Applications Of Molecular Dynamics Simulations In Research About Some Important Proteins

Rapid advances in computer science and technology provide unlimitedpossibilities for the development of other related disciplines. In many areas likebiology, chemistry, physics, etc., molecular dynamics simulation technology showingmore powerful capabilities based on the devolpment of the computer science andtechnology. With the help of molecular dynamics simulation technology, on one handwe can observe the dynamic process of protein structure change at the molecular level,on the other hand, we can also use this technique to gain a clearer understanding ofthe energy information in the relevant reaction. I In this dissertation, we investigatedseveral important biological macromolecules by means of molecular dynamicssimulation method, mainly included the following parts:1. Exploring the Molecular Basis of Fosfomycin Induced Structural Change inFosfomycin Resistance Kinases FomAFosfomycin resistance kinases FomA, one of the key enzymes responsible forbacterial resistances to fosfomycin, has gained much attention recently due to theraising public concern for multi-drug resistant bacteria. Using moleculardocking followed by molecular dynamics simulations, our group illustrated theprocess of fosfomycin induced conformational change of FomA. The detailed roles ofthe catalytic residues (Lys18, His58and Thr210) during the formation of theenzyme-substrate complex were shown in our research. The organization functions ofGly53, Gly54, Ile61and Leu75were also highlighted. Furthermore, the cation-πinteraction between Arg62and Trp207was observed and speculated to play anauxiliary role in the conformation change process of the enzyme. This detailedmolecular level illustration of the formation of FomA·ATP·Mg·Fosfomycin complexcould provide insight for both anti-biotic discovery and improvement of fosfomycinin the future. 2. Insights Into the Urea Binding and K166R Mutation Stabilizing Mechanismof TlpBThe chemoreceptor TlpB, which has being demonstrated to respond for pHsensing function, is crucial for survival of H. pylori in host stomach. Urea wasproposed to be essential for TlpB’s pH sensing function by binding with thePer-ARNT-Sim (PAS) domain of TlpB. Additionally, K166R mutation of the TlpBprotein has also been proven to have similar effect on TlpB pH sensing as ureabinding. Although X-ray crystallographic studies have been carried out forurea-bound TlpB, the molecular mechanism for the stabilization of TlpB induced byurea binding and K166R mutation remains to be elucidated. In this study, moleculardynamics simulations combined with principal component analysis (PCA) for thesimulation results were used to gain insights into the molecular mechanism behind thestabilization of urea on TlpB protein. The formulation of H-bonds and salt-bridgessurrounding Asp114, which induced by both urea binding and K166R mutation ofTlpB, were important to the stabilization of urea. The similarity between the ureabinding and K166R mutation, as well as their differences has been explicitlydemonstrated with molecular-leve computer simulations. The findings may pave theway for the further researches of the TlpB.3. Theoretical Studies on Substrate Binding Mode and Regioselectivity ofHuman CYP2C9with S-and R-warfarinCytochrome P450(CYP)2C9, a member of the2C subfamily of CYPs, playsimportant role in the oxidative metabolism of amount of current clinical drugs.CYP2C9shows the substrate regioselectivity toward warfarin. The currently availableX-ray structure of CYP2C9-S-warfarin complex (PDB ID:1OG5) shows anon-productive orientation of the S-warfarin bound in the active site of CYP2C9. Aseries of investigations including automatic docking, molecular dynamics (MD)simulation, combined with tunnel analysis and the MM-GB/SA calculation, identifieda6-7-hydroxylation state of the substrate binding mode in the re-dock complexstructure, as well as the “metastable state” in the crystal structure. In addition, thecomparison of the CYP2C9binding to S-warfarin and R-warfarin shows the structuralfeatures relevant to the substrate regioselectivity of CYP2C9. According to100nsMD simulations, the key residues that, in the active binding site, particularly Phe cluster residues, are proposed to play indispensable role in the stabilization ofsubstrates. The investigation of CYP2C9–substrate binding modes provides detailedinsights into the structural features of human CYP2C9toward warfarin at the atomiclevel, and will be valuable information for drug development.