Hydropathy analysis to correlate structure and function of proteins

Biochem Biophys Res Commun. 2004 Oct 22;323(3):996-1002. doi: 10.1016/j.bbrc.2004.08.186.

Abstract

In post-genomic era, a plethora of protein structures have been solved but the functions of some of them are unknown. In this context, the role of hydropathy index of amino acids in predicting the function of a structurally known and functionally unknown protein was explored. Initially serine protease class was taken for analysis. Various methodologies like calculation of average hydropathy index for a five-residue window of a given sequence, hydropathy cluster analyses, etc., were done. Among these, the distribution of hydropathy clusters seems to suggest that the location of these clusters is conserved for a given class of proteins. Hence, this methodology was extended to different classes of proteins and to a protein with unknown function.

Publication types

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

MeSH terms

  • Algorithms*
  • Amino Acid Sequence
  • Amino Acids / chemistry
  • Computer Simulation
  • Hydrophobic and Hydrophilic Interactions
  • Models, Chemical*
  • Models, Molecular*
  • Molecular Sequence Data
  • Proteins / chemistry*
  • Proteins / classification*
  • Sequence Analysis, Protein / methods*
  • Structure-Activity Relationship*

Substances

  • Amino Acids
  • Proteins