Development of Martini 2.2 parameters for N-glycans: a case study of the HIV-1 Env glycoprotein dynamics

Lopez Bautista, Cesar Augusto; Wagh, Kshitij; Chakraborty, Srirupa; Gnanakaran, Sandrasegaram

doi:10.1093/glycob/cwab017

Title: Development of Martini 2.2 parameters for N-glycans: a case study of the HIV-1 Env glycoprotein dynamics

Journal Article · Sat Mar 20 00:00:00 EDT 2021 · Glycobiology (Online)

DOI:https://doi.org/10.1093/glycob/cwab017· OSTI ID:1822782

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Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

N-linked glycans are ubiquitous in nature and play key roles in biology. For example, glycosylation of pathogenic proteins is a common immune evasive mechanism, hampering the development of successful vaccines. Due to their chemical variability and complex dynamics, an accurate molecular understanding of glycans is still limited by the lack of effective resolution of current experimental approaches. Here, we have developed and implemented a reductive model based on the popular Martini 2.2 coarse-grained force field for the computational study of N-glycosylation. We used the HIV-1 Env as a direct applied example of a highly glycosylated protein. Finally, our results indicate that the model not only reproduces many observables in very good agreement with a fully atomistic force field but also can be extended to study large amount of glycosylation variants, a fundamental property that can aid in the development of drugs and vaccines.

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Research Organization:: Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

Sponsoring Organization:: USDOE Laboratory Directed Research and Development (LDRD) Program; National Institutes of Health (NIH)

Grant/Contract Number:: 89233218CNA000001; 20190441ER; UM1 AI100645; UM1 AI14437

OSTI ID:: 1822782

Report Number(s):: LA-UR-20-26658

Journal Information:: Glycobiology (Online), Vol. 31, Issue 7; ISSN 1460-2423

Publisher:: Oxford University PressCopyright Statement

Country of Publication:: United States

Language:: English

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