ArticleJournal of the American Chemical Society2015
Interaction Networks in Protein Folding via Atomic-Resolution Experiments and Long-Time-Scale Molecular Dynamics Simulations.
Article in Journal of the American Chemical Society, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed.
- The Role of the Electronic Structure during Protein Folding through Electron Density-Based Quantum Chemical Descriptors.ACS omega · 2026Article
- Unveiling the Conformational Dynamics of the Histone Tails Using Markov State Modeling.Journal of chemical theory and computation · 2025Article
- Physics-Based Protein Networks Might Recover Effectful Mutations─a Case Study on Cathepsin G.The journal of physical chemistry. B · 2024Article
- Natural and Engineered Isoforms of the Inflammasome Adaptor ASC Form Noncovalent, pH-Responsive Hydrogels.Biomacromolecules · 2023Article
- A modular approach to map out the conformational landscapes of unbound intrinsically disordered proteins.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- The anatomy of unfolding of Yfh1 is revealed by site-specific fold stability analysis measured by 2D NMR spectroscopy.Communications chemistry · 2021Article
- Identification of unique subtype-specific interaction features in Class II zinc-dependent HDAC subtype binding pockets: A computational study.Journal of biosciences · 2021Article
- Investigating the trade-off between folding and function in a multidomain Y-family DNA polymerase.eLife · 2020Article
- Simple Model of Protein Energetics To Identify Ab Initio Folding Transitions from All-Atom MD Simulations of Proteins.Journal of chemical theory and computation · 2020Article
- Curvature and Torsion of Protein Main Chain as Local Order Parameters of Protein Unfolding.The journal of physical chemistry. B · 2020Article
- Graph-Directed Approach for Downselecting Toxins for Experimental Structure Determination.Marine drugs · 2020Article
- Amyloid assembly is dominated by misregistered kinetic traps on an unbiased energy landscape.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Confinement and Crowding Effects on Folding of a Multidomain Y-Family DNA Polymerase.Journal of chemical theory and computation · 2020Article
- Dissecting C-H∙∙∙π and N-H∙∙∙π Interactions in Two Proteins Using a Combined Experimental and Computational Approach.Scientific reports · 2019Article
- Learning dynamical information from static protein and sequencing data.Nature communications · 2019Article
- Snails In Silico: A Review of Computational Studies on the Conopeptides.Marine drugs · 2019Review
- Using correlated motions to determine sufficient sampling times for molecular dynamics.Physical review. E · 2018Article
- Molecular Modeling for Structural Insights Concerning the Activation Mechanisms of F1174L and R1275Q Mutations on Anaplastic Lymphoma Kinase.Molecules (Basel, Switzerland) · 2018Article
- Simultaneous determination of fast and slow dynamics in molecules using extreme CPMG relaxation dispersion experiments.Journal of biomolecular NMR · 2018Article
- Simple MD-based model for oxidative folding of peptides and proteins.Scientific reports · 2017Article
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9 authors.
Funding
Abstract
The integration of atomic-resolution experimental and computational methods offers the potential for elucidating key aspects of protein folding that are not revealed by either approach alone. Here, we combine equilibrium NMR measurements of thermal unfolding and long molecular dynamics simulations to investigate the folding of gpW, a protein with two-state-like, fast folding dynamics and cooperative equilibrium unfolding behavior. Experiments and simulations expose a remarkably complex pattern of structural changes that occur at the atomic level and from which the detailed network of residue-residue couplings associated with cooperative folding emerges. Such thermodynamic residue-residue couplings appear to be linked to the order of mechanistically significant events that take place during the folding process. Our results on gpW indicate that the methods employed in this study are likely to prove broadly applicable to the fine analysis of folding mechanisms in fast folding proteins.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.