A Mechanistic Understanding of Allosteric Immune Escape Pathways in the HIV-1 Envelope Glycoprotein

Viral Escape from Neutralizing Antibodies in Early Subtype A HIV-1 Infection Drives an Increase in Autologous Neutralization Breadth

(2013) Megan K. Murphy et al.   PLoS Pathogens

Dynamics based alignment of proteins: an alternative approach to quantify dynamic similarity

(2012) M�rton M�nz et al.   BMC BIOINFORMATICS

Exploring Residue Component Contributions to Dynamical Network Models of Allostery

(2012) Adam T. VanWart et al.   Journal of Chemical Theory and Computation

Neutralizing Antibody Escape during HIV-1 Mother-to-Child Transmission Involves Conformational Masking of Distal Epitopes in Envelope

(2012) Leslie Goo et al.   JOURNAL OF VIROLOGY

Solution Structure, Conformational Dynamics, and CD4-Induced Activation in Full-Length, Glycosylated, Monomeric HIV gp120

(2012) Miklos Guttman et al.   JOURNAL OF VIROLOGY

Immune-Correlates Analysis of an HIV-1 Vaccine Efficacy Trial

(2012) Barton F. Haynes et al.   NEW ENGLAND JOURNAL OF MEDICINE

Allosteric pathways in imidazole glycerol phosphate synthase

(2012) I. Rivalta et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Allosteric networks in thrombin distinguish procoagulant vs. anticoagulant activities

(2012) P. M. Gasper et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Unliganded HIV-1 gp120 core structures assume the CD4-bound conformation with regulation by quaternary interactions and variable loops

(2012) Y. D. Kwon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structural basis for germ-line gene usage of a potent class of antibodies targeting the CD4-binding site of HIV-1 gp120

(2012) Anthony P. West et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Early Low-Titer Neutralizing Antibodies Impede HIV-1 Replication and Select for Virus Escape

(2012) Katharine J. Bar et al.   PLoS Pathogens

Global trends in molecular epidemiology of HIV-1 during 2000–2007

(2011) Joris Hemelaar et al.   AIDS

Isolation of a Monoclonal Antibody That Targets the Alpha-2 Helix of gp120 and Represents the Initial Autologous Neutralizing-Antibody Response in an HIV-1 Subtype C-Infected Individual

(2011) E. S. Gray et al.   JOURNAL OF VIROLOGY

Structure of HIV-1 gp120 V1/V2 domain with broadly neutralizing antibody PG9

(2011) Jason S. McLellan et al.   NATURE

Trimeric HIV-1 glycoprotein gp140 immunogens and native HIV-1 envelope glycoproteins display the same closed and open quaternary molecular architectures

(2011) A. Harris et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Sequence and Structural Convergence of Broad and Potent HIV Antibodies That Mimic CD4 Binding

(2011) J. F. Scheid et al.   SCIENCE

A Potent and Broad Neutralizing Antibody Recognizes and Penetrates the HIV Glycan Shield

(2011) R. Pejchal et al.   SCIENCE

Coherent Conformational Degrees of Freedom as a Structural Basis for Allosteric Communication

(2011) Simon Mitternacht et al.   PLoS Computational Biology

Binding Leverage as a Molecular Basis for Allosteric Regulation

(2011) Simon Mitternacht et al.   PLoS Computational Biology

Is My Network Module Preserved and Reproducible?

(2011) Peter Langfelder et al.   PLoS Computational Biology

Recurrent Signature Patterns in HIV-1 B Clade Envelope Glycoproteins Associated with either Early or Chronic Infections

(2011) S. Gnanakaran et al.   PLoS Pathogens

Global Dynamics of Proteins: Bridging Between Structure and Function

(2010) Ivet Bahar et al.   Annual Review of Biophysics

Local Conformational Stability of HIV-1 gp120 in Unliganded and CD4-Bound States as Defined by Amide Hydrogen/Deuterium Exchange

(2010) L. Kong et al.   JOURNAL OF VIROLOGY

Structure of a clade C HIV-1 gp120 bound to CD4 and CD4-induced antibody reveals anti-CD4 polyreactivity

(2010) Ron Diskin et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Transmission of Single HIV-1 Genomes and Dynamics of Early Immune Escape Revealed by Ultra-Deep Sequencing

(2010) Will Fischer et al.   PLoS One

An Ensemble View of Allostery

(2010) V. J. Hilser   SCIENCE

Structural Basis for Broad and Potent Neutralization of HIV-1 by Antibody VRC01

(2010) T. Zhou et al.   SCIENCE

Identification of amino acid substitutions associated with neutralization phenotype in the human immunodeficiency virus type-1 subtype C gp120

(2010) Jennifer L. Kirchherr et al.   VIROLOGY

Genetic Signatures in the Envelope Glycoproteins of HIV-1 that Associate with Broadly Neutralizing Antibodies

(2010) S. Gnanakaran et al.   PLoS Computational Biology

Appreciating HIV Type 1 Diversity: Subtype Differences in Env

(2009) Rebecca M. Lynch et al.   AIDS RESEARCH AND HUMAN RETROVIRUSES

Normal Mode Analysis of Biomolecular Structures: Functional Mechanisms of Membrane Proteins

(2009) Ivet Bahar et al.   CHEMICAL REVIEWS

A new human immunodeficiency virus derived from gorillas

(2009) Jean-Christophe Plantier et al.   NATURE MEDICINE

Structure of HIV-1 gp120 with gp41-interactive region reveals layered envelope architecture and basis of conformational mobility

(2009) M. Pancera et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dynamical networks in tRNA:protein complexes

(2009) A. Sethi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structural Basis of Immune Evasion at the Site of CD4 Attachment on HIV-1 gp120

(2009) L. Chen et al.   SCIENCE

The Origin of Allosteric Functional Modulation: Multiple Pre-existing Pathways

(2009) Antonio del Sol et al.   STRUCTURE

HIV-1-specific antibody responses during acute and chronic HIV-1 infection

(2009) Georgia D Tomaras et al.   Current Opinion in HIV and AIDS

Limited Neutralizing Antibody Specificities Drive Neutralization Escape in Early HIV-1 Subtype C Infection

(2009) Penny L. Moore et al.   PLoS Pathogens

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

(2009) Rong Rong et al.   PLoS Pathogens

Energy Flow in Proteins

(2008) David M. Leitner   Annual Review of Physical Chemistry

Dynamics of Recognition between tRNA and Elongation Factor Tu

(2008) John Eargle et al.   JOURNAL OF MOLECULAR BIOLOGY

Molecular architecture of native HIV-1 gp120 trimers

(2008) Jun Liu et al.   NATURE

The Challenge of HIV-1 Subtype Diversity

(2008) Barbara S. Taylor et al.   NEW ENGLAND JOURNAL OF MEDICINE

Allostery and cooperativity revisited

(2008) Qiang Cui et al.   PROTEIN SCIENCE

Flexible Fitting of Atomic Structures into Electron Microscopy Maps Using Molecular Dynamics

(2008) Leonardo G. Trabuco et al.   STRUCTURE

Contact rearrangements form coupled networks from local motions in allosteric proteins

(2007) Michael D. Daily et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Estimating drug efficacy and viral dynamic parameters: HIV and HCV

(2007) Alan S. Perelson et al.   STATISTICS IN MEDICINE