HIV-1 GP120 V3 conformational and informational entropies

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.