Parameter-Free Hydrogen-Bond Definition to Classify Protein Secondary Structure

J Phys Chem B. 2016 Aug 25;120(33):8566-70. doi: 10.1021/acs.jpcb.6b02571. Epub 2016 Apr 25.

Abstract

DSSP is the most commonly used method to assign protein secondary structure. It is based on a hydrogen-bond definition with an energy cutoff. To assess whether hydrogen bonds defined in a parameter-free way may give more generality while preserving accuracy, we examine a series of hydrogen-bond definitions to assign secondary structure for a series of proteins. Assignment by the strongest-acceptor bifurcated definition with provision for unassigned donor hydrogens, termed the SABLE method, is found to match DSSP with 95% agreement. The small disagreement mainly occurs for helices, turns, and bends. While there is no absolute way to assign protein secondary structure, avoiding molecule-specific cutoff parameters should be advantageous in generalizing structure-assignment methods to any hydrogen-bonded system.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Hydrogen / chemistry
  • Hydrogen / metabolism
  • Hydrogen Bonding*
  • Models, Molecular*
  • Protein Structure, Secondary*
  • Static Electricity

Substances

  • Hydrogen