Study On Protein Allostery And Protein-ligand Interactions By Using Molecular Simulations

Proteins are essential biomolecules in the cell,which can fold into specific tertiary structures and play important roles in various cellular life processes.With the rapid growth of protein structure data obtained by the X-ray crystallography and cryo-electron microscopy technologies,the study of protein structure-function relationship has become a scientific problem of significance that needs to be solved in the field of molecular biology.Allosteric effect and protein-ligand interactions are important ways for the performance and regulation of protein functions.How to predict the allosteric pathway from protein tertiary structure and identify the key residues involved in protein-ligand interactions are important contents in the study of protein structure-function relationship.The researches on the above problems are helpful to reveal the molecular mechanism behind protein functions,and meanwhile,these studies could provide effective targets for protein engineering and drug design,which has important scientific significance and application value.In this thesis,based on the Elastic Network Model(ENM)and the theory of statistical physics,a non-equilibrium dynamics simulation method was developed to identify the allosteric pathway within protein structures.Besides that,an internal force distribution calculation method within proteins in response to external force perturbation was proposed to investigate the physical mechanism behind the allosteric regulation of protein mechanical stability.In addition,by using Molecular Dynamics(MD)simulation combined with molecular mechanics/generalized Born surface area(MMGBSA)method,the key residues and evolutionary mechanism for the interactions of severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)and norovirus(No V)with their receptors were explored.The main study contents of this thesis are as follows:Firstly,an ENM-based non-equilibrium dynamics simulation method was proposed to investigate the transduction pathway of allosteric signals within protein structures.In this method,the allosteric site in the protein was perturbed,and the propagation of perturbation energy was simulated in the normal mode space.Then,the simulation results were transformed into the Cartesian coordinate space to identify the allosteric signal propagation pathway in protein structure.The effectiveness of the proposed method was verified by using two protein systems,i.e.,myosin and the third PDZ domain of PSD-95,as case studies.According to the excitation time and response intensity of the residues in the protein,the allosteric signal transduction pathways were identified for these two studied proteins,and the prediction results were consistent with experimental observations and MD simulations.Besides that,our study also demonstrated that the proposed method was more efficient in revealing the specific anisotropic allosteric pathway than the conventional cross-correlation dynamics analysis method.Secondly,based on ENM and a linear response approach,an inter-residue force distribution calculation method was developed,and the impact of ligand binding on the mechanical stability of GB1 and CBDChe A proteins were studied by using the proposed method.In this method,the N-and C-terminus of the protein were stretched with external forces,and then the deformation and internal force distributions within the protein in response to the external forces were calculated under linear approximation.The changes of intra-protein force distributions between the systems with and without ligand binding were analyzed and the long-range coupling between the ligand-binding site and the force-resistant region was revealed.Based on these analyses,a physical mechanism behind the enhancement of the mechanical stability of GB1 by the binding of ligand was proposed.Our studies provided a valuable theoretical analysis method for the regulation of protein mechanical stability and the design of biosensors.Finally,the interactions of SARS-CoV-2 and No V with their host cell receptors were investigated by using MD simulations and MMGBSA method,and the key residues involved in the interactions were revealed.For SARS-CoV-2,the binding free energy of the receptor binding domain of spike protein with its receptor human angiotensin-converting enzyme 2and with several neutralizing antibodies were calculated,and the influences of the mutation of the key residue E484 K on the binding affinities were analyzed.Our calculation results showed that the binding affinities were significantly changed due to the reversal of residue charges and the conformational adjustments in the binding interface.Then,based on these calculations,a mechanism for the improvements of the transmissibility and immune-evasive capability of SARS-CoV-2 was proposed.For No V,the evolution of the binding free energy between the capsid protein VP1 of various No V strains and the receptor histo-blood group antigens was evaluated,and the contribution of each residue to the binding free energy was calculated by using energy decomposition method.Our simulation results showed that the evolution of the virus led to conformational changes in the receptor binding pocket,which tightened the binding affinity of VP1 with the receptor HBGA.Based on these analyses,the molecular mechanism for the improvement of the infectivity of No V was proposed.