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We probe the stability and near-native energy landscape of protein fold space using powerful conformational sampling methods together with simple reduced models and statistical potentials. Fold space is represented by a set of 280 protein domains spanning all topological classes and having a wide range of lengths (33-300 residues) amino acid composition and number of secondary structural elements. The degrees of freedom are taken as the loop torsion angles. This choice preserves the native secondary structure but allows the tertiary structure to change. The proteins are represented by three-point per residue, three-dimensional models with statistical potentials derived from a knowledge-based study of known protein structures. When this space is sampled by a combination of parallel tempering and equi-energy Monte Carlo, we find that the three-point model captures the known stability of protein native structures with stable energy basins that are near-native (all alpha: 4.77 A, all beta: 2.93 A, alpha/beta: 3.09 A, alpha+beta: 4.89 A on average and within 6 A for 71.41%, 92.85%, 94.29% and 64.28% for all-alpha, all-beta, alpha/beta and alpha+beta, classes, respectively). Denatured structures also occur and these have interesting structural properties that shed light on the different landscape characteristics of alpha and beta folds. We find that alpha/beta proteins with alternating alpha and beta segments (such as the beta-barrel) are more stable than proteins in other fold classes.

Original publication

DOI

10.1016/j.jmb.2007.10.087

Type

Journal article

Journal

J Mol Biol

Publication Date

25/01/2008

Volume

375

Pages

920 - 933

Keywords

Amino Acid Sequence, Computer Simulation, Databases, Protein, Energy Transfer, Markov Chains, Models, Molecular, Molecular Sequence Data, Monte Carlo Method, Protein Conformation, Protein Denaturation, Protein Folding, Protein Structure, Secondary, Protein Structure, Tertiary, Proteins, Software, Temperature, Thermodynamics