Protein Dynamics Studied By All-Atom Simulations Combined With Experimental Data

The proteins in solution are not static.They undergo both random thermal fluctuations near a given equilibrium state,and transitions between different substates.These motions are usually intricately associated with the function of the proteins.Therefore,it is very important to understand the dynamics of proteins for gaining insights into the mechanisms of many biological phenomena.Only the combination of structure and dynamics can accurately and properly describe the functional proteins(or biomolecules).Therefore,this thesis is centered on dynamics computations and structural studies of protein.Due to the low spatial and temporal resolution of traditional experimental methods,it is not enough to directly and accurately study the dynamic of proteins in solution.Theoretical calculation,especially molecular dynamics simulation,is an important tool for studying the microstructure and dynamics of proteins at the atomic level,which can make up for the deficiencies of experimental methods.In the first part of the thesis,we investigate the intrinsic structural instability of the second helix(all)of IFABP in comparison with other segments of the protein,using hydrogen-exchange nuclear magnetic resonance(NMR)spectroscopy,microsecond molecular dynamics simulations,and enhanced sampling techniques,and then elucidate the functional mechanism of its binding with ligands.While tertiary interactions positively contribute to the stability of helices in IFABP,the intrinsic unfolding tendency of all is encoded in its primary sequence and can be described by the Lifson-Roig theory in the absence of tertiary interactions.The unfolding pathway of all in intact proteins involves an on-pathway intermediate state that is characterized with the fraying of the last helical turn,captured by independent enhanced sampling methods.The simulations in this work,combined with hydrogen-exchange NMR data provide new atomistic insights into the functional local unfolding of FABPs.In the second part of the thesis,we propose a new method for screening the structural ensemble of flexible proteins based on small-angle X-ray scattering(SAXS)data.It iteratively runs multiple independent enhanced sampling simulations such as amplified collective motions and accelerated molecular dynamics,and an ensemble optimization method to drive the biomolecule towards an ensemble that fits the SAXS data well.In addtion,this method can also be applied to nucleic acid system.At present,the method has been verified by a protein and a nucleic acid system,i.e.,the tandem WW domains of formin-binding protein 21(FBP21-WWs)and the aptamer domain of SAM-1 riboswitch(free SAM-1 aptamer),respectively.In the protein system,we found that the two tandem WW domains of FBP21-WWs have both compact and extended conformations in solution according to the final structural ensemble;In nucleic acid system,orientations of the subdomains P1 and P3 of free SAM-1 aptamer,as well as their distances,are variable,which result in the opening/closing of the ligand-binding site.In summary,the dynamics of biomolecules,especially protein molecules,was studied by computer simulation combined with hydrogen-exchange NMR and SAXS.The results show that the computational methods and experimental techniques can produce good complementarity and are ideally used to study protein dynamics and to gain insights into observed biological phenomena at atomic resolution.