Conformational Heterogeneity of the HIV Envelope Glycan Shield

Yang, Mingjun; Huang, Jing; Simon, Raphael; Wang, Lai‐Xi; MacKerell, Alexander D.

doi:10.1038/s41598-017-04532-9

Sci Rep

2017

DOI: 10.1038/s41598-017-04532-9

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Conformational Heterogeneity of the HIV Envelope Glycan Shield

Mingjun Yang

¹

,

Jing Huang

²

,

Raphael Simon

³

et al.

Abstract: To better understand the conformational properties of the glycan shield covering the surface of the HIV gp120/gp41 envelope (Env) trimer, and how the glycan shield impacts the accessibility of the underlying protein surface, we performed enhanced sampling molecular dynamics (MD) simulations of a model glycosylated HIV Env protein and related systems. Our simulation studies revealed a conformationally heterogeneous glycan shield with a network of glycan-glycan interactions more extensive than those observed to … Show more

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Cited by 50 publications

(61 citation statements)

References 71 publications

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“…A threshold of 0.1 Å has been used for this purpose in a previous study. 50 In the structure of the antibody 87G7 bound to its RBD epitope (PDB 7N4l), 51 the lowest per-residue AASA among the non-glycine residues Y421, L455, F456, F486 and Y489 is 3.6 Å, comparable to our 1 Å threshold. The frames were binned by angle in increments of 2.75°, and for each bin, the largest number of exposed residues is reported.…”

Section: Methodssupporting

confidence: 71%

Predicting the feasibility of targeting a conserved region on the S2 domain of the SARS-CoV-2 spike protein

Garg

¹

,

Hsueh

²

,

Plotkin

³

2023

Preprint

0

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Exaggerated anticipatory anxiety is common in social anxiety disorder (SAD). Neuroimaging studies have revealed altered neural activity in response to social stimuli in SAD, but fewer studies have examined neural activity during anticipation of feared social stimuli in SAD. The current study examined the time course and magnitude of activity in threat processing brain regions during speech anticipation in socially anxious individuals and healthy controls (HC). Method Participants (SAD n = 58; HC n = 16) underwent functional magnetic resonance imaging (fMRI) during which they completed a 90s control anticipation task and 90s speech anticipation task.

show abstract

“…A threshold of 0.1 Å has been used for this purpose in a previous study. 50 In the structure of the antibody 87G7 bound to its RBD epitope (PDB 7N4l), 51 the lowest per-residue AASA among the non-glycine residues Y421, L455, F456, F486 and Y489 is 3.6 Å, comparable to our 1 Å threshold. The frames were binned by angle in increments of 2.75°, and for each bin, the largest number of exposed residues is reported.…”

Section: Methodssupporting

confidence: 71%

Predicting the feasibility of targeting a conserved region on the S2 domain of the SARS-CoV-2 spike protein

Garg

¹

,

Hsueh

²

,

Plotkin

³

2023

Preprint

0

Get access via publisher Add to dashboard Cite

Exaggerated anticipatory anxiety is common in social anxiety disorder (SAD). Neuroimaging studies have revealed altered neural activity in response to social stimuli in SAD, but fewer studies have examined neural activity during anticipation of feared social stimuli in SAD. The current study examined the time course and magnitude of activity in threat processing brain regions during speech anticipation in socially anxious individuals and healthy controls (HC). Method Participants (SAD n = 58; HC n = 16) underwent functional magnetic resonance imaging (fMRI) during which they completed a 90s control anticipation task and 90s speech anticipation task.

show abstract

“…The number of glycan conformers per glycosylation site also varies with clades, even for conserved sites. We observed that bNAbs interact with more glycans than previously reported in experimental and computational studies 24,48 .Our analysis suggests that all the 50 bNAbs have at least one glycan making on average more than 10 atomic contacts. The V3-glycan bNAb PGT135 has more than ten atom contacts with 31 glycans, the highest.…”

Section: Introductionsupporting

confidence: 63%

“…All known bNAbs must navigate the glycan shield to bind to their epitopes 10,24,55 . The number of glycan contacts can vary depending on both the specific bNAb and the HIV-1 clade.…”

Section: Resultsmentioning

confidence: 99%

Clade-specific influences of glycans on the interactions between HIV-1 envelope and broadly neutralizing antibodies

Arandhara

¹

,

Kumar

²

,

Dixit

³

et al. 2025

Preprint

0

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Exaggerated anticipatory anxiety is common in social anxiety disorder (SAD). Neuroimaging studies have revealed altered neural activity in response to social stimuli in SAD, but fewer studies have examined neural activity during anticipation of feared social stimuli in SAD. The current study examined the time course and magnitude of activity in threat processing brain regions during speech anticipation in socially anxious individuals and healthy controls (HC). Method Participants (SAD n = 58; HC n = 16) underwent functional magnetic resonance imaging (fMRI) during which they completed a 90s control anticipation task and 90s speech anticipation task.

show abstract

“…1,51 Recently, it has attracted attention and become a hot topic through the rapid exploration of structures of the SARS-CoV-2 spike protein.15−18 Advances in both experimental techniques and MD simulations now enable us to analyze glycan shielding at atomic resolution 52,53. Our results, together with previous simulations on SARS-CoV-2 spike proteins, 15−17 illustrate the diversity of glycan shielding, encompassing a variety of structures and interactions.…”

mentioning

confidence: 68%

Glycan Cluster Shielding and Antibody Epitopes on Lassa Virus Envelop Protein

Re

¹

,

Mizuguchi

²

2021

Get access via publisher Add to dashboard Cite

Exaggerated anticipatory anxiety is common in social anxiety disorder (SAD). Neuroimaging studies have revealed altered neural activity in response to social stimuli in SAD, but fewer studies have examined neural activity during anticipation of feared social stimuli in SAD. The current study examined the time course and magnitude of activity in threat processing brain regions during speech anticipation in socially anxious individuals and healthy controls (HC). Method Participants (SAD n = 58; HC n = 16) underwent functional magnetic resonance imaging (fMRI) during which they completed a 90s control anticipation task and 90s speech anticipation task.

show abstract

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