Computational Analysis of Residue Interaction Networks and Coevolutionary Relationships in the Hsp70 Chaperones: A Community-Hopping Model of Allosteric Regulation and Communication

CoeViz: a web-based tool for coevolution analysis of protein residues

(2016) Frazier N. Baker et al.   BMC BIOINFORMATICS

Probing Allosteric Inhibition Mechanisms of the Hsp70 Chaperone Proteins Using Molecular Dynamics Simulations and Analysis of the Residue Interaction Networks

(2016) Gabrielle Stetz et al.   Journal of Chemical Information and Modeling

Molecular dynamics simulations and modelling of the residue interaction networks in the BRAF kinase complexes with small molecule inhibitors: probing the allosteric effects of ligand-induced kinase dimerization and paradoxical activation

(2016) G. M. Verkhivker   Molecular BioSystems

Residues Coevolution Guides the Systematic Identification of Alternative Functional Conformations in Proteins

(2016) Pedro Sfriso et al.   STRUCTURE

An atomistic view of Hsp70 allosteric crosstalk: from the nucleotide to the substrate binding domain and back

(2016) Federica Chiappori et al.   Scientific Reports

The anisotropic network model web server at 2015 (ANM 2.0)

(2015) E. Eyal et al.   BIOINFORMATICS

Covariation Is a Poor Measure of Molecular Coevolution

(2015) David Talavera et al.   MOLECULAR BIOLOGY AND EVOLUTION

Integrated Analysis of Residue Coevolution and Protein Structures Capture Key Protein Sectors in HIV-1 Proteins

(2015) Yuqi Zhao et al.   PLoS One

Molecular Determinants Underlying Binding Specificities of the ABL Kinase Inhibitors: Combining Alanine Scanning of Binding Hot Spots with Network Analysis of Residue Interactions and Coevolution

(2015) Amanda Tse et al.   PLoS One

Dancing through Life: Molecular Dynamics Simulations and Network-Centric Modeling of Allosteric Mechanisms in Hsp70 and Hsp110 Chaperone Proteins

(2015) Gabrielle Stetz et al.   PLoS One

Nucleotides regulate the mechanical hierarchy between subdomains of the nucleotide binding domain of the Hsp70 chaperone DnaK

(2015) Daniela Bauer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Substrate-binding domain conformational dynamics mediate Hsp70 allostery

(2015) Anastasia Zhuravleva et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

From residue coevolution to protein conformational ensembles and functional dynamics

(2015) Ludovico Sutto et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

In silicomutational studies of Hsp70 disclose sites with distinct functional attributes

(2015) Gizem Ozbaykal et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Pathways of allosteric regulation in Hsp70 chaperones

(2015) Roman Kityk et al.   Nature Communications

Large-Scale Conformational Transitions and Dimerization Are Encoded in the Amino-Acid Sequences of Hsp70 Chaperones

(2015) Duccio Malinverni et al.   PLoS Computational Biology

Biophysics of protein evolution and evolutionary protein biophysics

(2014) T. Sikosek et al.   Journal of the Royal Society Interface

The ensemble nature of allostery

(2014) Hesam N. Motlagh et al.   NATURE

Common functionally important motions of the nucleotide-binding domain of Hsp70

(2014) Ewa I. Gołaś et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

ATPase Subdomain IA Is a Mediator of Interdomain Allostery in Hsp70 Molecular Chaperones

(2014) Ignacio J. General et al.   PLoS Computational Biology

A Unified View of “How Allostery Works”

(2014) Chung-Jung Tsai et al.   PLoS Computational Biology

Computational Modeling of Allosteric Regulation in the Hsp90 Chaperones: A Statistical Ensemble Analysis of Protein Structure Networks and Allosteric Communications

(2014) Kristin Blacklock et al.   PLoS Computational Biology

Real-time observation of the conformational dynamics of mitochondrial Hsp70 by spFRET

(2013) Martin Sikor et al.   EMBO JOURNAL

The Complex Evolutionary Dynamics of Hsp70s: A Genomic and Functional Perspective

(2013) Jacek Kominek et al.   Genome Biology and Evolution

Network deconvolution as a general method to distinguish direct dependencies in networks

(2013) Soheil Feizi et al.   NATURE BIOTECHNOLOGY

Emerging methods in protein co-evolution

(2013) David de Juan et al.   NATURE REVIEWS GENETICS

Allosteric opening of the polypeptide-binding site when an Hsp70 binds ATP

(2013) Ruifeng Qi et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

iPfam: a database of protein family and domain interactions found in the Protein Data Bank

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Coevolutionary signals across protein lineages help capture multiple protein conformations

(2013) F. Morcos et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

3Drefine: Consistent protein structure refinement by optimizing hydrogen bonding network and atomic-level energy minimization

(2013) Debswapna Bhattacharya et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Hsp70 chaperone dynamics and molecular mechanism

(2013) Matthias P. Mayer   TRENDS IN BIOCHEMICAL SCIENCES

Using Steered Molecular Dynamics to Predict and Assess Hsp70 Substrate-Binding Domain Mutants that Alter Prion Propagation

(2013) Linan Xu et al.   PLoS Computational Biology

Identification of Key Hinge Residues Important for Nucleotide-Dependent Allostery in E. coli Hsp70/DnaK

(2013) Peter Man-Un Ung et al.   PLoS Computational Biology

Decipher the Mechanisms of Protein Conformational Changes Induced by Nucleotide Binding through Free-Energy Landscape Analysis: ATP Binding to Hsp70

(2013) Adrien Nicolaï et al.   PLoS Computational Biology

Structural and Energetic Basis of Allostery

(2012) Vincent J. Hilser et al.   Annual Review of Biophysics

Identifying structural domains of proteins using clustering

(2012) Howard J Feldman   BMC BIOINFORMATICS

Disentangling evolutionary signals: conservation, specificity determining positions and coevolution. Implication for catalytic residue prediction

(2012) Elin Teppa et al.   BMC BIOINFORMATICS

Rigidity and flexibility of biological networks

(2012) M. E. Gaspar et al.   Briefings in Functional Genomics

An Interdomain Energetic Tug-of-War Creates the Allosterically Active State in Hsp70 Molecular Chaperones

(2012) Anastasia Zhuravleva et al.   CELL

Disordered Proteins and Network Disorder in Network Descriptions of Protein Structure, Dynamics and Function: Hypotheses and a Comprehensive Review

(2012) Peter Csermely et al.   CURRENT PROTEIN & PEPTIDE SCIENCE

Molecular dynamics simulations and statistical coupling analysis reveal functional coevolution network of oncogenic mutations in the CDKN2A-CDK6 complex

(2012) Jingwen Wang et al.   FEBS LETTERS

Conformational dynamics of full-length inducible human Hsp70 derived from microsecond molecular dynamics simulations in explicit solvent

(2012) Adrien Nicolaï et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Simulation of the Opening and Closing of Hsp70 Chaperones by Coarse-Grained Molecular Dynamics

(2012) Ewa Gołaś et al.   Journal of Chemical Theory and Computation

Sequence Evolution Correlates with Structural Dynamics

(2012) Ying Liu et al.   MOLECULAR BIOLOGY AND EVOLUTION

Structure and Dynamics of the ATP-Bound Open Conformation of Hsp70 Chaperones

(2012) Roman Kityk et al.   MOLECULAR CELL

The spatial architecture of protein function and adaptation

(2012) Richard N. McLaughlin Jr et al.   NATURE

Probing Molecular Mechanisms of the Hsp90 Chaperone: Biophysical Modeling Identifies Key Regulators of Functional Dynamics

(2012) Anshuman Dixit et al.   PLoS One

Mapping the Mutual Information Network of Enzymatic Families in the Protein Structure to Unveil Functional Features

(2012) Daniel Aguilar et al.   PLoS One

Evaluation of competing J domain:Hsp70 complex models in light of existing mutational and NMR data

(2012) R. Sousa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular Mechanism of Allosteric Communication in Hsp70 Revealed by Molecular Dynamics Simulations

(2012) Federica Chiappori et al.   PLoS Computational Biology

Probing the Allosteric Mechanism in Pyrrolysyl-tRNA Synthetase Using Energy-Weighted Network Formalism

(2011) Moitrayee Bhattacharyya et al.   BIOCHEMISTRY

Unique Peptide Substrate Binding Properties of 110-kDa Heat-shock Protein (Hsp110) Determine Its Distinct Chaperone Activity

(2011) Xinping Xu et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Molecular Evolution of Protein Conformational Changes Revealed by a Network of Evolutionarily Coupled Residues

(2011) Jouhyun Jeon et al.   MOLECULAR BIOLOGY AND EVOLUTION

Substrate discrimination of the chaperone BiP by autonomous and cochaperone-regulated conformational transitions

(2011) Moritz Marcinowski et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Mechanics of Hsp70 chaperones enables differential interaction with client proteins

(2011) Rainer Schlecht et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Direct-coupling analysis of residue coevolution captures native contacts across many protein families

(2011) F. Morcos et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Heat shock protein 70 kDa chaperone/DnaJ cochaperone complex employs an unusual dynamic interface

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

Allosteric signal transmission in the nucleotide-binding domain of 70-kDa heat shock protein (Hsp70) molecular chaperones

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

Global Dynamics of Proteins: Bridging Between Structure and Function

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

Energetics of Nucleotide-Induced DnaK Conformational States

(2010) Stefka G. Taneva et al.   BIOCHEMISTRY

Functional Modes and Residue Flexibility Control the Anisotropic Response of Guanylate Kinase to Mechanical Stress

(2010) Sophie Sacquin-Mora et al.   BIOPHYSICAL JOURNAL

Interaction Energy Based Protein Structure Networks

(2010) M.S. Vijayabaskar et al.   BIOPHYSICAL JOURNAL

Correlating allostery with rigidity

(2010) A. J. Rader et al.   Molecular BioSystems

Gymnastics of Molecular Chaperones

(2010) Matthias P. Mayer   MOLECULAR CELL

The Conformational Dynamics of the Mitochondrial Hsp70 Chaperone

(2010) Koyeli Mapa et al.   MOLECULAR CELL

An interdomain sector mediating allostery in Hsp70 molecular chaperones

(2010) Robert G Smock et al.   Molecular Systems Biology

Structural and Functional Roles of Coevolved Sites in Proteins

(2010) Saikat Chakrabarti et al.   PLoS One

Elucidation of the conformational free energy landscape in H.pylori LuxS and its implications to catalysis

(2010) Moitrayee Bhattacharyya et al.   BMC STRUCTURAL BIOLOGY

Networks of High Mutual Information Define the Structural Proximity of Catalytic Sites: Implications for Catalytic Residue Identification

(2010) Cristina Marino Buslje et al.   PLoS Computational Biology

Role of Hsp70 ATPase Domain Intrinsic Dynamics and Sequence Evolution in Enabling its Functional Interactions with NEFs

(2010) Ying Liu et al.   PLoS Computational Biology

Correction for phylogeny, small number of observations and data redundancy improves the identification of coevolving amino acid pairs using mutual information

(2009) C. M. Buslje et al.   BIOINFORMATICS

Protein Sectors: Evolutionary Units of Three-Dimensional Structure

(2009) Najeeb Halabi et al.   CELL

Computing Highly Correlated Positions Using Mutual Information and Graph Theory for G Protein-Coupled Receptors

(2009) Sarosh N. Fatakia et al.   PLoS One

Correlated Mutation Analysis on the Catalytic Domains of Serine/Threonine Protein Kinases

(2009) Feng Xu et al.   PLoS One

Solution conformation of wild-type E. coli Hsp70 (DnaK) chaperone complexed with ADP and substrate

(2009) E. B. Bertelsen 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

Allostery and conformational free energy changes in human tryptophanyl-tRNA synthetase from essential dynamics and structure networks

(2009) Moitrayee Bhattacharyya et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Variations in Clique and Community Patterns in Protein Structures during Allosteric Communication: Investigation of Dynamically Equilibrated Structures of Methionyl tRNA Synthetase Complexes†

(2008) Amit Ghosh et al.   BIOCHEMISTRY

Structural Basis for the Cooperation of Hsp70 and Hsp110 Chaperones in Protein Folding

(2008) Sigrun Polier et al.   CELL

From hatching to dispatching: the multiple cellular roles of the Hsp70 molecular chaperone machinery

(2008) Eirini Meimaridou et al.   JOURNAL OF MOLECULAR ENDOCRINOLOGY

Insights into the structural dynamics of the Hsp110-Hsp70 interaction reveal the mechanism for nucleotide exchange activity

(2008) C. Andreasson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Coevolution in defining the functional specificity

(2008) Saikat Chakrabarti et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

The solution structure of the bacterial HSP70 chaperone protein domain DnaK(393-507) in complex with the peptide NRLLLTG

(2003) Shawn Y. Stevens et al.   PROTEIN SCIENCE