Hindawi Publishing Corporation Journal of Biomedicine and Biotechnology Volume 2012, Article ID 959057, 12 pages doi:10.1155/2012/959057 Research Article Combined QM/MM Study of Thyroid and Steroid Hormone Analogue Interactions with αvβ3 Integrin Marek Freindorf, 1 Thomas R. Furlani, 1 Jing Kong, 2 Vivian Cody, 3, 4 Faith B. Davis, 5 and Paul J. Davis 5 1 Center for Computational Research, State University of New York at Buffalo, Buffalo, NY 14260, USA 2 Q-Chem, Inc., Pittsburgh, PA 15213, USA 3 Structural Biology Department, Hauptman-Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203, USA 4 School of Medicine and Biological Sciences, State University of New York at Buffalo, Buffalo, NY 14260, USA 5 Pharmaceutical Research Institute, Albany College of Pharmacy and Health Sciences, Albany, NY 12208, USA Correspondence should be addressed to Vivian Cody, cody@hwi.buffalo.edu Received 12 July 2011; Revised 29 November 2011; Accepted 2 December 2011 Academic Editor: Paolo Ruggerone Copyright © 2012 Marek Freindorf et al. 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. Recent biochemical studies have identified a cell surface receptor for thyroid and steroid hormones that bind near the arginine-glycine-aspartate (RGD) recognition site on the heterodimeric αvβ3 integrin. To further characterize the intermolecular interactions for a series of hormone analogues, combined quantum mechanical and molecular mechanical (QM/MM) methods were used to calculate their interaction energies. All calculations were performed in the presence of either calcium (Ca 2+ ) or magnesium (Mg 2+ ) ions. These data reveal that 3,5 ′ -triiodothyronine (T 3 ) and 3,5,3 ′ ,5 ′ -tetraiodothyroacetic acid (T 4 ac) bound in two different modes, occupying two alternate sites, one of which is along the Arg side chain of the RGD cyclic peptide site. These orientations differ from those of the other ligands whose alternate binding modes placed the ligands deeper within the RGD binding pocket. These observations are consistent with biological data that indicate the presence of two discrete binding sites that control distinct downstream signal transduction pathways for T 3 . 1. Introduction Integrins are plasma membrane proteins that generate com- plex and intracellular signals during morphogenesis, tissue remodeling, and repair [1]. Interactions of integrins with specific extracellular matrix proteins and growth factors or with certain small molecules generate ligand-specific signals. The integrin superfamily of heterodimeric glycoproteins consists of α- and β-monomers that associate in defined combinations that include more than twenty different mam- malian subtypes, of which at least eight are characterized by the presence of an Arg-Gly-Asp (RGD) site used in the process of recognition of different protein ligands [1–3]. The combination of αvβ3 subunits is the most abundant integrin expressed in mammalian cells [1]. Structural data have revealed that the extracellular seg- ment of integrin αvβ3 (i.e., lacking the transmembrane and cytoplasmic tails) is V shaped with the 4-domain αv subunit and the 8-domain β3 subunit bent by 135 ◦ [4–6]. Data for the RGD cyclic pentapeptide complex reveals that the RGD peptide occupies a shallow crevice between the propeller and βA domains in the integrin head. The X-ray structure of apo αvβ3 has been determined in the presence of Ca 2+ ions [6] and in the presence of Mn 2+ as a complex with the cyclic pentapeptide Arg-Gly-Asp-{D- Phe}-{N-methyl-Val} (Figure 1)[4]. These data showed that replacement of Ca 2+ with Mn 2+ in the αvβ3 integrin did not result in any important structural changes to the protein. There are also relatively small changes in the αvβ3 structure with and without the cyclic pentapeptide bound in the RGD site of integrin. Ligand binding to integrins is dependent upon bivalent- cation interactions that are generally stimulated by Mg 2+ or Mn 2+ and inhibited by Ca 2+ . Competitive binding data