Application Of MM/GBSA-based Interaction Entropy Method On The Protein-protein And Protein-Nucleic Acid Systems

The binding mechanisms of the protein-micromolecule,protein-protein and protein-RNA interactions are very instructive for the understanding of physiological processes,explaining of diseases and designing of new drugs.Although experimental methods can provide some information on the interactions between protein and ligand,it is always time-consuming,material-wasting and cash-demanding.Theoretical and computational calculations have shown their advantages in scientific research fields with the development of computer power.Molecular dynamics simulations,quantum chemical calculations and molecular docking have been established to uncover the bindings details of biological complexes with acceptable accuracy.High efficiency and low cost are the great advantages of calculation methods compared with experimental means.One of the most difficult and challenging work in the computational and theoretical calculations on the binding free energy of large biomolecular systems is the treatment to binding entropies and solvent models.Traditional methods,like Normal Mode Analysis,have many limitations and uncertainty.In order to solve this problem,our group have developed the Interactional Entropy(IE)methods to quickly and accurately calculate the entropy contributions to binding free energies.Combined with MM/PB(GB)SA method and alanine scanning(AS),both the contribution of single residue and the total binding free energy of biomolecular systems can be calculated.In this thesis,MM/GB/ASIE and other structure-based methods are applied to explore several protein-protein and protein-RNA interactions which are very helpful for the promotion of tumor therapy and the application to the researches on genetics and evolution.The second chapter of this thesis applies the MM/GB/ASIE method to detect the binding mechanisms of PD-L1 and its monoclonal antibodies(mAbs).The PD-L1 mAbs are very promising immunotherapy drugs for many cancers.This study calculated the important residues of 5 PD-L1/mAb systems and analyzed their binding mechanisms to their mAbs.Our results show that PD-L1M115 and PD-L1Y123 are two relatively important hotspots in all the five PD-L1/mAb binding complexes.It is also found that important residues of mAbs binding to PD-L1M1 15 and PD-L1Y123 are similar to each other.The results of computational alanine scanning are compared to the experimental measurements that are available for two of the mAbs(KN035 and atezolizumab).The calculated alanine scanning results are in good agreement with the experimental data with the correlation coefficient of 0.87 for PD-L1/KN035 and 0.6 for PD-L1/atezolizumab.Our computation is also compared with other free-energy-predicting method,which indicates a more reliable and stable result shown by MM/GB/ASIE.Our present work provides important insights for the designs of new mAbs targeting PD-L1.In the third chapter of this thesis,we calculated the binding free energy contribution of residues in two PD-1/mAb systems by MM/GB/ASIE methods.PD-1 mAbs are also important treatments for cancers.The comparation between the predicted hotspots and the important residues in PD-1/PD-L1 complex shows that pembrolizumab combines with PD-1 in a way similar to PD-L1,while nivolumab combines with PD-1 in a more different way by N-loop.PD-1K131 is the only hotspot shared by the two PD-1/mAb complexes.It is also found that key residues of mAbs binding to PD-1K131 are similarly dominated by the Van der Waals(VDW)energy.Furthermore,the electrostatic contributions of hotspots on both the monoclonal antibodies are small,which suggests that we can consider increasing the electrostatic energy contribution of monoclonal antibodies to improve the binding ability of antibodies.In the fourth chapter of this thesis,the ASIE method was adjusted and promoted to quantitatively analyze the free energy contributions of the binding pocket residues in the complex of Mmil proteins and its specific binding site,DSR(determinant of selective removal)motif on mRNA.Previously,ASIE method was rarely applied to the systems containing nucleic acids,because nucleic acids are biological molecules with high electrostatic energy,and its calculation accuracy was lower than that of macromolecular system with low electrostatic energy.Therefore,we determined the force field parameters and GB models which were suitable for nucleic acid and protein in this research.Furthermore,we used the optimized MM/GB/ASIE method to quantitively predict hotspots in the Mmil YTH/DSR motif complex and analyzed the mechanism of the vital specific binding.We found that a packed hydrophobic groove was formed by ?-? stackings between the hydroxyphenyl groups of multi TYRs and aromatic rings in nucleotide acid bases.Besides,a smaller hydrophobic core surrounded by 4 basic hotspots was formed to hold the 5'-terminal of RNA,and a basic clip was formed to clamp the RNA 3'-terminal.Good consistency was revealed between the calculation results and experimental data except an experimental warm spot YTHS333,whose contribution detected by traditional one-trajectory ASIE was little.We used the double-trajectory ASIE method to explain that the reason for the false negative was the conformational changes in the YTHS333 alanine mutant type,which was mutually verified by the experiment.By adjusting and optimizing the traditional ASIE method,we expand its application scope to protein-nucleic acid systems,which provides strong help for the study of many important physiological processes involving nucleic acid and the design of nucleic acid drugs.