Skip to main content

Advertisement

SpringerLink
Log in

HIV-1 GP120 V3 conformational and informational entropies

  • Original paper
  • Published:
Journal of Molecular Modeling Aims and scope Submit manuscript

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.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3

Similar content being viewed by others

References

  1. Jensen MA, van ’t Wout AB (2003) AIDS Rev 5:104–112

    PubMed  Google Scholar 

  2. Sharon M, Kessler N, Levy R, Zolla-Pazner S, Gorlach M, Anglister J (2002) NMR Structure of a V3 (MN Isolate) Peptide Bound to 447-52D, a Human HIV-1 Neutralizing Antibody. Protein Data Bank PDB 1NJ0

  3. Sharon M, Kessler N, Levy R, Zolla-Pazner S, Gorlach M, Anglister J (2003) Structure 11:225–236

    Article  PubMed  CAS  Google Scholar 

  4. Schmidt MW, Baldridge KK, Boatz JA, Elbert ST, Gordon MS, Jensen JH, Kosek S, Matsunaga N, Nguyen KA, Su S, Windus TL, Dupuis M, Montgomery JA (1993) J Comput Chem 14:1347–1363

    Article  CAS  Google Scholar 

  5. Weltman JK, Skowron G, Loriot GB (2004) J Mol Model 10:367–372

    Article  CAS  Google Scholar 

  6. Kirkwood JG (1934) J Chem Phys 2:351–363

    Article  CAS  Google Scholar 

  7. Onsager L (1936) J Am Chem Soc 58:1486–1493

    Article  CAS  Google Scholar 

  8. Schlitter J (1993) Chem Phys Lett 215:617–621

    Article  CAS  Google Scholar 

  9. Shäfer H, Smith LJ, Mark AE, van Gunsteren (2002) Proteins 46:215–224

    Article  PubMed  CAS  Google Scholar 

  10. Arun KS, Huang TS, Blostein SD (1987) IEEE Trans Patt Anal Mach Intell PAMI-9 698–700

  11. Vasil S, Thakallapally R, Korber BT, Foley BT (1998) Global variation in the HIV-1 V3 region. Los Alamos National Laboratory Compendium. III-118, p 6

  12. a) Shannon CE (1948) Bell Sys Tech J 27:379–423 b)Shannon CE (1948) Bell Sys Tech J 27:623–656

    Google Scholar 

  13. Sharpe S, Kessler N, Anglister JA, Yau WM, Tycko R (2004) J Am Chem Soc 126:4979–4990

    Article  PubMed  CAS  Google Scholar 

  14. Moore WJ (1962) Entropy changes in isolated systems. In: Physical Chemistry. Longmans, London, pp 78–79

    Google Scholar 

  15. Hsu ST, Peter C, van Gunsteren WF, Bonvin AM (2005) Biophys J 88:15–24

    Article  PubMed  CAS  Google Scholar 

  16. Tolman RC (1962) Thermodynamic quantities in terms of the free energy. In: The Principles of Statistical Mechanics. Oxford, pp 565–570

  17. Yockey HP (1992) The criterion for isomorphism between probability spaces: when are they the same? In Information theory and molecular biology. Cambridge, pp 69–70 and pp 86–89

  18. Krieger F, Moglich A, Kiefhaber T (2005) J Am Chem Soc 127:3346–3352

    Article  PubMed  CAS  Google Scholar 

  19. Jacob J, Duclohier H, Cafiso DS (1999) Biophys J 76:1367–1376

    Article  PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Medicine, Brown Medical School, Brown University, Providence, RI, 02912, USA

    Joel K. Weltman & Gail Skowron

  2. Brown AIDS Program, Roger Williams Medical Center and Boston University School of Medicine, Brown University, Providence, RI, 02912, USA

    Gail Skowron

  3. Center for Computation and Visualization, Brown University, Providence, RI, 02912, USA

    George B. Loriot

Authors
  1. Joel K. Weltman
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Gail Skowron
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. George B. Loriot
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Joel K. Weltman.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Weltman, J.K., Skowron, G. & Loriot, G.B. HIV-1 GP120 V3 conformational and informational entropies. J Mol Model 12, 362–365 (2006). https://doi.org/10.1007/s00894-005-0054-2

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00894-005-0054-2

Keywords

Search

Navigation