Molecular Dynamics Simulations Study On The Structural Featuresand Reactional Mechanisms Of Several Impotrant Proteins Related With Diseases

Protein conformation, which has been a research hotspot for humandiseases, is an important factor of protein properties. Recently, a series ofapproaches have been utilized to investigate the conformational changes underdifferent conditions, such as the pH environment, the mutation of someimportant residues, etc. Some of them have gained promising achievements, butit is still deficient in the detail researches at the atomic level.There are seven parts in this contribution. In Chapter I, we made an briefintroduction of the proteins and amino acids, some serious human diseases andthe proteins related with the diseases, the characters and the computationalmethods of the reactions catalyzed by enzymes. In Chapter II, we summarize thetheoretical methods used in this contribution, including the computationalmethods of the quantum chemistry, molecular mechanics, and moleculardynamics. In addition, other methods such as molecular docking, REMDmethod, and QM/MM method are also reviewed in this part. Then, we carried onthe theoretically investigations on the structural changes and properties of threedifferent kinds of protein systems in Chapter III to Chapter VII.1. Molecular dynamics studies of insect ordorant binding proteinpH-induced ligand releasing mechanismPart A: Constant pH molecular dynamics (CpHMD) and molecular docking studies of CquiOBP1pH-induced ligand releasing mechanismThe odorant binding protein of Culex quinquefasciatus (CquiOBP1),expressed on the insect antenna, is crucial for the investigation of trappingbaited with oviposition semi-chemicals and controlling mosquito populations.The acidic titratable residues pKa prediction and the ligand binding posesinvestigation in two systems (pH7and pH5) are studied by constant pHmolecular dynamics (CpHMD) and molecular docking methods. Researchresults reveal that the change of the protonation states would disrupt someimportant H-bonds, such as Asp66-Asp70, Glu105-Asn102, etc. The cleavage ofthese H-bonds leads to the movement of the relative position of hydrophobictunnel, N-and C-termini loops and pH-sensing triad (His23-Tyr54-Val125) inacid solution. Ligand MOP has lower affinity and shows different binding posesto protein CquiOBP1at pH5. This ligand may be released from another tunnelbetween helices α3and α4in acidic environment. However, it would bind to theprotein with high affinity in neutral environment. This work could provide morepenetrating understanding of the pH-induced ligandreleasing mechanism.Part B: Constant pH Molecular Dynamics (CpHMD) and mutation studies:Insights into AaegOBP1pH-induced ligand releasing mechanismAaegOBP1, isolated from the male and female antenna of yellow fevermosquitoes, may serve as crucial molecular targets for the development ofmosquitoes’ attractants and for the control of mosquito populations. Nowadayscrystal structures of AaegOBP1in the neutral environment have been obtained,whereas little research is focused on the conformational change of AaegOBP1inthe acid solution. In our study, the conformational change and the ligand boundposes in different solution pH were investigated using constant pH moleculardynamics (CpHMD) as well as mutation studies. Results demonstrate that theprotein changes dramatically in low pH solution and that the pH-sensing triad(Arg23-Tyr54-Ile125) plays an indispensable role in the structural stability and ligand binding. In addition, we have proved that the residue Arg23is the mostimportant one of the pH-sensing triad. This work could provide morepenetrating understanding of the pH-induced ligand-releasing mechanism.2. Insights into the folding and unfolding processes of wild-type andmutated SH3domain by molecular dynamics and replica exchangemolecular dynamics simulationsSrc-homology regions3(SH3) domain is essential for the down-regulationof tyrosine kinase activity. Mutation A39V/N53P/V55L of SH3is found to berelative to the urgent misfolding diseases. To gain insight, the human and gallusSH3domains (PDB ID:1NYG and2LP5), including58amino acids in eachprotein, were selected for MD simulations (Amber11, ff99SB force field) andcluster analysis to investigate the influence of mutations on the spatial structureof the SH3domain. It is found that the large conformational change of mutationsmainly exists in three areas in the vicinity of protein core: RT loop, N-src loop,distal b-hairpin to310helix. The C-terminus of the mutated gallus SH3isdisordered after simulation, which represents the intermediate state ofaggregation. The disappeared strong Hbond net in the mutated human and gallussystems will make these mutated proteins looser than the wild-type proteins.Additionally, by performing the REMD simulations on the gallus SH3domain,the mutated domain is found to have an obvious effect on the unfolding process.These studies will be helpful for further aggregation mechanisms investigationson SH3family.3. Molecular dynamics (MD) simulations and binding free energycalculation studies between inhibitors and type II dehydroquinase(DHQ2)Type II dehydroquinase (DHQ2) is the third enzyme of the shikimic acidpathway, and it has been the effective target for tuberculosis (TB). So far, developing multiple potent inhibitors of the DHQ2of Mycobacteriumtuberculosis (DHQ2-Mt) has been considered to be the new therapy to TB.Molecular dynamics simulations followed by molecular mechanicsgeneralisedBorn surface area were carried out to calculate the free binding energy and todetermine the affinity ability of the four chosen inhibitor molecules, L1, L2, L3and L4. Energy decomposition analyses show the electrostatic interaction andvan der Waals interaction of the ligands to every residue of the DHQ2-Mt. Theresults suggest that some important residues have different interactions with thefour ligands, such as Arg19and Tyr24. These interactions may have an effect onthe ligand binding affinity. The binding affinity of monosubstituted inhibitor ishigher than that of disubstituted inhibitor, due to some important interactionswith the DHQ2-Mt residues. These computational works will be significant tothe theoretical research in the future.4. Insights into the drug resistance induced by the BaDHPS mutations:molecular dynamic simulations and MM/GBSA studiesDihydropteroate synthase (DHPS) is essential for the folic acid biosyntheticpathway in prokaryotes; the mutation forms for DHPS are found to be relative tothe urgent drug resistance problems. In our study, the Bacillus anthracis DHPS(BaDHPS) was selected for molecular dynamics and binding free energy studiesto investigate the biochemistry behaviors of the wild-type and mutation formBaDHPS proteins (D184N and K220Q). It is found that the conformationalchange of the ligand dihydropteroate sulfathiazole binding site in mutationD184N and K220Q systems is mainly attributed from the Loop1, Loop2, andLoop7regions, and the binding free energy of these mutation systems is lowerthan that of the wild-type system. Additionally, some important hydrogen bondsof the mutation systems are disrupted during the simulations. But the shorteningof the distance between residue Thr67and the ligand would cause significant change of the binding pose in the K220Q system. These studies of DHPS familywill be helpful for further drug resistance investigations.5. Insights into the phosphatase and the synthase activities of humanbisphosphoglycerate mutase: a quantum mechanics/molecularmechanics simulationBisphosphoglycerate mutase (BPGM) is a multi-activity enzyme. Its mainfunction is to synthesize the2,3-bisphosphoglycerate, the allosteric effector ofhemoglobin. This enzyme can also catalyze the2,3-bisphosphoglycerate to the3-phosphoglycerate. In this study, the reaction mechanisms of both thephosphatase and the synthase activities of human bisphosphoglycerate mutasewere theoretically calculated by using the quantum mechanics/molecularmechanics method based on the metadynamics and umbrella samplingsimulations. The simulation results not only show the free energy curve of thephosphatase and the synthase reactions, but also reveal the important role ofsome residues in the active site. Additionally, the energy barriers of the tworeactions indicate that the activity of the synthase in human bisphosphoglyceratemutase is much higher than that of the phosphatase. The estimated reactionbarriers are consistent with the experimental data. Therefore, our work can giveimportant information to understand the catalytic mechanism of thebisphosphoglycerate mutase family.