The occurrence of C-H...O hydrogen bonds in alpha-helices and helix termini in globular proteins

Manikandan, K and Ramakumar, S (2004) The occurrence of C-H...O hydrogen bonds in alpha-helices and helix termini in globular proteins. In: Proteins: Structure, Function, and Genetics, 56 (4). pp. 768-781.

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Abstract

A comprehensive database analysis of C-H...O hydrogen bonds in 3124 \alpha helices and their corresponding helix termini has been carried out from a nonredundant data set of high-resolution globular protein structures resolved at better than 2.0 Angstrom in order to investigate their role in the helix, the important protein secondary structural element. The possible occurrence of 5 \rightarrow 1 C -- H...O hydrogen bond between the ith residue CH group and (\imath - 4)th residue C=O with C...O \le 3.8 Angstrom is studied, considering as potential donors the main-chain C\alpha and the side-chain carbon atoms C\beta, G\gamma, C\delta and C\epsilon. Similar analysis has been carried out for 4 \rightarrow 1C-H...O hydrogen bonds, since the C-H...O hydrogen bonds found in helices are predominantly of type 5 \rightarrow 1 or 4 \rightarrow 1. A total of 17,367 (9310 of type 5 \rightarrow 1 and 8057 of type 4 \rightarrow 1) C-H...O hydrogen bonds are found to satisfy the selected criteria. The average stereochemical parameters for the data set suggest that the observed C-H...O hydrogen bonds are attractive interactions. Our analysis reveals that the C\gamma and C\beta hydrogen atom(s) are frequently involved in such hydrogen bonds. A marked preference is noticed for aliphatic \beta-branched residue Ile to participate in 5 --> 1 C-H...O hydrogen bonds involving methylene C\gamma 1 atom as donor in \alpha-helices. This may be an enthalpic compensation for the greater loss of side-chain conformational entropy for \beta-branched amino acids due to the constraint on side-chain torsion angle, namely, chi(1), when they occur in helices. The preference of amino acids for 4 --> 1 C-H...O hydrogen bonds is found to be more for Asp, Cys, and for aromatic residues Trp, Phe, and His. Interestingly, overall propensity for C-H...O hydrogen bonds shows that a majority of the helix favoring residues such as Met, Glu, Arg, Lys, Len, and Gln, which also have large side-chains, prefer to be involved in such types of weak attractive interactions in helices. The amino acid side-chains that participate in C-H...O interactions are found to shield the acceptor carbonyl oxygen atom from the solvent. In addition, C-H...O hydrogen bonds are present along with helix stabilizing salt bridges. A novel helix terminating interaction motif, X-Gly with Gly at C_cap position having 5 \rightarrow 1 C\alpha-H...O, and a chain reversal structural motif having 1 \rightarrow 5 C\alpha-H...O have been identified and discussed. Our analysis highlights that a multitude of local C-H...O hydrogen bonds formed by a variety of amino acid side-chains and C\alpha hydrogen atoms occur in helices and more so at the helix termini. It may be surmised that the main-chain C\alpha and the side-chain CH that participate in C-H...O hydrogen bonds collectively augment the cohesive energy and thereby contribute together with the classical N-H...O hydrogen bonds and other interactions to the overall stability of helix and therefore of proteins.

Item Type:	Journal Article
Publication:	Proteins: Structure, Function, and Genetics
Publisher:	John Wiley and Sons
Additional Information:	Copyright for this article belongs to John Wiley and Sons.
Keywords:	CHO hydrogen bond;alpha-helix;hydrogen bonding potentials;solvent shielding;side-chain conformational entropy;helix propensity;helix capping;chain reversal motif
Department/Centre:	Division of Information Sciences (Doesn't exist now) > BioInformatics Centre Division of Physical & Mathematical Sciences > Physics
Date Deposited:	03 Dec 2004
Last Modified:	17 Jan 2012 06:58
URI:	http://eprints.iisc.ac.in/id/eprint/2222

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