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We demonstrate in this work that the surface tension, water-organic solvent, transfer-free energies and the thermodynamics of melting of linear alkanes provide fundamental insights into the nonpolar driving forces for protein folding and protein binding reactions. We first develop a model for the curvature dependence of the hydrophobic effect and find that(More)
Current techniques for the prediction of side-chain conformations on a fixed backbone have an accuracy limit of about 1.0-1.5 A rmsd for core residues. We have carried out a detailed and systematic analysis of the factors that influence the prediction of side-chain conformation and, on this basis, have succeeded in extending the limits of side-chain(More)
We have devised and implemented in PrISM (protein informatics system for modeling) a new measure of protein structural relationships, the protein structural distance (PSD). The PSD is designed to describe relationships between protein structures in quantitative rather than descriptive terms and is applicable both when two structures are very similar, and(More)
The application of all-atom force fields (and explicit or implicit solvent models) to protein homology-modeling tasks such as side-chain and loop prediction remains challenging both because of the expense of the individual energy calculations and because of the difficulty of sampling the rugged all-atom energy surface. Here we address this challenge for the(More)
The magnitude of the hydrophobic effect, as measured from the surface area dependence of the solubilities of hydrocarbons in water, is generally thought to be about 25 calories per mole per square angstrom (cal mol-1 A-2). However, the surface tension at a hydrocarbon-water interface, which is a "macroscopic" measure of the hydrophobic effect, is(More)
A detailed treatment is provided of the various free-energy terms that contribute to the transfer of a polyalanine alpha-helix from the aqueous phase into lipid bilayers. In agreement with previous work, the hydrophobic effect is found to provide the major driving force for helix insertion. However, an opposing effect of comparable magnitude is also(More)
Crystal structures of classical cadherins have revealed two dimeric configurations. In the first, N-terminal beta-strands of EC1 domains 'swap' between partner molecules. The second configuration (the 'X dimer'), also observed for T-cadherin, is mediated by residues near the EC1-EC2 calcium binding sites, and N-terminal beta-strands of partner EC1 domains,(More)