Characterizing Conformational Transition Between Two Primary States Of HIV-1 Gp120

Envelope trimer(Env trimer)located on the membrane of HIV-1 virus is composed of three gp 120 and three gp41 subunits held together by weak noncovalent interactions.Only through a series of conformational changes in Env trimer induced by interactions of gp120 with the receptor and coreceptor located on the immune-cell surface can HIV-1 accomplish its invasion into the host cell.In addition,the conformational changes of gp 120 is also directly related to the viral immune evasion.For the CD4-dependent HIV-I isolates,the first step of infection is gp120's binding to the cell surface receptor molecule CD4,which leads to the dissociation of the gp120 V1/V2 region from the structural core,thus resulting in the formation and exposure of the coreceptor binding site and related binding epitopes of certain related antibodies.Furthermore,the binding of coreceptor CCR5 or CXCR4 to gp120 induces further conformational changes in Env trimer which in turn establish the conformational condition that allows gp41 fusion peptide to insert into the host cell membrane.The conformational states of gp120 before and after CD4/coreceptor binding are defined as the unliganded state and liganded state,respectively,in this thesis.Understanding the detailed process of gp120 conformational transition from the unliganded state to the liganded state will not only facilitate a better understanding of the infection and immune evasion mechanisms of HIV-1,but is also of great significance to the development of anti-HIV-1 drugs and vaccines.Although the experimentally determined structures of gp120 are either in the unliganded or in the liganded states,the single molecule fluorescence resonance energy transfer experiment(FRET)shows that gp 120 possesses at least one intermediate state besides the two primary conformational states(i.e.,the unliganded and liganded states).Details of the conformational transition between the two primary states of gp120 still remain unknown.In order to investigate the detailed process of the gp120 conformational transition and find out the factors influencing the conformational transition,we has constructed two structural models of the monomeric gp 120(from the CD4 dependent HIV-1 strain JR-FL)in the unliganded and liganded states using homology modeling method,based on which we have performed conformational transition simulation using the well-tempered metadynamics followed by,reconstructing the free energy landscape and dynamic network.The analysis of the free energy landscape reveal that:i)the transition of gp120 from the unliganded to liganded states needs to overcome a energy barrier of about 60 kJ/mol,while the transition from the liganded to the liganded states needs to cover a higher barrier of about 80-120 kJ/mol,indicating that the transition from the unliganded to liganded states is easier than the reverse transition;?)there is a intermediate state during the interconversion between the the two gp 120 primary states,and in this intermediate state,the V1/V2 region has completely detached from the structural core while V3 loop still adhering to the top of the core,which indicates that the dissociation or attachment of V1/V2 loop to the structural core is the key of gp120 conformational transition;?)the liganded state consists of three main substates which are located separately in the three local free energy minima/wells that are separated by energy barriers and have low free-energy levels,while the unliganded state contains no substate and is located in a single free energy well/minima with a high free energy level,indicating that the liganded state has more conformational substates,greater flexibility and higher thermal stability than the unliganded state.Comparative analysis of the dynamic network models of the two states reveal that the gp 120 outer domain plays a central role in the distant allosteric signal transmission,and that the conformational perturbation of the CD4 binding fragments in the outer domain may also be one of the factors causing the conformational transition.Our results not only provide the explanations,from the perspectives of energetics and conformational changes,for the immune evasion of HIV-1,but also provide new ideas for the design and development of anti-HIV-1 drugs and vaccines.we recommend that the key for the development of anti-HIV-1 drugs lies in the discovery or design of small molecules capable of ?)blocking the V1/V2 reorientation relative to the structural core and ?)preventing allosteric signal transmission via the outer structural domain.The key for the development of anti-HIV-1 vaccines is the selective fixation of distinctive conformational states of the gp120 in the the inactivated or artificial virus,and as such,the fixation of the unliganded state and the intermediate state seems likely to be a more effective way for vaccine design.