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The Patterns of Coevolution in Clade B HIV Envelope's N-Glycosylation Sites

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  • Swetha Garimalla
  • Thomas Kieber-Emmons
  • Anastas D Pashov

Abstract

The co-evolution of the potential N-glycosylation sites of HIV Clade B gp120 was mapped onto the coevolution network of the protein structure using mean field direct coupling analysis (mfDCA). This was possible for 327 positions with suitable entropy and gap content. Indications of pressure to preserve the evolving glycan shield are seen as well as strong dependencies between the majority of the potential N-glycosylation sites and the rest of the structure. These findings indicate that although mainly an adaptation against antibody neutralization, the evolving glycan shield is structurally related to the core polypeptide, which, thus, is also under pressure to reflect the changes in the N-glycosylation. The map we propose fills the gap in previous attempts to tease out sequon evolution by providing a more general molecular context. Thus, it will help design strategies guiding HIV gp120 evolution in a rational way.

Suggested Citation

  • Swetha Garimalla & Thomas Kieber-Emmons & Anastas D Pashov, 2015. "The Patterns of Coevolution in Clade B HIV Envelope's N-Glycosylation Sites," PLOS ONE, Public Library of Science, vol. 10(6), pages 1-18, June.
    • Handle: RePEc:plo:pone00:0128664
    DOI: 10.1371/journal.pone.0128664
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    References listed on IDEAS

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    1. Simona Cocco & Remi Monasson & Martin Weigt, 2013. "From Principal Component to Direct Coupling Analysis of Coevolution in Proteins: Low-Eigenvalue Modes are Needed for Structure Prediction," PLOS Computational Biology, Public Library of Science, vol. 9(8), pages 1-17, August.
    2. Richard Wyatt & Peter D. Kwong & Elizabeth Desjardins & Raymond W. Sweet & James Robinson & Wayne A. Hendrickson & Joseph G. Sodroski, 1998. "The antigenic structure of the HIV gp120 envelope glycoprotein," Nature, Nature, vol. 393(6686), pages 705-711, June.
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