Prog Biophys Mol Biol. 2007 Sep-Nov;95(1-3):83-137. doi: 10.1016/j.pbiomolbio.2007.03.016. Epub 2007 Jun 5.

Authors

Affiliation

• 1 Department of Biochemistry and Bioinformatics Centre, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata 700054, India. pinak@boseinst.ernet.in

• PMID: 17629549

• DOI: 10.1016/j.pbiomolbio.2007.03.016

Abstract

Although hydrophobic interaction is the main contributing factor to the stability of the protein fold, the specificity of the folding process depends on many directional interactions. An analysis has been carried out on the geometry of interaction between planar moieties of ten side chains (Phe, Tyr, Trp, His, Arg, Pro, Asp, Glu, Asn and Gln), the aromatic residues and the sulfide planes (of Met and cystine), and the aromatic residues and the peptide planes within the protein tertiary structures available in the Protein Data Bank. The occurrence of hydrogen bonds and other nonconventional interactions such as C-H...pi, C-H...O, electrophile-nucleophile interactions involving the planar moieties has been elucidated. The specific nature of the interactions constraints many of the residue pairs to occur with a fixed sequence difference, maintaining a sequential order, when located in secondary structural elements, such as alpha-helices and beta-turns. The importance of many of these interactions (for example, aromatic residues interacting with Pro or cystine sulfur atom) is revealed by the higher degree of conservation observed for them in protein structures and binding regions. The planar residues are well represented in the active sites, and the geometry of their interactions does not deviate from the general distribution. The geometrical relationship between interacting residues provides valuable insights into the process of protein folding and would be useful for the design of protein molecules and modulation of their binding properties.

Publication types

• Research Support, Non-U.S. Gov’t
• Review

MeSH terms

• Amino Acids / chemistry*
• Amino Acids, Acidic / chemistry
• Amino Acids, Aromatic / chemistry
• Amino Acids, Basic / chemistry
• Binding Sites
• Hydrogen Bonding
• Models, Molecular
• Peptides / chemistry*
• Protein Folding
• Protein Structure, Secondary
• Proteins / chemistry*
• Sulfides / chemistry

Substances

• Amino Acids
• Amino Acids, Acidic
• Amino Acids, Aromatic
• Amino Acids, Basic
• Peptides
• Proteins
• Sulfides