Theoretical Studies On Structure And Docking Of Protein

With the rapid development of protein sequencing, computer aidedmolecular modeling has become a very important and active research fieldin chemistry, biochemistry and molecular biology. By the theoreticalsimulation and structure prediction method, the three dimension (3D)structure, energy changes, electron transport and conformationtransformation of biomacromolecule in biochemical reaction can beobtained. In this doctoral thesis, the homology modeling and moleculardynamics simulations are used to build 3D models of four proteins andinvestigate their structure properties in detail. Based on the 3D model, thedocking studies with ligand are performed. The main results are summarizedas follows:1. Homology modeling and PAPS ligand (cofactor) bingding study ofbovine phenol sulfotransferaseSulfate conjugation is mainly catalyzed by cytosolic sulfotransferase.The sulfotransferase enzyme can alter biology activities of numerouscarcinogenic and mutagenic compounds and play an important role inchemical defense mechanisms through sulfation.Using homology modeling and molecular dynamics methods, the 3Dstructure of bSULT1A1 is created and refined. With this model, a flexibledocking study is performed and the results indicate that PAPS is a morepreferred ligand than CoA, which is consistent with the experimental factsby Leach et al. From the docking studies, we also suggest that His108,Phe255, Phe142 and Tyr169 are four important determinant residues inbinding as they have strong interactions with the ligand.2. Theoretical study of 3-hydroxykynurenine transaminase3-Hydroxykynurenine (3-HK) is a metabolic intermediate of thekynurenine pathway. Several studies showed that 3-HK concentration iselevated in the brains of patients with AIDS-related dementia, Parkinson'sdisease, Huntington's disease, and hepatic encephalopathy. 3-HKT has anefficient mechanism for controlling the level of 3-HK through theconversion of the chemically reactive and potentially toxic to a chemicallystable XA.With the aid of the molecular modeling and molecular dynamicsmethods, the 3D model of 3-HKT is constructed. The docking study isperformed on the basis of 3-HKT 3D structure. The results indicate thathydrogen bond plays an important role for structure and function of 3-HKTand the residues of Pro211, Gln204, Ser77 and Lys205 are four importantdeterminant residues in the binding site and act as vital role in catalysis of3-HKT.3. Homology modeling and substrate binding study of Nudix hydrolaseNdx1 from Thermos thermophlius HB8Nudix proteins as housecleaning enzymes have been proposed todegrade compounds that either are deleterious to the cell or are normalmetabolites presented in excessive concentrations, and play protective,regulatory, and signaling roles in metabolism.With homology modeling techniques, molecular mechanics andmolecular dynamics methods, a 3D structure model of Ndx1 is created andrefined. Based on this 3D model, a flexible docking study is performed andthe result indicates that Glu46, Arg88, and Glu90 are three importantdeterminant residues in binding, as they have strong hydrogen bondinginteractions and electrostatic interactions with Ap6A. In addition, we furtherfind that three residues, Ser38, Leu39 and Glu46, coordinate enzyme-boundMg2+ ions in complex N–A. The result about Glu46 is consistent with theexperimental result by Iwai et al., and the other four residues mentionedabove may also play important roles in catalysis of Ndx1.4. Molecular simulation studies of Human inosine triphosphatepyrophosphataseInosine triphosphate (ITP) exists in all cells, and its intracellularconcentration is determined by the activity of cytosolic inosinetriphosphatase (ITPase;EC 3.6.1.19). ITPase acts as a putative role inrecycling purines trapped in the form of ITP and protecting the cell from theaccumulation of "rogue" nucleotides, such as ITP, dITP or xanthosinetriphosphate (XTP), that may be incorporated into RNA and DNA.By means of the homology modeling and docking methods, atheoretical study on ITPase is performed. The 3D structure of ITPase isgenerated based on 1B78. With this 3D model, the P32T substitution anddocking study are perfomed. The mutation results indicate that the P32Tsubstitution alters the α-helices of ITPase but the β-sheets are nearly notchanged, and the mutation induces the interaction energy increased betweenITPase and ITP, which is consistent with the conclusion predicted by Sumiet al. The docking results show that Arg178, Lys 19, Glu44 and Ser176 arefour important determinant residues in substrate binding.The structure information, the interaction energy of ligand with each ofthe residues in the active site of protein and the important determinantresidues in binding may be helpful for further experimental studies, and mayguide the selection of candidate sites for further experimentally ofsite-directed mutagenesis.