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Models of S/π interactions in protein structures: Comparison of the H2S–benzene complex with PDB data

  1. Ashley L. Ringer,
  2. Anastasia Senenko,
  3. C. David Sherrill*

Article first published online: 1 JAN 2009

DOI: 10.1110/ps.073002307

Issue

Protein Science

Protein Science

Volume 16, Issue 10, pages 2216–2223, October 2007

Additional Information

How to Cite

Ringer, A. L., Senenko, A. and Sherrill, C. D. (2007), Models of S/π interactions in protein structures: Comparison of the H2S–benzene complex with PDB data. Protein Science, 16: 2216–2223. doi: 10.1110/ps.073002307

Author Information

  1. 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

*School of Chemistry and Biochemistry, 901 Atlantic Drive, Atlanta, GA 30332-0400, USA; fax: (404) 894-7452.

Publication History

  1. Issue published online: 1 JAN 2009
  2. Article first published online: 1 JAN 2009
  3. Manuscript Revised: 3 JUL 2007
  4. Manuscript Accepted: 3 JUL 2007
  5. Manuscript Received: 16 MAY 2007

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Keywords:

  • molecular recognition;
  • protein structure;
  • computational analysis of protein structure;
  • forces and stability

Abstract

S/π 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.

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