Molecular Simulation Of Protein Functional Dynamics Modulated By Mechanical Force

Cell adhesion is an important cellular and molecular biological process that plays a key role in the process of bacterial growth and reproduction,tissue structure maintenance of multicellular organisms,and immune response.Cell adhesion pro-cesses are typically achieved by non-covalent binding of receptor proteins on the cell surface to small molecule ligand/protein or cell interstitium on the surface of adj acent cells.Unlike normal adhesion,cell adhesion needs to meet more complex biological requirements and is dynamically regulated by a variety of factors.In particular,the cell adhesion process generally relies on the adhesion-enhancing phenomenon caused by a tensile force,a so-called catch-bond effect.The important biological and medical significance of cell adhesion under the control of mechanical signals has prompted people to begin to think about the physical basis of the cell adhesion process response to mechanical signals and the microscopic molecular mechanism generated by the catch-bond effect,attracting physical,chemistry,and biological researchers.At present,the research on the regulation of cell adhesion by mechanical signals mainly uses experimental methods,and the related computer simulation research is still very limited.In this thesis,the microscopic physical mechanism of the binding of leukocyte surface receptor protein CD44 to ligand molecules is studied by coarse-grained molecular simulation.In addition,folding assembly of single-stranded DNA on the corresponding binding protein is critical for transcription,replication,and repair of DNA,but the molecular mechanisms remain unclear.This paper will also explore the folding assembly process of single-stranded DNA on binding proteins and its regulation by mechanical external forces.The details are as follows:1.Study on the mechanism of the catch-bond effect of cell adhesion protein CD44 regulated by mechanical force..The immune response requires leukocytes to be enriched at the site of infection.The rolling of leukocytes on the inner wall of blood vessels is a critical step in achieving enrichment from the blood to the site of infection and is dependent on CD44-mediated cell adhesion.It has been found that the rolling motion of such leukocytes depends on the pulling force generated in the fluid environment(blood flow,etc.).In a static environment,leukocytes are mainly free-moving,limiting their rolling adhesion to the vessel wall.At a certain flow rate,leukocytes tend to adhere to the vessel wall and undergo rolling motion.It is speculated that the rolling motion caused by this fluid pull may be related to the CD44-mediated catch-bond effect,but the related microscopic physical mechanism is still unclear.Based on the protein energy surface theory and multi-well model,this paper establishes a coarse-grained model describing the allosteric motion of protein molecules and ligand binding under mechanical control,and uses molecular dynamics simulation to study the conformational motion of CD44 and binding or dissociation processes of corresponding ligand molecules under mechanical external force.The simulation results show that with the increase of mechanical external force,the C-terminal helix of CD44 unfolds and separates from the core domain of CD44,which leads to the conformational change of CD44 core domain and the increase of ligand molecule' s affinity,showing catch-bond effect.As the mechanical external force continues to increase,the ligand molecule affinity decreases.Therefore,the molecular simulation results of this paper support the allosteric mechanism of the CD44 receptor protein catch-bond effect,which can explain the phenomenon that the observed leukocytes tend to roll on the inner wall of the blood vessel in the fluid environment.The relevant results are significant for understanding the cellular immune response mechanism.2.The folding assembly dynamics of single-stranded DNA in binding proteins and its mechanical regulation.Single-stranded DNA(ssDNA)produced during transcription,replication,and repair processes of DNA needs to bind to other proteins(binding proteins)to maintain stability and avoid damage by hydrolysis.It has been found that there are multiple binding models for ssDNA and binding proteins,and they are regulated by external factors such as mechanical tension and salt concentration,but the related molecular mechanisms remain unclear.In this paper,we attempt to establish a coarse-grained model describing the interaction between ssDNA and binding protein,and based on molecular dynamics simulation,folding assembly and its mechanical regulation of ssDNA are studied on Ecoli single-stranded DNA binding protein(SSB)and replication protein A(PRA).Molecular simulation can successfully realize the folding assembly of ssDNA,and the resulting composite structure can be well matched with the experimental results.In addition,through the depiction of the free energy surface,it is found that the ssDNA-SSB complex changes among multiple binding modes as the tensile force increases,which explains the experimental data to some extent.The content of this thesis is as follows:The first chapter reviews the cell adhesion phenomenon controlled by mechanical force,the assembly kinetics of ssDNA,and the molecular simulation method.The second chapter gives the coarse-grained model of interaction between CD44 and ligand.And the molecular simulation results of the mechanism of the catch-bond effect;The third chapter gives the coarse-grained model of the interaction between ssDNA and binding protein and discusses the ssDNA folding and assembly process and its mechanical regulation;The fourth chapter is the paper summary and prospects for related research.