Recursive domains in proteins

Protein Sci. 2002 Feb;11(2):409-17. doi: 10.1110/ps.24701.

Abstract

The domain is a fundamental unit of protein structure. Numerous studies have analyzed folding patterns in protein domains of known structure to gain insight into the underlying protein folding process. Are such patterns a haphazard assortment or are they similar to sentences in a language, which can be generated by an underlying grammar? Specifically, can a small number of intuitively sensible rules generate a large class of folds, including feasible new folds? In this paper, we explore the extent to which four simple rules can generate the known all-beta folds, using tools from graph theory. As a control, an exhaustive set of beta-sandwiches was tested and found to be largely incompatible with such a grammar. The existence of a protein grammar has potential implications for both the mechanism of folding and the evolution of domains.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Dimerization
  • Kinetics
  • Models, Molecular
  • Protein Conformation
  • Protein Folding
  • Protein Structure, Tertiary
  • Proteins / chemistry*

Substances

  • Proteins