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PEDS Advance Access originally published online on December 2, 2004
Protein Engineering Design and Selection 2004 17(11):795-808; doi:10.1093/protein/gzh093
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Protein Engineering, Design & Selection vol. 17 no. 11 © Oxford University Press 2004; all rights reserved

Disulfide bonds, their stereospecific environment and conservation in protein structures

Rajasri Bhattacharyya, Debnath Pal1 and Pinak Chakrabarti2

Department of Biochemistry, Bose Institute, P-1/12 CIT Scheme VIIM, Calcutta 700 054, India

2 To whom correspondence should be addressed. E-mail: pinak{at}boseinst.ernet.in or pinak_chak{at}yahoo.co.in

We studied the specificity of the non-bonded interaction in the environment of 572 disulfide bonds in 247 polypeptide chains selected from the Protein Data Bank. The preferred geometry of interaction of peptide oxygen atoms is along the back of the two covalent bonds at the sulfur atom of half cystine. With aromatic residues the geometries that direct one of the sulfur lone pair of electrons into the aromatic {pi}-system are avoided; an orientation in which the sulfide plane is normal or inclined to the aromatic plane and on top of its edge is normally preferred. The importance of the S···aromatic interaction is manifested in the high degree of its conservation across members in homologous protein families. These interactions, while providing extra overall stability to the native fold and reducing the accessibility of the disulfide bond and thereby preventing exchange reactions, also set the orientation of the conserved aromatic rings for further interactions and binding to another molecule. The conformational features and the mode of interactions of disulfide bridges should be useful for molecular design and protein engineering experiments.

Received September 2, 2004; revised November 2, 2004; accepted November 27, 2004.

Edited by P.Balaram


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