Theoretical Study Of Typical Zinc Protein System

Among the chemical and life processes,zinc protein plays a very important role.Zinc ions in proteins usually act as catalytic active center,and/or play the role of maintaining a stable protein structure.So the study of zinc protein has important significance.Details are as follows:1.Theoretical study of the interaction of zinc ions and histidine residues,cysteine residues and water moleculesIn the gas phase,all the complex structures were fully optimized and calculated the frequency by B3LYP/6-311++G(d,p)?,and then calculated the energy,including BSSE correction,at the MP2/6-311++G(2d,2p)level.The Mulliken charge of monomers and complexes was calculated by HF/STO-3G.We compared the coordination ability of coordinating atoms and we found the difference between binding energy and charge transfer when cysteine was protonated or deprotonated.2.Theoretical study of conformational transition in zinc finger protein for Zn2+-Cys3His typeA series of calculation were completed by B3LYP/6-311++G(d,p),including optimization,frequency,Gibbs free energy,salvation free energy and NBO charge.When the conformation changed,coordination number of zinc ions also changed.The activation energy in the reaction process was less than 21 kcal mol-1,which was described that the reaction could be carried out at room temperature.The binding ability of Zn-S was stronger than Zn-O by charge transfer.3.Theoretical study of the interaction between Zn(H2O)62+and amino acid side chainsIn the gas phase and aqueous phase,all the complex structures were optimized and the frequency was calculated by B3LYP/6-311++G(d,p),and then calculated the energy at the MP2/6-311++G(2d,2p)level,where Zn2+ used pseudo potential basis set Lanl2dz.The Mulliken charge of complexes were calculated by HF/STO-3G,and then compared with Mulliken charge and ABEEM?? charge.We found the stability of the order from strong to weak between Zn(H2O)62+and amino acid side chains.For O…H type hydrogen bond,single hydrogen bond length and the corresponding second-order stabilizing energy had exponential relationship,which the correlation coefficient was 0.9648.It had a good linear correlation between ABEEM?? charge and Mulliken charge calculated by HF/STO-3G.4.The calculation of charge distribution and the preliminary study for kinetic properties of zinc proteinWe fitted a set of parameters used to calculate ABEEM?? charge by selecting more than 30 kinds of model molecules and more than 100 training molecules.we also got the suitable force field parameters for zinc protein through the zinc protein fragments,3 c5k1,2v5w0 and 41d21,optimized by ABEEM?? fluctuating charge polarizable force field.In order to test the reasonableness of the force field parameters,we simulated the protein fragment 3c5k and analyzed the properties of the root mean square deviation,radial distribution function and the charge changes.