Titlebook: Statistical Mechanics, Protein Structure, and Protein Substrate Interactions; Sebastian Doniach Book 1994 Springer Science+Business Media

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The Molecular Origin of the Large Entropies of Hydrophobic Hydrations to the entropy of hydration of simple, hydrophobic solutes. With a factorization assumption for the solute-water correlation function we have been able to separate the contributions to the entropy of hydration due to translational and orientational solute-water correlations. The required correlati

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Hydrophobic Zippers: A Conformational Search Strategy for Proteinsomers. We call the method “hydrophobic zippers.”. We have used hydrophobic zippers to construct conformational ensembles that resemble the compact denatured and molten globule states of proteins. We have also used hydrophobic zippers to attempt to find global minimum (“native”) conformations of simp

SHOCK

Theoretical Perspectives on In Vitro and In Vivo Protein Foldingdiverse biological demands placed on proteins are probably the reason why one observes seemingly large classes of protein structures. However, the process by which proteins acquire their three dimensional structure remains an unsolved problem in biochemistry and molecular biology. The text book desc

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On the Configurations Accessible to Folded and to Denatured Proteinsding and function. X-ray crystallography and NMR spectroscopy furnish detailed information on the average structures of folded proteins. The configurations accessible to most folded proteins can be described in terms of fluctuations of the atoms of ~ 1 Å about their average positions. Data on the co

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Constrained Langevin Dynamics of Polypeptide Chainsthe the planar geometry of the peptide bonds. We show that for overdamped dynamics the constraints can be implemented at each time step by inversion of a banded matrix. This inversion is computationally very efficient. The forces which are included are those due to the non-bonding interactions betwe

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Moil: A Molecular Dynamics Program with Emphasis on Conformational Searches and Reaction Path Calculnd the interactions that lead to stability of macromolecules has been obtained. Crucial in bringing these changes was the introduction of “user friendly” computer programs so that the number of potential users expanded considerably. It is now possible to visualize complex molecules and to study thei

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Flexibility in the Fc Region of Immunoglobulin GFc region. The length and sequence of the hinge varies between different Ig classes and subclasses, and these differences are implicated in differential binding to membrane-bound cellular receptors known as Fc receptors (FcR) (Burton et al., 1985; Burton, 1990). In particular, the human IgG binding

MOCK

Computer-Supported Protein Structure Determination by NMRas of molecular biology and biochemistry. In this context, the three-dimensional (3D) structure has a pivotal role, as its knowledge is a prerequisite to understanding the physical, chemical, and biological properties of a protein (Schulz and Schirmer, 1979). Until 1984, structural information at at

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Enumeration with Constraints: A Possible Approach to Protein Structure Reconstruction from NMR Datainteratomic contacts. The algorithm is very effective and allowed to investigate the dependence of number of protein conformations on the number of constraints. This dependence is very dramatic so that introduction of few constraints decrease the number of conformations significantly making their en