Determination of optimal effective interactions between amino acids in globular proteins

Abstract

An optimization technique is used to determine the pairwise interactions between amino acids in globular proteins. A numerical strategy is applied to a set of proteins for maximizing the native fold stability with respect to alternative structures obtained by gapless threading. The extracted parameters are shown to be very reliable for identifying the native states of proteins (unrelated to those in the training set) among thousands of conformations. The only poor performers are proteins with heme groups and/or poor compactness whose complexity cannot be captured by standard pairwise energy functionals.

20 pages, 6 figures, submitted to J. Mol. Biol

References in corpus (5)

• A New Algorithm for Protein Design
• Protein folding using contact maps
• Folding, Design and Determination of Interaction Potentials Using Off-Lattice Dynamics of Model Heteropolymers
• Variational approach to protein design and extraction of interaction potentials
• Determination of Interaction Potentials of Amino Acids from Native Protein Structures: Test on Simple Lattice Models