Does Secondary Structure Determine Tertiary Structure in Proteins?

Proteins. 2005 Nov 1;61(2):338-43. doi: 10.1002/prot.20622.

Abstract

Is highly approximate knowledge of a protein's backbone structure sufficient to successfully identify its family, superfamily, and tertiary fold? To explore this question, backbone dihedral angles were extracted from the known three-dimensional structure of 2,439 proteins and mapped into 36 labeled, 60 degrees x 60 degrees bins, called mesostates. Using this coarse-grained mapping, protein conformation can be approximated by a linear sequence of mesostates. These linear strings can then be aligned and assessed by conventional sequence-comparison methods. We report that the mesostate sequence is sufficient to recognize a protein's family, superfamily, and fold with good fidelity.

Publication types

  • Comparative Study
  • Evaluation Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms*
  • Molecular Structure
  • Monte Carlo Method
  • Protein Structure, Secondary*
  • Protein Structure, Tertiary*
  • Proteins / chemistry
  • Proteins / classification
  • Sequence Alignment
  • Sequence Analysis, Protein

Substances

  • Proteins