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Insights into the Structure, Correlated Motions, and Electrostatic Properties of Two HIV-1 gp120 V3 Loops

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  • Aliana López de Victoria
  • Phanourios Tamamis
  • Chris A Kieslich
  • Dimitrios Morikis

Abstract

The V3 loop of the glycoprotein 120 (gp120) is a contact point for cell entry of HIV-1 leading to infection. Despite sequence variability and lack of specific structure, the highly flexible V3 loop possesses a well-defined role in recognizing and selecting cell-bound coreceptors CCR5 and CXCR4 through a mechanism of charge complementarity. We have performed two independent molecular dynamics (MD) simulations to gain insights into the dynamic character of two V3 loops with slightly different sequences, but significantly different starting crystallographic structures. We have identified highly populated trajectory-specific salt bridges between oppositely charged stem residues Arg9 and Glu25 or Asp29. The two trajectories share nearly identical correlated motions within the simulations, despite their different overall structures. High occupancy salt bridges play a key role in the major cross-correlated motions in both trajectories, and may be responsible for transient structural stability in preparation for coreceptor binding. In addition, the two V3 loops visit conformations with similarities in spatial distributions of electrostatic potentials, despite their inherent flexibility, which may play a role in coreceptor recognition. It is plausible that cooperativity between overall electrostatic potential, charged residue interactions, and correlated motions could be associated with a coreceptor selection and binding.

Suggested Citation

  • Aliana López de Victoria & Phanourios Tamamis & Chris A Kieslich & Dimitrios Morikis, 2012. "Insights into the Structure, Correlated Motions, and Electrostatic Properties of Two HIV-1 gp120 V3 Loops," PLOS ONE, Public Library of Science, vol. 7(11), pages 1-15, November.
    • Handle: RePEc:plo:pone00:0049925
    DOI: 10.1371/journal.pone.0049925
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    References listed on IDEAS

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    1. Peter D. Kwong & Richard Wyatt & James Robinson & Raymond W. Sweet & Joseph Sodroski & Wayne A. Hendrickson, 1998. "Structure of an HIV gp120 envelope glycoprotein in complex with the CD4 receptor and a neutralizing human antibody," Nature, Nature, vol. 393(6686), pages 648-659, June.
    2. Matthias T. Dittmar & Áine McKnight & Graham Simmons & Paul R. Clapham & Robin A. Weiss & Peter Simmonds, 1997. "HIV-1 tropism and co-receptor use," Nature, Nature, vol. 385(6616), pages 495-496, February.
    3. Suryani Lukman & Barry J Grant & Alemayehu A Gorfe & Guy H Grant & J Andrew McCammon, 2010. "The Distinct Conformational Dynamics of K-Ras and H-Ras A59G," PLOS Computational Biology, Public Library of Science, vol. 6(9), pages 1-9, September.
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