Application Of Coarse-grained Force Field Model In Molecular Dynamics Simulation Studies Of ABC Exporter And RNA

Biological macromolecules(including proteins,DNA,RNA and their complexes)often achieve their biological properties through conformational changes.Therefore,the study on the dynamics of the conformational changes of biological macromolecules has attracted increasing attention in the field of modern biology.However,since the structural change process of macromolecules involves hundreds of thousands to hundreds of millions of atoms,the conformational changes have large scales and long time(reaching the order of microseconds and milliseconds).With the current computer capability,the traditional all-atom molecular dynamics(AA-MD)method is difficult to carry out a complete dynamic simulation of these molecular systems effectively.To this end,we introduced the coarse-grained molecular dynamics(CG-MD)simulation study on ATP binding cassette exporter(ABC exporter)and ribonucleic acid(RNA)macromolecules,which effectively improved the simulation efficiency.1.ATP-binding cassette(ABC)exporters are a class of molecular machines that transport substrates out of biological membranes via gating movements leading to transitions between outward-facing(OF)and inward-facing(IF)conformational states.Despite significant advances in structural and functional studies,the molecular mechanism underlying conformational gating in ABC exporters is not completely understood.A complete elucidation of the state transitions during the transport cycle is beyond the capability of all-atom molecular dynamics(MD)method because of the limited time-scale of MD.In the present work,coarse-grained molecular dynamics(CG-MD)methods with improved sampling strategies were performed for the bacteria ABC exporters,P-gp and MsbA.2.In the study of P-gp exporter,the potential of mean force(PMF)is obtained to identify a reliable pathway where the predicted OF and IF structures are in good agreement with available experiments.Notably,the CG-MD trajectories showed that the periplasmic gate is closed before the cytoplasmic gate is opened during the OF to IF conformational transition,capturing the unidirectional feature of substrate translocation through the exporter.The present work also sheds light on how the mechanical force generated upon the NBD dissociation is transferred to the periplasmic end at a distance over 70 (?) to close the gate,and subsequently to open the cytoplasmic gate.3.In order to further explore the conformational transition path and intermediate state in detail,we used the latest high-precision experimental structure of ABC exporter MsbA for simulation research.The resultant PMF along the center-of-mass(COM)distances,d1 and d2 between the two opposing subunits of the internal and external gate,respectively,are obtained,delicately showing the details of the OF→IF transition occurring via an occluded(OC)state,in which the internal and external gate are both closed.The OC state has an important role for the unidirectionality of the transport function of the ABC exporters.Our CG-MD simulations dynamically show that upon NBD dissociation the opening of the internal gate occurs in a highly cooperative manner with the closure of the external gate.Based on our PMF calculations and CG-MD simulations,we proposed a mechanistic model,which is significantly different from those published in literature recently,shedding light on the molecular mechanism by which the ABC exporter executes conformational gating for substrate translocation.4.Latest molecular biology research shows that not only RNA sequences can fold into highly sophisticated three-dimensional structures like proteins,but also has complex and diverse biological functions.RNA macromolecules are even considered as the most functional biological macromolecules in cells,and its biological importance is no less than that of protein.For example,none-coding RNA can not only regulate gene expression,signal transduction and gene editing,but also catalyze many important biochemical reactions in cells.To study RNA-protein complexes,we need to establish a general coarse-grained force field that can describe both protein and RNA,and the interactions between them.For this reason,we specifically optimized a set of RNA coarse-grained force field models based on the original MARTINI coarse-grained force field.Compared with the simple coarse-grained force field established for DNA and RNA in the MARTINI force field,our optimized coarse-grained force field are able to better characterize the charge polarity within RNA molecules and the stacking effect of RNA bases.We simulated several RNA single strands accordingly.At the end of this paper,several new systems that can be extended by these methods and the directions for further improvement of these methods are also discussed.