title: Exploring the role of C-H....pi interactions on the structural stability of single chain "all-alpha" proteins.
abstract: C-H....pi interactions are known to be important contributors to protein stability. In this study, we have analyzed the influence of C-H....pi interactions in single chain "all-alpha" proteins. In the data set, a total of 181 C-H....pi interactions were observed. The most prominent representatives are the interactions between aromatic C-H donor groups and aromatic pi acceptors. Eighty-one percent of the C-H....pi interactions between side chain to side chain and remaining19% of the C-H....pi interactions were observed between side-chain to side-chain five-member aromatic ring. The donor atom contribution to C-H....pi interactions was mainly from Phe, Tyr, and Trp residues. The acceptor atom contribution to C-H....pi interactions was mainly from Phe, Tyr, Trp, and His. The highest percentage of C-H....pi interactions were observed form Phe residue. The secondary structure preference analysis of all C-H....pi interacting residues showed that Phe, Tyr, Trp, and His preferred to be in helix. Long-range C-H....pi interactions are the predominant type of interactions in single chain all-alpha proteins data set. All the C-H....pi interactions forming residues in the data set preferred to be in the buried region. Seventy-three percent of the donor residues and 65% of the acceptor residues are highly conserved.
authors.affiliation: School of Biotechnology, Chemical and Biomedical Engineering, Bioinformatics Division, Vellore Institute of Technology, Vellore 632014, Tamil Nadu, India.
authors.forename: V
authors.initials: V
authors.lastname: Shanthi
authors.forename: K
authors.initials: K
authors.lastname: Ramanathan
authors.forename: Rao
authors.initials: R
authors.lastname: Sethumadhavan
mesh_terms: D000596:Amino Acids / Q000737:chemistry; D017124:Conserved Sequence; D055550:Protein Stability; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D012997:Solvents
chemical_list: D000596:Amino Acids; D011506:Proteins; D012997:Solvents