Thermodynamics of stacking interactions in proteins

Phys Chem Chem Phys. 2008 May 21;10(19):2673-85. doi: 10.1039/b718519g. Epub 2008 Apr 9.

Abstract

Using a database of 6166 experimental structures taken from the Protein Data Bank, we have studied pair interactions between planar residues (Phe, Tyr, His, Arg, Glu and Asp) in proteins, known as pi-pi interactions. On the basis of appropriate coordinates defining the mutual arrangement of two residues, we have calculated 2-D potentials of mean force aimed at determining the stability of the most probable structures for aromatic-aromatic, aromatic-cation and aromatic-anion bound pairs. Our analysis reveals the thermodynamic relevance and the ubiquity of stacked complexes in proteins.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Databases, Protein
  • Proteins / chemistry*
  • Thermodynamics*

Substances

  • Proteins