Molecular Dynamics Simulations On Intrinsically Disordered Proteins By Enhanced Sampling And NMR Restraints

Intrinsically disordered proteins(IDPs)are a class of protein which lacks well defined three-dimensional structure under native states while possessing normal biological function.They play an important role in various processes such as molecular recognition,signal transduction and cell regulation.IDPs involved in various human diseases,such as cancer,neurodegeneration,cardiovascular diseases and type 2 diabetes mellitus.IDPs is characterized with structural ensembles,and obtained accurately the structural ensembles of IDPs is of great significance for understanding protein functioning and diseases pathogenesis.Because of high dynamic nature of IDPs,it is very difficult to determine their complete structure ensemble by current experimental technologies.With the increasing power of computers,as well as the improvements in force fields,molecular dynamics(MD)simulation has been providing increasing support for the study of protein structures,ligand binding,and kinetic and thermodynamics properties.However,it meets two basic challenges to study the disordered proteins:the insufficient of configuration sampling and the inaccuracy of force fields.Concerning this issue,the integrating of the enhanced sampling technologies and experimental data,especially the nuclear magnetic resonance(NMR)data,in the molecular simulations could be improved the simulation accuracy greatly.In this study,the structure ensembles of a typical intrinsically disordered protein,islet amyloid polypeptide(IAPP)and ?-amyloid(A?42),were investigated by the unbiased molecular dynamics simulation,enhanced sampling without NMR data restraints and enhanced sampling with NMR chemical shift data,respectively.In addition,we also tested the prediction accuracy of the new disordered protein field ff14IDPSFF in IDPs.The main results are as follows:(1)The enhanced samplingtechnique could improve the sampling accuracy of IAPP and A?42,and the NMR restraints will further improve the simulation accuracy.(2)By compared with the non-amyloidosis of rIAPP,we speculated that the formation of helical structure on aggregation core and C-terminus(residues 20 to 37)rather than the N-terminal helix is the determinate factor for the IAPP aggregation.(3)The structures ensemble of A?42 obtained by ffl4IDPSFF force filed are better agreed with the experiments than the Amber99sb-ildn,but performed poorly in hIAPP.In both systems,there is a high propensity helix structure in Amber99sb-ildn force field.In contrast,the ff14IDPSFF force filed prefers ?-sheet and random coil structure.The paper is divided into six parts.The first chapter is introduction.It mainly introduces the intrinsically disorderly protein,including the structural properties,physiological function,human-related diseases and current challenges in experiments and computational simulation,and followd by a brief introduction to IAPP and A?42.The second chapter describes the main theory of molecular dynamics simulation,force filed,and some related data processing and analysis methods in this study.In chapter three,we tested the simulation accuracy of the IDPs force fields ff14IDPSFF in IAPP and A?42.In chapter four and chapter five,islet amyloid polypeptide(IAPP)and ?-amyloid(A?42)were investigated by the unbiased molecular dynamics simulation,enhanced sampling without NMR data restraints and enhanced sampling with NMR chemical shift data respectively.The structural ensemble of IAPP and A?42 was obtained,free energy surface was reconstructed and atomic resolution informationwas provided for further aggregation principle.The sixth chapter is the summary and prospect.