title: Structural dynamics of V3 loop in a trimeric ambiance, a molecular dynamics study on gp120-CD4 trimeric mimic.
abstract: Entry of HIV virus into the host cell is initiated by the interaction of its surface exposed gp120 protein with the cell surface CD4 receptor and a co-receptor that can be either CCR5 or CXCR4. The third variable region (V3 loop) of gp120 has an important role in co-receptor selection by gp120 and forms an epitope for neutralizing antibodies. In this work the dynamical behavior of the V3 loop in a trimeric environment has been investigated by generating an atomistic trimer model of gp120-CD4 complex and has been compared with the result of a monomeric gp120-CD4 complex. The main results coming from this work are that the three V3 loops belonging to the three subunits of the trimer display a different dynamical behavior in terms of its flexibility, spatial orientation, motion along the principal modes, conformations, solvent exposure and electrostatic potential distribution. We propose that the ability of the V3 loop to present, in the trimeric environment, simultaneous multiple alternative conformations that increase its capability of co-receptor recognition, is at least in part due to the effect of electrostatic potential generated by two subunits over the third one.
authors.affiliation: Department of Biology, University of Rome Tor Vergata, Via Della Ricerca Scientifica, Rome 00133, Italy.
authors.forename: Balasubramanian
authors.initials: B
authors.lastname: Chandramouli
authors.affiliation: CASPUR Inter-universities Consortium for Supercomputing Applications, Via dei Tizii 6b, Rome 00185, Italy.
authors.forename: Giovanni
authors.initials: G
authors.lastname: Chillemi
authors.affiliation: Department of Biology, University of Rome Tor Vergata, Via Della Ricerca Scientifica, Rome 00133, Italy. Electronic address: desideri@uniroma2.it.
authors.forename: Alessandro
authors.initials: A
authors.lastname: Desideri
mesh_terms: D020816:Amino Acid Motifs; D015704:CD4 Antigens / Q000737:chemistry*; D015699:HIV Envelope Protein gp120 / Q000737:chemistry*; D015497:HIV-1; D006801:Humans; D056004:Molecular Dynamics Simulation; D011485:Protein Binding; D054730:Protein Interaction Domains and Motifs; D020836:Protein Structure, Quaternary
chemical_list: D015704:CD4 Antigens; D015699:HIV Envelope Protein gp120
keywords: Co-receptor recognition; Molecular dynamics; V3 loop; gp120