained by using chemotherapy for treatment of metastatic osteolysis.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01806717
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  • 28
    Electronic Resource
    Electronic Resource
    Evolution des conceptions en matière de radiothérapie des métastases osseuses (1994)
    Springer
    European journal of orthopaedic surgery & traumatology 4 (1994), S. 11-12 
    Details
    ISSN: 1432-1068
    Keywords: Radiotherapy ; Metastases ; Bone ; Radiothérapie ; Métastases osseuses
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Description / Table of Contents: Résumé Les techniques d'irradiation antalgique sont différentes s'il s'agit de métastases uniques (champs séparés) ou multiples (irradiation hémicorporelle antalgique). Un procédé original d'irradiation hémicorporelle précoce est décrit.
    Notes: Abstract Irradiation for bone pain depends on whether the metastasis is solitary (separate field) or disseminated (antalgic half body irradiation). A new original procedure of early halfbody irradiation is described.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01806720
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  • 29
    Electronic Resource
    Electronic Resource
    Métastases osseuses d'origine thyroïdienne (1994)
    Springer
    European journal of orthopaedic surgery & traumatology 4 (1994), S. 13-15 
    Details
    ISSN: 1432-1068
    Keywords: Thyroid ; Bone ; Metastases ; Métastases osseuses ; Thyroïde
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Description / Table of Contents: Résumé En 25 ans, 1061 cancers de la thyroïde ont été pris en charge. 42 patients étaient atteints de métastases osseuses, unique ou multiples. La forme histologique la moins métastasiante est le cancer papillaire qui de plus, survient chez les sujets jeunes. Deux stades doivent être différentiés dans la maladie métastasiante. La métastase osseuse, unique, est découverte à la scintigraphie, les radiographies sont normales, l'irradiation à l'iode éventuellement associée au cobalt peut la stériliser. La métastase osseuse est visible sur les radiographies, elle n'est pas unique, la scintigraphie objectivera d'autres foyers hyperfixants, le traitement chirurgical, palliatif, aura pour effet de réduire la taille tumorale pour que l'irradiation puisse la stériliser ainsi que les autres foyers fixants.
    Notes: Abstract Over 25 years, 1601 thyroid cancers were treated. 42 patients had solitary or multiple bony metastases. The least metastatic histological form is papillary cancer, which in addition occurs in young subjects. There are two stages of the metastatic disease. The solitary bony metastasis, discovered on scintigraphy with normal Xrays, may be effectively treated by irradiation with iodine with the possible addition of cobalt. Multiple metastases, visible on plain X-ray with other hyperfixation areas on scintigraphy, is best treated by palliative surgery to reduce size so that it can be sterilised by irradiation at the same time as other hyperfixation sites.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01806721
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  • 30
    Electronic Resource
    Electronic Resource
    Aspects actuels de la prise en charge des métastases osseuses en milieu oncologique (1994)
    Springer
    European journal of orthopaedic surgery & traumatology 4 (1994), S. 9-10 
    Details
    ISSN: 1432-1068
    Keywords: Metastases ; Bone ; Métastases osseuses
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Description / Table of Contents: Résumé L'histo-pronostic, comme l'utilisation de marqueurs, sont des notions relativement nouvelles qui facilitent la prise en charge de certains cancers. Hormonothérapie et chimiothérapie doivent être discutées en fonction de leurs avantages et de leurs inconvénients. Toutes les ressources modernes contre la douleur doivent être utilisées.
    Notes: Abstract The histological prognosis and use of markers are new concepts, which are of value in managing some cancers. Hormonal therapy and chemotherapy should be considered, along with their advantages and disadvantages. All contemporary modalities of treatment against pain should be used.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01806719
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  • 31
    Electronic Resource
    Electronic Resource
    EEG profile of intravenous zolpidem in healthy volunteers (1994)
    Springer
    Psychopharmacology 114 (1994), S. 138-146 
    Details
    ISSN: 1432-2072
    Keywords: Zolpidem ; EEG ; Non benzodiazepine hypnotic ; Clinical pharmacology ; Healthy volunteers ; Psychopharmacology
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract Zolpidem is an imidazopyridine which binds specifically to the ω1 receptor. Zolpidem demonstrated potent hypnotic activity at a dose of 10 mg. Pharmacodynamics and pharmacokinetics of zolpidem were studied after daytime administration in a randomised, double-blind, placebo-controlled, cross-over trial. Single doses of zolpidem (10 mg IV as a 3-min infusion and 20 mg orally) and placebo were firstly tested in 12 healthy young male volunteers. Two other doses (5 mg IV and orally) were then evaluated in 6 out of these 12 subjects. EEG (4 leads = Fp2-T4, Fp1-T3, T4-02 and T3-01), and Stanford Sleepiness Scale (SSS) were measured up to 5 h post-dosing. Blood samples were also collected up to 24 h. The time course of the hypnotic activity of zolpidem, assessed by the score obtained on SSS, showed a similar profile whatever the route or the dose administered: slightly earlier onset after IV but sedative scores were reached at 30 min and the effect peaked between 1 and 1.5 h and lasted 4 h in both conditions. The EEG profile of zolpidem was characterised by a decrease of alpha activity and an increase in delta and in beta activity. The effect on beta activity was marked within the first hour and then disappeared. The time course of delta and alpha activities indicated a rapid onset (10 min after IV, 30 min after oral route) and a duration of 3–4 h. The amplitude of these relative EEG changes and their duration were independent of the route of administration and the dose administered. AUC and Cmax increased proportionally to the administered dose and elimination half life (2 h), clearance and volume of distribution did not change according to the dose or the route of administration. Tmax was 1 h after the oral administration. The absolute bioavailability was about 70%. In conclusion, EEG induced changes and score of SSS were in good correlation with what has been observed with insomniac patients: zolpidem has a rapid onset and a short duration of action.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02245455
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  • 32
    Electronic Resource
    Electronic Resource
    Psychopharmacological treatment of social phobia; a double blind placebo controlled study with fluvoxamine (1994)
    Springer
    Psychopharmacology 115 (1994), S. 128-134 
    Details
    ISSN: 1432-2072
    Keywords: Social phobia ; Psychopharmacology ; Serotonin reuptake inhibitors ; Fluvoxamine
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract Previous studies have shown selective and non-selective monoamine oxidase inhibitors (MAOIs) to be effective in the treatment of social phobia. In this study we investigated the efficacy of selective serotonin reuptake inhibitors (SSRIs) in social phobia. Thirty patients with social phobia (DSM-IIIR) were treated with the SSRI fluvoxamine (150 mg daily) using a 12-week double-blind placebo controlled design. A substantial improvement was observed in seven (46%) patients on fluvoxamine and in one (7%) on placebo. Statistically significant effects were seen on measures of social anxiety and general (or anticipatory) anxiety in patients treated with fluvoxamine compared with placebo. The level of phobic avoidance decreased also but the difference at endpoint between fluvoxamine and placebo failed to reach statistical significance. It is concluded that treatment with the SSRI fluvoxamine has beneficial effects in patients suffering from social phobia, suggesting that serotonergic mechanisms might be implicated in social anxiety.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02244762
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  • 33
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    Electronic Resource
    Cystic angiomatosis of bone with sclerotic changes mimicking osteoblastic metastases (1994)
    Springer
    Skeletal radiology 23 (1994), S. 247-252 
    Details
    ISSN: 1432-2161
    Keywords: Cystic angiomatosis ; Hemangiomatosis ; Lymphangiomatosis ; Osteosclerosis ; Bone
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract Five unusual cases of cystic angiomatosis of bone which presented with the radiologic appearance of osteoblastic lesions are reported. Three patients were female (ages 37, 41, and 65 years) and two were male (ages 24 and 66 years). Although cystic angiomatosis of bone usually produces widespread osteolytic lesions with a honeycombed appearance in the skeletal system, multiple osteoblastic lesions mimicking metastatic osteoblastic carcinoma are sometimes seen. This radiological presentation has not been well emphasized in previous reports. Histologically, in addition to the angiomatous lesions, both mature thickened lamellar bone trabeculae and immature trabeculae of woven bone were found. In one of our patients, increasing density of the osteoblastic lesions was noted over time. One previous study has suggested that the age of the lesions of cystic angiomatosis is related to radiographic density. It is important to recognize this uncommon variant of cystic angiomatosis and to include this entity among the radiologic differential diagnoses when multiple osteoblastic lesions are encountered.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02412356
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  • 34
    Electronic Resource
    Electronic Resource
    Immunologicalization of complement C1s and matrix metalloproteinase 9 (92kDa gelatinase/type IV collagenase) in the primary ossification center of the human femur (1994)
    Springer
    Cell & tissue research 277 (1994), S. 239-245 
    Details
    ISSN: 1432-0878
    Keywords: Bone ; Ossification ; Cartilage ; Matrix ; Chondrocytes ; Complement ; Matrix metalloproteinase ; Immunocytochemistry ; Man
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract The first component of complement $$C\bar 1s$$ has been shown to degrade type I and type II collagens (Yamaguchi et al. 1990), the latter of which is a major constituent of the cartilage matrix. In order to understand the physiological roles of $$C\bar 1s$$ in cartilage resorption, the expression of C1s was examined by immunohistochemistry in the primary ossification center where the matrix is removed and replaced by bone marrow. Hypertrophic chondrocytes, endothelium and hematogenous elements in the capillary buds were intensely stained by a monoclonal antibody against C1s. Matrix metalloproteinase 9 (MMP-9, 92kDa gelatinase/type IV collagenase) was also immunolocalized in hypertrophic chondrocytes, mesenchymal cells in the primitive bone marrow and the cartilage matrix adjacent to the marrow. In addition, $$C\bar 1s$$ was found to activate the zymogen of MMP-9. These observations suggest that $$C\bar 1s$$ and MMP-9 coordinately participate in matrix degradation in cartilage.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00327771
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  • 35
    Electronic Resource
    Electronic Resource
    The effect ofin vitro fluoride ion treatment on the ultrasonic properties of cortical bone (1994)
    Springer
    Annals of biomedical engineering 22 (1994), S. 404-415 
    Details
    ISSN: 1573-9686
    Keywords: Bone ; Ultrasound ; Interfacial bonding ; Anisotropy ; Fluoride
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine , Technology
    Notes: Abstract The mechanical properties of composites are influenced, in part, by the volume fraction, orientation, constituent mechanical properties, and interfacial bonding. Cortical bone tissue represents a short-fibered biological composite where the hydroxyapatite phase is embedded in an organic matrix composed of type I collagen and other noncollagenous proteins. Destructive mechanical testing has revealed that fluoride ion treatment significantly lowers theZ-axis tensile and compressive properties of cortical bone through a constituent interfacial debonding mechanism. The present ultrasonic data indicates that fluoride ion treatment significantly alters the longitudinal velocity in theZ-axis as well as the circumferential and radial axes of cortical bone. This suggests that the distribution of constituents and interfacial bonding amongst them may contribute to the anisotropic nature of bone tissue.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02368247
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  • 36
    Electronic Resource
    Electronic Resource
    Statistical model of the habit and arrangement of mineral crystals in the collagen of bone (1994)
    Springer
    Journal of statistical physics 77 (1994), S. 125-143 
    Details
    ISSN: 1572-9613
    Keywords: Bone ; collagen ; Voronoi tesselations ; small-angle scattering ; structure function ; calcified tissue
    Source: Springer Online Journal Archives 1860-2000
    Topics: Physics
    Notes: Abstract Randomly colored space tesselations are considered as models for the mineral/organic structure of bone. First, it is shown that the structure function for such models is always proportional to the average form factor of the individual tiles and hence independent of the mineral density in the sample. Then the structure function is calculated for three such models: for model I, based on a hexagonal, and model 2, on a Poisson-Voronoi tesselation of the plane and for model 3, based on a random tesselation of the line. These results are compared to experimental structure functions measured by small-angle scattering and excellent agreement is obtained between model 2 and the bone from mice and rats, as well as between model 3 and calcified turkey leg tendon. Divergent conclusions following recent experiments by small-angle x-ray scattering and by electron microscopy are discussed in the light of these structural models and an explanation is proposed which might remove the discrepancy.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02186835
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  • 37
    Electronic Resource
    Electronic Resource
    Solution structure of a core peptide derived from scyllatoxin (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 18 (1994), S. 205-215 
    Details
    ISSN: 0887-3585
    Keywords: peptide folding ; disulfide framework ; insect toxins ; NMR ; distance geometry ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: An analysis of the sequences of scyllatoxin and charybdotoxin suggested that it would be possible to design a core peptide sequence which would still fold to give the β-hairpin and helix seen in the toxins, but which would eliminate one disulfide and connecting residues. The core sequence was modeled, then synthesized and purified. The cysteines oxidize in air to give the same disulfide pairings as seen in the parent toxins as the major product. The three-dimensional structure of the core sequence peptide, termed Max, was determined using proton NMR spectroscopy and found to be identical in secondary structure to the toxins. However differences were found in the relative orientation of the β-hairpin and helix. The use of this structural motif, found in many insect toxins, as a disulfide framework for exploring sequence/structure/activity relationships is discussed. © 1994 John Wiley & Sons, Inc.
    Additional Material: 9 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340180302
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    Thermodynamics of ubiquitin unfolding (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 18 (1994), S. 246-253 
    Details
    ISSN: 0887-3585
    Keywords: microcalorimetry ; heat capacity ; enthalpy ; hydrogen bonding ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The energetics of ubiquitin unfolding have been studied using differential scanning microcalorimetry. For the first time it has been shown directly that the enthalpy of protein unfolding is a nonlinear function of temperature. Thermodynamic parameters of ubiquitin unfolding were correlated with the structure of the protein. The enthalpy of hydrogen bonding in ubiquitin was calculated and compared to that obtained for other proteins. It appears that the energy of hydrogen bonding correlates with the average length of the hydrogen bond in a given protein structure. © 1994 John Wiley & Sons, Inc.
    Additional Material: 6 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340180305
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    Hydrogen bond strength and β-sheet propensities: The role of a side chain blocking effect (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 18 (1994), S. 262-266 
    Details
    ISSN: 0887-3585
    Keywords: protein structure prediction ; protein stability ; hydrogen bond ; β-sheet ; amino acid propensity ; steric effect ; hydrogen exchange ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Amino acid side chains can enhance peptide group hydrogen bond strength in protein structures by obstructing the competing hydrogen bond to solvent in the unfolded state. Available data indicate that the steric blocking effect contributes an average of 0.5 kJ per residue to protein hydrogen bond strength and accounts for the intrinsic α-sheet propensities of the amino acids. In available data for helical models, the contribution to α-helix propensities is obscured especially by large context-dependent effects. These issues are all related by a common side chain-dependent steric clash which disfavors peptide to water H-bond formation, peptide to catalyst complexation in hydrogen exchange reactions (Bai et al., Proteins 17:75-86, 1993), and peptide to peptide H-bonding in the helical main chain conformation (Creamer and Rose, Proc. Natl. Acad. Sci. U.S.A. 89:5937-5941, 1992) but not in α-strands. © 1994 John Wiley & Sons, Inc.
    Additional Material: 4 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340180307
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    A method for α-helical integral membrane protein fold prediction (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 18 (1994), S. 281-294 
    Details
    ISSN: 0887-3585
    Keywords: membrane ; protein ; structure ; prediction ; G-protein coupled receptor ; rhodopsin ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Integral membrane proteins (of the α-helical class) are of central importance in a wide variety of vital cellular functions. Despite considerable effort on methods to predict the location of the helices, little attention has been directed toward developing an automatic method to pack the helices together. In principle, the prediction of membrane proteins should be easier than the prediction of globular proteins: there is only one type of secondary structure and all helices pack with a common alignment across the membrane. This allows all possible structures to be represented on a simple lattice and exhaustively enumerated. Prediction success lies not in generating many possible folds but in recognizing which corresponds to the native. Our evaluation of each fold is based on how well the exposed surface predicted from a multiple sequence alignment fits its allocated position. Just as exposure to solvent in globular proteins can be predicted from sequence variation, so exposure to lipid can be recognized by variable-hydrophobic (variphobic) positions. Application to both bacteriorhodopsin and the eukaryotic rhodopsin/opsin families revealed that the angular size of the lipid-exposed faces must be predicted accurately to allow selection of the correct fold. With the inherent uncertainties in helix prediction and parameter choice, this accuracy could not be guaranteed but the correct fold was typically found in the top six candidates. Our method provides the first completely automatic method that can proceed from a scan of the protein sequence databanks to a predicted three-dimensional structure with no intervention required from the investigator. Within the limited domain of the seven helix bundle proteins, a good chance can be given of selecting the correct structure. However, the limited number of sequences available with a corresponding known structure makes further characterization of the method difficult. © 1994 John Wiley & Sons, Inc.
    Additional Material: 5 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340180309
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    Crystallization and preliminary crystallographic studies of the precursor and mature forms of a neutral lipase from the fungus Rhizopus delemar (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 18 (1994), S. 301-306 
    Details
    ISSN: 0887-3585
    Keywords: triglyceride lipase ; proenzyme ; molecular replacement ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A neutral lipase from the filamentous fungus Rhizopus delemar has been crystallized in both its proenzyme and mature forms. Although the latter crystallizes readily and produces a variety of crystal forms, only one was found to be suitable for X-ray studies. It is monoclinic (C2, a = 92.8 Å, b = 128.9 Å, c = 78.3 Å, β = 135.8) with two molecules in the asymmetric unit related by a noncrystallographic diad. The prolipase crystals are orthorhombic (P212121, with a = 79.8 Å, b = 115.2 Å, c = 73.0 Å) and also contain a pair of molecules in the asymmetric unit. Initial results of molecular replacement calculations using the refined coordinates of the related lipase from Rhizomucor miehei identified the correct orientations and positions of the protein molecules in the unit cells of crystals of both proenzyme and the mature form. © 1994 John Wiley & Sons, Inc.
    Additional Material: 2 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340180311
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    Correlated mutations and residue contacts in proteins (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 18 (1994), S. 309-317 
    Details
    ISSN: 0887-3585
    Keywords: protein structure prediction ; predicted contact maps ; correlated mutations ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The maintenance of protein function and structure constrains the evolution of amino acid sequences. This fact can be exploited to interpret correlated mutations observed in a sequence family as an indication of probable physical contact in three dimensions. Here we present a simple and general method to analyze correlations in mutational behavior between different positions in a multiple sequence alignment. We then use these correlations to predict contact maps for each of 11 protein families and compare the result with the contacts determined by crystallography. For the most strongly correlated residue pairs predicted to be in contact, the prediction accuracy ranges from 37 to 68% and the improvement ratio relative to a random prediction from 1.4 to 5.1. Predicted contact maps can be used as input for the calculation of protein tertiary structure, either from sequence information alone or in combination with experimental information. © 1994 John Wiley & Sons, Inc.
    Additional Material: 6 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340180402
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    Analysis of Cα geometry in protein structures (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 18 (1994), S. 324-337 
    Details
    ISSN: 0887-3585
    Keywords: protein structure ; secondary structure ; peptide geometry ; Ramachandran plot ; β-turns ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The polypeptide of a protein molecule can be considered as a chain of Cα atoms linked by pseudobonds between the Cα atoms of successive amino acid residues. This paper presents an analysis of the angle and dihedral angles made by these pseudobonds in protein structures determined at high resolution by X-ray crystallography. This analysis reveals a strong correlation between Cα geometry and the protein fold. The regular features of protein secondary structure such as α-helix and α-sheet are very clearly defined. In addition, it is possible to identify with some confidence the discrete populations of particular conformations of α-turn. Comparison with the traditional Ramachandran type of plot demonstrates that an analysis of protein structure on the basis of Cα geometry provides a richer description of protein conformation. In addition, the characteristics of this geometry could be a useful guide in model building of protein structure. © 1994 John Wiley & Sons, Inc.
    Additional Material: 5 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340180404
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    Crystallization of a fragment of human fibronectin: Introduction of methionine by site-directed mutagenesis to allow phasing via selenomethionine (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 19 (1994), S. 48-54 
    Details
    ISSN: 0887-3585
    Keywords: X-ray crystallography ; extracellular matrix ; multiwavelength anomalous diffraction (MAD) ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Crystals of a fragment of human fibronectin encompassing the 7th through the RGD-containing 10th type III repeats (FN7-10) have been produced with protein expressed in E. coli. The crystals are monoclinic with one molecule in the asymmetric unit and diffract to beyond 2.0 Å Bragg spacings. A mutant FN7-10 was produced in which three methionines, in addition to the single native methionine already present, have been introduced by site-directed mutagenesis. Diffraction-quality crystals of this mutant protein have been grown in which methionine was replaced with selenomethionine. The introduction of methionine by site-directed mutagenesis to allow phasing from selenomethionyl-substituted crystals is shown to be feasible by this example and is proposed as a general approach to solving the crystallographic phase problem. Strategies for selecting propitious sites for methionine mutations are discussed. © 1994 Wiley-Liss, Inc.
    Additional Material: 1 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340190107
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    Combining evolutionary information and neural networks to predict protein secondary structure (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 19 (1994), S. 55-72 
    Details
    ISSN: 0887-3585
    Keywords: secondary structure prediction ; prediction of secondary structure class ; prediction of secondary structure content ; evolutionary information ; multiple alignment profiles ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Using evolutionary information contained in multiple sequence alignments as input to neural networks, secondary structure can be predicted at significantly increased accuracy. Here, we extend our previous three-level system of neural networks by using additional input information derived from multiple alignments. Using a position-specific conservation weight as part of the input increases performance. Using the number of insertions and deletions reduces the tendency for overprediction and increases overall accuracy. Addition of the global amino acid content yields a further improvement, mainly in predicting structural class. The final network system has a sustained overall accuracy of 71.6% in a multiple cross-validation test on 126 unique protein chains. A test on a new set of 124 recently solved protein structures that have no significant sequence similarity to the learning set confirms the high level of accuracy. The average cross-validated accuracy for all 250 sequence-unique chains is above 72%. Using various data sets, the method is compared to alternative prediction methods, some of which also use multiple alignments: the performance advantage of the network system is at least 6 percentage points in three-state accuracy. In addition, the network estimates secondary structure content from multiple sequence alignments about as well as circular dichroism spectroscopy on a single protein and classifies 75% of the 250 proteins correctly into one of four protein structural classes. Of particular practical importance is the definition of a position-specific reliability index. For 40% of all residues the method has a sustained three-state accuracy of 88%, as high as the overall average for homology modelling. A further strength of the method is greatly increased accuracy in predicting the placement of secondary structure segments. © 1994 Wiley-Liss, Inc.
    Additional Material: 8 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340190108
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    Expression, purification, and crystallization of restriction endonuclease PvuII with DNA containing its recognition site (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 19 (1994), S. 77-79 
    Details
    ISSN: 0887-3585
    Keywords: endonuclease overexpression ; crystallization ; X-ray diffraction ; protein-DNA complex ; Type II restriction enzyme ; vapor diffusion ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We have overexpressed the type II restriction endonuclease PvuII (R.PvuII) in E. coli, prepared large amounts of the homogeneous enzyme, and crystallized it with an oligonucleotide carrying a PvuII recognition site. The cocrystals are orthorhombic space group P212121 with cell constants a = 95.8 Å, b = 86.3 Å, c = 48.5 Å, and diffract X-rays to at least 2.7 Å. There is a complex of two protein subunits and one oligonucleotide duplex in the asymmetric unit. © 1994 Wiley-Liss, Inc.
    Additional Material: 2 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340190110
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    Masthead (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 19 (1994) 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340190201
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  • 48
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    Crystallization and preliminary X-ray crystallographic analysis of phospholipid transfer protein from maize seedlings (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 19 (1994), S. 80-83 
    Details
    ISSN: 0887-3585
    Keywords: maize protein ; crystals ; X-ray diffraction ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Phospholipid transfer protein from maize seedlings has been crystallized using trisodium citrate as precipitant. The crystal belongs to the orthorhombic space group P212121 with unit cell dimensions of a = 24.46 Å, b = 49.97 Å, and c = 69.99 Å. The presence of one molecule in the asymmetric unit gives a crystal volume per protein mass (Vm) of 2.36 Å 3/Da and a solvent content of 48% by volume. The X-ray diffraction pattern extends at least to 1.6 Å Bragg spacing when exposed to both CuKα and synchrotron X-rays. A set of X-ray data to approximately 1.9 Å Bragg spacing has been collected from a native crystal. © 1994 Wiley-Liss, Inc.
    Additional Material: 1 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340190111
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  • 49
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    α-Helix-forming propensities in peptides and proteins (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 19 (1994), S. 85-97 
    Details
    ISSN: 0887-3585
    Keywords: protein conformation ; secondary structure ; protein folding ; helix stability ; helix formation ; conformational entropy ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Much effort has been invested in seeking to understand the thermodynamic basis of helix stability in both peptides and proteins. Recently, several groups have measured the helix-forming propensities of individual residues (Lyu, P. C., Liff, M. I., Marky, L. A., Kallenbach, N. R. Science 250:669-673, 1990; O'Neil, K. T., DeGrado, W. F. Science 250:646-651, 1990; Padmanabhan, S., Marqusee, S., Ridgeway, T., Laue, T. M., Baldwin, R. L. Nature (London) 344:268-270, 1990). Using Monte Carlo computer simulations, we tested the hypothesis that these differences in measured helix-forming propensity are due primarily to loss of side chain conformational entropy upon helix formation (Creamer, T. P., Rose, G. D. Proc. Natl. Acad. Sci. U.S.A. 89:5937-5941, 1992). Our previous study employed a rigid helix backbone, which is here generalized to a completely flexible helix model in order to ensure that earlier results were not a methodological artifact. Using this flexible model, side chain rotamer distributions and entropy losses are calculated and shown to agree with those obtained earlier. We note that the side chain conformational entropy calculated for Trp in our previous study was in error; a corrected value is presented. Extending earlier work, calculated entropy losses are found to correlate strongly with recent helix propensity scales derived from substitutions made within protein helices (Horovitz, A., Matthews, J. M., Fersht, A. R. J. Mol. Biol. 227:560-568, 1992; Blaber, M., Zhang, X.-J., Matthews, B. M. Science 260:1637-1640, 1993). In contrast, little correlation is found between these helix propensity scales and the accessible surface area buried upon formation of a model polyalanyl α-helix. Taken in sum, our results indicate that loss of side chain entropy is a major determinant of the helix-forming tendency of residues in both peptide and protein helices. © 1994 Wiley-Liss, Inc.
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    URL: http://dx.doi.org/10.1002/prot.340190202
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  • 50
    Electronic Resource
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    1.56 Å structure of mature truncated human fibroblast collagenase (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 19 (1994), S. 98-109 
    Details
    ISSN: 0887-3585
    Keywords: crystallography ; hydroxamate ; high resolution ; metalloproteinase ; zinc ; X-ray ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The X-ray crystal structure of a 19 kDa active fragment of human fibroblast collagenase has been determined by the multiple isomorphous replacement method and refined at 1.56 Å resolution to an R-factor of 17.4%. The current structure includes a bound hydroxamate inhibitor, 88 waters and three metal atoms (two zincs and a calcium). The overall topology of the enzyme, comprised of a five stranded β-sheet and three α-helices, is similar to the thermolysin-like metalloproteinases. There are some important differences between the collagenase and thermolysin families of enzymes. The active site zinc ligands are all histidines (His-218, His-222, and His-228). The presence of a second zinc ion in a structural role is a unique feature of the matrix metalloproteinases. The binding properties of the active site cleft are more dependent on the main chain conformation of the enzyme (and substrate) compared with thermolysin. A mechanism of action for peptide cleavage similar to that of thermolysin is proposed for fibroblast collagenase. © 1994 Wiley-Liss, Inc.
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    URL: http://dx.doi.org/10.1002/prot.340190203
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    Kinetic study on myoglobin refolding monitored by five optical probe stopped-flow methods (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 19 (1994), S. 110-119 
    Details
    ISSN: 0887-3585
    Keywords: folding intermediate ; urea denaturation ; stopped-flow circular dichroism ; molten globule ; hemindicyanide ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The refolding kinetics of horse cyanometmyoglobin induced by concentration jump of urea was investigated by five optical probe stopped-flow methods: absorption at 422 nm, tryptophyl fluorescence at around 340 nm, circular dichroism (CD) at 222 nm, CD at 260 nm, and CD at 422 nm. In the refolding process, we detected three phases with rate constants of 〉 1 × 102 s-1, (4.5-9.3) S-1, and (2-5) × 10-3 s-1. In the fastest phase, a substantial amount of secondary structure (40%) is formed within the dead time of the CD stopped-flow apparatus (10.7 ms). The kinetic intermediate populated in the fastest phase is shown to capture a hemindicyanide, suggesting that a “heme pocket precursor” recognized by hemindicyanide must be constructed within the dead time. In the middle phase, most of secondary and tertiary structures, especially around the captured hemindicyanide, have been constructed. In the slowest phase, we detected a minor structural rearrangement accompanying the ligand-exchange reaction in the fifth coordination of ferric iron. We present a possible model for the refolding process of myoglobin in the presence of the heme group. © 1994 Wiley-Liss, Inc.
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    URL: http://dx.doi.org/10.1002/prot.340190204
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    Decoupling of melting domains in immobilized ribonuclease A (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 19 (1994), S. 120-131 
    Details
    ISSN: 0887-3585
    Keywords: enzymes ; protein immobilization ; microcalorimetry ; protein melting domains ; protein DSC ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Ribonuclease A has been immobilized on silica beads through glutaraldeyde-mediated chemical coupling in order to improve the stability of the protein against thermal denaturation. The thermodynamic and binding properties of the immobilized enzyme have been studied and compared with those of the free enzyme. The parameters describing the binding of the inhibitor 3′ -CMP (Ka and ΔH) as monitored by spectrophotometry and calorimetry were not significantly affected after immobilization. Conversely both the stability and unfolding mechanism drastically changed. Thermodynamic analysis of the DSC data suggests that uncoupling of protein domains has occurred as a consequence of the immobilization. The two state approximation of the protein unfolding process is not longer valid for the immobilized RNase. Protein stability strongly depends on the hydrophobicity properties of the support surface as well as on the presence of the inhibitor and pH. For example, after immobilization on a highly hydrophobic surface, the enzyme is partially in the unfolded state. The binding of a ligand is able to reorganize the protein structure into a native-like conformation. The refolding rates are different for the two protein domains and vary as a function of pH and presence of the inhibitor 3′-CMP. © 1994 Wiley-Liss, Inc.
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    URL: http://dx.doi.org/10.1002/prot.340190205
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    Temperature-induced complementarity as a mechanism for biomolecular assembly (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 19 (1994), S. 73-76 
    Details
    ISSN: 0887-3585
    Keywords: molecular recognition ; protein assembly ; protein folding ; protein interactions ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Recent advances in the measurement and theory of “hydration” interactions between biomolecules provide a basis on which to formulate mechanisms of biomolecular recognition. In this paper we have developed a mathematical formalism for analyzing specificity encoded in dynamic distributions of surface polar groups, a formalism that incorporates newly recognized properties of directly measured “hydration” forces. As expected, attraction between surfaces requires complementary patterns of surface polar groups. In contrast to usual expectations, thermal motion can create these complementary surface configurations. We have demonstrated that assembly can occur with an increase in conformational entropy of polar residues. Elevated temperature then facilitates recognition rather than hinders it. This mechanism might underlie some temperature-favored assembly reactions common in biological systems that are usually associated with the “hydrophobic effect” only. © 1994 Wiley-Liss, Inc.
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    URL: http://dx.doi.org/10.1002/prot.340190109
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    Coiled-coil stutter and link segments in keratin and other intermediate filament molecules: A computer modeling study (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 20 (1994), S. 174-184 
    Details
    ISSN: 0887-3585
    Keywords: coiled-coils ; keratin ; intermediate filament proteins ; link segments ; heptad phasing ; computer modeling ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Structural discontinuities have previously been identified in four regions of the coiled-coil rod domain structure present in intermediate filament (IF) protein molecules. These include a point at which a phase shift occurs in the heptad periodicity characteristic of the sequence of polar and apolar residues in α-helical coiled-coils, and three links that lack a heptad substructure. We have studied these regions by computer-based molecular modeling and comparative sequence analysis and conclude that the phasing discontinuity can be accommodated without significant distortion of the overall double-helical chain conformation; the L2 link has a similar conformation in all different types of IF molecules, a favorable conformation being one in which the two strands wrap tightly around each other; the L12 links vary in length between different IF types but contain important sequence similarities suggestive of a partial β structure; the L1 links show larger variations in length, a lower degree of similarity, and probably diverse structures. Variations in the overall charges of the different links suggest that ionic interactions may playa significant role in filament assembly. The results also have general significance for other α-fibrous proteins in which either the characteristic heptad phasing undergoes a discontinuity or where a short non-coiled-coil sequence occurs within a coiled-coil rod domain structure. © 1994 Wiley-Liss, Inc.
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    URL: http://dx.doi.org/10.1002/prot.340200207
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    Crystallization and characterization of the recombinant human Clara cell 10-kDa protein (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 20 (1994), S. 191-196 
    Details
    ISSN: 0887-3585
    Keywords: human Clara cell 10-kDa protein ; X-ray diffraction ; phospholipase A2 inhibitor ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Crystals of recombinant human Clara cell 10-kDa protein were grown both from ammonium sulfate and polyethylene glycol (PEG) solutions. Crystals grown from ammonium sulfate solution have been characterized by X-ray diffraction studies as monoclinic with the space group C2 and lattice constants a = 69.2 Å, b = 83.0 Å, c = 58.3 Å, and β = 99.7°. The monoclinic crystals diffract to beyond 2.5 Å. Some of the crystals grown from PEG were of a similar habit to those grown from ammonium sulfate, but others were triclinic with the space group P1 and cell constants a = 40.3 Å, b = 46.3 Å, c = 51.3 Å, α = 117.7°, β = 102.3°, and γ = 71.4°. These crystals diffract to beyond 3.2 Å. © 1994 Wiley-Liss, Inc.
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    URL: http://dx.doi.org/10.1002/prot.340200209
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    Conformational analysis of hemopexin by fourier-transform infrared and circular dichroism spectroscopy (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 20 (1994), S. 185-190 
    Details
    ISSN: 0887-3585
    Keywords: heme ; secondary structure ; conformation ; hemopexin ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Hemopexin is a serum glyco-protein that binds heme with the highest known affinity of any characterized heme-binding protein and plays an important role in receptormediated cellular heme uptake. Complete understanding of the function of hemopexin will require the elucidation of its molecular structure. Previous analysis of the secondary structure of hemopexin by far-UV circular dichroism (CD) failed due to the unusual positive ellipticity of this protein at 233 nm. In this paper, we present an examination of the structure of hemopexin by both Fourier-transform infrared (FTIR) and circular dichroism spectroscopy. Our studies show that hemopexin contains about 55% β-structure, 15% α-helix, and 20% turns. The two isolated structural domains of hemopexin each have secondary structures similar to hemopexin. Although there are significant tertiary conformational changes indicated by the CD spectra, the overall secondary structure of hemopexin is not affected by binding heme. However, moderate changes in secondary structure do occur when the heme-binding domain of hemopexin associates with heme. In spite of the exceptionally tight binding at neutral pH, heme is released from the bis-histidyl heme-hemopexin complex at pH 5.0. Under this acidic condition, hemopexin maintains the same overall secondary structure as the native protein and is able to resume the heme-binding function and the native structure of the hemeprotein (as indicated by the CD spectra) when returned to neutral pH. We propose that the state of hemopexin identified in vitro at pH 5.0 resembles that of this protein in the acidic environment of the endosomes in vivo when hemopexin releases heme during receptor-mediated endocytosis. © 1994 Wiley-Liss, Inc.
    Additional Material: 6 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340200208
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    Masthead (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 20 (1994) 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340200301
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    Preliminary crystallographic analysis of an enzyme involved in erythromycin biosynthesis: Cytochrome P450eryF (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 20 (1994), S. 197-201 
    Details
    ISSN: 0887-3585
    Keywords: cytochrome P450 ; erythromycin ; P450eryF ; crystallization ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Cytochrome P450eryF was overexpressed in Escherichia coli and purified in high yield. Crystals of the protein in the presence of the substrate, 6-deoxyerythronolide B, have been obtained by the hanging drop vapor diffusion method, using polyethylene glycol 4000 as a precipitant. The crystals belong to the orthorhombic space group P212121 with unit cell dimensions of a = 54.16 Å, b = 79.67 Å, and c = 99.48 Å and one molecule per asymmetric unit. A complete native data set has been collected to a resolution of 2.1 Å, and anomalous dispersion difference Patterson maps have revealed the location of the single heme iron atom. © 1994 Wiley-Liss, Inc.
    Additional Material: 5 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340200210
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    Homology modeling of the Abl-SH3 domain (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 20 (1994), S. 203-215 
    Details
    ISSN: 0887-3585
    Keywords: SH3 ; Abl ; molecular modeling ; homology modeling ; molecular dynamics ; protein structure prediction ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A tertiary structure model of the Abl-SH3 domain is predicted by using homology modeling techniques coupled to molecular dynamics simulations. Two template proteins were used, Fyn-SH3 and Spc-SH3. The refined model was extensively checked for errors using criteria based on stereochemistry, packing, solvation free-energy, accessible surface areas, and contact analyses. The different checking methods do not totally agree, as each one evaluates a different characteristic of protein structures. Several zones of the protein are more susceptible to incorporating errors. These include residues 13, 15, 35, 39, 45, 46, 50, and 60. An interesting finding is that the measurement of the Cα chirality correlated well with the rest of the criteria, suggesting that this parameter might be a good indicator of correct local conformation. Deviations of more than 4 degrees may be indicative of poor local structure. © 1994 Wiley-Liss, Inc.
    Additional Material: 7 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340200302
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    Homologous modeling of the lysosomal protective protein/carboxypeptidase L: Structural and functional implications of mutations identified in galactosialidosis patients (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 18 (1994), S. 81-93 
    Details
    ISSN: 0887-3585
    Keywords: serine carboxypeptidase ; protein modeling ; mutation analysis ; comparative modeling ; cathepsin A ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The deficiency of the lysosomal protective protein/carboxypeptidase L (CARB L) causes the lysosomal storage disorder, galactosialidosis, characterized by neuraminidase and β-galactosidase deficiencies in patients' cells. The three enzymes form a complex inside the lysosome, and the neuraminidase and β-galactosidase deficiencies are secondary to CARB L deficiency. Sequence similarity and common enzymological properties suggest that the protomeric tertiary structure of CARB L is conserved within a family of serine carboxypeptidases which includes the yeast carboxypeptidase Y, killer expression I gene product and several plant carboxypeptidases. We used this homology to build a model of the CARB L structure based on the recently published X-ray atomic coordinates of the wheat carboxypeptidase II (CPDW-II) which shares 32% primary structure identity with CARB L. Small insertions and deletions were accommodated into the model structure by energy minimization using the DREIDING II force field. The Cα atomic-coordinates of the final CARB L model have a RMS shift of 1.01 Å compared to the corresponding conserved residues in the CPDW-II template structure. The correct orientation of the homologous catalytic triad residues Ser150, His429 and Asp392, the potential energy calculations and the distribution of hydrophobic and hydrophillic residues in the structure all support the validity of the CARB L model. Most missense mutations identified in galactosialidosis patients were located in secondary structural elements except for the Tyr211→Asn mutation which is in a loop. The other mutant residues have their side chains deeply buried in the central β-sheet of the model structure except for the Phe412→Val mutation which is located in the dimer interface. The predicted effects of specific mutations on CARB L structural stability correlates well with recently published transient expression studies of mutant CARB L (Shimmoto, M. et al., J. Clin. Invest., 91:2393-2399, 1993). © 1994 John Wiley & Sons, Inc.
    Additional Material: 6 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340180110
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    Protein simulations using techniques suitable for very large systems: The cell multipole method for nonbond interactions and the Newton-Euler inverse mass operator method for internal coordinate dynamics (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 20 (1994), S. 227-247 
    Details
    ISSN: 0887-3585
    Keywords: cell multipole method ; Newton-Euler inverse mass operator ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Two new methods developed for molecular dynamics simulations of very large proteins are applied to a series of proteins ranging up to the protein capsid of tomato bushy stunt virus (TBSV).For molecular dynamics of very large proteins and polymers, it is useful to carry out the dynamics using internal coordinates (say, torsions only) rather than Cartesian coordinates. This allows larger time steps, eliminates problems with the classical description of high energy modes, and focuses on the important degrees of freedom. The resulting equation of motion has the form where for T is the vector of generalized forces, M(θ) is the moments of inertia tensor, is the vector of torsions, and C is a vector containing Coriolis forces and nonbond forces. The problem is that to calculate the acceleration vector from M, C, and Trequires inverting. M(θ), an order N3calculation. Since the number of degrees of freedom might be 300,000 for a million atom system, solving these equations every time step is impractical, restricting internal coordinate methods to small systems. The new method, Newton-Euler Inverse Mass Operator (NEIMO) dynamics, constructs the torsional accelerations vector directly by an order N process, allowing internal-coordinate dynamics to be solved for super larger (million atom) systems, The first use of the NEIMO method for molecular dynamics of proteins is presented here.A second serious difficulty for large proteins is calculation of the nonbond forces. We report here the first application to proteins of the new Cell Multipole Method (CMM) to evaluate the Coulomb and van der Waals interactions. The cost of CMM scales linearly with the number of particles while retaining an accuracy significantly better than standard non bond methods (involving cutoffs).Results for NEIMO and CMM are given for simulations of a wide range of peptide and protein systems, including the protein capsid of TBSV with 488,000 atoms. The computational times for NEIMO and CMM are demonstrated to scale linearly with size. With NEIMO the dynamics time steps can be as large as 20 fs (for small peptides), much larger than possible with standard Cartesian coordinate dynamics.For TBSV we considered both the normal form and the high pH form, in which the Ca2+ ions are removed. These calculations lead to a contraction of the protein for both forms (probably because of ignoring the RNA core not observed in the X-ray). © 1994 Wiley-Liss, Inc.
    Additional Material: 21 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340200304
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    Estimation of changes in side chain configurational entropy in binding and folding: General methods and application to helix formation (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 20 (1994), S. 68-84 
    Details
    ISSN: 0887-3585
    Keywords: side chain conformation ; protein folding ; protein binding ; helix formation ; helix stability ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Theoretical estimations of changes in side chain configurational entropy are essential for understanding the different contributions to the overall thermodynamic behavior of important biological processes like folding and binding. The configurational entropy of any given side chain in any particular protein can be evaluated from the complete energy profile of the side chain. Calculations of the energy profiles can be performed using the side chain single bond dihedrals as the only independent variables as long as the structures at each value of the dihedrals are allowed to relax through small changes in the valence bond angles. The probabilities of different side chain conformers obtained from these energy profiles are very similar to the conformer populations obtained by analysis of side chain preferences in the proteins of the Protein Data Bank. Also, side chain conformational entropies obtained from the energy profiles agree extremely well with those obtained from the Protein Data Bank conformer populations. Changes in side chain configurational entropy in binding and folding can be computed as differences in conformational entropy because, in most cases, the frequency of the rotational oscillation around the energy minimum of any given conformer does not appear to change significantly in the reaction. Changes of side chain conformational entropy calculated in this way were compared with experimental values. The only available experimental data-the effect of side chain substitution on the stability of α-helices-were used for this comparison. The experimental values were corrected to subtract the solvent contributions. This comparison yields an excellent agreement between calculated and experimental values, validating not only the theoretical estimates but also the separability of the entropic contributions into configurational terms and solvation related terms. © 1994 Wiley-Liss, Inc.
    Additional Material: 4 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340200108
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    Microtube batch protein crystallization: Applications to human immunodeficiency virus type 2 (HIV-2) protease and human renin (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 20 (1994), S. 98-102 
    Details
    ISSN: 0887-3585
    Keywords: X-ray diffraction ; aspartic protease ; AIDS ; recombinant protein ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: For therapeutically relevant targets, the evaluation of enzymes in complex with their inhibitors by cocrystallization and high resolution structural analysis has become a vital component of structure-driven drug design and development. Two approaches, hanging drop vapor diffusion and a novel microtube batch method, were utilized in parallel to grow crystals of recombinant HIV -2 protease and recombinant human renin in complex with inhibitors. In the case of HIV -2 protease in complex with a reduced amide inhibitor, crystallization was achieved only by the microbatch method. In the case of human renin, the addition of precipitant was required for crystal growth. The microbatch method described here is a useful supplementary or alternative approach for screening parameters and generating crystals suitable for high resolution structural analysis. © 1994 Wiley-Liss, Inc.
    Additional Material: 1 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340200110
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    Solvent-induced organization: A physical model of folding myoglobin (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 20 (1994), S. 124-138 
    Details
    ISSN: 0887-3585
    Keywords: leghemoglobin ; hydrophobic ; interactions ; hydrophobicity ; protein folding ; structure prediction ; protein dynamics ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The essential features of the in vitro refolding of myoglobin are expressed in a solvable physical model. Alpha helices are taken as the fundamental collective coordinates of the system, while the refolding is assumed to be mainly driven by solvent-induced hydrophobic forces. A quantitative model of these forces is developed and compared with experimental and theoretical results. The model is then tested by being employed in a simulation scheme designed to mimic solvent effects. Realistic dynamic trajectories of myoglobin are shown as it folds from an extended conformation to a close approximation of the native state. Various suggestive features of the process are discussed. The tenets of the model are further tested by folding the single-chain plant protein leghemoglobin. © 1994 Wiley-Liss, Inc.
    Additional Material: 9 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340200203
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    An evaluation of implicit and explicit solvent model systems for the molecular dynamics simulation of bacteriophage T4 lysozyme (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 18 (1994), S. 19-33 
    Details
    ISSN: 0887-3585
    Keywords: Discover program ; protein dynamics ; computer simulation ; protein motions ; counterions ; dielectric ; protein electrostatics ; aqueous simulation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: In this report we examine several solvent models for use in molecular dynamics simulations of protein molecules with the Discover program from Biosym Technologies. Our goal was to find a solvent system which strikes a reasonable balance among theoretical rigor, computational efficiency, and experimental reality. We chose phage T4 lysozyme as our model protein and analyzed 14 simulations using different solvent models. We tested both implicit and explicit solvent models using either a linear distance-dependent dielectric or a constant dielectric. Use of a linear distance-dependent dielectric with implicit solvent significantly diminished atomic fluctuations in the protein and kept the protein close to the starting crystal structure. In systems using a constant dielectric and explicit solvent, atomic fluctuations were much greater and the protein was able to sample a larger portion of conformational space. A series of nonbonded cutoff distances (9.0, 11.5, 15.0, 20.0 Å) using both abrupt and smooth truncation of the nonbonded cutoff distances were tested. The method of dual cutoffs was also tested. We found that a minimum nonbonded cutoff distance of 15.0 Å was needed in order to properly couple solvent and solute. Distances shorter than 15.0 Å resulted in a significant temperature gradient between the solvent and solute. In all trajectories using the proprietary Discover switching function, we found significant denaturation in the protein backbone; we were able to run successful trajectories only in those simulations that used no switching function. We were able to significantly reduce the computational burden by using dual cutoffs and still calculate a quality trajectory. In this method, we found that an outer cutoff distance of 15.0 Å and an inner cutoff distance of 11.5 worked well. While a 10 Å shell of explicit water yielded the best results, a 6 A shell of water yielded satisfactory results with nearly a 40% reduction in computational cost. © 1994 John Wiley & Sons, Inc.
    Additional Material: 8 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340180105
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    Molecular surface representations by sparse critical points (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 18 (1994), S. 94-101 
    Details
    ISSN: 0887-3585
    Keywords: surface representation ; molecular recognition ; protein docking ; surface triangulation ; molecular graphics ; molecular visualization ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We have defined a molecular surface representation that describes precisely and concisely the complete molecular surface. The representation consists of a limited number of critical points disposed at key locations over the surface. These points adequately represent the shape and the important characteristics of the surface, despite the fact that they are modest in number. We expect the representation to be useful in areas such as molecular recognition and visualization. In particular, using this representation, we are able to achieve accurate and efficient protein-protein and protein-small molecule docking. © 1994 John Wiley & Sons, Inc.
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    URL: http://dx.doi.org/10.1002/prot.340180111
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    Lobster enolase crystallized by serendipity (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 18 (1994), S. 390-393 
    Details
    ISSN: 0887-3585
    Keywords: protein crystallization ; enzyme copurification ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: An unknown protein crystallized from a lobster muscle preparation in which arginine kinase was the majority component. It was identified as enolase by peptide sequencing and activity testing, and a SIRAS electron density map showed its three-dimensional structure to be very similar to that of yeast enolase. © 1994 John Wiley & Sons, Inc.
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    URL: http://dx.doi.org/10.1002/prot.340180409
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    Crystallographic analysis of oxygenated and deoxygenated states of arthropod hemocyanin shows unusual differences (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 19 (1994), S. 302-309 
    Details
    ISSN: 0887-3585
    Keywords: dinuclear copper site ; hemocyanin ; oxygen binding ; allosteric regulation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The X-ray structure of an oxygenated hemocyanin molecule, subunit II of Limulus polyphemus hemocyanin, was determined at 2.4 Å resolution and refined to a crystallographic R-factor of 17.1%. The 73-kDa subunit crystallizes with the symmetry of the space group R32 with one subunit per asymmetric unit forming hexamers with 32 point group symmetry. Molecular oxygen is bound to a dinuclear copper center in the protein's second domain, symmetrically between and equidistant from the two copper atoms. The copper-copper distance in oxygenated Limulus hemocyanin is 3.6 ± 0.2 Å, which is surprisingly 1 Å less than that seen previously in deoxygenated Limulus polyphemus subunit II hemocyanin (Hazes et al., Protein Sci. 2:597, 1993). Away from the oxygen binding sites, the tertiary and quaternary structures of oxygenated and deoxygenated Limulus subunit II hemocyanins are quite similar. A major difference in tertiary structures is seen, however, when the Limulus structures are compared with deoxygenated Panulirus interruptus hemocyanin (Volbeda, A., Hol, W. G. J. J. Mol. Biol. 209:249, 1989) where the position of domain 1 is rotated by 8° with respect to domains 2 and 3. We postulate this rotation plays an important role in cooperativity and regulation of oxygen affinity in all arthropod hemocyanins. © 1994 Wiley-Liss, Inc.
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    URL: http://dx.doi.org/10.1002/prot.340190405
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    Conservation and prediction of solvent accessibility in protein families (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 20 (1994), S. 216-226 
    Details
    ISSN: 0887-3585
    Keywords: evolutionary information ; multiple alignments ; neural networks ; protein structure prediction ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Currently, the prediction of three-dimensional (3D) protein structure from sequence alone is an exceedingly difficult task. As an intermediate step, a much simpler task has been pursued extensively: predicting 1D strings of secondary structure. Here, we present an analysis of another 1D projection from 3D structure: the relative solvent accessibility of each residue. We show that solvent accessibility is less conserved in 3D homologues than is secondary structure, and hence is predicted less accurately from automatic homology modeling; the correlation coefficient of relative solvent accessibility between 3D homologues is only 0.77, and the average accuracy of predictions based on sequence alignments is only 0.68. The latter number provides an effective upper limit on the accuracy of predicting accessibility from sequence when homology modeling is not possible. We introduce a neural network system that predicts relative solvent accessibility (projected onto ten discrete states) using evolutionary profiles of amino acid substitutions derived from multiple sequence alignments. Evaluated in a cross-validation test on 238 unique proteins, the correlation between predicted and observed relative accessibility is 0.54. Interpreted in terms of a three-state (buried, intermediate, exposed) description of relative accessibility, the fraction of correctly predicted residue states is about 58%. In absolute terms this accuracy appears poor, but given the relatively low conservation of accessibility in 3D families, the network system is not far from its likely optimal performance. The most reliably predicted fraction of the residues (50%) is predicted as accurately as by automatic homology modeling. Prediction is best for buried residues, e.g., 86% of the completely buried sites are correctly predicted as having 0% relative accessibility. © 1994 Wiley-Liss, Inc.
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    URL: http://dx.doi.org/10.1002/prot.340200303
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    Molecular dynamics simulations of trp apo-and holorepressors: Domain structure and ligand-protein interaction (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 20 (1994), S. 248-258 
    Details
    ISSN: 0887-3585
    Keywords: molecular dynamics ; trp-repressor ; ligand ; domain ; dynamic cross-correlation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Molecular dynamics simulations of the apo- and holo-forms of thetrp-repressor protein were performed under extensively solvated conditions in order to elucidate their dynamic structures and ligand-protein interactions. The root mean square fluctuations calculated from the trajectories agreed with those calculated from X-ray temperature factors. Distance, distance fluctuation, and dynamic cross-correlation maps were drawn to provide information on the dynamic structures and communications among the domains. A three-domain format has been proposed for the crystal structure (Zhang et at., Nature 327:591-597, 1987) namely, helices A-C and F of both subunits make up a central core, and D and E of each subunit forms a DNA binding head. The results of the simulations were mostly consistent with the three-domain format. However, helix F was more flexible and freer than other parts of the central core. The turn DE, the helix-turn-helix DNA binding motif, was free from interactions and correlations with other domains in both forms of the repressor. A comparison of the simulations of the aporepressor and holorepressor showed that tryptophan binding made the DNA-binding helix D more flexible but helix F less flexible. Several amino acid residues in contact with the bound tryptophan were identified as making concerted motions with it. Interaction energies between the corepressor and the amino acid residues of the protein were analyzed; the results were mostly consistent with the mutational experiments. © 1994 Wiley-Liss, Inc.
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    URL: http://dx.doi.org/10.1002/prot.340200305
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    Magnetic resonance studies of the binding of oligonucleotide substrates to mutants of staphylococcal nuclease (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 18 (1994), S. 68-80 
    Details
    ISSN: 0887-3585
    Keywords: staphylococcal nuclease ; nonproductive substrate binding to ; subsites of ; active site mutants of ; oligonucleotide binding to ; Ca2+ binding to ; Mn2+ binding to ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: By a combination of NMR docking and model building, the substrate binding site on staphylococcal nuclease was found to accommodate a trinucleotide and to consist of three subsites, each interacting with a single nucleotidyl unit of DNA. Binding of the essential Ca2+ activator and substrate cleavage occur between subsites 1 and 2. Hence, catalytically productive binding would span subsites 1 and 2 while nonproductive binding would span subsites 2 and 3. Lys-49 is near subsite 1, and Lys-84 and Tyr-115 interact with substrates at sub site 3 [Weber, D. J., Gittis, A. G., Mullen, G. P., Abeygunawardana, C., Lattman, E. E., Mildvan, A. S. Proteins 13:275-287, 1992]. The proposed locations of these subsites were independently tested by the effects of the K49A, K84A, and Y115A mutations of staphylococcal nuclease on the binding of Mn2+, Ca2+, and the dinucleotide and trinucleotide substrates, 5′-pdTdA, dTdA, and dTdAdG. These three mutants have previously been shown to be fully active and to have CD and 2D NMR spectra very similar to those of the wild-type enzyme (Chuang, W.-J., Weber, D. J., Gittis, A. G., Mildvan, A. S. Proteins 17:36-48, 1993). All three mutant enzymes and their pdTdA and dTdA complexes (but not their dTdAdG complex) bind Mn2+ and Ca2+ more weakly than the wild-type enzyme by factors ranging from 2 to 11. The presence of a terminal phosphate as in 5′-pdTdA raises the affinity of the substrate for staphylococcal nuclease and its three mutants by two orders of magnitude and for the corresponding enzyme-metal complexes by three to four orders of magnitude, suggesting that the terminal phosphate is coordinated by the enzyme-bound divalent cation. Such complexation would result in the nonproductive binding of 5′-pdTdA at subsites 2 and 3. Accordingly, the K84A and Y115A mutations significantly weaken the binding of 5′-pdTdA and its metal to staphylococcal nuclease by factors of 2.2 to 37.8, while the K49A mutation has much smaller or no effect. Such nonproductive binding explains the low activity of staphylococcal nuclease with small substrates, especially those With a terminal phosphate. Similarly, the K84A and Y115A mutations weaken the binding of dTdA and its metal complexes to the enzyme by factors of 3.4 to 13.1 while the K49A mutation has smaller effects indicating significant nonproductive binding of dTdA. The trinucleotide dTdAdG binds more tightly to wild-type and mutant staphylococcal nuclease and to its metal complexes than does the dinucleotide dTdA by factors of 2.4 to 12.2, reflecting the occupancy of an additional subsite. Predominantly productive binding of dTdAdG is indicated by the 1.7- to 8.3-fold lower affinities of the K49A, K84A, and Y115A mutants for the trinucleotide and its metal complexes. The largest effects on dTdAdG binding are seen with the Y115A mutation presumably reflecting the dual role of Tyr-115 both in donating a hydrogen bond to a phosphodiester oxygen between subsites 2 and 3 and in stacking onto the guanine base at subsite 3. © 1994 John Wiley & Sons, Inc.
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    New Developments at PROTEINS (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 18 (1994), S. i 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340180102
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    Rigid-body docking with mutant constraints of influenza hemagglutinin with antibody HC19 (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 18 (1994), S. 8-18 
    Details
    ISSN: 0887-3585
    Keywords: docking algorithm ; antigen-antibody complex ; epitope ; influenza virus hemagglutinin ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: An automatic docking algorithm has been applied to the modeling of the complex between hemagglutinin from influenza virus and the Fab fragment of a monoclonal antibody raised against this antigen. We have introduced here the use of biochemical information provided by mutants of hemagglutinin. The docking procedure finds a small number of candidate solutions where three sites of escape mutations are buried and form hydrogen bonds in the interface. The localization of the epitope is improved by additional biochemical data about mutants that do not affect antibody binding. Five candidate solutions with low energy, reasonably well-packed interfaces, and six to ten hydrogen bonds are compatible with mutant information. One of the five stands out as generally better than the others from these points of views. © 1994 John Wiley & Sons, Inc.
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    URL: http://dx.doi.org/10.1002/prot.340180104
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    Alpha helix capping in synthetic model peptides by reciprocal side chain-main chain interactions: Evidence for an N terminal “capping box” (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 18 (1994), S. 1-7 
    Details
    ISSN: 0887-3585
    Keywords: α-helix capping ; α-helix initiation ; α-helix termination ; synthetic peptides ; protein folding ; circular dichroism ; 1H nmr ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A significant fraction of the amino acids in proteins are alpha helical in conformation. Alpha helices in globular proteins are short, with an average length of about twelve residues, so that residues at the ends of helices make up an important fraction of all helical residues. In the middle of a helix, H-bonds connect the NH and CO groups of each residue to partners four residues along the chain. At the ends of a helix, the H-bond potential of the main chain remains unfulfilled, and helix capping interactions involving bonds from polar side chains to the NH or CO of the backbone have been proposed and detected. In a study of synthetic helical peptides, we have found that the sequence Ser-Glu-Asp-Glu stabilizes the alpha helix in a series of helical peptides with consensus sequences. Following the report by Harper and Rose, which identifies SerXaaXaaGlu as a member of a class of common motifs at the N termini of alpha helices in proteins that they refer to as “capping boxes,” we have reexamined the side chain-main chain interactions in a varient sequence using 1H NMR, and find that the postulated reciprocal side chain-backbone bonding between the first Ser and last Glu side chains and their peptide NH partners can be resolved: Deletion of two residues N terminal to the Ser-Glu-Asp-Glu sequence in these peptides has no effect on the initiation of helical structure, as defined by two-dimensional (2D) NMR experiments on this variant. Thus the capping box sequence Ser-Glu-Asp-Glu inhibits N terminal fraying of the N terminus of alpha helix in these peptides, and shows the side chain-main chain interactions proposed by Harper and Rose. It thus acts as a helix initiating signal. Since normal a helix cannot propagate beyond the N terminus of this structure, the box acts as a termination signal in this direction as well. © 1994 John Wiley & Sons, Inc.
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    URL: http://dx.doi.org/10.1002/prot.340180103
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    Cold adaption of enzymes: Structural comparison between salmon and bovine trypsins (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 20 (1994), S. 149-166 
    Details
    ISSN: 0887-3585
    Keywords: crystal structure ; cold adaption ; catalytic efficiency ; protein stability ; anionic ; ectotherm ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The crystal structure of an anionic form of salmon trypsin has been determined at 1.82 Å resolution. We report the first structure of a trypsin from a phoikilothermic organism in a detailed comparison to mammalian trypsins in order to look for structural rationalizations for the cold-adaption features of salmon trypsin. This form of salmon trypsin (T II) comprises 222 residues, and is homologous to bovine trypsin (BT) in about 65% of the primary structure. The tertiary structures are similar, with an overall displacement in main chain atomic positions between salmon trypsin and various crystal structures of bovine trypsin of about 0.8 Å. Intramolecular hydrogen bonds and hydrophobic interactions are compared and discussed in order to estimate possible differences in molecular flexibility which might explain the higher catalytic efficiency and lower thermostability of salmon trypsin compared to bovine trypsin. No overall differences in intramolecular interactions are detected between the two structures, but there are differences in certain regions of the structures which may explain some of the observed differences in physical properties. The distribution of charged residues is different in the two trypsins, and the impact this might have on substrate affinity has been discussed. © 1994 Wiley-Liss, Inc.
    Additional Material: 10 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340200205
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    Collective motions in proteins investigated by X-ray diffuse scattering (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 18 (1994), S. 34-48 
    Details
    ISSN: 0887-3585
    Keywords: normal mode refinement ; correlation function ; intra- and intermolecular correlation ; higher order scattering ; human lysozyme ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We have developed theoretical models for analysis of X-ray diffuse scattering from protein crystals. A series of models are proposed to be used for experimental data with different degrees of precision. First, we propose the normal mode model, where conformational dynamics of a protein is assumed to occur mostly in a limited conformational subspace spanned by a small number of low-frequency normal modes in the protein. When high precision data are available, variances and covariances of the normal mode variables can be determined from experimental data using this model. For experimental data with lower degrees of precision, we introduce a series of simpler models. These models express the covariance matrix using relatively simple empirical correlation functions by assuming the correlation between a pair of atoms to be isotropic. As an application of these simpler models, we calculate diffuse-scattering patterns from a human lysozyme crystal to examine how each adjustable parameter in the models affects general features of the resulting patterns. The results of the calculation are summarized as follows. (1) The higher order scattering makes a significant contribution at high resolutions. (2) The resulting simulated patterns are sensitive to changes in correlation lengths of about 1 Å, as well as to changes of the functional form of the correlation function. (3) But only the “average” value of the intra- and intermolecular correlation lengths seems to determine the gross features of the pattern. (4) The effect of the atom-dependent amplitude of fluctuations is difficult to observe. © 1994 John Wiley & Sons, Inc.
    Additional Material: 4 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340180106
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    The enzymatic mechanism of carboxypeptidase: A molecular dynamics study (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 18 (1994), S. 186-197 
    Details
    ISSN: 0887-3585
    Keywords: carboxypeptidas ; molecular dynamics ; enzymatic mechanisms ; peptidase mechanism ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: An MD simulation of the system carboxypeptidase A (CPA) with the tetrapeptide Val-Leu-Phe-Phe has been performed in order to learn about the substrate disposition just prior to nucleophilic attack. We have explored the model in which the substrate does not substitute the zinc-coordinated water (the “water” mechanism). The simulations do suggest as feasible that the Zn-OH2 group performs a nucleophilic attack on the Phe-Phe peptidic bond. We have also investigated the model in which the carbonyl oxygen displaces the zinc-coordinated water. In this case the substrate and Glu-270 orient themselves to allow an anhydride intermediate during the peptidic bond cleavage (the “anhydride” mechanism). Based on the results of the simulations, both “water” and “anhydride” mechanisms are structurally feasible, although the former model seems more probable on chemical grounds. © 1994 John Wiley & Sons, Inc.
    Additional Material: 5 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340180210
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    A molecular dynamics approach for the generation of complete protein structures from limited coordinate data (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 18 (1994), S. 174-185 
    Details
    ISSN: 0887-3585
    Keywords: computer modeling ; protein structure prediction ; α-carbons ; structure evaluation ; molecular dynamics ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Generation of full protein coordinates from limited information, e.g., the Cα coordinates, is an important step in protein homology modeling and structure determination, and molecular dynamics (MD) simulations may prove to be important in this task. We describe a new method, in which the protein backbone is built quickly in a rather crude way and then refined by minimization techniques. Subsequently, the side chains are positioned using extensive MD calculations. The method is tested on two proteins, and results compared to proteins constructed using two other MD-based methods. In the first method, we supplemented an existing backbone building method with a new procedure to add side chains. The second one largely consists of available methodology. The constructed proteins are compared to the corresponding X-ray structures, which became available during this study, and they are in good agreement (backbone RMS values of 0.5-0.7 Å, and all-atom RMS values of 1.5-1.9 Å). This comparative study indicates that extensive MD simulations are able, to some extent, to generate details of the native protein structure, and may contribute to the development of a standardized methodology to predict reliably (parts of) protein structures when only partial coordinate data are available. © 1994 John Wiley & Sons, Inc.
    Additional Material: 3 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340180209
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    Introducing “Future Directions” (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 18 (1994), S. i 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340180202
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    Crystallization and characterization of colicin E1 channel-forming polypeptides (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 19 (1994), S. 150-157 
    Details
    ISSN: 0887-3585
    Keywords: X-ray crystallography ; membrane protein ; ion channels ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Crystals of the channel-forming domain of colicin E1 from E. coli were grown by vapor diffusion at pH 6.4 and higher pH values. Cleavage of the colicin molecule with trypsin or thermolysin produced two of the pore-forming polypeptides used in these experiments. The third polypeptide was purified from a constructed plasmid that overexpresses only the C-terminal domain of colicin E1. Polypeptide crystals are tetragonal with space group I4, have one monomer in the asymmetric unit, and diffract to 2.2-2.4 Å. Unit cell parameters for the tryptic and thermolytic polypeptides are a = 102.9 Å and c = 35.6 Å. Crystals of the overexpressed polypeptide have unit cell parameters of a =87.2 Å and c =59.1 Å. The crystals were characterized by precession photography, and native data sets of each channel-forming fragment were collected on a Siemens-Nicolet area detector. The crystallization and characterization of these polypeptides are the first steps in the structure determination of the channel-forming domain of colicin E1. © 1994 Wiley-Liss, Inc.
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    URL: http://dx.doi.org/10.1002/prot.340190208
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    A model for the structure of a homodimeric prohormone: The precursor to the locust neuropeptide AKH I (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 20 (1994), S. 356-366 
    Details
    ISSN: 0887-3585
    Keywords: NMR ; structure determination ; coiled coil ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We have determined the structure in solution of a homodimeric protein that is a precursor to the locust neuropeptide adipokinetic hormone I using nuclear magnetic resonance spectroscopy. This precursor, called P1, is comprised of two 41 residue strands joined by a single inter-chain disulphide at Cys39. We have also determined the structure of an end product of P1 processing, called APRP1; this is a homodimer comprised of residues 14-41 of PI. Nuclear Overhauser Effect (nOe) data indicate that in both P1 and APRP1, residues 22-37 (numbered with respect to P1) form pairs of α-helices, with no evidence for any other secondary structure. © 1994 Wiley-Liss, Inc.
    Additional Material: 10 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340200408
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    Molecular dynamics simulation of the docking of substrates to proteins (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 19 (1994), S. 174-182 
    Details
    ISSN: 0887-3585
    Keywords: molecular dynamics ; docking ; computer simulation ; substrate docking ; immunoglobulin ; rational drug design ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A simple method is described to perform docking of subtrates to proteins or probes to receptor molecules by a modification of molecular dynamics simulations. The method consists of a separation of the center-of-mass motion of the substrate from its internal and rotational motions, and a separate coupling to different thermal baths for both types of motion of the substrate and for the motion of the receptor. Thus the temperatures and the time constants of coupling to the baths can be arbitrarily varied for these three types of motion, allowing either a frozen or a flexible receptor and allowing control of search rate without disturbance of internal structure. In addition, an extra repulsive term between substrate and protein was applied to smooth the interaction. The method was applied to a model substrate docking onto a model surface, and to the docking of phosphocholine onto immunoglobulin McPC603, in both cases with a frozen receptor. Using transrational temperatures of the substrate in the range of 1300-1700 K and room temperature for the internal degrees of freedom of the substrate, an efficient nontrapping exploratory search (“helicopter view”) is obtained, which visits the correct binding sites. Low energy conformations can then be further investigated by separate search or by dynamic simulated annealing. In both cases the correct minima were identified. The possibility to work with flexible receptors is discussed. © 1994 Wiley-Liss, Inc.
    Additional Material: 9 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340190303
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    Spatial optimization of electrostatic interactions between the ionized groups in globular proteins (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 19 (1994), S. 222-229 
    Details
    ISSN: 0887-3585
    Keywords: protein electrostatics ; energy calculations ; ion pairs ; Monte-Carlo simulations ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A model approach is suggested to estimate the degree of spatial optimization of the electrostatic interactions in protein molecules. The method is tested on a set of 44 globular proteins, representative of the available crystallographic data. The theoretical model is based on macroscopic computation of the contribution of charge-charge interactions to the electrostatic term of the free energy for the native proteins and for a big number of virtual structures with randomly distributed on protein surface charge consetellations (generated by a Monte-Carlo technique). The statistical probability of occurrence of random structures with electrostatic energies lower than the energy of the native protein is suggested as a criterion for spatial optimization of the electrostatic interactions. The results support the hypothesis that the folding process optimizes the stabilizing effect of electrostatic interactions, but to very different degree for different proteins. A parallel analysis of ion pairs shows that the optimization of the electrostatic term in globular proteins has increasingly gone in the direction of rejecting the repulsive short contacts between charges of equal sign than of creating of more salt bridges (in comparison with the statistically expected number of shortrange ion pairs in the simulated random structures). It is observed that the decrease in the spatial optimization of the electrostatic interactions is usually compensated for by an appearance of disulfide bridges in the covalent structure of the examined proteins. © 1994 Wiley-Liss, Inc.
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    URL: http://dx.doi.org/10.1002/prot.340190306
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    Energy minimization method using automata network for sequence and side-chain conformation prediction from given backbone geometry (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 19 (1994), S. 244-255 
    Details
    ISSN: 0887-3585
    Keywords: energy minimization ; rotamers ; automaton ; de novo design ; sequence prediction ; side-chain conformation prediction ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Globular proteins have high packing densities as a result of residue side chains in the core achieving a tight, complementary packing. The internal packing is considered the main determinant of native protein structure. From that point of view, we present here a method of energy minimization using an automata network to predict a set of amino acid sequences and their side-chain conformations from a desired backbone geometry for de novo design of proteins. Using discrete side-chain conformations, that is, rotamers, the sequence generation problem from a given backbone geometry becomes one of combinatorial problems. We focused on the residues composing the interior core region and predicted a set of amino acid Sequences and their side-chain conformations only from a given backbone geometry. The kinds of residues were restricted to six hydrophobic amino acids (Ala, Ile, Met, Leu, Phe, and Val) because the core regions are almost always composed of hydrophobic residues. The obtained sequences were well packed as was the native sequence. The method can be used for automated sequence generation in the de novo design of proteins. © 1994 Wiley-Liss, Inc.
    Additional Material: 6 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340190308
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    Parser for protein folding units (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 19 (1994), S. 256-268 
    Details
    ISSN: 0887-3585
    Keywords: unfolding ; solvation ; contact maps ; protein design ; structural domains ; normal modes ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: General patterns of protein structural organization have emerged from studies of hundreds of structures elucidated by X-ray crystallography and nuclear magnetic resonance. Structural units are commonly identified by visual inspection of molecular models using qualitative criteria. Here, we propose an algorithm for identification of structural units by objective, quantitative criteria based on atomic interactions. The underlying physical concept is maximal interactions within each unit and minimal interaction between units (domains). In a simple harmonic approximation, interdomain dynamics is determined by the strength of the interface and the distribution of masses. The most likely domain decomposition involves units with the most correlated motion, or largest interdomain fluctuation time. The decomposition of a convoluted 3-D structure is complicated by the possibility that the chain can cross over several times between units. Grouping the residues by solving an eigenvalue problem for the contact matrix reduces the problem to a one-dimensional search for all reasonable trial bisections. Recursive bisection yields a tree of putative folding units. Simple physical criteria are used to identify units that could exist by themselves. The units so defined closely correspond to crystallographers' notion of structural domains. The results are useful for the analysis of folding principles, for modular protein design and for protein engineering. © 1994 Wiley-Liss, Inc.
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    URL: http://dx.doi.org/10.1002/prot.340190309
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    Crystallization and preliminary X-ray diffraction study of the green flavoenzyme 5-Hydroxyvaleryl-CoA dehydratase/dehydrogenase from Clostridium aminovalericum (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 19 (1994), S. 269-271 
    Details
    ISSN: 0887-3585
    Keywords: acyl-CoA dehydrogenase ; bifunctional enzyme ; charge-transfer complex ; clostridial metabolism ; FAD, x-ray diffraction ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The bifunctional flavoenzyme 5-hydroxyvaleryl-CoA dehydratase/ dehydrogenase has been crystallized from solutions containing ammonium sulfate (form I) or polyethylene glycol (form II) as precipitant. In both cases, the crystals grew in the monoclinic space group C2. The unit cell dimensions for form I crystals were determined as a = 162.8 Å, b = 71.8 Å, c = 83.5 Å, β = 109.1°. Corresponding values for form II crystals were a = 161.2 Å, b = 71.6 Å, c = 82.2 Å, β = 109.3°. In both cases most probably there are two monomers per asymmetric unit. The crystals diffract to about 2 Å resolution and are rather stable in the X-ray beam. © 1994 Wiley-Liss, Inc.
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    URL: http://dx.doi.org/10.1002/prot.340190310
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    Torsion angle dynamics: Reduced variable conformational sampling enhances crystallographic structure refinement (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 19 (1994), S. 277-290 
    Details
    ISSN: 0887-3585
    Keywords: simulated annealing ; molecular dynamics ; torsion angle dynamics ; conformational sampling ; X-ray crystallography ; refinement ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A reduced variable conformational sampling strategy for macromolecules based on molecular dynamics in torsion angle space is evaluated using crystallographic refinement as a prototypical search problem. Bae and Haug's algorithm for constrained dynamics [Bae, D. S., Haug, E. J. A recursive formulation for constrained mechanical system dynamics. Mech. Struct. Mach. 15:359-382, 1987], originally developed for robotics, was used. Their formulation solves the equations of motion exactly for arbitrary holonomic constraints, and hence differs from commonly used approximation algorithms. It uses gradients calculated in Cartesian coordinates, and thus also differs from internal coordinate formulations. Molecular dynamics can be carried out at significantly higher temperatures due to the elimination of the high frequency bond and angle vibrations. The sampling strategy presented here combines high temperature torsion angle dynamics with repeated trajectories using different initial velocities. The best solutions can be identified by the free R value, or the R value if experimental phase information is appropriately included in the refinement. Applications to crystallographic refinement show a significantly increased radius of convergence over conventional techniques. For a test system with diffraction data to 2 Å resolution, slow-cooling protocols fail to converge if the backbone atom root mean square (rms) coordinate deviation from the crystal structure is greater than 1.25 Å, but torsion angle refinement can correct backbone atom rms coordinate deviations up to approximately 1.7 Å. © 1994 Wiley-Liss, Inc.
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    URL: http://dx.doi.org/10.1002/prot.340190403
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    Helix-capping interaction in λ cro protein: A free energy simulation analysis (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 19 (1994), S. 310-323 
    Details
    ISSN: 0887-3585
    Keywords: protein stability ; free energy simulations ; molecular dynamics calculations ; helix-capping interactions ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The stability mutant Tyr-26 → Asp was studied in the Cro protein from bacteriophage λ using free energy molecular dynamics simulations. The mutant was calculated to be more stable than the wild type by 3.0 ± 1.7 kcal/mol/monomer, in reasonable agreement with experiment (1.4 kcal/mol/monomer). Moreover, the aspartic acid in the mutant was found to form a capping interation with the amino terminus of the third α-helix of Cro. The simulations were analyzed to understand better the source of the stability of this helix-capping interaction and to examine the results in light of previous explanations of stabilizing helix caps-namely, a model of local unsatisfied hydrogen bonds at the helix termini and the helix macro dipole model. Analysis of the simulations shows that the stabilizing effect of this charged helical cap is due both to favorable hydrogen bonds with backbone NH groups at the helix terminus and to favorable electrostatic interactions (but not hydrogen bonds) with their carbonyls (effectively the next row of local dipoles in the helix). However, electrostatic interactions are weak or negligible with backbone dipolar groups in the helix further away from the terminus. Moreover, the importance of other local electrostatic interactions with polar side chains near the helix terminus, which are neglected in most treatments of this effect, are shown to be important. Thus, the results support a model that is intermediate between the two previous explanations: both unsatisfied hydrogen bonds at the helix terminus and other, local preoriented dipolar groups stabilize the helix cap. These findings suggest that similar interactions with preoriented dipolar groups may be important for cooperativity in other charge-dipole interactions and may be employed to advantage for molecular design. © 1994 Wiley-Liss, Inc.
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    URL: http://dx.doi.org/10.1002/prot.340190406
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    Multiple copy sampling: Rigid versus flexible protein (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 19 (1994), S. 324-329 
    Details
    ISSN: 0887-3585
    Keywords: multiple copy conformational sampling ; protein flexibility ; sampling convergence ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Effects of protein flexibility on multiple copy conformational sampling were systematically evaluated by studying the side-chain placement of Phe-14 in protein Zif268. The multiple copy sampling is shown to be significantly more efficient when a flexible but harmonically constrained protein is used instead of a rigid protein. A range of constraint force from 1 to 25 kcal/mol. Å per atom is determined to be sufficient to prevent the protein from distortion while allowing the protein to fluctuate for enhanced sampling. The protein fluctuations are essential in smoothing the effective energy surface as shown by the opening-closing of a protein hydrophobic pocket during a multiple copy energy minimization, a phenomenon that has been previously observed only in molecular dynamics. These results provide a practical guidance for applying the multiple copy techniques to molecular modeling and computer-aided drug design. © 1994 Wiley-Liss, Inc.
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    URL: http://dx.doi.org/10.1002/prot.340190407
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    Protein stability parameters measured by hydrogen exchange (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 20 (1994), S. 4-14 
    Details
    ISSN: 0887-3585
    Keywords: thermodynamic parameters ; cytochrome c ; protein folding ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The hydrogen exchange (HX) rates of the slowest peptide group NH hydrogens in oxidized cytochrome c (equine) are controlled by the transient global unfolding equilibrium. These rates can be measured by one-dimensional nuclear magnetic resonance and used to determine the thermodynamic parameters of global unfolding at mild solution conditions well below the melting transition. The free energy for global unfolding measured by hydrogen exchange can differ from values found by standard denaturation methods, most notably due to the slow cis-trans isomerization of the prolyl peptide bond. This difference can be quantitatively calculated from basic principles. Even with these corrections, HX experiments at low denaturant concentration measure a free energy of protein stability that rises above the usual linear extrapolation from denaturation data, as predicted by the denaturant binding model of Tanford. © 1994 Wiley-Liss, Inc.
    Additional Material: 9 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340200103
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  • 91
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    Protein folding: Predicting predicting (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 19 (1994), S. 1-3 
    Details
    ISSN: 0887-3585
    Keywords: protein folding ; protein conformation ; Paracelsus award ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Additional Material: 1 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340190102
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  • 92
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    Structure of trichosanthin at 1.88 Å resolution (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 19 (1994), S. 4-13 
    Details
    ISSN: 0887-3585
    Keywords: trichosanthin ; ribosome-inactivating proteins ; crystal structure ; orthorhombic ; molecular replacement ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Trichosanthin (TCS) is one of the single chain ribosome-inactivating proteins (RIPs). The crystals of the orthorhombic form of trichosanthin have been obtained from a citrate buffer (pH 5.4) with KC1 as the precipitant. The crystal belongs to the space group P212121 with a = 38.31, b = 76.22, c = 79.21 Å. The structure was solved by molecular replacement method and refined using the programs XPLOR and PROLSQ to an R-factor of 0.191 for the reflections within the 6-1.88 Å resolution range. The bond length and bond angle in the protein molecule have root-mean-square deviations from ideal value of 0.013 Å and 3.3°, respectively. The refined model includes 247 residues and 197 water molecules. The TCS molecule consists of two structural domains. The large domain contains six α-helices, a six stranded sheet, and an antiparallel β-sheet. The small domain has a largest α-helix, which shows a distinct bend. The possible active site of the molecule located on the cleft between two domains was proposed. In the active site Arg-163 and Glu-160, Glu-189 and Arg-122 form two ion pairs, Glu-189 and Gln-156 are hydrogen bonded to each other. Three water molecules are bonded to the residues in the active site region. The structures of TCS molecule and ricin A-chain (RTA) superimpose quite well, showing that the structures of the two protein molecules are homologous. Comparison of the structures of the TCS molecule in this orthorhombic crystal with that in the monoclinic crystal indicates that there are no essential differences of the structures between the two protein crystals. © 1994 Wiley-Liss, Inc.
    Additional Material: 10 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340190103
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  • 93
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    Monte carlo simulations of protein folding. I. Lattice model and interaction scheme (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 18 (1994), S. 338-352 
    Details
    ISSN: 0887-3585
    Keywords: tertiary structure prediction ; reduced protein model ; lattice protein models ; dynamic Monte Carlo simulations ; potentials of mean force ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A new hierarchical method for the simulation of the protein folding process and the de novo prediction of protein three-dimensional structure is proposed. The reduced representation of the protein α-carbon backbone employs lattice discretizations of increasing geometrical resolution and a single ball representation of side chain rotamers. In particular, coarser and finer lattice backbone descriptions are used. The coarser (finer) lattice represents Cα traces of native proteins with an accuracy of 1.0 (0.7) Å rms. Folding is simulated by means of very fast Monte Carlo lattice dynamics. The potential of mean force, predominantly of statistical origin, contains several novel terms that facilitate the cooperative assembly of secondary structure elements and the cooperative packing of the side chains. Particular contributions to the interaction scheme are discussed in detail. In the accompanying paper (Kolinski, A., Skolnick, J. Monte Carlo simulation of protein folding. II. Application to protein A, ROP, and crambin. Proteins 18:353-366, 1994), the method is applied to three small globular proteins. © 1994 John Wiley & Sons, Inc.
    Additional Material: 7 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340180405
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  • 94
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    Investigation of the functional interplay between the primary site and the subsite of RNase T1: Kinetic analysis of single and multiple mutants for modified substrates (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 18 (1994), S. 318-323 
    Details
    ISSN: 0887-3585
    Keywords: ribonuclease T1 ; functional cooperativity ; double mutant cycle ; subsite ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We report on the functional cooperativity of the primary site and the sub-site of ribonuclease T1 (RNase T1; EC 3.1.27.3). The kinetic properties of the single Tyr-38-Phe and Asn-98-Ala mutants have been compared with those of the corresponding double mutant. The Tyr-38-Phe mutation has been used to probe enzyme-substrate interactions at the primary site; the Asn-98-Ala mutation monitors subsite interactions.1 In addition to the dinucleoside phosphate substrate GpC, we measured the kinetics for GpMe, a synthetic substrate in which the leaving nucleoside cytosine has been replaced by methanol. All data were combined in a triple mutant box to analyze the interplay between Tyr-38, Asn-98, and the leaving group. The free energy barriers to kcat, introduced by the single Tyr-38-Phe and Asn-98-Ala mutations are not additive in the corresponding double mutant. The energetic coupling between both mutations is independent of the binding of the leaving cytosine at the subsite. We conclude that the coupling of the Tyr-38-Phe and Asn-98-Ala mutations arises through distortion or reorientation of the 3′-guanylic acid moiety bound at the primary site. The experimental data indicate that the enzyme-substrate interactions beyond the scissile phosphodiester bond contribute to catalysis through the formation of new or improved contacts in going from ground state to transition state, which are functionally independent of primary site interactions. © 1994 John Wiley & Sons, Inc.
    Additional Material: 1 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340180403
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  • 95
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    Recognition of distantly related proteins through energy calculations (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 19 (1994), S. 132-140 
    Details
    ISSN: 0887-3585
    Keywords: distant protein folds ; sequence homology ; database searching ; profile analysis ; protein structure comparison ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A new method to detect remote relationships between protein sequences and known three-dimensional structures based on direct energy calculations and without reliance on statistics has been developed. The likelihood of a residue to occupy a given position on the structural template was represented by an estimate of the stabilization free energy made after explicit prediction of the substituted side chain conformation. The profile matrix derived from these energy values and modified by increasing the residue self-exchange values successfully predicted compatibility of heatshock protein and globin sequences with the three-dimensional structures of actin and phycocyanin, respectively, from a full protein sequence databank search. The high sensitivity of the method makes it a unique tool for predicting the three-dimensional fold for the rapidly growing number of protein sequences. © 1994 Wiley-Liss, Inc.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340190206
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  • 96
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    Characterization of two crystal forms of Clostridium thermocellum endoglucanase CelC (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 19 (1994), S. 158-160 
    Details
    ISSN: 0887-3585
    Keywords: crystallization ; cellulases ; X-ray crystallography ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Endoglucanase CelC from Clostridium thermocellum expressed in Escherichia coli has been crystallized in two different crystal forms by the hanging drop method. Crystals of form I were grown with polyethylene glycol as a precipitant. They are orthorhombic, space group P212121, with cell dimensions a =51.4 Å, b =84.3 Å, and c =87.5 Å. Crystals of form II, obtained in ammonium sulfate solutions, belong to the tetragonal space group P41212 (or P43212) with cell dimensions of a = b = 130.7 Å and c = 69.6 Å. Diffraction data to 2.8 Å resolution were observed for both crystal forms with a rotating anode generator. Preliminary oscillation images of the orthorhombic form I crystals using a synchrotron radiation source show diffraction to 2.2 Å resolution, indicating that these crystals are suitable for high resolution crystallographic analysis. © 1994 Wiley-Liss, Inc.
    Additional Material: 1 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340190209
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  • 97
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    Masthead (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 19 (1994) 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340190301
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  • 98
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    Searching protein structure databases has come of age (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 19 (1994), S. 165-173 
    Details
    ISSN: 0887-3585
    Keywords: algoriths ; structure alignment ; Protein Data Bank ; protein superfamilies ; structural homology ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The number of protein structures known in atomic detail has increased from one in 1960 (Kendrew, J. C., Strandberg, B. E., Hart, R. G., Davies, D. R., Phillips, D. C., Shore, V. C. Nature (London) 185:422-427, 1960) to more than 1000 in 1994. The rate at which new structures are being published exceeds one a day as a result of recent advances in protein engineering, crystallography, and spectroscopy. More and more frequently, a newly determined structure is similar in fold to a known one, even when no sequence similarity is detectable. A new generation of computer algorithms has now been developed that allows routine comparison of a protein structure with the database of all known structures. Such structure database searches are already used daily and they are beginning to rival sequence database searches as a tool for discovering biologically interesting relationships. © 1994 Wiley-Liss, Inc.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340190302
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  • 99
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    The closed conformation of a highly flexible protein: The structure of E. coli adenylate kinase with bound AMP and AMPPNPThe structure is listed as 1ANK in the Brookhaven Protein Data Bank. (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 19 (1994), S. 183-198 
    Details
    ISSN: 0887-3585
    Keywords: X-ray crystallography ; Rfree ; ATP and AMP binding sites ; Mg2+ coordination ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The structure of E. coli adenylate kinase with bound AMP and AMPPNP at 2.0 Å resolution is presented. The protein crystallizes in space group C2 with two molecules in the asymmetric unit, and has been refined to an R factor of 20.1% and an Rfree of 31.6%. In the present structure, the protein is in the closed (globular) form with the large flexible lid domain covering the AMPPNP molecule. Within the protein, AMP and AMPPNP, an ATP analog, occupy the AMP and ATP sites respectively, which had been suggested by the most recent crystal structure of E. coli adenylate kinase with AP5A bound (Müller and Schulz, 1992, ref. 1) and prior fluorescence studies (Liang et al., 1991, ref. 2). The binding of substrates and the positions of the active site residues are compared between the present structure and the E. coli adenylate kinase/Ap5A structure. We failed to detect a peak in the density map corresponding to the Mg2+ ion which is required for catalysis, and its absence has been attributed to the use of ammonium sulfate in the crystallization solution. Finally, a comparison is made between the present structure and the structure of the heavy chain of muscle myosin. © 1994 Wiley-Liss, Inc.
    Additional Material: 13 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340190304
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  • 100
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    HOOK: A program for finding novel molecular architectures that satisfy the chemical and steric requirements of a macromolecule binding site (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 19 (1994), S. 199-221 
    Details
    ISSN: 0887-3585
    Keywords: multicopy simulation search ; rational drug design ; database search ; computer-aided design ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A program (HOOK) is described for generating potential ligands that satisfy the chemical and steric requirements of the binding region of a macromolecule. Functional group sites with defined positions and orientations are derived from known ligand structures or the multicopy simulation search (MCSS) method (Miranker, A., Karplus, M. Proteins 11:29-34, 1991). HOOK places molecular “skeletons” from a database into the protein binding region by making bonds between sites (“hooks”) on the skeleton and functional groups. The nonpolar interactions with the binding region of candidate molecules are assessed by use of a simplified van der Waals potential. The method is illustrated by constructing ligands for the sialic acid binding site of the hemagglutinin from the influenza A virus and the active site of chloramphenicol acetyltransferase. Aspects of the HOOK program that lead to a highly efficient search of 105 or more skeletons for binding to 102 or more functional group minima are outlined. © 1994 Wiley-Liss, Inc.
    Additional Material: 9 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340190305
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