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

Rigidity versus flexibility: the dilemma of understanding protein thermal stability

(2015) Andrey Karshikoff et al.   FEBS Journal

Exact milestoning

(2015) Juan M. Bello-Rivas et al.   JOURNAL OF CHEMICAL PHYSICS

Mechanism of Substrate Translocation by a Ring-Shaped ATPase Motor at Millisecond Resolution

(2015) Wen Ma et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Allostery vs. “allokairy”: Fig. 1.

(2015) Vincent J. Hilser 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

Pathways of allosteric regulation in Hsp70 chaperones

(2015) Roman Kityk et al.   Nature Communications

Investigating Drug–Target Association and Dissociation Mechanisms Using Metadynamics-Based Algorithms

(2014) Andrea Cavalli et al.   ACCOUNTS OF CHEMICAL RESEARCH

Quantitative method for the assignment of hinge and shear mechanism in protein domain movements

(2014) Daniel Taylor et al.   BIOINFORMATICS

Molecular Dynamics Simulation Studies on the Positive Cooperativity of the Kemptide Substrate with Protein Kinase A Induced by the ATP Ligand

(2014) Chaoqun Li et al.   JOURNAL OF PHYSICAL CHEMISTRY B

The ensemble nature of allostery

(2014) Hesam N. Motlagh et al.   NATURE

iMODS: internal coordinates normal mode analysis server

(2014) José Ramón López-Blanco et al.   NUCLEIC ACIDS RESEARCH

DUET: a server for predicting effects of mutations on protein stability using an integrated computational approach

(2014) D. E. V. Pires et al.   NUCLEIC ACIDS RESEARCH

Redistribution of Flexibility in Stabilizing Antibody Fragment Mutants Follows Le Châtelier’s Principle

(2014) Tong Li et al.   PLoS One

Activation pathway of Src kinase reveals intermediate states as targets for drug design

(2014) Diwakar Shukla et al.   Nature Communications

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

Exploring the Conformational Transitions of Biomolecular Systems Using a Simple Two-State Anisotropic Network Model

(2014) Avisek Das 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

Molecular Chaperone Functions in Protein Folding and Proteostasis

(2013) Yujin E. Kim et al.   Annual Review of Biochemistry

The Underappreciated Role of Allostery in the Cellular Network

(2013) Ruth Nussinov et al.   Annual Review of Biophysics

Exploration of conformational transition pathways from coarse-grained simulations

(2013) Pedro Sfriso et al.   BIOINFORMATICS

mCSM: predicting the effects of mutations in proteins using graph-based signatures

(2013) Douglas E. V. Pires et al.   BIOINFORMATICS

Allostery in Disease and in Drug Discovery

(2013) Ruth Nussinov et al.   CELL

Identification of an Allosteric Pocket on Human Hsp70 Reveals a Mode of Inhibition of This Therapeutically Important Protein

(2013) Anna Rodina et al.   CHEMISTRY & BIOLOGY

Allo-Network Drugs: Extension of the Allosteric Drug Concept to Protein- Protein Interaction and Signaling Networks

(2013) Andras Szilagyi et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

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

(2013) Martin Sikor et al.   EMBO JOURNAL

Stability Mechanisms of Laccase Isoforms using a Modified FoldX Protocol Applicable to Widely Different Proteins

(2013) Niels J. Christensen et al.   Journal of Chemical Theory and Computation

Grcarma: A fully automated task-oriented interface for the analysis of molecular dynamics trajectories

(2013) Panagiotis I. Koukos et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Chaperone machines for protein folding, unfolding and disaggregation

(2013) Helen Saibil   NATURE REVIEWS MOLECULAR CELL BIOLOGY

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

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

Depth: a web server to compute depth, cavity sizes, detect potential small-molecule ligand-binding cavities and predict the pKa of ionizable residues in proteins

(2013) Kuan Pern Tan et al.   NUCLEIC ACIDS RESEARCH

Structure and dynamics of molecular networks: A novel paradigm of drug discovery

(2013) Peter Csermely et al.   PHARMACOLOGY & THERAPEUTICS

Differential Modulation of Functional Dynamics and Allosteric Interactions in the Hsp90-Cochaperone Complexes with p23 and Aha1: A Computational Study

(2013) Kristin Blacklock et al.   PLoS One

Effects of oncogenic mutations on the conformational free-energy landscape of EGFR kinase

(2013) L. Sutto et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Allosteric Conformational Barcodes Direct Signaling in the Cell

(2013) Ruth Nussinov et al.   STRUCTURE

Hsp70 chaperone dynamics and molecular mechanism

(2013) Matthias P. Mayer   TRENDS IN BIOCHEMICAL SCIENCES

Mutational Analysis of Sse1 (Hsp110) Suggests an Integral Role for this Chaperone in Yeast Prion Propagation In Vivo

(2013) Ciara Moran et al.   G3-Genes Genomes Genetics

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

Protein function and allostery: a dynamic relationship

(2012) Charalampos G. Kalodimos   Annals of the New York Academy of Sciences

Allostery and the Monod-Wyman-Changeux Model After 50 Years

(2012) Jean-Pierre Changeux   Annual Review of Biophysics

Structural and Energetic Basis of Allostery

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

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

Hsp70 Protein Complexes as Drug Targets

(2012) Victoria A. Assimon et al.   CURRENT PHARMACEUTICAL DESIGN

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

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

Accurate Stabilities of Laccase Mutants Predicted with a Modified FoldX Protocol

(2012) Niels J. Christensen et al.   Journal of Chemical Information and Modeling

Finding Conformational Transition Pathways from Discrete Molecular Dynamics Simulations

(2012) Pedro Sfriso et al.   Journal of Chemical Theory and Computation

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

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

(2012) Roman Kityk et al.   MOLECULAR CELL

Protein activity regulation by conformational entropy

(2012) Shiou-Ru Tzeng 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

Structure-based model of allostery predicts coupling between distant sites

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

Agonism/antagonism switching in allosteric ensembles

(2012) H. N. Motlagh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Entropy-enthalpy transduction caused by conformational shifts can obscure the forces driving protein-ligand binding

(2012) A. T. Fenley 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

A graphical interface for the FoldX forcefield

(2011) J. Van Durme et al.   BIOINFORMATICS

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

How do dynamic cellular signals travel long distances?

(2011) Ruth Nussinov   Molecular BioSystems

Molecular chaperones in protein folding and proteostasis

(2011) F. Ulrich Hartl et al.   NATURE

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

SDM--a server for predicting effects of mutations on protein stability and malfunction

(2011) C. L. Worth et al.   NUCLEIC ACIDS RESEARCH

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

Dynamic Allostery: Linkers Are Not Merely Flexible

(2011) Buyong Ma et al.   STRUCTURE

Energetics of Nucleotide-Induced DnaK Conformational States

(2010) Stefka G. Taneva et al.   BIOCHEMISTRY

Interaction Energy Based Protein Structure Networks

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

Targeting biomolecular flexibility with metadynamics

(2010) Vanessa Leone et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Protein dynamics and allostery: an NMR view

(2010) Shiou-Ru Tzeng et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Heat Shock Protein 70 (Hsp70) as an Emerging Drug Target

(2010) Christopher G. Evans et al.   JOURNAL OF MEDICINAL CHEMISTRY

Interaction of the Hsp110 Molecular Chaperones from S. cerevisiae with Substrate Protein

(2010) Sigrun Polier et al.   JOURNAL OF MOLECULAR BIOLOGY

Lactose Binding to Galectin-1 Modulates Structural Dynamics, Increases Conformational Entropy, and Occurs with Apparent Negative Cooperativity

(2010) Irina V. Nesmelova et al.   JOURNAL OF MOLECULAR BIOLOGY

Correlating allostery with rigidity

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

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

Induced fit, conformational selection and independent dynamic segments: an extended view of binding events

(2010) Peter Csermely et al.   TRENDS IN BIOCHEMICAL SCIENCES

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

ATP-Induced Conformational Changes in Hsp70: Molecular Dynamics and Experimental Validation of an in Silico Predicted Conformation

(2009) Hyung-June Woo et al.   BIOCHEMISTRY

Allostery in Hsp70 Chaperones Is Transduced by Subdomain Rotations

(2009) Akash Bhattacharya et al.   JOURNAL OF MOLECULAR BIOLOGY

Protein allostery, signal transmission and dynamics: a classification scheme of allosteric mechanisms

(2009) Chung-Jung Tsai et al.   Molecular BioSystems

Prodepth: Predict Residue Depth by Support Vector Regression Approach from Protein Sequences Only

(2009) Jiangning Song 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

Protein flexibility from discrete molecular dynamics simulations using quasi-physical potentials

(2009) Agustí Emperador et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

(2009) Antonio del Sol et al.   STRUCTURE

Allosteric Communication Occurs via Networks of Tertiary and Quaternary Motions in Proteins

(2009) Michael D. Daily et al.   PLoS Computational Biology

Exploring the Suitability of Coarse-Grained Techniques for the Representation of Protein Dynamics

(2008) Agustí Emperador et al.   BIOPHYSICAL JOURNAL

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

(2008) Sigrun Polier et al.   CELL

Crystal Structures of the 70-kDa Heat Shock Proteins in Domain Disjoining Conformation

(2008) Yi-Wei Chang et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Hsp110 Is a Nucleotide-activated Exchange Factor for Hsp70

(2008) Claes Andréasson et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Allostery: Absence of a Change in Shape Does Not Imply that Allostery Is Not at Play

(2008) Chung-Jung Tsai et al.   JOURNAL OF MOLECULAR BIOLOGY

Finding Transition Pathways Using the String Method with Swarms of Trajectories

(2008) Albert C. Pan et al.   JOURNAL OF PHYSICAL CHEMISTRY B

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

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