title: HIV-1 GP120 V3 conformational and informational entropies.
abstract: In an attempt to analyze structure, function and evolution of HIV-1 GP120 V3, interactions among the Hartree-Fock energy, the conformational entropy and the Shannon entropy were determined for the 1NJ0 set of antibody-bound V3 loop conformers. The Hartree-Fock energy of each conformer was determined at the MINI level with GAMESS. The conformational entropy was determined per conformer and per residue from the mass-weighted covariance matrices. The Shannon entropy per residue was determined from sequence-substitution frequencies. Correlations were determined by linear regression analysis. There was a negative correlation between the Hartree-Fock energy and the conformational entropy (R=-0.4840, p=0.0078, df =28) that enhanced the negative Helmholtz-free-energy change for the binding of the GP120 ligand to target CD4. The Shannon entropy of V3 was a function of the conformational entropy variance (R=0.7225, p=0.00157, df=15) and of the V3 Hartree-Fock energy. Biological implications of this work are that (1) conformational entropy interacts with V3 Hartree-Fock energy to enhance GP120 binding to CD4 cell receptors and that (2) the Hartree-Fock energy of V3 interacts with the evolutionary system to participate in the regulation of V3 diversity.
authors.affiliation: Department of Medicine, Brown Medical School, Brown University, Providence, RI 02912, USA. joel_weltman@brown.edu
authors.forename: Joel K
authors.initials: JK
authors.lastname: Weltman
authors.forename: Gail
authors.initials: G
authors.lastname: Skowron
authors.forename: George B
authors.initials: GB
authors.lastname: Loriot
mesh_terms: D019277:Entropy; D015699:HIV Envelope Protein gp120 / Q000737:chemistry*; D015497:HIV-1 / Q000737:chemistry*; D011487:Protein Conformation
chemical_list: D015699:HIV Envelope Protein gp120