Exploring the environmental preference of weak interactions in (alpha/beta)8 barrel proteins.
The environmental preference for the occurrence of noncanonical hydrogen bonding and cation-pi interactions, in a data set containing 71 nonredundant (alpha/beta)(8) barrel proteins, with respect to amino acid type, secondary structure, solvent accessibility, and stabilizing residues has been performed. Our analysis reveals some important findings, which include (a) higher contribution of weak interactions mediated by main-chain atoms irrespective of the amino acids involved; (b) domination of the aromatic amino acids among interactions involving side-chain atoms; (c) involvement of strands as the principal secondary structural unit, accommodating cross strand ion pair interaction and clustering of aromatic amino acid residues; (d) significant contribution to weak interactions occur in the solvent exposed areas of the protein; (e) majority of the interactions involve long-range contacts; (f) the preference of Arg is higher than Lys to form cation-pi interaction; and (g) probability of theoretically predicted stabilizing amino acid residues involved in weak interaction is higher for polar amino acids such as Trp, Glu, and Gln. On the whole, the present study reveals that the weak interactions contribute to the global stability of (alpha/beta)(8) TIM-barrel proteins in an environment-specific manner, which can possibly be exploited for protein engineering applications.
Chakkaravarthi
S
S
School of Biotechnology and Chemical Engineering, Vellore Institute of Technology, Vellore, India.
Babu
M Madan
MM
Gromiha
M Michael
MM
Jayaraman
G
G
Sethumadhavan
R
R
D000596:Amino Acids / Q000737:chemistry*; D006860:Hydrogen Bonding; D017433:Protein Structure, Secondary; D012997:Solvents / Q000737:chemistry
D000596:Amino Acids; D012997:Solvents