ArticlePLoS computational biology2013
Decipher the mechanisms of protein conformational changes induced by nucleotide binding through free-energy landscape analysis: ATP binding to Hsp70.
Article in PLoS computational biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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29 citing papers in PubMed, 38 citations in OpenAlex.
- Development of domain-specific probes ofAntimicrobial agents and chemotherapy · 2026Article
- Disarming the Hsp70-Bim Alliance: Small-Molecule and Peptidic Disruptors of a Chaperone-Apoptotic Switch in Cancer.ChemistryOpen · 2026Review
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- Navigating Uncertainty: Assessing Variants of Uncertain Significance in the CDKL5 Gene for Developmental and Epileptic Encephalopathy Using In Silico Prediction Tools and Computational Analysis.Journal of molecular neuroscience : MN · 2025Article
- Structural insights into GrpEL1-mediated nucleotide and substrate release of human mitochondrial Hsp70.Nature communications · 2024Article
- Molecular characterization of heat shock protein 70 and 90 genes and their expression analysis in air-breathing magur catfish (Clarias magur) while exposed to zinc oxide nanoparticles.Fish physiology and biochemistry · 2024Article
- Structural insights into GrpEL1-mediated nucleotide and substrate release of human mitochondrial Hsp70.bioRxiv : the preprint server for biology · 2024Article
- Protein conformational ensembles in function: roles and mechanisms.RSC chemical biology · 2023Review
- Megahertz pulse trains enable multi-hit serial femtosecond crystallography experiments at X-ray free electron lasers.Nature communications · 2022Article
- Peroxidase from foxtail millet bran exerts anti-colorectal cancer activityActa pharmaceutica Sinica. B · 2022Article
- Comparative analysis of the coordinated motion of Hsp70s from different organelles observed by single-molecule three-color FRET.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Structural Communication between theInternational journal of molecular sciences · 2021Article
- Conformational Changes of Glutamine 5'-Phosphoribosylpyrophosphate Amidotransferase for Two Substrates Analogue Binding: Insight from Conventional Molecular Dynamics and Accelerated Molecular Dynamics Simulations.Frontiers in chemistry · 2021Article
- Two-step mechanism of J-domain action in driving Hsp70 function.PLoS computational biology · 2020Article
- Energy flow and intersubunit signalling in GSAM: A non-equilibrium molecular dynamics study.Computational and structural biotechnology journal · 2020Article
- Mechanistic Insights into the Effect of Ligands on Structural Stability and Selectivity of Sulfotransferase 2A1 (SULT2A1).ACS omega · 2019Article
- Hsp70 molecular chaperones: multifunctional allosteric holding and unfolding machines.The Biochemical journal · 2019Review
- Probing inhibition mechanisms of adenosine deaminase by using molecular dynamics simulations.PloS one · 2018Article
- Adaptive Steered Molecular Dynamics Combined With Protein Structure Networks Revealing the Mechanism of Y68I/G109P Mutations That Enhance the Catalytic Activity of D-psicose 3-Epimerase FromFrontiers in chemistry · 2018Article
- Understanding the differences of the ligand binding/unbinding pathways between phosphorylated and non-phosphorylated ARH1 using molecular dynamics simulations.Scientific reports · 2017Article
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3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
ATP regulates the function of many proteins in the cell by transducing its binding and hydrolysis energies into protein conformational changes by mechanisms which are challenging to identify at the atomic scale. Based on molecular dynamics (MD) simulations, a method is proposed to analyze the structural changes induced by ATP binding to a protein by computing the effective free-energy landscape (FEL) of a subset of its coordinates along its amino-acid sequence. The method is applied to characterize the mechanism by which the binding of ATP to the nucleotide-binding domain (NBD) of Hsp70 propagates a signal to its substrate-binding domain (SBD). Unbiased MD simulations were performed for Hsp70-DnaK chaperone in nucleotide-free, ADP-bound and ATP-bound states. The simulations revealed that the SBD does not interact with the NBD for DnaK in its nucleotide-free and ADP-bound states whereas the docking of the SBD was found in the ATP-bound state. The docked state induced by ATP binding found in MD is an intermediate state between the initial nucleotide-free and final ATP-bound states of Hsp70. The analysis of the FEL projected along the amino-acid sequence permitted to identify a subset of 27 protein internal coordinates corresponding to a network of 91 key residues involved in the conformational change induced by ATP binding. Among the 91 residues, 26 are identified for the first time, whereas the others were shown relevant for the allosteric communication of Hsp70 s in several experiments and bioinformatics analysis. The FEL analysis revealed also the origin of the ATP-induced structural modifications of the SBD recently measured by Electron Paramagnetic Resonance. The pathway between the nucleotide-free and the intermediate state of DnaK was extracted by applying principal component analysis to the subset of internal coordinates describing the transition. The methodology proposed is general and could be applied to analyze allosteric communication in other proteins.
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