Search Menu
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information
Search Scholarly Publications

Title: Effect of glycosylation on an immunodominant region in the V1V2 variable domain of the HIV-1 envelope gp120 protein

Abstract

Heavy glycosylation of the envelope (Env) surface subunit, gp120, is a key adaptation of HIV-1; however, the precise effects of glycosylation on the folding, conformation and dynamics of this protein are poorly understood. Here we explore the patterns of HIV-1 Env gp120 glycosylation, and particularly the enrichment in glycosylation sites proximal to the disulfide linkages at the base of the surface-exposed variable domains. To dissect the influence of glycans on the conformation these regions, we focused on an antigenic peptide fragment from a disulfide bridge-bounded region spanning the V1 and V2 hyper-variable domains of HIV-1 gp120. We used replica exchange molecular dynamics (MD) simulations to investigate how glycosylation influences its conformation and stability. Simulations were performed with and without N-linked glycosylation at two sites that are highly conserved across HIV-1 isolates (N156 and N160); both are contacts for recognition by V1V2-targeted broadly neutralizing antibodies against HIV-1. Glycosylation stabilized the pre-existing conformations of this peptide construct, reduced its propensity to adopt other secondary structures, and provided resistance against thermal unfolding. Simulations performed in the context of the Env trimer also indicated that glycosylation reduces flexibility of the V1V2 region, and provided insight into glycan-glycan interactions in this region. These stabilizing effectsmore » were influenced by a combination of factors, including the presence of a disulfide bond between the Cysteines at 131 and 157, which increased the formation of beta-strands. Together, these results provide a mechanism for conservation of disulfide linkage proximal glycosylation adjacent to the variable domains of gp120 and begin to explain how this could be exploited to enhance the immunogenicity of those regions. Furthermore, these studies suggest that glycopeptide immunogens can be designed to stabilize the most relevant Env conformations to focus the immune response on key neutralizing epitopes.« less

Authors:
 [1];  [2];  [3];  [4];  [5];  [2];  [2];  [6]
+ Show Author Affiliations
  1. Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
  2. Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
  3. Emory Univ., Atlanta, GA (United States)
  4. Univ. of California, Berkeley, CA (United States)
  5. Rutgers Univ., Newark, NJ (United States)
  6. National Cancer Institute - Frederick, Frederick, MD (United States)
Publication Date:
Research Org.:
Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)
Sponsoring Org.:
USDOE Laboratory Directed Research and Development (LDRD) Program
OSTI Identifier:
1338782
Report Number(s):
LA-UR-16-26334
Journal ID: ISSN 1553-7358
Grant/Contract Number:  
AC52-06NA25396
Resource Type:
Accepted Manuscript
Journal Name:
PLoS Computational Biology (Online)
Additional Journal Information:
Journal Name: PLoS Computational Biology (Online); Journal Volume: 12; Journal Issue: 10; Journal ID: ISSN 1553-7358
Publisher:
Public Library of Science
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Biological Science

Citation Formats

Tian, Jianhui, Lopez, Cesar Augusto, Derdeyn, Cynthia A., Jones, Morris S., Pinter, Abraham, Korber, Bette Tina Marie, Gnanakaran, Sandrasegaram, and Rein, Alan. Effect of glycosylation on an immunodominant region in the V1V2 variable domain of the HIV-1 envelope gp120 protein. United States: N. p., 2016. Web. doi:10.1371/journal.pcbi.1005094.
Copy to clipboard
Tian, Jianhui, Lopez, Cesar Augusto, Derdeyn, Cynthia A., Jones, Morris S., Pinter, Abraham, Korber, Bette Tina Marie, Gnanakaran, Sandrasegaram, & Rein, Alan. Effect of glycosylation on an immunodominant region in the V1V2 variable domain of the HIV-1 envelope gp120 protein. United States. https://doi.org/10.1371/journal.pcbi.1005094
Copy to clipboard
Tian, Jianhui, Lopez, Cesar Augusto, Derdeyn, Cynthia A., Jones, Morris S., Pinter, Abraham, Korber, Bette Tina Marie, Gnanakaran, Sandrasegaram, and Rein, Alan. Fri . "Effect of glycosylation on an immunodominant region in the V1V2 variable domain of the HIV-1 envelope gp120 protein". United States. https://doi.org/10.1371/journal.pcbi.1005094. https://www.osti.gov/servlets/purl/1338782.
Copy to clipboard
@article{osti_1338782,
title = {Effect of glycosylation on an immunodominant region in the V1V2 variable domain of the HIV-1 envelope gp120 protein},
author = {Tian, Jianhui and Lopez, Cesar Augusto and Derdeyn, Cynthia A. and Jones, Morris S. and Pinter, Abraham and Korber, Bette Tina Marie and Gnanakaran, Sandrasegaram and Rein, Alan},
abstractNote = {Heavy glycosylation of the envelope (Env) surface subunit, gp120, is a key adaptation of HIV-1; however, the precise effects of glycosylation on the folding, conformation and dynamics of this protein are poorly understood. Here we explore the patterns of HIV-1 Env gp120 glycosylation, and particularly the enrichment in glycosylation sites proximal to the disulfide linkages at the base of the surface-exposed variable domains. To dissect the influence of glycans on the conformation these regions, we focused on an antigenic peptide fragment from a disulfide bridge-bounded region spanning the V1 and V2 hyper-variable domains of HIV-1 gp120. We used replica exchange molecular dynamics (MD) simulations to investigate how glycosylation influences its conformation and stability. Simulations were performed with and without N-linked glycosylation at two sites that are highly conserved across HIV-1 isolates (N156 and N160); both are contacts for recognition by V1V2-targeted broadly neutralizing antibodies against HIV-1. Glycosylation stabilized the pre-existing conformations of this peptide construct, reduced its propensity to adopt other secondary structures, and provided resistance against thermal unfolding. Simulations performed in the context of the Env trimer also indicated that glycosylation reduces flexibility of the V1V2 region, and provided insight into glycan-glycan interactions in this region. These stabilizing effects were influenced by a combination of factors, including the presence of a disulfide bond between the Cysteines at 131 and 157, which increased the formation of beta-strands. Together, these results provide a mechanism for conservation of disulfide linkage proximal glycosylation adjacent to the variable domains of gp120 and begin to explain how this could be exploited to enhance the immunogenicity of those regions. Furthermore, these studies suggest that glycopeptide immunogens can be designed to stabilize the most relevant Env conformations to focus the immune response on key neutralizing epitopes.},
doi = {10.1371/journal.pcbi.1005094},
journal = {PLoS Computational Biology (Online)},
number = 10,
volume = 12,
place = {United States},
year = {Fri Oct 07 00:00:00 EDT 2016},
month = {Fri Oct 07 00:00:00 EDT 2016}
}
Copy to clipboard
Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
https://doi.org/10.1371/journal.pcbi.1005094
Copyright Statement
Other availability
Search WorldCat Search WorldCat to find libraries that may hold this journal
Citation Metrics:
Cited by: 15 works
Citation information provided by
Web of Science
Save / Share:
Export Metadata
Save to My Library
You must Sign In or Create an Account in order to save documents to your library.

Works referenced in this record:

Thermodynamics of Unfolding for Kazal-Type Serine Protease Inhibitors:  Entropic Stabilization of Ovomucoid First Domain by Glycosylation †
journal, February 1997

  • DeKoster, Gregory T.; Robertson, Andrew D.
  • Biochemistry, Vol. 36, Issue 8
  • DOI: 10.1021/bi962580b

Sequence Note : Rapid Sequon Evolution in Human Immunodeficiency Virus Type 1 Relative to Human Immunodeficiency Virus Type 2
journal, September 1996

  • Wills, Christopher; Farmer, Andrew; Myers, Gerald
  • AIDS Research and Human Retroviruses, Vol. 12, Issue 14
  • DOI: 10.1089/aid.1996.12.1383

Tyrosine Sulfation of the Amino Terminus of CCR5 Facilitates HIV-1 Entry
journal, March 1999

Structure of HIV-1 gp120 V1/V2 domain with broadly neutralizing antibody PG9
journal, November 2011

  • McLellan, Jason S.; Pancera, Marie; Carrico, Chris
  • Nature, Vol. 480, Issue 7377
  • DOI: 10.1038/nature10696

Escape from Autologous Neutralizing Antibodies in Acute/Early Subtype C HIV-1 Infection Requires Multiple Pathways
journal, September 2009

The core trisaccharide of an N-linked glycoprotein intrinsically accelerates folding and enhances stability
journal, February 2009

  • Hanson, S. R.; Culyba, E. K.; Hsu, T. -L.
  • Proceedings of the National Academy of Sciences, Vol. 106, Issue 9
  • DOI: 10.1073/pnas.0810318105

The HIV-1 Envelope Glycoproteins: Fusogens, Antigens, and Immunogens
journal, June 1998

How Hydrophobicity and the Glycosylation Site of Glycans Affect Protein Folding and Stability: A Molecular Dynamics Simulation
journal, December 2011

  • Lu, Diannan; Yang, Cheng; Liu, Zheng
  • The Journal of Physical Chemistry B, Vol. 116, Issue 1
  • DOI: 10.1021/jp203926r

Stereochemistry of the N-glycosylation sites in glycoproteins
journal, July 1995

Envelope glycans of immunodeficiency virions are almost entirely oligomannose antigens
journal, July 2010

  • Doores, K. J.; Bonomelli, C.; Harvey, D. J.
  • Proceedings of the National Academy of Sciences, Vol. 107, Issue 31
  • DOI: 10.1073/pnas.1006498107

A Next-Generation Cleaved, Soluble HIV-1 Env Trimer, BG505 SOSIP.664 gp140, Expresses Multiple Epitopes for Broadly Neutralizing but Not Non-Neutralizing Antibodies
journal, September 2013

Structures of HIV-1 Env V1V2 with broadly neutralizing antibodies reveal commonalities that enable vaccine design
journal, December 2015

  • Gorman, Jason; Soto, Cinque; Yang, Max M.
  • Nature Structural & Molecular Biology, Vol. 23, Issue 1
  • DOI: 10.1038/nsmb.3144

Context-Dependent Effects of Asparagine Glycosylation on Pin WW Folding Kinetics and Thermodynamics
journal, November 2010

  • Price, Joshua L.; Shental-Bechor, Dalit; Dhar, Apratim
  • Journal of the American Chemical Society, Vol. 132, Issue 43
  • DOI: 10.1021/ja106896t

Effects of Disulfide Bonds on Folding Behavior and Mechanism of the β-Sheet Protein Tendamistat
journal, January 2006

Glycoproteins: glycan presentation and protein-fold stability
journal, July 1999

Synthetic glycopeptides reveal the glycan specificity of HIV-neutralizing antibodies
journal, June 2013

  • Amin, Mohammed N.; McLellan, Jason S.; Huang, Wei
  • Nature Chemical Biology, Vol. 9, Issue 8
  • DOI: 10.1038/nchembio.1288

Glycosylation Enhances Peptide Hydrophobic Collapse by Impairing Solvation
journal, June 2010

N-linked oligosaccharides as outfitters for glycoprotein folding, form and function
journal, March 2006

  • Mitra, Nivedita; Sinha, Sharmistha; Ramya, Thirumalai N. C.
  • Trends in Biochemical Sciences, Vol. 31, Issue 3
  • DOI: 10.1016/j.tibs.2006.01.003

Replica-exchange molecular dynamics method for protein folding
journal, November 1999

The CCN family of proteins: structure–function relationships
journal, October 2008

  • Holbourn, Kenneth P.; Acharya, K. Ravi; Perbal, Bernard
  • Trends in Biochemical Sciences, Vol. 33, Issue 10
  • DOI: 10.1016/j.tibs.2008.07.006

Crystal Structure of a Soluble Cleaved HIV-1 Envelope Trimer
journal, October 2013

Oxidative Refolding of Bovine Pancreatic RNases A and B Promoted by Asn-Glycans
journal, March 1998

The O-Glycosylated Linker from the Trichoderma reesei Family 7 Cellulase Is a Flexible, Disordered Protein
journal, December 2010

  • Beckham, Gregg T.; Bomble, Yannick J.; Matthews, James F.
  • Biophysical Journal, Vol. 99, Issue 11
  • DOI: 10.1016/j.bpj.2010.10.032

The Glycan Shield of HIV Is Predominantly Oligomannose Independently of Production System or Viral Clade
journal, August 2011

Asymmetric recognition of the HIV-1 trimer by broadly neutralizing antibody PG9
journal, February 2013

  • Julien, Jean-Philippe; Lee, Jeong Hyun; Cupo, Albert
  • Proceedings of the National Academy of Sciences, Vol. 110, Issue 11
  • DOI: 10.1073/pnas.1217537110

 -Helical stabilization by side chain shielding of backbone hydrogen bonds
journal, February 2002

  • Garcia, A. E.; Sanbonmatsu, K. Y.
  • Proceedings of the National Academy of Sciences, Vol. 99, Issue 5
  • DOI: 10.1073/pnas.042496899

Broad neutralization coverage of HIV by multiple highly potent antibodies
journal, September 2011

  • Walker, Laura M.; Huber, Michael; Doores, Katie J.
  • Nature, Vol. 477, Issue 7365
  • DOI: 10.1038/nature10373

Do asparagine-linked carbohydrate chains in glycoproteins have a preference for β-bends?
journal, August 1986

The interplay of glycosylation and disulfide formation influences fibrillization in a prion protein fragment
journal, June 2003

  • Bosques, C. J.; Imperiali, B.
  • Proceedings of the National Academy of Sciences, Vol. 100, Issue 13
  • DOI: 10.1073/pnas.1232504100

GLYCAM06: A generalizable biomolecular force field. Carbohydrates: GLYCAM06
journal, September 2007

  • Kirschner, Karl N.; Yongye, Austin B.; Tschampel, Sarah M.
  • Journal of Computational Chemistry, Vol. 29, Issue 4
  • DOI: 10.1002/jcc.20820

Analysis of the Disulfide Bond Arrangement of the HIV-1 Envelope Protein CON-S gp140 ΔCFI Shows Variability in the V1 and V2 Regions
journal, February 2011

  • Go, Eden P.; Zhang, Ying; Menon, Sushma
  • Journal of Proteome Research, Vol. 10, Issue 2
  • DOI: 10.1021/pr100764a

Composition and Antigenic Effects of Individual Glycan Sites of a Trimeric HIV-1 Envelope Glycoprotein
journal, March 2016

Perturbing the folding energy landscape of the bacterial immunity protein Im7 by site-specific N-linked glycosylation
journal, December 2010

  • Chen, M. M.; Bartlett, A. I.; Nerenberg, P. S.
  • Proceedings of the National Academy of Sciences, Vol. 107, Issue 52
  • DOI: 10.1073/pnas.1015356107

HIV Evolution in Early Infection: Selection Pressures, Patterns of Insertion and Deletion, and the Impact of APOBEC
journal, May 2009

Parallel β-Sheet Secondary Structure Is Stabilized and Terminated by Interstrand Disulfide Cross-Linking
journal, December 2011

  • Almeida, Aaron M.; Li, Rebecca; Gellman, Samuel H.
  • Journal of the American Chemical Society, Vol. 134, Issue 1
  • DOI: 10.1021/ja208856c

Trimeric HIV-1-Env Structures Define Glycan Shields from Clades A, B, and G
journal, May 2016

Effect of glycosylation on protein folding: A close look at thermodynamic stabilization
journal, June 2008

  • Shental-Bechor, D.; Levy, Y.
  • Proceedings of the National Academy of Sciences, Vol. 105, Issue 24
  • DOI: 10.1073/pnas.0801340105

Particle mesh Ewald: An N ⋅log( N ) method for Ewald sums in large systems
journal, June 1993

  • Darden, Tom; York, Darrin; Pedersen, Lee
  • The Journal of Chemical Physics, Vol. 98, Issue 12
  • DOI: 10.1063/1.464397

Molecular dynamics with coupling to an external bath
journal, October 1984

  • Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.
  • The Journal of Chemical Physics, Vol. 81, Issue 8
  • DOI: 10.1063/1.448118

The CCN family of proteins: structure–function relationships
journal, October 2008

  • Holbourn, Kenneth P.; Acharya, K. Ravi; Perbal, Bernard
  • Trends in Biochemical Sciences, Vol. 33, Issue 10
  • DOI: 10.1016/j.tibs.2008.07.006

Competition between folding and glycosylation in the endoplasmic reticulum.
journal, July 1996

Analysis of V2 Antibody Responses Induced in Vaccinees in the ALVAC/AIDSVAX HIV-1 Vaccine Efficacy Trial
journal, January 2013

HIV Glycosylation: What Does It Portend?
journal, August 1992

  • Myers, Gerald; Lenroot, Rhoshell
  • AIDS Research and Human Retroviruses, Vol. 8, Issue 8
  • DOI: 10.1089/aid.1992.8.1459

Antibody neutralization and escape by HIV-1
journal, March 2003

  • Wei, Xiping; Decker, Julie M.; Wang, Shuyi
  • Nature, Vol. 422, Issue 6929
  • DOI: 10.1038/nature01470

N-linked oligosaccharides as outfitters for glycoprotein folding, form and function
journal, March 2006

  • Mitra, Nivedita; Sinha, Sharmistha; Ramya, Thirumalai N. C.
  • Trends in Biochemical Sciences, Vol. 31, Issue 3
  • DOI: 10.1016/j.tibs.2006.01.003

Removal of N-glycosylation sites of the yeast acid phosphatase severely affects protein folding.
journal, January 1991

Developmental pathway for potent V1V2-directed HIV-neutralizing antibodies
journal, March 2014

  • Doria-Rose, Nicole A.; Schramm, Chaim A.; Gorman, Jason
  • Nature, Vol. 509, Issue 7498
  • DOI: 10.1038/nature13036

Synthetic glycopeptides reveal the glycan specificity of HIV-neutralizing antibodies
journal, June 2013

  • Amin, Mohammed N.; McLellan, Jason S.; Huang, Wei
  • Nature Chemical Biology, Vol. 9, Issue 8
  • DOI: 10.1038/nchembio.1288

 -Helical stabilization by side chain shielding of backbone hydrogen bonds
journal, February 2002

  • Garcia, A. E.; Sanbonmatsu, K. Y.
  • Proceedings of the National Academy of Sciences, Vol. 99, Issue 5
  • DOI: 10.1073/pnas.042496899

Effect of N-linked glycosylation on glycopeptide and glycoprotein structure
journal, December 1999

Chaperone-Like Functions of High-Mannose Type and Complex-Type N-Glycans and Their Molecular Basis
journal, November 2002

Sequence Note : Rapid Sequon Evolution in Human Immunodeficiency Virus Type 1 Relative to Human Immunodeficiency Virus Type 2
journal, September 1996

  • Wills, Christopher; Farmer, Andrew; Myers, Gerald
  • AIDS Research and Human Retroviruses, Vol. 12, Issue 14
  • DOI: 10.1089/aid.1996.12.1383

Structural comparison of protein sequences around potential N-glycosylation sites
journal, August 1984

  • Mononen, Ilkka; Karjalainen, Erkki
  • Biochimica et Biophysica Acta (BBA) - Protein Structure and Molecular Enzymology, Vol. 788, Issue 3
  • DOI: 10.1016/0167-4838(84)90050-5

Chemical Synthesis of Highly Congested gp120 V1V2 N -Glycopeptide Antigens for Potential HIV-1-Directed Vaccines
journal, August 2013

  • Aussedat, Baptiste; Vohra, Yusuf; Park, Peter K.
  • Journal of the American Chemical Society, Vol. 135, Issue 35
  • DOI: 10.1021/ja405990z

Effects of Disulfide Bonds on Folding Behavior and Mechanism of the β-Sheet Protein Tendamistat
journal, January 2006

Specific and Nonspecific Effects of Glycosylation
journal, April 2012

  • Ellis, Christopher R.; Maiti, Buddhadev; Noid, William G.
  • Journal of the American Chemical Society, Vol. 134, Issue 19
  • DOI: 10.1021/ja301005f

The HIV-1 Envelope Glycoproteins: Fusogens, Antigens, and Immunogens
journal, June 1998

New Monte Carlo algorithms for protein folding
journal, April 1999

The B Cell Response Is Redundant and Highly Focused on V1V2 during Early Subtype C Infection in a Zambian Seroconverter
journal, October 2010

  • Lynch, R. M.; Rong, R.; Boliar, S.
  • Journal of Virology, Vol. 85, Issue 2
  • DOI: 10.1128/jvi.02006-10

Structural basis for diverse N-glycan recognition by HIV-1–neutralizing V1–V2–directed antibody PG16
journal, May 2013

  • Pancera, Marie; Shahzad-ul-Hussan, Syed; Doria-Rose, Nicole A.
  • Nature Structural & Molecular Biology, Vol. 20, Issue 7
  • DOI: 10.1038/nsmb.2600

Broad neutralization coverage of HIV by multiple highly potent antibodies
journal, September 2011

  • Walker, Laura M.; Huber, Michael; Doores, Katie J.
  • Nature, Vol. 477, Issue 7365
  • DOI: 10.1038/nature10373

Thermodynamics of Unfolding for Kazal-Type Serine Protease Inhibitors:  Entropic Stabilization of Ovomucoid First Domain by Glycosylation †
journal, February 1997

  • DeKoster, Gregory T.; Robertson, Andrew D.
  • Biochemistry, Vol. 36, Issue 8
  • DOI: 10.1021/bi962580b

HIV-1 Vaccine-Induced C1 and V2 Env-Specific Antibodies Synergize for Increased Antiviral Activities
journal, May 2014

  • Pollara, Justin; Bonsignori, Mattia; Moody, M. Anthony
  • Journal of Virology, Vol. 88, Issue 14
  • DOI: 10.1128/JVI.00156-14

Water penetration and escape in proteins
journal, February 2000

The O-Glycosylated Linker from the Trichoderma reesei Family 7 Cellulase Is a Flexible, Disordered Protein
journal, December 2010

  • Beckham, Gregg T.; Bomble, Yannick J.; Matthews, James F.
  • Biophysical Journal, Vol. 99, Issue 11
  • DOI: 10.1016/j.bpj.2010.10.032

Evolution of an HIV glycan–dependent broadly neutralizing antibody epitope through immune escape
journal, October 2012

  • Moore, Penny L.; Gray, Elin S.; Wibmer, C. Kurt
  • Nature Medicine, Vol. 18, Issue 11
  • DOI: 10.1038/nm.2985

Recognition of synthetic glycopeptides by HIV-1 broadly neutralizing antibodies and their unmutated ancestors
journal, October 2013

  • Alam, S. M.; Dennison, S. M.; Aussedat, B.
  • Proceedings of the National Academy of Sciences, Vol. 110, Issue 45
  • DOI: 10.1073/pnas.1317855110

The core trisaccharide of an N-linked glycoprotein intrinsically accelerates folding and enhances stability
journal, February 2009

  • Hanson, S. R.; Culyba, E. K.; Hsu, T. -L.
  • Proceedings of the National Academy of Sciences, Vol. 106, Issue 9
  • DOI: 10.1073/pnas.0810318105

The interplay of glycosylation and disulfide formation influences fibrillization in a prion protein fragment
journal, June 2003

  • Bosques, C. J.; Imperiali, B.
  • Proceedings of the National Academy of Sciences, Vol. 100, Issue 13
  • DOI: 10.1073/pnas.1232504100

The Influence of N-Linked Glycans on the Molecular Dynamics of the HIV-1 gp120 V3 Loop
journal, November 2013

Structural comparison of protein sequences around potential N-glycosylation sites
journal, August 1984

  • Mononen, Ilkka; Karjalainen, Erkki
  • Biochimica et Biophysica Acta (BBA) - Protein Structure and Molecular Enzymology, Vol. 788, Issue 3
  • DOI: 10.1016/0167-4838(84)90050-5

Estimation of absolute and relative entropies of macromolecules using the covariance matrix
journal, December 1993

Simulation Studies of Protein Folding/Unfolding Equilibrium under Polar and Nonpolar Confinement
journal, September 2011

  • Tian, Jianhui; Garcia, Angel E.
  • Journal of the American Chemical Society, Vol. 133, Issue 38
  • DOI: 10.1021/ja2054572

The Effect of Glycosylation on the Folding Kinetics of Erythropoietin
journal, September 2011

Crystal Structure of a Soluble Cleaved HIV-1 Envelope Trimer
journal, October 2013

Antibody neutralization and escape by HIV-1
journal, March 2003

  • Wei, Xiping; Decker, Julie M.; Wang, Shuyi
  • Nature, Vol. 422, Issue 6929
  • DOI: 10.1038/nature01470

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit
journal, February 2013

Early Low-Titer Neutralizing Antibodies Impede HIV-1 Replication and Select for Virus Escape
journal, May 2012

Chemical Synthesis of Highly Congested gp120 V1V2 N -Glycopeptide Antigens for Potential HIV-1-Directed Vaccines
journal, August 2013

  • Aussedat, Baptiste; Vohra, Yusuf; Park, Peter K.
  • Journal of the American Chemical Society, Vol. 135, Issue 35
  • DOI: 10.1021/ja405990z

Specific and Nonspecific Effects of Glycosylation
journal, April 2012

  • Ellis, Christopher R.; Maiti, Buddhadev; Noid, William G.
  • Journal of the American Chemical Society, Vol. 134, Issue 19
  • DOI: 10.1021/ja301005f

Comparison of multiple Amber force fields and development of improved protein backbone parameters
journal, November 2006

  • Hornak, Viktor; Abel, Robert; Okur, Asim
  • Proteins: Structure, Function, and Bioinformatics, Vol. 65, Issue 3
  • DOI: 10.1002/prot.21123

Structures of HIV-1 Env V1V2 with broadly neutralizing antibodies reveal commonalities that enable vaccine design
journal, December 2015

  • Gorman, Jason; Soto, Cinque; Yang, Max M.
  • Nature Structural & Molecular Biology, Vol. 23, Issue 1
  • DOI: 10.1038/nsmb.3144

Glycosylation Enhances Peptide Hydrophobic Collapse by Impairing Solvation
journal, June 2010

How Hydrophobicity and the Glycosylation Site of Glycans Affect Protein Folding and Stability: A Molecular Dynamics Simulation
journal, December 2011

  • Lu, Diannan; Yang, Cheng; Liu, Zheng
  • The Journal of Physical Chemistry B, Vol. 116, Issue 1
  • DOI: 10.1021/jp203926r

Co-evolution of a broadly neutralizing HIV-1 antibody and founder virus
journal, April 2013

  • Liao, Hua-Xin; Lynch, Rebecca; Zhou, Tongqing
  • Nature, Vol. 496, Issue 7446
  • DOI: 10.1038/nature12053

Envelope glycans of immunodeficiency virions are almost entirely oligomannose antigens
journal, July 2010

  • Doores, K. J.; Bonomelli, C.; Harvey, D. J.
  • Proceedings of the National Academy of Sciences, Vol. 107, Issue 31
  • DOI: 10.1073/pnas.1006498107

Stereochemistry of the N-glycosylation sites in glycoproteins
journal, July 1995

HIV Glycosylation: What Does It Portend?
journal, August 1992

  • Myers, Gerald; Lenroot, Rhoshell
  • AIDS Research and Human Retroviruses, Vol. 8, Issue 8
  • DOI: 10.1089/aid.1992.8.1459

Evolution of an HIV glycan–dependent broadly neutralizing antibody epitope through immune escape
text, January 2012

  • Tandile, Hermanus,; Abdool, Karim, Quarraisha; E., Lambson, Bronwen
  • The University of North Carolina at Chapel Hill University Libraries
  • DOI: 10.17615/e8bk-6082

Structure of HIV-1 gp120 V1/V2 domain with broadly neutralizing antibody PG9
journal, November 2011

  • McLellan, Jason S.; Pancera, Marie; Carrico, Chris
  • Nature, Vol. 480, Issue 7377
  • DOI: 10.1038/nature10696

Analysis of the Disulfide Bond Arrangement of the HIV-1 Envelope Protein CON-S gp140 ΔCFI Shows Variability in the V1 and V2 Regions
journal, February 2011

  • Go, Eden P.; Zhang, Ying; Menon, Sushma
  • Journal of Proteome Research, Vol. 10, Issue 2
  • DOI: 10.1021/pr100764a

LINCS: A linear constraint solver for molecular simulations
journal, September 1997

Composition and Antigenic Effects of Individual Glycan Sites of a Trimeric HIV-1 Envelope Glycoprotein
journal, March 2016

Perturbing the folding energy landscape of the bacterial immunity protein Im7 by site-specific N-linked glycosylation
journal, December 2010

  • Chen, M. M.; Bartlett, A. I.; Nerenberg, P. S.
  • Proceedings of the National Academy of Sciences, Vol. 107, Issue 52
  • DOI: 10.1073/pnas.1015356107

The V1V2 Region of HIV-1 gp120 Forms a Five-Stranded Beta Barrel
journal, May 2015

  • Pan, Ruimin; Gorny, Miroslaw K.; Zolla-Pazner, Susan
  • Journal of Virology, Vol. 89, Issue 15
  • DOI: 10.1128/JVI.00754-15

Asymmetric recognition of the HIV-1 trimer by broadly neutralizing antibody PG9
journal, February 2013

  • Julien, Jean-Philippe; Lee, Jeong Hyun; Cupo, Albert
  • Proceedings of the National Academy of Sciences, Vol. 110, Issue 11
  • DOI: 10.1073/pnas.1217537110

Removal of N-glycosylation sites of the yeast acid phosphatase severely affects protein folding.
journal, January 1991

Oxidative Refolding of Bovine Pancreatic RNases A and B Promoted by Asn-Glycans
journal, March 1998

Chaperone-Like Functions of High-Mannose Type and Complex-Type N-Glycans and Their Molecular Basis
journal, November 2002

HIV-1 Envelope Proteins and V1/V2 Domain Scaffolds with Mannose-5 to Improve the Magnitude and Quality of Protective Antibody Responses to HIV-1
journal, May 2014

  • Morales, Javier F.; Morin, Trevor J.; Yu, Bin
  • Journal of Biological Chemistry, Vol. 289, Issue 30
  • DOI: 10.1074/jbc.m114.554089

Evolution Rescues Folding of Human Immunodeficiency Virus-1 Envelope Glycoprotein GP120 Lacking a Conserved Disulfide Bond
journal, November 2008

  • Sanders, Rogier W.; Hsu, Shang-Te D.; van Anken, Eelco
  • Molecular Biology of the Cell, Vol. 19, Issue 11
  • DOI: 10.1091/mbc.E08-07-0670

Probing the Effect of the Outer Saccharide Residues of N -Linked Glycans on Peptide Conformation
journal, June 2001

  • O'Connor, Sarah E.; Pohlmann, Jens; Imperiali, Barbara
  • Journal of the American Chemical Society, Vol. 123, Issue 25
  • DOI: 10.1021/ja010094s

The Glycan Shield of HIV Is Predominantly Oligomannose Independently of Production System or Viral Clade
journal, August 2011

Parallel β-Sheet Secondary Structure Is Stabilized and Terminated by Interstrand Disulfide Cross-Linking
journal, December 2011

  • Almeida, Aaron M.; Li, Rebecca; Gellman, Samuel H.
  • Journal of the American Chemical Society, Vol. 134, Issue 1
  • DOI: 10.1021/ja208856c

Synthetic carbohydrate antigens for HIV vaccine design
journal, December 2013

Comparative Protein Structure Modeling Using MODELLER
journal, November 2007

  • Eswar, Narayanan; Webb, Ben; Marti-Renom, Marc A.
  • Current Protocols in Protein Science, Vol. 50, Issue 1
  • DOI: 10.1002/0471140864.ps0209s50

Simulation Studies of Protein Folding/Unfolding Equilibrium under Polar and Nonpolar Confinement
journal, September 2011

  • Tian, Jianhui; Garcia, Angel E.
  • Journal of the American Chemical Society, Vol. 133, Issue 38
  • DOI: 10.1021/ja2054572

The Effect of Glycosylation on the Folding Kinetics of Erythropoietin
journal, September 2011

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit
journal, February 2013

Context-Dependent Effects of Asparagine Glycosylation on Pin WW Folding Kinetics and Thermodynamics
journal, November 2010

  • Price, Joshua L.; Shental-Bechor, Dalit; Dhar, Apratim
  • Journal of the American Chemical Society, Vol. 132, Issue 43
  • DOI: 10.1021/ja106896t

Molecular dynamics with coupling to an external bath
journal, October 1984

  • Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.
  • The Journal of Chemical Physics, Vol. 81, Issue 8
  • DOI: 10.1063/1.448118

Co-evolution of a broadly neutralizing HIV-1 antibody and founder virus
journal, April 2013

  • Liao, Hua-Xin; Lynch, Rebecca; Zhou, Tongqing
  • Nature, Vol. 496, Issue 7446
  • DOI: 10.1038/nature12053

Exchange Monte Carlo Method and Application to Spin Glass Simulations
journal, June 1996

  • Hukushima, Koji; Nemoto, Koji
  • Journal of the Physical Society of Japan, Vol. 65, Issue 6
  • DOI: 10.1143/jpsj.65.1604

Structural Requirements for Additional N -Linked Carbohydrate on Recombinant Human Erythropoietin
journal, February 2004

  • Elliott, Steve; Chang, David; Delorme, Evelyne
  • Journal of Biological Chemistry, Vol. 279, Issue 16
  • DOI: 10.1074/jbc.m311095200

Comparison of multiple Amber force fields and development of improved protein backbone parameters
journal, November 2006

  • Hornak, Viktor; Abel, Robert; Okur, Asim
  • Proteins: Structure, Function, and Bioinformatics, Vol. 65, Issue 3
  • DOI: 10.1002/prot.21123

Effect of glycosylation on protein folding: A close look at thermodynamic stabilization
journal, June 2008

  • Shental-Bechor, D.; Levy, Y.
  • Proceedings of the National Academy of Sciences, Vol. 105, Issue 24
  • DOI: 10.1073/pnas.0801340105

Escape from Autologous Neutralizing Antibodies in Acute/Early Subtype C HIV-1 Infection Requires Multiple Pathways
journal, September 2009

Protein-disulfide Isomerase-mediated Reduction of Two Disulfide Bonds of HIV Envelope Glycoprotein 120 Occurs Post-CXCR4 Binding and Is Required for Fusion
journal, September 2002

  • Barbouche, Rym; Miquelis, Raymond; Jones, Ian M.
  • Journal of Biological Chemistry, Vol. 278, Issue 5
  • DOI: 10.1074/jbc.m205467200
    Sort by:
    [ × clear filter / sort ]

    Works referencing / citing this record:

    Visualization of the HIV-1 Env glycan shield across scales
    journal, October 2020

    • Berndsen, Zachary T.; Chakraborty, Srirupa; Wang, Xiaoning
    • Proceedings of the National Academy of Sciences, Vol. 117, Issue 45
    • DOI: 10.1073/pnas.2000260117

    Role of glycosylation in nucleating protein folding and stability
    journal, July 2017

    • Jayaprakash, Nisha Grandhi; Surolia, Avadhesha
    • Biochemical Journal, Vol. 474, Issue 14
    • DOI: 10.1042/bcj20170111

    Exploiting glycan topography for computational design of Env glycoprotein antigenicity
    journal, April 2018

    Completeness of HIV-1 Envelope Glycan Shield at Transmission Determines Neutralization Breadth
    journal, October 2018

    Exploiting glycan topography for computational design of Env glycoprotein antigenicity
    journal, April 2018

    HIV-1 Envelope Glycoproteins from Diverse Clades Differentiate Antibody Responses and Durability among Vaccinees
    journal, January 2018

    • Yates, Nicole L.; deCamp, Allan C.; Korber, Bette T.
    • Journal of Virology, Vol. 92, Issue 8
    • DOI: 10.1128/jvi.01843-17
      Sort by:
      [ × clear filter / sort ]

      Similar Records in DOE PAGES and OSTI.GOV collections: