Comparative Study On Dynamics And Free Energy Landscapes Of HIV-1 Gp120 In The Unliganded And CD4-bound State

The entry of HIV-1 into target cells is mediated by the viral envelope glycoprotein trimer(Env trimer),which is composed of three gp120 subunits and three gp41 subunits.Binding of gp120 subunit to CD4 receptor triggers confrontational changes in gp120,which in turn induces conformational changes of Env trimer from a functionally “closed” state to a more “open” conformation,However,the detailed mechanism involving conformational changes of gp120 still remains elusive.Despite numerous studies on the dynamics behavior of HIV-1 gp120,they mainly focused on the dynamics of the gp120 core structure and as such may not fully interpret the detailed structure-dynamics-function relationship of gp120.In this thesis,two near-full-length gp120 structural models,one in the unliganded state(before CD4 binding)and the other in the CD4-bound state(after CD4 receptor binding)were built using homology modeling method;subseqently,these two models were subjected to multiple-replica molecular dynamics(MD)simulations;finally,the differences in the structural/geometrical properties,conformational flexibility,large-scale concerted motions,and free energy landscapes(FELs)between these two gp120 s were analyzed and compared based on the obtained concatenated equilibrium trajectories.The comparative analysis of geometrical paramters indicates that during simulations the main-body structure(i.e.,the structure contains no V1/V2 region)of the bound gp120 was more stable and compact than that of the unliganded gp120.The comparison of local conformational flexibility reveals that although the outer domains of both gp120 states demonstrate very similar conformational flexibility,the V1/V2 region in the inner domain of the bound gp120 exhibits significantly higher conformational flexibility than that of unliganded gp120,and the other regions of the inner domain are more flexible in the unliganded gp120 than in the bound gp120.The most significant motion modes derived from the essential dynamics(ED)analysis reveal that the differences in fluctuating amplitude and moving directions between the these two gp120 s can cause different conformational effects of gp120.In the case of the unliganded gp120,the clockwise vortical rotation of the outer domain and the inward movement of the lower half of the inner domain will cause the lower halves of the two domain to be close to each other,thus likely facilitating the formation of bridge sheet and the conformational transition from the unliganded to the bound state.In the case of the bound gp120,the clockwise vortical rotation of the core structure will bring the inner domain,outer domain,and bridging sheet closer to one another,thus benefiting to maintaining the stability of CD4-binding cavity.Moreover,the outward movement of the V3 loop in the bound gp120 may benefit to the recognition and binding of co-receptor.The results of combined ED analysis,conformational space sampling,and free energy landscape reconstruction collectively indicate that the bound gp120 has greater conformational entropy,richer conformational diversity,and lower thermostability than the unliganded gp120.Based on the synthetic differences in the static structures,dynamic behavior,and free energy landscapes between the unliganded and bound gp120,we consider that the orientation of the V1/V2 region relative to the main-body structure of gp120 is likely the key factor in determining the properties of gp120 dynamics,kinetics,and thermodynamics.For the unliganded gp120,its complex dynamic behaviors and rich conformational substates on the one hand may interfere with the recognition and binding of antibodies through the conformational screening effect,on the other hand may be conducive to information transmisson between gp120 and gp41 in the Env quaternary structural context,which could trigger the formation of a helix-bundle and the exposure of the fusion peptide in gp41,thus allowing the fusion of viral and cell membranes.Our study reveals the differences in conformational flexibility,molecular motions,and free energy landscapes between the unliganded and bound gp120 s,thus facilitating a better understanding of the structure-dynamics-function relationship of gp120 and providing a theoretical guidance for designing and developing of anti-HIV-1 drugs and vaccines.To sample sufficiently and comprehensively the conformational space of gp120,we have attempted to apply an enhanced sampling technique — parallel tempering in well-tempered ensemble(PT-WTE)to the two structural models of gp120,and reconstructed the free energy landscapes based on the effective trajectory at 300 K with probability density function.Through comparison between the free energy landscapes derived from the multiple-replica MD simulations and PT-WTE simulations,we find that although both methods can provide sufficient conformational sampling,more conformaiotnal transition events required for crossing local energy barriers can be observed in PT-WTE simulation than in tranditional MD simulations.As a result,the free energy landscapes derived from PT-WTE are more complete and feature a higher resolution than those from the traditional MD simulation.This exploratory study lays the foundation for the subsequent studies relevant to protein free energy landscape in our laboratory.