Molecular Dynamics Simulations Of Protein Dynamics And High Efficiency Sampling Methods

As the main participants of biological activities,proteins attract widespread concerns from physicists,chemists,biologists and so on.Molecular dynamics(MD)simulations can provide conformational and dynamic information with both high spatial and time resolution,thus become a very important research technique.However,owing to the limitation of computing resource,relatively accurate all-atom MD simulations can hardly reach the typical timescale of protein functional dynamics,which somewhat limits their applications.To overcome this difficulty,a number of methods have be developed to improve the sampling efficiency of MD simulations,including:1)Using coarse-grained force fields.2)Developing enhanced sampling method to accelerate MD simulations based on the statistical mechanics principle.In this work,we carried out both of the above two ideas.On the one hand,we developed a coarse-grained model describing the protein allostery and functional dynamics regulated by mechanical force and chemical factor.We used it to study the cytotoxicity mechanism of typical hydrophobic nanotubes to a classic signaling protein and investigate the catch-bond mechanism of E.coli adhesin Fim H.This model can also be used to study the dynamics processes of other proteins such as molecular motor and molecular chaperone.On the other hand,we developed a novel enhanced sampling method based on the coarse-graining of conformation space.This method enables us to enhance the sampling efficiency without modifying the force field,applying high temperatures or biasing temperatures,and shows high portability.In addition,to overcome the accuracy bottleneck of coarse-grained models,we developed an integrative molecular simulation scheme in which we improve the model by the experimental data of hydrogen exchange.Our work mainly consists of the following four parts:(1)Consequences of hydrophobic nanotube binding on the functional dynamics of signaling protein calmodulin.The wide applications of nanomaterials in industry and our daily life have raised growing concerns on their toxicity to human body.Increasing evidence links the cytotoxicity of nanoparticles to the disruption of cellular signaling pathways.Here,we report a computational study on the mechanisms of the cytotoxicity of carbon nanotubes(CNTs)by investigating the direct impacts of CNTs on the functional motions of calmodulin(Ca M),which is one of the most important signaling proteins in a cell,and its signaling function relies on the Ca²⁺-binding-coupled conformational switching.Computational simulations with a coarse-grained model showed that binding of CNTs modifies the conformational equilibrium of Ca M and induces the closed-to-open conformational transition,leading to the loss of its Ca²⁺-sensing ability.In addition,the binding of CNTs drastically increases the calcium affinity of Ca M,which may disrupt the Ca²⁺homeostasis in a cell.These results suggest that the binding of hydrophobic nanotubes not only inhibits the signaling function of Ca M as a calcium sensor but also renders Ca M to toxic species through sequestering Ca²⁺from other competing Ca²⁺-binding proteins,suggesting a new physical mechanism of the cytotoxicity of nanoparticles.(2)Fim H-mediated catch-bond mechanism by coarse-grained simulationsResearch shows that mechanical force can be an important biological signal to regulate molecular and cellular activities.For example,the binding strength between the Escherichia coli adhesin Fim H and its ligand can be counter-intuitively strengthened by the drag force,namely the so-called catch-bond effect.This effect is very important to the bacterial adhesion and the infection by Escherichia coli.To further understand the molecular mechanism,we developed a coarse-grained model within the framework of energy landscape view that can describe the Fim H catch-bond effect.The corresponding simulations can well reproduce the catch-bond phenomena observed experimentally,providing a comprehensive picture of force-regulated bacterial adhesion.In addition,the simulations also revealed the dual-directional coupling in protein allostery,e.g.,the force-induced increase of the ligand binding strength and the binding-induced decrease of the threshold force for the catch-bond effect.Besides,we also investigated the detailed pathways of domain separation,protein allostery and ligand binding,showing how the catch-bond processes can benefit from multi-pathway dynamics.These results provide a detailed molecular mechanism of force-regulated protein adhesion,deepening our understanding to the force-regulated biological processes.(3)An enhanced sampling method with coarse-graining of conformational space.The sampling of conformations in the molecular simulations for systems with complicated free energy landscapes is always difficult.Here,we report a novel method for enhanced sampling based on the coarse-graining of conformational space.In this method,the locally converged region of the conformational space is coarse-grained with its population characterized by the related average residence time and visiting number,and at the same time,the direct simulations inside it are eliminated.The detailed balance is satisfied by updating the visiting number and generating outgoing trajectories of this region.This kind of coarse-graining operation can be further carried out by merging all the neighboring regions which are already converged together.The global equilibrium is achieved when the local equilibrated regions cover all the interested areas of the landscape.We tested the method by applying it to two model potentials and one protein system with multiple-basin energy landscapes.The sampling efficiency is found to be enhanced by more than three orders of magnitude compared to conventional molecular simulations,and are comparable with other widely used enhanced sampling methods.In addition,the kinetic information can also be well captured.All these results demonstrate that our method can help to solve the sampling problems efficiently and precisely without applying high temperatures or biasing potentials.(4)Modeling hydrogen exchange of proteins by a multiscale method.In this work,we proposed a practical way for mapping the results of coarse-grained molecular simulations to the observables in hydrogen change experiments.By combining an atomic-interaction based coarse-grained model with an all-atom structure reconstruction algorithm,we reproduced the experimental hydrogen exchange data with reasonable accuracy using molecular dynamics simulations.We also showed that the coarse-grained model can be further improved by imposing experimental restraints from hydrogen exchange data via an iterative optimization strategy.These results suggest that it is feasible to develop an integrative molecular simulation scheme by incorporating the hydrogen exchange data into the coarse-grained molecular dynamics simulations and therefore help to overcome the accuracy bottleneck of coarse-grained models.