Molecular Simulation Study On The Effects Of Post-translational Modification On Protein Structure And Function

Objective: Protein post-translational modification acts as an effectively means to regulate protein structure and function,and plays an important roles in various physiological and pathological processes.It also contributes to the formation of cellular biomarkers in Alzheimer’s disease.The studies have found that the deamidation of N27 residue could significantly affect Aβ42 polymerization ability,but the specific mechanism is not yet clear.This study aims to investigate the effect of deamidationof N27 on the structure of Aβ42 monomer from the molecular structure level,and to reveal the molecular mechanism of the deamidation modification of N27 to inhibit Aβ42 polymerization.Additionally,the post-translational modification of histone is also an important type of epigenetic regulation,and the interaction between different post-translational modifications of histone can change to some extent the intensity and specificity of regulation The acetylation of Lysine 14 on histone H3(H3K14ace)is associated with transcription by binding to BPTF-BRD domain.Due to their weak recognition,other modifications can influence the association between H3K14 ace and BPTF-BRD.This study explores the effect of H3K4me3,an other common post translational modification,on the binding of H3K14 ace to BPTF-BRD,and to reveal the potential mechanism for this effect at the molecular structure level.Methods: In order to analyze the molecular mechanism of N27 deamidation modification inhibiting Aβ42 polymerization and the effect of H3(1-17)K4me3 on the interaction of K14 ace and BPTF-BRD protein.Two simulation systems were constructed,the model of unmodified Aβ42 monomer and modified Aβ42 monomer with deamidation at N27 and the model of complex between single H3 modification(H3K14ace)and BPTF-BRD and between two H3 modification(H3K4me3and H3K14ace)and BPTF-BRD.In this study,the modified and unmodified protein structure were obtained from Vienna-PTM website and PDB database,respectively.For the Aβ42 monomer system and the H3-BPTF protein complex system,performing 100 ns and 50 ns balance simulation respectively,using conventional molecular dynamics simulation.Use GROMACS built-in module program,Python script and MM-PBSA method to analyze the structure and interaction of proteins in the equilibrium trajectory.Results: The results that analysis of the structure and residue interactions using molecular dynamics simulation methods suggested that the deamidation modification of N27 changed the residues’ flexibility of Aβ42.Among them,the flexibility of residues in CHC and Turn region decreased,and the flexibility of residues in CTR(I31-V39)and NTR(S8-Q15)region increased.The secondary structure of modified Aβ42 monomers mainly consisted of random coils and turn structures.The tendency of NTR and CTR regions to form β-sheet structure decreased,and the distance between them increased.The distance between D23 and K28 also increased to 1.03 nm,resulting in the destruction of the conditions for the formation of salt bridges between them.In addition,the deamidation modification of N27 weakens the interaction between Aβ42 residues,especially the van der Waals interaction between residues,and the number of residues with strong interactions is significantly reduced.The cluster analysis of Aβ42 structure suggested that the number of clusters of modified Aβ42 structure increased,and all the conformations were loose and flexible,with a rich random coil structure,but no β-sheet structure.The results that analysis of the structure and residue interactions of H3 and BPTF protein complex using molecular dynamics simulation methods suggest that K4me3 can promoted the structural stability of the K14ace-BRD complex and inhibit the flexibility of the BRD region and most residues of the H3 short peptide.And changing the contact between the residues,which decreases the distance between residues 8-17 of H3 short peptide and residues 90-106 and 48-162 of BRD region,increases the distance between residues 1-8 and residues 95-110.This makes K14 more closely contact with residues in the BRD domain,while providing a greater chance of interaction.The binding energy analysis of H3 and BRD domain residues suggested that K4me3 can promote the interaction between K14 ace and BRD domain,and enhance the recognition of K14 and BRD domain residues.The main mode of interaction between them is that there is a strong interaction between K4 and PHD,which promotes H3 to be in a stable structure.In turn,the number of residues in the BRD domain with a distance K14 of 8 ? increased,and K14 formed relatively stable hydrogen bonds with S152 and P96.Conclusions: Deamidation modification can induce the structural changes of Aβ42 monomer and destroy the salt bridge formed between D23-K28.As a result,these changes inhibit the formation of β-turn structure in Turn regionand of antiparallel β sheets between the C-terminal and N-terminal regions,which consequently weakens the intra-peptide interaction between the residues on these regions.In addition,the formation of D23–K28 salt bridges plays an important role in promoting the polymerization of Aβ42.Therefore,the deamidation modification of N27 caused the decrease of polymerization ability.H3K4me3 can enhance the binding of H3K14 ace into BPTF-BRD domain.The potential reason for such effect is the stable binding of K4me3 to PHD domain.It promotes the stable structure of H3 and makes a more stable binding of K14 ace into BRD domain by formation of hydrogen bonds between K14 and S152 and P96.