Improving prediction of helix-helix packing in membrane proteins using predicted contact numbers as restraints.

Li B, Mendenhall J, Nguyen ED, Weiner BE, Fischer AW, Meiler J
Proteins. 2017 85 (7): 1212-1221

PMID: 28263405 · PMCID: PMC5476507 · DOI:10.1002/prot.25281

One of the challenging problems in tertiary structure prediction of helical membrane proteins (HMPs) is the determination of rotation of α-helices around the helix normal. Incorrect prediction of helix rotations substantially disrupts native residue-residue contacts while inducing only a relatively small effect on the overall fold. We previously developed a method for predicting residue contact numbers (CNs), which measure the local packing density of residues within the protein tertiary structure. In this study, we tested the idea of incorporating predicted CNs as restraints to guide the sampling of helix rotation. For a benchmark set of 15 HMPs with simple to rather complicated folds, the average contact recovery (CR) of best-sampled models was improved for all targets, the likelihood of sampling models with CR greater than 20% was increased for 13 targets, and the average RMSD100 of best-sampled models was improved for 12 targets. This study demonstrated that explicit incorporation of CNs as restraints improves the prediction of helix-helix packing. Proteins 2017; 85:1212-1221. © 2017 Wiley Periodicals, Inc.

© 2017 Wiley Periodicals, Inc.

MeSH Terms (11)

Algorithms Amino Acids Benchmarking Binding Sites Membrane Proteins Models, Molecular Protein Binding Protein Conformation, alpha-Helical Protein Folding Protein Interaction Domains and Motifs Protein Structure, Tertiary

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