Closed loops of TIM barrel protein fold

J Biomol Struct Dyn. 2005 Jun;22(6):643-56. doi: 10.1080/07391102.2005.10507032.

Abstract

The closed loops within the proteins of the TIM-barrel fold family are analyzed and compared sequence- and structure-wise. The size distribution of the closed loops of the TIM-barrels confirms universal preference to the standard size of 25-30 residues. 3D structural RMSD comparisons of the closed loops and presentation of their sequences in binary form suggest that the TIM-barrel proteins are built from descendants of several types of basic closed loop prototypes. Comparison of these prototypes points to a likely common ancestor--the alpha helix containing closed loops of 28 amino acids. The presumed ancestor is characterized by specific binary consensus sequence.

Publication types

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

MeSH terms

  • Amino Acid Sequence
  • Conserved Sequence
  • Databases, Factual
  • Evolution, Molecular
  • Hydrophobic and Hydrophilic Interactions
  • Models, Molecular
  • Molecular Sequence Data
  • Protein Conformation
  • Protein Folding*
  • Protein Structure, Secondary
  • Proteins / chemistry*
  • Sequence Homology, Amino Acid
  • Structure-Activity Relationship

Substances

  • Proteins