The Computational Simulation Study On The Binding/Unbinding Mechanism Of Fatty Acid Binding Protein And Ligand

Protein is the main undertaker of biological activities and plays key roles in the growth,development and evolution of life.In many cases,proteins need to interact with ligands to perform corresponding functions.Studying of the interaction between protein and ligand is not only helpful to reveal the influence of ligand binding on the protein structure,but also to understanding of protein function and many biological regulatory mechanisms,and has important guiding significance for drug research and development.As a carrier protein,fatty acid binding protein(FABP)binds to fatty acids in cells and plays the significance role of transporting fatty acids.As the main energy source of the body,fatty acids can regulate immune response and inflammatory response,promote cell differentiation and apoptosis,and inhibit tumor growth.The molecular mechanism of the binding of fatty acids to FABP is of great significance for understanding the function and regulation of FABP,as well as for understanding the transport mechanism of ligands and drugs in cells.The fatty acid binding pocket is located inside the FABP.The result shows that there is no significant difference between the crystal structure of ligand-bound FABP(holo-FABP)and the ligand-free FABP(apo-FABP).It is difficult to elucidate the binding and dissociation mechanism of fatty acids in FABP through the static structure.Molecular dynamics simulation can effectively derive the dynamic change process of protein structure and the molecular mechanism of ligand regulation.In this paper,the structure of H-FABP and its kinetic and thermodynamic changes with ligand stearic acid were studied at the atomic level by the conventional molecular dynamics simulation method and enhanced sampling technique.The dissertation is organized as follows:First of all,to introduce the background of the interaction between proteins and ligands,especially the research status of molecular dynamics simulation,especially the enhanced sampling method,and the related research of FABP.In Chapter 2,the observation of ligand-binding-relevant open states of fatty acid binding protein by molecular dynamics simulations and a Markov State Model.In this chapter,conventional molecular dynamics simulation and Markov state model(MSM)were performed to characterize the structural properties of nativelike intermediate states.Based on the MD simulations and MSM analysis,several;"open" intermediate states were observed.Ligand binding would stabilize the "closed" structure of H-FABP,which would facilitate the transportation of the fatty acids.And there are two kinds of ligand-bound "open" structures,which might relate to different ligand releasing pathways.Our results provide atomic-level descriptions of the binding-relevant intermediate states and could improve our understanding of the binding mechanism.In Chapter 3,the molecular dynamics simulation of ligand dissociation pathways in H-FABP.Firstly,it was found that there are two pathways for the ligand to dissociate from H-FABP by full atom molecular dynamics simulation.Then,the free energy surface of the binding process of ligands was obtained by the bias exchange Metadynamics.In addition,the ligand-binding-relevant structures were found.The results show that there are two pathways for the ligand binding to or unbinding from H-FABP.In Chapter 4,the simulation of the best dissociation path and dissociation constant of the FA in H-FABP.The kinetic information of the dissociation of the ligand in H-FABP was studied by combining with conventional molecular dynamics(cMD)simulations and enhanced sampling technologies.Moreover,the optimal dissociation path was determined.There are significant differences in the interaction forces that ligands need to overcome to dissociate from different portals.The koff of portal 1 was larger than the value of the portal 2,indicating that the ligand could be more easily dissociated through the portal 1(Figure 1).These studies provide some theoretical basis for the design of FABP-related drugs.Figure 1 The ligand dissociation pathway of H-FABP.The dynamic portal regin wagcolored in yellow,and the ?D and ?E were colored in blue and the ligand dissociation path is marked with a red arrow.A:The portal 1;B:The portal 2.In Chapter 5,the summary and prospect.Summarize the research content of this paper,and look forward to further problems and research directions.