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Published online before print August 31, 2007, 10.1110/ps.073002307
Protein Science (2007), 16:2216-2223. Published by Cold Spring Harbor Laboratory Press. Copyright © 2007 The Protein Society
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Models of S/{pi} interactions in protein structures: Comparison of the H2S–benzene complex with PDB data

Ashley L. Ringer, Anastasia Senenko, and C. David Sherrill

Center for Computational Molecular Science and Technology, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA College of Computing, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA

(RECEIVED May 16, 2007; FINAL REVISION July 3, 2007; ACCEPTED July 3, 2007)

S/{pi} interactions are prevalent in biochemistry and play an important role in protein folding and stabilization. Geometries of cysteine/aromatic interactions found in crystal structures from the Brookhaven Protein Data Bank (PDB) are analyzed and compared with the equilibrium configurations predicted by high-level quantum mechanical results for the H2S–benzene complex. A correlation is observed between the energetically favorable configurations on the quantum mechanical potential energy surface of the H2S–benzene model and the cysteine/aromatic configurations most frequently found in crystal structures of the PDB. In contrast to some previous PDB analyses, configurations with the sulfur over the aromatic ring are found to be the most important. Our results suggest that accurate quantum computations on models of noncovalent interactions may be helpful in understanding the structures of proteins and other complex systems.

Keywords: molecular recognition; protein structure; computational analysis of protein structure; forces and stability


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