Computationally-Aided Modeling of Hsp70–Client Interactions: Past, Present, and Future

Mapping the degradation pathway of a disease-linked aspartoacylase variant

(2021) Sarah K. Gersing et al.   PLoS Genetics

Evaluation of in silico tools for the prediction of protein and peptide aggregation on diverse datasets

(2021) R Prabakaran et al.   BRIEFINGS IN BIOINFORMATICS

Molecular Dynamics Scoring of Protein–Peptide Models Derived from Coarse-Grained Docking

(2021) Mateusz Zalewski et al.   MOLECULES

Structure of Hsp90–Hsp70–Hop–GR reveals the Hsp90 client-loading mechanism

(2021) Ray Yu-Ruei Wang et al.   NATURE

Reversible amyloids of pyruvate kinase couple cell metabolism and stress granule disassembly

(2021) Gea Cereghetti et al.   NATURE CELL BIOLOGY

Selective promiscuity in the binding of E. coli Hsp70 to an unfolded protein

(2021) Eugenia M. Clerico et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Physics-based modeling provides predictive understanding of selectively promiscuous substrate binding by Hsp70 chaperones

(2021) Erik B. Nordquist et al.   PLoS Computational Biology

Bacterial Hsp70 resolves misfolded states and accelerates productive folding of a multi-domain protein

(2020) Rahmi Imamoglu et al.   Nature Communications

Selective Binding of HSC70 and its Co-Chaperones to Structural Hotspots on CFTR

(2020) Imad Baaklini et al.   Scientific Reports

Mutagenesis-Based Characterization and Improvement of a Novel Inclusion Body Tag

(2020) Wouter S. P. Jong et al.   Frontiers in Bioengineering and Biotechnology

KLR-70: A Novel Cationic Inhibitor of the Bacterial Hsp70 Chaperone

(2020) Matthew D. Dalphin et al.   BIOCHEMISTRY

Feedback regulation of heat shock factor 1 (Hsf1) activity by Hsp70‐mediated trimer unzipping and dissociation from DNA

(2020) Szymon W Kmiecik et al.   EMBO JOURNAL

Post-translational modifications of Hsp70 family proteins: Expanding the chaperone code

(2020) Nitika et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

ANuPP: A Versatile Tool to Predict Aggregation Nucleating Regions in Peptides and Proteins

(2020) R. Prabakaran et al.   JOURNAL OF MOLECULAR BIOLOGY

Hsp70 molecular chaperones: multifunctional allosteric holding and unfolding machines

(2019) Eugenia M. Clerico et al.   BIOCHEMICAL JOURNAL

Unveiling the Interplay between the TLR4/MD2 Complex and HSP70 in the Human Cardiovascular System: A Computational Approach

(2019) Amanda Almeida de Oliveira et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Regulation of the Hsf1-dependent transcriptome via conserved bipartite contacts with Hsp70 promotes survival in yeast

(2019) Sara Peffer et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The Hsp70 chaperone network

(2019) Rina Rosenzweig et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

ChaperISM: improved chaperone binding prediction using position-independent scoring matrices

(2019) M B B Gutierres et al.   BIOINFORMATICS

ERK-dependent phosphorylation of the linker and substrate-binding domain of HSP70 increases folding activity and cell proliferation

(2019) Semi Lim et al.   EXPERIMENTAL AND MOLECULAR MEDICINE

Fine Tuning: Effects of Post-Translational Modification on Hsp70 Chaperones

(2019) Alijah A. Griffith et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Heat shock-induced chaperoning by Hsp70 is enabled in-cell

(2019) Drishti Guin et al.   PLoS One

Efficient conversion of chemical energy into mechanical work by Hsp70 chaperones

(2019) Salvatore Assenza et al.   eLife

Roles of the nucleotide exchange factor and chaperone Hsp110 in cellular proteostasis and diseases of protein misfolding

(2018) Unekwu M. Yakubu et al.   BIOLOGICAL CHEMISTRY

Accurate Prediction of Protein-Ligand Binding by Combined Molecular Dynamics-Based Docking and QM/MM Methods

(2018) Iris Antes et al.   BIOPHYSICAL JOURNAL

Hsp70 at the membrane: driving protein translocation

(2018) Elizabeth A. Craig   BMC BIOLOGY

Cellular Handling of Protein Aggregates by Disaggregation Machines

(2018) Axel Mogk et al.   MOLECULAR CELL

Molecular Mechanism of J-Domain-Triggered ATP Hydrolysis by Hsp70 Chaperones

(2018) Roman Kityk et al.   MOLECULAR CELL

Intra-molecular pathways of allosteric control in Hsp70s

(2018) Matthias P. Mayer   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Conserved conformational selection mechanism of Hsp70 chaperone-substrate interactions

(2018) Ashok Sekhar et al.   eLife

Structure of the post-translational protein translocation machinery of the ER membrane

(2018) Xudong Wu et al.   NATURE

The Hsp70 interdomain linker is a dynamic switch that enables allosteric communication between two structured domains

(2017) Charles A. English et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design

(2017) Rebecca F. Alford et al.   Journal of Chemical Theory and Computation

Conformational heterogeneity in the Hsp70 chaperone-substrate ensemble identified from analysis of NMR-detected titration data

(2017) Ashok Sekhar et al.   PROTEIN SCIENCE

Promiscuous binding by Hsp70 results in conformational heterogeneity and fuzzy chaperone-substrate ensembles

(2017) Rina Rosenzweig et al.   eLife

The Role of the Multifunctional BAG3 Protein in Cellular Protein Quality Control and in Disease

(2017) Elisabeth Stürner et al.   Frontiers in Molecular Neuroscience

PBSA_E: A PBSA-Based Free Energy Estimator for Protein–Ligand Binding Affinity

(2016) Xiao Liu et al.   Journal of Chemical Information and Modeling

Clathrin-coat disassembly illuminates the mechanisms of Hsp70 force generation

(2016) Rui Sousa et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Hsp70 biases the folding pathways of client proteins

(2016) Ashok Sekhar et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

GGIP: Structure and sequence-based GPCR-GPCR interaction pair predictor

(2016) Wataru Nemoto et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

BiPPred: Combined sequence- and structure-based prediction of peptide binding to the Hsp70 chaperone BiP

(2016) Markus Schneider et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Clathrin-coat disassembly illuminates the mechanisms of Hsp70 force generation

(2016) Rui Sousa et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

In SilicoPrediction of the Effects of Mutations in the Human Mevalonate Kinase Gene: Towards a Predictive Framework for Mevalonate Kinase Deficiency

(2015) Claire Browne et al.   ANNALS OF HUMAN GENETICS

Designing Antigenic Peptides with Dual Binding Affinities for HSP70 and MHC

(2015) Tomonori Waku et al.   CHEMISTRY LETTERS

Molecular docking and molecular dynamics studies reveal structural basis of inhibition and selectivity of inhibitors EGCG and OSU-03012 toward glucose regulated protein-78 (GRP78) overexpressed in glioblastoma

(2015) Rituparna Bhattacharjee et al.   JOURNAL OF MOLECULAR MODELING

Heterogeneous binding of the SH3 client protein to the DnaK molecular chaperone

(2015) Jung Ho Lee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mapping the conformation of a client protein through the Hsp70 functional cycle

(2015) Ashok Sekhar et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

AMPylation matches BiP activity to client protein load in the endoplasmic reticulum

(2015) Steffen Preissler et al.   eLife

Prediction of Peptide and Protein Propensity for Amyloid Formation

(2015) Carlos Família et al.   PLoS One

Modeling and Docking Studies on Novel Mutants (K71L and T204V) of the ATPase Domain of Human Heat Shock 70 kDa Protein 1

(2014) Asita Elengoe et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Proteostasis and the Aging Proteome in Health and Disease

(2014) R. I. Morimoto et al.   JOURNALS OF GERONTOLOGY SERIES A-BIOLOGICAL SCIENCES AND MEDICAL SCIENCES

Single-molecule spectroscopy reveals chaperone-mediated expansion of substrate protein

(2014) Ruth Kellner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structural Identification of DnaK Binding Sites within Bovine and Sheep Bactenecin Bac7

(2014) Michael Zahn et al.   PROTEIN AND PEPTIDE LETTERS

Molecular Chaperone Functions in Protein Folding and Proteostasis

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

Regulation of molecular chaperones through post-translational modifications: Decrypting the chaperone code

(2013) Philippe Cloutier et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Tracking the Interplay between Bound Peptide and the Lid Domain of DnaK, Using Molecular Dynamics

(2013) Itzhaq Azoulay et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Identification and Characterization of a Novel Human Methyltransferase Modulating Hsp70 Protein Function through Lysine Methylation

(2013) Magnus E. Jakobsson et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Structural Studies on the Forward and Reverse Binding Modes of Peptides to the Chaperone DnaK

(2013) Michael Zahn et al.   JOURNAL OF MOLECULAR BIOLOGY

Molecular chaperone involvement in chloroplast protein import

(2012) Úrsula Flores-Pérez et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH

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

Conformational Selection in Substrate Recognition by Hsp70 Chaperones

(2012) Moritz Marcinowski et al.   JOURNAL OF MOLECULAR BIOLOGY

Molecular chaperones DnaK and DnaJ share predicted binding sites on most proteins in the E. coli proteome

(2012) Sharan R. Srinivasan et al.   Molecular BioSystems

DnaK Functions as a Central Hub in the E. coli Chaperone Network

(2012) Giulia Calloni et al.   Cell Reports

Molecular chaperones in protein folding and proteostasis

(2011) F. Ulrich Hartl et al.   NATURE

Single-molecule analysis of a molecular disassemblase reveals the mechanism of Hsc70-driven clathrin uncoating

(2011) Till Böcking et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Predicting MHC class I epitopes in large datasets

(2010) Kirsten Roomp et al.   BMC BIOINFORMATICS

Exploring the sequence determinants of amyloid structure using position-specific scoring matrices

(2010) Sebastian Maurer-Stroh et al.   NATURE METHODS

Cellular strategies for controlling protein aggregation

(2010) Jens Tyedmers et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Limitations of Ab Initio Predictions of Peptide Binding to MHC Class II Molecules

(2010) Hao Zhang et al.   PLoS One

Towards Universal Structure-Based Prediction of Class II MHC Epitopes for Diverse Allotypes

(2010) Andrew J. Bordner   PLoS One

Structure of clathrin coat with bound Hsc70 and auxilin: mechanism of Hsc70-facilitated disassembly

(2009) Yi Xing et al.   EMBO JOURNAL

BETASCAN: Probable β-amyloids Identified by Pairwise Probabilistic Analysis

(2009) Allen W. Bryan et al.   PLoS Computational Biology

Accurate Prediction of DnaK-Peptide Binding via Homology Modelling and Experimental Data

(2009) Joost Van Durme et al.   PLoS Computational Biology

Identification of Aggregation-Prone Elements by Using Interaction-Energy Matrices

(2008) Jennifer M. Bui et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Recent advances in implicit solvent-based methods for biomolecular simulations

(2008) Jianhan Chen et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Allosteric Coupling between the Lid and Interdomain Linker in DnaK Revealed by Inhibitor Binding Studies

(2008) M. Liebscher et al.   JOURNAL OF BACTERIOLOGY