Effect Of CD4 Binding On Dynamics Of HIV-1 Gp120 Core Structure In Its CD4-bound State

Entry of HIV-1 virus into the host cell is mediated by a series of"cascade"reactions between the viral envelope glycoprotein trimer(Env trimer)and the receptor and co-receptor molecules located on the host cell surface.First,the binding gp120subunit(which is within the Env trimer)to the receptor molecule CD4(which is located on the surface of the host cell)causes the Env trimer to switch from the closed state to the open state and simultaneously results in the formation and exposure of the co-receptor-binding site in gp120.Subsequently,the binding of gp120 to the co-receptor CCR5 or CXCR4 induces additional conformational changes in the Env trimer and results in the formation of the energetically stable six-helix bundle in gp41and the subsequent fusion of viral and cell membranes.Finally,the HIV-1 viron releases its nucleocapsid into the cytoplasm.Gp120 molecules/subunits in the Env trimer and its conformational changes play a crucial role in the entire process of viral entry into the cell.Elucidating the conformational control mechanism of gp120 is fundamentally important for undertanding the mechanisms of viral entry and immune evasion,as well as for developing and designing the vaccines and anti-HIV drugs.In order to investigate the effect of CD4 binding on the dynamic behavior of gp120core structure,in this thesis we constructed two structural models using the homology modeling method:the model of gp120 monomer in the CD4-bound state and the model of gp120-CD4 complex(referred to as the complexed gp120),and performed multiple-replica molecular dynamics(MD)simulations on these two structural models.The differences in the conformational flexibility,essential dynamics(ED)properties,and conformational space sampling between the monomeric and complexed gp120s were then compared and analyzed based on the sufficient conformational sampling in the obtained MD concatenated MD trajectories.The calculation and comparison of C_?atom root mean square fluctuations indicate that CD4 binding not only restrains to a certain extent the conformational flexibility at the CD4-binding site,but also significantly reduces the flexibility in partial peripheral loop regions outside the core structure and in the layer 1 of the inner domain.The results of essential dynamics analysis show that the motion modes of both gp120 core structures(i.e.,monomeric and complexed gp120 cores)along the first four eigenvectors are mainly manifested as the combinations of the rotations,translations,twistings,and bendings of gp120inner and outer domains and bridging sheet layer or of partial structural regions within them.The differences in moving directions of these regions can lead to different effects on local(such as the CD4-binding cavity)or overall conformation of gp120,and thus are likely to be related to the biological function of gp120 and conformational transition between different states.The results of combined ED analysis and the conformational space sampling analysisrevealed that although the monomeric gp120 has stronger conformational change capability(or higher conformational freedom)than the complexed gp120,the binding of CD4 to gp120appears not to completely restrain the conformational freedom of the complexed gp120 but merely limit the conformational changes to a relatively small range.As a result,the complexed gp120 still exhibits a relatively rich conformational diversity.We consider that the rich conformational diversity of gp120 could not only facilitate its binding to receptors and co-receptors via conformational selection or induced fit,but also be advantageous to the avoidance of neutralizing antibody attack via the effect of conformational masking.Previous studies have shown that the gp120 inner domain can be topologically divided into a structurally stable seven-stranded?-sandwich and three independent structural layers(i.e.,layers 1-3)that emanate from the?-sandwich.To investigate the difference in the capability for layer 1 to move away from the structural cores of the monomeric and complexed gp120s,the free energy landscapes(FELs)using the distance between centers of mass of layer 1 and structure core as a reaction coordinate were constructed based on pulling(or biased)MD simulations of monomeric gp120and gp120-CD4 complex.Comparison between the two FELs show that layer 1 in the monomeric gp120 can easily overcome free energy barriers when move away from the the core and convert readily between conformational substates when it is close to and far from the core structure,whereas in the gp120-CD4 complex,the changes in positional of layer 1 with respect to the core structure is difficult due to the higher barrier.The conformational alternativity/variability of layer 1 in the monomeric gp120 may not only facilitate its interaction with the gp41 subunit in the Env trimer,but also allow the gp120 inner domain to move among alternative conformations required for HIV immune evasion.Upon CD4 binding,the mobility of layer 1 is partially limited,making it difficult to move away from the core structure.The restrained mobility of layer 1 on the one hand may loosen the contact between layer 1and the gp41 fusion peptide and hence allow additional conformational changes in gp41 to transition to states suitable for membrane fusion.The structurally stable layer on the other hand enhances the overall stability of the inner domain,which in turn may contribute to the maintenance of the CD4-bound state necessary for further co-receptor binding.In this study,we have probed the structure-dynamics-function relationship of gp120 using molecular simulations methods.The results will facilitate a more thorough understanding of the gp120 conformational control mechanisms as well as the mechanisms of HIV-1 infection and immune evasion.The findings may also provide help to the development of HIV treatment drugs.