A global representation of the protein fold space

Proc Natl Acad Sci U S A. 2003 Mar 4;100(5):2386-90. doi: 10.1073/pnas.2628030100. Epub 2003 Feb 26.

Abstract

One of the principal goals of the structural genomics initiative is to identify the total repertoire of protein folds and obtain a global view of the "protein structure universe." Here, we present a 3D map of the protein fold space in which structurally related folds are represented by spatially adjacent points. Such a representation reveals a high-level organization of the fold space that is intuitively interpretable. The shape of the fold space and the overall distribution of the folds are defined by three dominant trends: secondary structure class, chain topology, and protein domain size. Random coil-like structures of small proteins and peptides are mapped to a region where the three trends converge, offering an interesting perspective on both the demography of fold space and the evolution of protein structures.

Publication types

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

MeSH terms

  • Bacterial Proteins / chemistry*
  • Biophysical Phenomena
  • Biophysics*
  • Models, Molecular
  • Phylogeny
  • Protein Folding
  • Protein Structure, Tertiary
  • Proteins / chemistry*

Substances

  • Bacterial Proteins
  • Proteins