Role of hydrophobic clusters and long-range contact networks in the folding of (alpha/beta)8 barrel proteins

Biophys J. 2003 Mar;84(3):1919-25. doi: 10.1016/s0006-3495(03)75000-0.

Abstract

Analysis on the three dimensional structures of (alpha/beta)(8) barrel proteins provides ample light to understand the factors that are responsible for directing and maintaining their common fold. In this work, the hydrophobically enriched clusters are identified in 92% of the considered (alpha/beta)(8) barrel proteins. The residue segments with hydrophobic clusters have high thermal stability. Further, these clusters are formed and stabilized through long-range interactions. Specifically, a network of long-range contacts connects adjacent beta-strands of the (alpha/beta)(8) barrel domain and the hydrophobic clusters. The implications of hydrophobic clusters and long-range networks in providing a feasible common mechanism for the folding of (alpha/beta)(8) barrel proteins are proposed.

MeSH terms

  • Algorithms*
  • Amino Acid Sequence
  • Amino Acids / chemistry*
  • Hydrophobic and Hydrophilic Interactions
  • Models, Molecular*
  • Molecular Sequence Data
  • Protein Conformation
  • Protein Folding*
  • Protein Structure, Secondary
  • Protein Structure, Tertiary
  • Proteins / chemistry*
  • Temperature

Substances

  • Amino Acids
  • Proteins