How frequent are correlated changes in families of protein sequences?

Proc Natl Acad Sci U S A. 1994 Jan 4;91(1):98-102. doi: 10.1073/pnas.91.1.98.

Abstract

A loss-of-function point mutation in a protein is often rescued by an additional mutation that compensates for the original physical change. According to one hypothesis, such compensation would be most effective in maintaining a structural motif if the two mutated residues were spatial neighbors. If this hypothesis were correct, one would expect that many such compensatory mutations have occurred during evolution and that present-day protein families show some degree of correlation in the occurrence of amino acid residues at positions whose side chains are in contact. Here, a statistical theory is presented which allows evaluation of correlations in a family of aligned protein sequences by assigning a scalar metric (such as charge or side-chain volume) to each type of amino acid and calculating correlation coefficients of these quantities at different positions. For the family of myoglobins it is found that there is a high correlation between fluctuations in neighboring charges. The correlation is close to what would be expected for total conservation of local charge. For the metric side-chain volume, on the other hand, no correlation could be found.

Publication types

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

MeSH terms

  • Amino Acid Sequence
  • Animals
  • Mutation*
  • Myoglobin / chemistry*
  • Protein Conformation
  • Sequence Alignment
  • Sequence Analysis / methods
  • Sequence Homology, Amino Acid
  • Structure-Activity Relationship

Substances

  • Myoglobin