Geometric characteristics of hydrogen bonds involving sulfur atoms in proteins

Abstract

Sulfur atoms have been known to participate in hydrogen bonds (H-bonds) and these sulfur-containing H-bonds (SCHBs) are suggested to play important roles in certain biological processes. This study aims to comprehensively characterize all the SCHBs in 500 high-resolution protein structures (< or =1.8 A). We categorized SCHBs into six types according to donor/acceptor behaviors and used explicit hydrogen approach to distinguish SCHBs from those of nonhydrogen bonding interactions. It is revealed that sulfur atom is a very poor H-bond acceptor, but a moderately good H-bond donor. In alpha-helix, considerable SCHBs were found between the sulphydryl group of cysteine residue i and the carbonyl oxygen of residue i-4, and these SCHBs exert effects in stabilizing helices. Although for other SCHBs, they possess no specific secondary structural preference, their geometric characteristics in proteins and in free small compounds are significantly distinct, indicating the protein SCHBs are geometrically distorted. Interestingly, sulfur atom in the disulfide bond tends to form bifurcated H-bond whereas in cysteine-cysteine pairs prefer to form dual H-bond. These special H-bonds remarkably boost the interaction between H-bond donor and acceptor. By oxidation/reduction manner, the mutual transformation between the dual H-bonds and disulfide bonds for cysteine-cysteine pairs can accurately adjust the structural stability and biological function of proteins in different environments. Furthermore, few loose H-bonds were observed to form between the sulphydryl groups and aromatic rings, and in these cases the donor H is almost over against the rim rather than the center of the aromatic ring.

A dynamic Asp–Arg interaction is essential for catalysis in microsomal prostaglandin E 2 synthase

“…Conversely, Arg-126 is observed in a single conformation with an Nη-GSH thiol distance of 3.4 Å. We believe that this active site geometry also substantiates strong evidence for a mechanism of GSH thiol activation by an Arg-126 guanidinium interaction (30). Hence, despite compelling structural evidence, Ser-127 does not play a critical role in mPGES-1 catalysis.…”

Repression of the Chromatin-Tethering Domain of Murine Leukemia Virus p12

“…Multiple potential roles of the M63 residue may be disrupted by the M63I substitution, resulting in the weakened repressor binding observed in p12-I63-GFP. Methionine residues are reported to interact with tyrosine residues (39). The phenolic group of tyrosine is also capable of attacking the sulfhydryl position of methionine during acid catalysis (40,41).…”

Changes in the hydrogen-bonding strength of internal water molecules and cysteine residues in the conductive state of channelrhodopsin-1

“…74,87 Consequently, a change in H-bonding strength of a cysteine side chain might originate either by a change in the pitch of the helix in the case of an intrahelical H-bond or a change in the relative orientation of two helices in the case of an interhelical H-bond. For CrChR2, it has been shown that the photocycle is associated with the movement of transmembrane helices, predominantly of helices B and F. 88 Because helix F of CaChR1 lacks cysteine residues, the cysteine residues in helix B (C133, C134, and C141) are prime candidates to undergo a measurable change in their S-H stretch frequency as a result of the structural changes.…”