Models of S/pi interactions in protein structures: comparison of the H2S benzene complex with PDB data.
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 H(2)S-benzene complex. A correlation is observed between the energetically favorable configurations on the quantum mechanical potential energy surface of the H(2)S-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.
Ringer
Ashley L
AL
Center for Computational Molecular Science and Technology, Georgia Institute of Technology, Atlanta, GA 30332-0400, USA.
Senenko
Anastasia
A
Sherrill
C David
CD
D001554:Benzene / Q000737:chemistry*; D019295:Computational Biology; D018360:Crystallography, X-Ray; D030562:Databases, Protein; D006862:Hydrogen Sulfide / Q000737:chemistry*; D008958:Models, Molecular; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry
D011506:Proteins; D001554:Benzene; D006862:Hydrogen Sulfide