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Bioinorganic Chemistry and Applications
Volume 2010, Article ID 724210, 9 pages
http://dx.doi.org/10.1155/2010/724210
Research Article

Modeling Cu(II) Binding to Peptides Using the Extensible Systematic Force Field

1Department of Chemistry, Emmanuel College, Boston, MA 02115, USA
2Carlson School of Chemistry and Biochemistry, Clark University, Worcester, MA 01610, USA

Received 10 October 2009; Accepted 5 January 2010

Academic Editor: Konstantinos Tsipis

Copyright © 2010 Faina Ryvkin and Frederick T. Greenaway. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

The utility of the extensible systematic force field (ESFF) was tested for copper(II) binding to a 34-amino-acid Cu(II) peptide, which includes five histidine residues and is the putative copper-binding site of lysyl oxidase. To improve computational efficiency, distance geometry calculations were used to constrain all combinations of three histidine ligands to be within bonding distance of the copper and the best results were utilized as starting structures for the ESFF computations. All likely copper geometries were modeled, but the results showed only a small dependence on the geometrical model in that all resulted in a distorted square pyramidal geometry about the copper, some of the imidazole rings were poorly oriented for ligation to the Cu(II), and the copper-nitrogen bond distances were too long. The results suggest that ESFF should be used with caution for Cu(II) complexes where the copper-ligand bonds have significant covalency and when the ligands are not geometrically constrained to be planar.