RESEARCH ARTICLE Copyright © 2014 American Scientific Publishers All rights reserved Printed in the United States of America Journal of Computational and Theoretical Nanoscience Vol. 11, 1081–1085, 2014 Effect of Divalent Metals on the Molecular Structure of Protein: Modeling and Spectroscopic Approaches Hanan Elhaes 1 , Nahla M. Elkashef 2 , Fagr Kh. Abdel-Gawad 3 4 , Ahmed Shabaan 4 , and Medhat Ibrahim 5 ∗ 1 Faculty of Women for Arts, Science and Education, Physics Department, Ain Shams University, 11757 Cairo, Egypt 2 Faculty of Science, Physics Department, Suez Canal University, Ismailia, Egypt 3 Centre of Excellence for Advanced Science (CEAS), Water Pollution Research Department, National Research Centre, 12311 Dokki, Cairo, Egypt 4 Water Pollution Research Department, National Research Centre, 12311 Dokki, Cairo, Egypt 5 Spectroscopy Department, National Research Center, 12311 Dokki, Cairo, Egypt HF/3-21g ∗∗ was used to study the possible interaction of Ca, Cd and Za with protein. Results indi- cate that each metal is attached with two hydrogen bondings in two hydrated protein chains. Protein structure has been affected as a result of interaction with the studied metals. The change was noticed in the bond lengths and bond angle of the COOH group. The interaction decreases the cal- culated band gap energy and increases the total dipole moment which is a good indication for the reactivity of protein after interaction with the studied metals. FTIR verifies experimentally the inter- action and indicates that the characteristic bands of metal carboxylate are shifted 190∼200 cm −1 through the lower wavenumbers. Keywords: Molecular Modeling, HF, FTIR, Protein, Heavy Metals, Fish. 1. INTRODUCTION Metalloproteins serve many important biological functions. Metals impart various effects on protein structure and bring about overall structural stability. 1 Metalloproteins have a metal ion or ions in their struc- ture and have a wide variety of functions in vivo. Zinc metalloproteins contain many attractive drug targets. 2 For example; inhibitors of angiotensin-converting enzyme (ACE), carbonic anhydrases (CAs), matrix metallopro- teinases (MMPs), TNF- converting enzyme (TACE), histone deacetylases (HDACs), and farnesyltransferase have been reported. 3–9 Cadmium may increase the amount of unbound free or chelated copper and iron ions (replacing them in var- ious proteins) that can participate in oxidative stress via Fenton reaction. 10 11 An oxidative damage to proteins and DNA was noticed in rats exposed to Cd and/or ethanol. 12 Calcium–protein binding gains considerable attention because a variety of biochemical and physical properties of proteins are regulated by calcium ions. 13–15 A variety of ∗ Author to whom correspondence should be addressed. biochemical and physical properties of proteins are regu- lated by calcium ion (Ca 2+  binding with varying speci- ficity and affinity. 16 Glycine is the simplest protein; and the smallest and unique non-chiral amino acid that can act as a neuro -inhibitor in mammalian nervous system. 17 18 Glycine among other amino acids were subjected to XRD; FTIR and molecular modeling study to investigate the effect of hydration upon amino acids. 19 Molecular model- ing was utilized extensively in biological systems to study some important biological interactions such as protein interactions in hydration; metal-protein interaction. 19–24 Recently, molecular modeling is being widely utilized for investigating electronic; structural as well as many other important physical parameters for many systems. 25–27 In the present work three units of glycine are designed as a model molecule for protein structure. HF/3-21g ∗∗ was utilized to study the effect of Ca, Cd and Zn upon two chains of hydrated proteins. The change in the geometrical parameters are introduced in terms the COOH structure. Vibrational frequencies are calculated at the same level of theory then experimental verification of such metal protein interaction was carried out after performing FTIR of fish samples. J. Comput. Theor. Nanosci. 2014, Vol. 11, No. 04 1546-1955/2014/11/001/005 doi:10.1166/jctn.2014.3465 1081