Assembly And Regulation Mechanism Of Membrane Protein System By Molecular Dynamics Simulations

The cell membrane is not only the fundamental part for cells to exist independently,but also the carrying platform for many life activities.Important processes such as signal transduction,substance exchange,and immune response depend on the self-assembly process of related proteins on the cell membrane.The dimer formation depending on the transmembrane regions is a common way in membrane protein self-assembly.The formation,maintenance,and transformation of the dimer structure not only respond to the conformational changes of the juxtamembrane regions of proteins,but also directly participate in the signal transduction processes.The membrane acts as the main body where the membrane proteins exist or attach upon.The membrane microenvironment,which is formed by diversity of membrane components and their structural heterogeneity,is not only the primary factor to influence the membrane protein association,but also the determinant for the targeting of self-assembling peptide drugs.Due to the technological limitations on measurement accuracy,and safe of protein expression,extraction under experimental conditions,traditional techniques are still difficult to provide detailed structural information of proteins under living cell conditions.The method of molecular dynamics simulation has been widely used in the related fields because of its high accuracy and dynamic visualization.Depending on further integration of neighboring atoms,the coarse-grained force field can not only ensure the accuracy of simulations,but also effectively expand the system size and simulation timescale,thus enable provides high-throughput,near-atomic level dynamic simulation results.In this dissertation,based on existing experimental results,we used molecular dynamics simulations to construct membrane models,to explore the self-assembly and conformational transition of membrane proteins,association of heterologous membrane proteins mediated by membrane environment,and interaction details between the bioactive peptides and membranes.We took the membrane proteins as the research thesis in this study.By constructing a variety of membrane models,series of analytical methods are employed to comprehensively explain the self-assembly characteristics,structural transition,lateral translocation,enzyme recognition,and cell damage associated with the biological function of membrane proteins.The main conclusions are as follows:1)Combining coarse grained model and all-atom model,the dimeric conformations and transition mechanisms during the dimerization process of the transmembrane domain of tyrosine kinase receptor EphA2 were analyzed.We found the assembly of transmembrane region can form two types of dimeric conformations.One is the left-handed parallel conformation controlled by the L535xxxG539xxA542xxxV546xxL549xxxG553 and FF557,which are consistent with the NMR results.The N-terminal G540xxxG544 is involved in the formation of the right-handed 20° mode,in accordance with previous experimental results.In addition,.a stable "riveting" structure can be established between FF557,thus it exhibits the comparable ability to control the left-hand parallel configuration as the upstream region.Moreover,it acts as a link of the conformational transition.At the same time,H559 is found to be favorable for the stability of the left-handed conformation by anchoring the polar head group of the membrane.The simulation results revealed the structural information of the dimerization of the transmembrane domains,which can enhance our understanding of membrane mediation and conformational transformation.It is hopeful to provide guiding information to understand the biological function of transmembrane proteins.2)By constructing a two-phase membrane model containing the lipid rafts,we further investigated the assembly of amyloid precursor protein transmembrane segment(C99)mediated by lipid rafts and the resultant amyloid pathways.The lipid raft compartment not only inhibits the dimerization of C99,but also affects its dimeric conformations.The mechanism includes the competitive binding of cholesterol molecules on the packing residue sites of C99,and the specific anchoring effect of the saturated phospholipid molecules in lipid rafts.Under the influence of lipid rafts,the enzyme recognition accessibility of the key amyloid site can be changed,thus potentially influence the pathway of enzymolysis.The results comprehensively expounded the intrinsic relationship of cholesterol,lipid rafts,and amyloid degradation pathways,which is helpful to gain understanding for the pathogenesis of Alzheimer's disease.3)The membrane microenvironmen plays an important role in the binding process between the transmembrane protein and the cytoplasmic protein receptor.By comparing the membrane environments with different lipid components in the inner layer,negatively charged lipid molecules is necessary for the cytosolic protein receptors to attach on the inner membrane surface.It is noteworthy that under the same charge concentration,phosphatidylinositol-3,4 diphosphate(PIP2)can remarkably promote the associating efficiency between the transmembrane protein and cytoplasmic receptor protein on the membrane,and form a more stable heterologous protein complexes.PIP2 can be clustered around the protein depending on the electrostatic force,and the final binding of the proteins is governed by further fusion of the PIP2 clusters.The results revealed the molecular regulation of the specific lipids on protein interaction in the cytoplasmic membrane surface area,which is favorable for further understanding the regulation mananism of membrane environment.4)The interplay of membrane and protein on the membrane surface is also reflected by self-assembling of bioactive peptide in disrupting the membrane structure.By constructing a membrane model with the characteristics of pathogenic cells,we found that the self-assembling peptide PTP-7b needs to be co-aggregated with lipid molecules under certain concentration conditions after being embedded in the membrane,resulting in obvious membrane deformation.PTP-7b exerts bioactive function dependent on the leading assembly of the membrane-embedded peptides and continued traction of the periplasmic polypeptides.It finally forms a "cage"-like peptide structure that pulls lipid molecules out of the cell membrane matrix,demonstrating a novel model of cell membrane lysis.The driving force of PTP-7b self-assembly to destroy cell membranes is derived from histidine interaction on one hand,it is also regulated by the amphiphilic properties that help it firmly attach to the membrane.The revealed information fully described the available conditions,contacting model and molecular mechanisms of lytic peptides in disrupting membranes.It is hopeful to guide the following design and development of the bioactive peptides.Overal,this study fully elucidated the intrinsic mechanism of membrane protein interaction,and discussed the implication with the biological function.The molecular information disclosed in this dissertation,such as the interaction details,transition mechanism,and acting mode,can provide references for the following research in related fields.