HIV-1 GP120 V3 conformational and informational entropies |
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Authors: | Joel K Weltman Gail Skowron George B Loriot |
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Institution: | (1) Department of Medicine, Brown Medical School, Brown University, Providence, RI 02912, USA;(2) Brown AIDS Program, Roger Williams Medical Center and Boston University School of Medicine, Brown University, Providence, RI 02912, USA;(3) Center for Computation and Visualization, Brown University, Providence, RI 02912, USA |
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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. |
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Keywords: | HIV-1 V3 loop GP120 HF-SCF Entropy Energy Conformational entropy Informational entropy Shannon entropy Entropy variance Molecular evolution |
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