Cargando…

Free Energy Perturbation Calculation of Relative Binding Free Energy between Broadly Neutralizing Antibodies and the gp120 Glycoprotein of HIV-1

Direct calculation of relative binding affinities between antibodies and antigens is a long-sought goal. However, despite substantial efforts, no generally applicable computational method has been described. Here, we describe a systematic free energy perturbation (FEP) protocol and calculate the bin...

Descripción completa

Detalles Bibliográficos
Autores principales:	Clark, Anthony J., Gindin, Tatyana, Zhang, Baoshan, Wang, Lingle, Abel, Robert, Murret, Colleen S., Xu, Fang, Bao, Amy, Lu, Nina J., Zhou, Tongqing, Kwong, Peter D., Shapiro, Lawrence, Honig, Barry, Friesner, Richard A.
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Elsevier 2017
Materias:	Article
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5383735/ https://www.ncbi.nlm.nih.gov/pubmed/27908641 http://dx.doi.org/10.1016/j.jmb.2016.11.021

Ejemplares similares

Free Energy Perturbation Calculations of Mutation Effects on SARS-CoV-2 RBD::ACE2 Binding Affinity
por: Sergeeva, Alina P., et al.
Publicado: (2023)

Calculation of the Free Energy and Cooperativity of Protein Folding
por: Kentsis, Alex, et al.
Publicado: (2007)

Predicting Binding Affinities for GPCR Ligands Using Free-Energy Perturbation
por: Lenselink, Eelke B., et al.
Publicado: (2016)

Internalization and Axonal Transport of the HIV Glycoprotein gp120
por: Berth, Sarah, et al.
Publicado: (2015)

Converging ligand‐binding free energies obtained with free‐energy perturbations at the quantum mechanical level
por: Olsson, Martin A., et al.
Publicado: (2016)

Free energy perturbation (FEP)-guided scaffold hopping
por: Wu, Deyan, et al.
Publicado: (2022)

Mammalian production of an isotopically enriched outer domain of the HIV-1 gp120 glycoprotein for NMR spectroscopy
por: Sastry, Mallika, et al.
Publicado: (2011)

Structural Plasticity and Conformational Transitions of HIV Envelope Glycoprotein gp120
por: Korkut, Anil, et al.
Publicado: (2012)

Backbone Free Energy Estimator Applied to Viral Glycoproteins
por: Penner, Robert C.
Publicado: (2020)

Evolution of the HIV-1 envelope glycoproteins with a disulfide bond between gp120 and gp41
por: Sanders, Rogier W, et al.
Publicado: (2004)

The maximal and current accuracy of rigorous protein-ligand binding free energy calculations
por: Ross, Gregory A., et al.
Publicado: (2023)

Use of multistate Bennett acceptance ratio method for free-energy calculations from enhanced sampling and free-energy perturbation
por: Matsunaga, Yasuhiro, et al.
Publicado: (2022)

Perturbation Free-Energy Toolkit: An Automated Alchemical Topology Builder
por: Petrov, Drazen
Publicado: (2021)

How To Deal with Multiple Binding Poses in Alchemical Relative Protein–Ligand Binding Free Energy Calculations
por: Kaus, Joseph W., et al.
Publicado: (2015)

Modeling of Oligosaccharides within Glycoproteins from Free-Energy Landscapes
por: Turupcu, Aysegül, et al.
Publicado: (2017)

Bispecific Anti-HIV Immunoadhesins That Bind Gp120 and Gp41 Have Broad and Potent HIV-Neutralizing Activity
por: Pincus, Seth H., et al.
Publicado: (2021)

Supersite of immune vulnerability on the glycosylated face of HIV-1 envelope glycoprotein gp120
por: Kong, Leopold, et al.
Publicado: (2013)

HIV-1 gp120 envelope glycoprotein determinants for cytokine burst in human monocytes
por: Levast, Benoît, et al.
Publicado: (2017)

Predicting resistance of clinical Abl mutations to targeted kinase inhibitors using alchemical free-energy calculations
por: Hauser, Kevin, et al.
Publicado: (2018)

Assessing the stability of free-energy perturbation calculations by performing variations in the method
por: Manzoni, Francesco, et al.
Publicado: (2018)

Large-scale application of free energy perturbation calculations for antibody design
por: Zhu, Fangqiang, et al.
Publicado: (2022)

Broad and potent HIV-1 neutralization by a human antibody that binds the gp41-120 interface
por: Huang, Jinghe, et al.
Publicado: (2014)

Structural definition of a conserved neutralization epitope on HIV-1 gp120
por: Zhou, Tongqing, et al.
Publicado: (2007)

NMR spectroscopy of HIV-1 gp120 outer domain
por: Sastry, M, et al.
Publicado: (2012)

Structural definition for a new modality of broad and potent antibody neutralization at the CD4-binding site on HIV-1 gp120
por: Zhou, T, et al.
Publicado: (2012)

Crystal Structures of HIV-1 gp120 Envelope Glycoprotein in Complex with NBD Analogues That Target the CD4-Binding Site
por: Kwon, Young Do, et al.
Publicado: (2014)

Exploring the Activity Profile of TbrPDEB1 and hPDE4 Inhibitors Using Free Energy Perturbation
por: Zara, Lorena, et al.
Publicado: (2022)

Identification and Characterization of a Broadly Cross-Reactive HIV-1 Human Monoclonal Antibody That Binds to Both gp120 and gp41
por: Zhang, Mei-Yun, et al.
Publicado: (2012)

Peptides presenting the binding site of human CD4 for the HIV-1 envelope glycoprotein gp120
por: Meier, Julia, et al.
Publicado: (2012)

Antigenic Properties of the Human Immunodeficiency Virus Envelope Glycoprotein Gp120 on Virions Bound to Target Cells
por: Mengistu, Meron, et al.
Publicado: (2015)

HIV Glycoprotein Gp120 Impairs Fast Axonal Transport by Activating Tak1 Signaling Pathways
por: Berth, Sarah H., et al.
Publicado: (2016)

Release of gp120 Restraints Leads to an Entry-Competent Intermediate State of the HIV-1 Envelope Glycoproteins
por: Herschhorn, Alon, et al.
Publicado: (2016)

Contribution of the gp120 V3 loop to envelope glycoprotein trimer stability in primate immunodeficiency viruses
por: Bowder, Dane, et al.
Publicado: (2018)

An Improved Free Energy Perturbation FEP+ Sampling Protocol for Flexible Ligand-Binding Domains
por: Fratev, Filip, et al.
Publicado: (2019)

Antiviral Activity and Crystal Structures of HIV-1 gp120 Antagonists
por: Curreli, Francesca, et al.
Publicado: (2022)

Neutralizing antibodies to human immunodeficiency virus type-1 gp120 induce envelope glycoprotein subunit dissociation
Publicado: (1996)

Correction: Antigenic Properties of the Human Immunodeficiency Virus Envelope Glycoprotein Gp120 on Virions Bound to Target Cells
Publicado: (2015)

Prediction of HIV-associated neurocognitive disorder (HAND) from three genetic features of envelope gp120 glycoprotein
por: Ogishi, Masato, et al.
Publicado: (2018)

Structure-Based Stabilization of HIV-1 gp120 Enhances Humoral Immune Responses to the Induced Co-Receptor Binding Site
por: Dey, Barna, et al.
Publicado: (2009)

Broad-high operating temperature range and enhanced energy storage performances in lead-free ferroelectrics
por: Zhao, Weichen, et al.
Publicado: (2023)

Cannot write session to /tmp/vufind_sessions/sess_e97am13l6hbpi5kkq3ihb3ki46