Multiscaled Theoretical Study And Computational Method For Biomolecular Conformational Dynamics

Biomolecules,such as proteins and nucleic acid,are the basic substances that constitute life organisms,and the main bearers of life activities.The proteins almost appear in every organic structure and cellular activity.The nucleic acids are responsible for depositing and delivering genetic information.The functionality of biomolecules has been thought to be derived from three dimensional structures,however,more and more scientific studies propose that the dynamic conformational changes play a key role in biological functions,such as protein folding,protein binding,molecular recognition,and transcriptional regulation.My work is mainly about exploring the conformational dynamics of biomolecules using molecular dynamics simulations based on the energy landscape theory.My work combines the theory with experiments to deepen our understanding of the functional mechanism of biomolecular systems.The main contents of this thesis contain the following two aspects:Firstly,we explore the multistate conformational dynamics upon ligand binding of a monomeric enzyme involved in pyrophosphoryl transfer.Biomolecules are generally not static three-dimensional structures under physiological conditions,but can adopt multiple conformations.The dynamic conformational changes play an important role in substrate recognition and the functionality of enzymatic catalysis.HPPK(6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase)is a small and stable protein with 158 residues.It catalyzes the transfer of pyrophosphate from ATP to 6-hydroxymethyl-7,8-dihydropterin(HP),leading to the biosynthesis of folate,a vitamin essential for all forms of life.In this work,we studied the structures of three states of HPPK to explore the conformational transition mechanism.We extended our previous structure-based model by introducing explicit ligands,which were typically ignored or implicitly considered in most SBMs.We revealed the intrinsic conformational fluctuations between the apo and open states of HPPK.The holo state can be induced upon the ordered ligand binding with ATP first.We uncovered the underlying mechanism by which major induced fit and minor population shift pathways coexist upon ligand binding by quantitative flux analysis.Additionally,we pointed out the structural origin for the conformational changes and identified the key residues as well as contact interactions.We further explored the temperature effect on the conformational distributions and pathway weights.It gave strong support that higher temperatures promote population shift,while the induced fit pathway is always the predominant activation route of the HPPK system.These findings will provide significant insights of the mechanisms of the multistate conformational dynamics of HPPK upon ligand binding.Secondly,we explore the mechanism of the coupled folding and binding in the RNA recognition by intrinsically disordered protein DCL1-A.Intrinsically disordered proteins(IDP)are a class of naturally abundant proteins and protein regions that lack well-defined three-dimensional structures in their free forms under physiological conditions.Such IDPs play essential roles in various biological functions,frequently related to signaling,molecular recognition,cell regulation,and closely implicated in some human diseases.A number of experimental data suggested that the unbound IDPs often transiently acquire the secondary structures present in the well-ordered complexes,that is,they are not totally unfolded random coils.Since IDPs can fold into ordered structures after engagement with their interaction partners,the binding process from isolated unfolded states towards the well-structured native bound state involves significant disorder-to-order transitions.However,the mechanisms of the coupled binding and folding are not yet well understood.Although we have seen impressive progress in biophysical techniques in recent years,it is still challenging to obtain a detailed description of the intrinsic flexibility of the disordered structures and of the mechanism of the coupled folding and binding,due to the limited spatial and temporal resolution of these measurements.Here we have developed a coarse-grained structure-based model with consideration of electrostatic interactions to explore the mechanism of the coupled folding and binding.Our approach led to remarkable agreements with both experimental and theoretical results.We quantified the global binding-folding landscape,which indicates a synergistic binding induced folding mechanism.We further investigated the effect of electrostatic interactions in this coupled folding and binding process.It reveals that non-native electrostatic interactions dominate the initial stage of the recognition.Our results help improve our understanding of the induced folding of the IDP DCL1-A upon binding to dsRNA.Such methods developed here can be applied for further explorations of the dynamics of coupled folding and binding systems.