Homology modeling of histidine-containing phosphocarrier protein and eosinophil-derived neurotoxin: Construction of models and comparison with experiment

Homology modeling methods have been used to construct models of two proteins—the histidine-containing phosphocarrier protein (HPr) from Mycoplasma capricolum and human eosinophil-derived neurotoxin (EDN). Comparison of the models with the subsequently determined X-ray crystal structures indicates that the core regions of both proteins are reasonably well reproduced, although the template structures are closer to the X-ray structures in these regions—possible enhancements are discussed. The conformations of most of the side chains in the core of HPr are well reproduced in the modeled structure. As expected, the conformations of surface side chains in this protein differ significantly from the X-ray structure. The loop regions of EDN were incorrectly modeled—reasons for this and possible enhancements are discussed. © 1995 Wiley-Liss, Inc.     

Quantum-mechanical kinetic study of the primary reaction of the photochemical cycle of Halobacterium halobium

A two-frequency oscillator model for the primary photochemical reaction bacteriorhodopsin batho-bacteriorhodopsin (K₆₁₀) is proposed. According to this model two conformational changes in the reaction are considered to take place: the first one is a distortion of the retinal in the bacteriorhodopsin active site and the second one is a conformational transition of the bacterioopsin, affecting the native structure hydrogen bonds. On the basis of this model the temperature dependences of the rate constants for normal and deuterated reactants are calculated in good agreement with the available experimental data. The relations of the reaction considered to the primary photochemical reaction of vision are discussed.     

Determination of window size for analyzing DNA sequences

Summary DNA sequences are generally not random sequences. To show such nonrandomness visually, DNA sequence data are often plotted as moving averages for a certain length of window slid along a sequence. Here a simple algorithm is presented for determining the window size and for finding a nonrandom region of sequence.     

Possible role of cell cycle-dependent morphology,geometry, and mechanical properties in tumor cell metastasis

Studies that examine the shear- and abrasion-sensitivity of proliferating cells are important in order to understand the behavior of hybridoma cells in bioreactor culture and metastasizing cancer cells in the bloodstream. Little is known about the link between morphology, structure, and mechanical properties of a given cell line, especially with respect to variations throughout the cell cycle. In our experiments with GAP A3 hybridoma cells, distinct cell morphologies were identified and correlated with phases of the cell cycle by video microscopic observation of synchronized cells, and of individual cells that were followed throughout their cell cycle. Micropipet manipulation was used to measure the geometrical (cell volume) and mechanical (apparent cell viscosity) properties of single cells. As the cell cycle progressed at 37°C, an increase in cell volume from 1400 μm³ to 5700 μm³ was accompanied by an increase in apparent cell viscosity from 430 poise to 12,000 poise, consistent with an accumulation of more cytoplasmic material in the “older” cells. Hybridomas are representative of the various leukemias derived from hemopoietic cells, and even though as a whole, they appeared to be rather shear-insensitive, the wide range of property values demonstrates that a given cell line cannot be characterized by a single value for any one property, and that properties must be related to the cell cycle when considering proliferating cells. It is interesting to see if distinct stages in the metastatic sequence of events might correlate with any of these physical features of the cell cycle, irrespective of cell type or cell line. For example, the cytokinetic doublet could represent a fragile structure that may fail and produce cell death under fluid-shear conditions that would not affect the cells at any other stage in the cell cycle. Identifying such cell cycle-dependent features in metastasizing cancer cells could lead to a better understanding of the metastatic process and to possible clinical treatments directed at making cells more shear- and abrasion-sensitive, and therefore, more likely to be killed by the natural hydrodynamic forces of the circulatory system.     

Statistical assessment of population variability: a methodological approach

We have implemented a multivariate statistical methodology to assess the degree and pattern of cranial variability in skeletal samples. Specifically, the method is designed to test whether variability in a skeletal sample exceeds "normal within-group variability" defined in the present instance as variability present among crania from a cemetery associated with a village. It involves comparing a covariance matrix derived from a sample of unknown composition to one representing "normal within-group variability." The method has been applied to two Plains Indian craniometric samples. The Leavenworth site (39CO9) represents the remnants of previously autonomous Arikara Indian villages devastated by epidemic diseases in the late 1700s. The Bad River 2 Phase is an archaeological designation grouping together closely related sites in the Bad-Cheyenne region of South Dakota dating from 1740-1795 AD. We were able to show substantial heterogeneity among crania from Leavenworth. District burial areas at Leavenworth account for some of the heterogeneity, supporting the notion that they represent an attempt to maintain former social distinctions. We were unable to differentiate among sites within the Bad River 2 Phase, suggesting that it is a valid biological unit.     

Un modèle d'ontogenèse: La croissancede Toxaster granosus kiliani (Lambert)), échinide spatangoide du Valanginien

A complete study of the ontogeny of the irregular urchin Toxaster granosus kiliani (Lambert)) was achieved from an important lower cretaceous sample. In a first time, ontogenic variations of each character were analysed versus length chosen as size reference. This first step had shown that very important changes in shape take place during the development of the young urchin: increase in height, downward migration of the periproct, forward movement of the peristome… In a second time, a growth crisis was proved and described. Such a crisis occurs, from 12 mm to 16 mm length, as a momentary acceleration of the growth (i.e. the rate of growth increases during a short time). The reality of this crisis was demonstrated by both mathematical and biological ways and also by comparing with other actual and fossil populations. The whole of these results leads to a synthetical pattern of growth divided into three main stages which are successively a juvenile, a preadult and an adult stage. This division was proved also by a principal components analysis.     

A theory of the electric field-induced phase transition of phospholipid bilayers

Improving the statistical mechanical model of Jacobs et al. (Jacobs, R.E., Hudson, B. and Andersen, H.C. (1975) Proc. Natl. Acad. Sci. U.S. 72, 3993–3997) we have constructed a model which describes not only the temperature but also the external field dependence of the membrane structure of phospholipid bilayers. In addition to the interactions between head groups, between hydrocarbon chains, and the internal conformational energy of the chains (which were considered in Jacobs' model), our model includes the energy of deformation and the field energy as well.By the aid of this model we can explain the phenomenon of dielectric breakdown, the non-linearity of current-voltage characteristics, and the mechanism of membrane elasticity.The free energy of the membrane, the average number of the gauche conformations in the hydrocarbon interior and at the membrane surface, gauche distribution along the chain, the membrane thickness, area and volume are calculated at different temperatures and voltages. The calculation also gives the temperature dependence of Young's modulus and that of the linear thermal expansion coefficient.     

蛋白质-RNA序列结构界面偏好性及用于对接打分统计势的构建

本文对来自PDB (Protein Data Bank)数据库的蛋白质-RNA复合物结构构建了非冗余非核糖体数据库(694个结构),并对此数据库统计了蛋白质和RNA序列及二级结构的界面偏好性.结果发现,蛋白质β折叠、3₁₀-helix和RNA未配对核苷酸,尤其是未配对中空间排列不规整的核苷酸,具有显著的界面偏好性.据此,对二级结构进行归类,建立了考虑序列和二级结构信息的60×12氨基酸-核苷酸成对偏好势,并将其作为打分函数用于蛋白质-RNA对接中近天然结构的筛选.结果表明,该60×12统计势的打分成功率为65.77%,优于考虑蛋白质或RNA二级结构信息的统计势,及我们小组之前在251个结构上构建的60×8^*统计势.该工作有助于加深对蛋白质-RNA特异性识别的理解,可推动复合物结构预测的进展.