The spatial architecture of protein function and adaptation

Nature. 2012 Nov 1;491(7422):138-42. doi: 10.1038/nature11500. Epub 2012 Oct 7.

Abstract

Statistical analysis of protein evolution suggests a design for natural proteins in which sparse networks of coevolving amino acids (termed sectors) comprise the essence of three-dimensional structure and function. However, proteins are also subject to pressures deriving from the dynamics of the evolutionary process itself--the ability to tolerate mutation and to be adaptive to changing selection pressures. To understand the relationship of the sector architecture to these properties, we developed a high-throughput quantitative method for a comprehensive single-mutation study in which every position is substituted individually to every other amino acid. Using a PDZ domain (PSD95(pdz3)) model system, we show that sector positions are functionally sensitive to mutation, whereas non-sector positions are more tolerant to substitution. In addition, we find that adaptation to a new binding specificity initiates exclusively through variation within sector residues. A combination of just two sector mutations located near and away from the ligand-binding site suffices to switch the binding specificity of PSD95(pdz3) quantitatively towards a class-switching ligand. The localization of functional constraint and adaptive variation within the sector has important implications for understanding and engineering proteins.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adaptation, Physiological* / genetics
  • Adaptation, Physiological* / physiology
  • Amino Acid Sequence
  • Amino Acid Substitution*
  • Binding Sites / genetics
  • Evolution, Molecular
  • Ligands
  • Models, Molecular
  • Molecular Sequence Data
  • Mutant Proteins / chemistry*
  • Mutant Proteins / genetics
  • Mutant Proteins / metabolism
  • Mutation
  • PDZ Domains / genetics*
  • PDZ Domains / physiology*
  • Proteins / chemistry*
  • Proteins / genetics
  • Proteins / metabolism*

Substances

  • Ligands
  • Mutant Proteins
  • Proteins