ArticleProceedings of the National Academy of Sciences of the United States of America2011
Frustration, specific sequence dependence, and nonlinearity in large-amplitude fluctuations of allosteric proteins.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 71 papers.
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Who cites it
71 citing papers in PubMed.
- Role of Hsp70 chaperone in client-protein folding elucidated by Markov state modeling and NMR restraint-assisted molecular dynamics simulations.Biophysical journal · 2026Article
- Advances and challenges in multiscale biomolecular simulations: artificial intelligence-driven paradigm shift.Quantitative biology (Beijing, China) · 2026Article
- Allosteric regulation of enzymatic catalysis by molecular crowding.Communications chemistry · 2026Article
- H4K16 acylations destabilize chromatin architecture and facilitate transcriptional response during metabolic perturbations.Molecular cell · 2026Article
- Role of frustrations in cell reprogramming.PNAS nexus · 2025Article
- Sodium Ion-Induced Structural Transition on the Surface of a DNA-Interacting Protein.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- A Molecular View into the Structure and Dynamics of Phase-Separated Chromatin.The journal of physical chemistry. B · 2024Article
- Illuminating Protein Allostery by Chemically Accurate Contact Response Analysis (ChACRA).Journal of chemical theory and computation · 2024Article
- Fusion Dynamics and Size-Dependence of Droplet Microstructure in ssDNA-Mediated Protein Phase Separation.JACS Au · 2024Article
- Predicting protein conformational motions using energetic frustration analysis and AlphaFold2.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- From Nucleosomes to Compartments: Physicochemical Interactions Underlying Chromatin Organization.Annual review of biophysics · 2024Review
- Article
- Evolution shapes interaction patterns for epistasis and specific protein binding in a two-component signaling system.Communications chemistry · 2024Article
- The Statistical Trends of Protein Evolution: A Lesson from AlphaFold Database.Molecular biology and evolution · 2022Article
- Frustration and the Kinetic Repartitioning Mechanism of Substrate Inhibition in Enzyme Catalysis.The journal of physical chemistry. B · 2022Article
- Role of water-bridged interactions in metal ion coupled protein allostery.PLoS computational biology · 2022Article
- Enhanced Conformational Sampling with an Adaptive Coarse-Grained Elastic Network Model Using Short-Time All-Atom Molecular Dynamics.Journal of chemical theory and computation · 2022Article
- Multiscale modeling of genome organization with maximum entropy optimization.The Journal of chemical physics · 2021Article
- Energy landscape remodeling mechanism of Hsp70-chaperone-accelerated protein folding.Biophysical journal · 2021Article
- Optimizing Gō-MARTINI Coarse-Grained Model for F-BAR Protein on Lipid Membrane.Frontiers in molecular biosciences · 2021Article
11 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors.
Funding
Abstract
Proteins have often evolved sequences so as to acquire the ability for regulation via allosteric conformational change. Here we investigate how allosteric dynamics is designed through sequences with nonlinear interaction features. First, for 71 allosteric proteins of which two, open and closed, structures are available, a statistical survey of interactions using an all-atom model with effective solvation shows that those residue contact interactions specific to one of the two states are significantly weaker than are the contact interactions shared by the two states. This interaction feature indicates there is underlying sequence design to facilitate conformational change. Second, based on the energy landscape theory, we implement these interaction features into a new atomic-interaction-based coarse-grained model via a multiscale simulation protocol (AICG). The AICG model outperforms standard coarse-grained models for predictions of the native-state mean fluctuations and of the conformational change direction. Third, using the new model for adenylate kinase, we show that intrinsic fluctuations in one state contain rare and large-amplitude motions nearly reaching the other state. Such large-amplitude motions are realized partly by sequence specificity and partly by the nonlinear nature of contact interactions, leading to cracking. Both features enhance conformational transition rates.
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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.