Abstract
C–H….π interactions are known to be important contributors to protein stability. In this study, we have analyzed the influence of C–H….π interactions in single chain “all-alpha” proteins. In the data set, a total of 181 C–H….π interactions were observed. The most prominent representatives are the interactions between aromatic C–H donor groups and aromatic π acceptors. Eighty-one percent of the C–H….π interactions between side chain to side chain and remaining19% of the C–H….π interactions were observed between side-chain to side-chain five-member aromatic ring. The donor atom contribution to C–H….π interactions was mainly from Phe, Tyr, and Trp residues. The acceptor atom contribution to C–H….π interactions was mainly from Phe, Tyr, Trp, and His. The highest percentage of C–H….π interactions were observed form Phe residue. The secondary structure preference analysis of all C–H….π interacting residues showed that Phe, Tyr, Trp, and His preferred to be in helix. Long-range C–H….π interactions are the predominant type of interactions in single chain all-alpha proteins data set. All the C–H….π 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.
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The authors thank the management of Vellore Institute of Technology for providing the facilities to carry out this work. The authors also thank the reviewers for their suggestions in the improvement of this manuscript.
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Shanthi, V., Ramanathan, K. & Sethumadhavan, R. Exploring the Role of C–H….π Interactions on the Structural Stability of Single Chain “All-Alpha” Proteins. Appl Biochem Biotechnol 160, 1473–1483 (2010). https://doi.org/10.1007/s12010-009-8584-1
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DOI: https://doi.org/10.1007/s12010-009-8584-1