ArticleThe journal of physical chemistry. B2014
Extensive conformational heterogeneity within protein cores.
Article in The journal of physical chemistry. B, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Unfolding of the Villin Headpiece Domain: Revealing Structural Heterogeneity with Time-Resolved X-Ray Solution Scattering and Markov State Modeling.Chemphyschem : a European journal of chemical physics and physical chemistry · 2025Article
- Advances in uncovering the mechanisms of macromolecular conformational entropy.Nature chemical biology · 2025Review
- Folding@home: Achievements from over 20 years of citizen science herald the exascale era.Biophysical journal · 2023Review
- Folding@home: achievements from over twenty years of citizen science herald the exascale era.ArXiv · 2023Article
- Flexible CDOCKER: Hybrid Searching Algorithm and Scoring Function with Side Chain Conformational Entropy.Journal of chemical information and modeling · 2021Article
- A Minireview on Temperature Dependent Protein Conformational Sampling.The protein journal · 2021Review
- Novel insights in linking solvent relaxation dynamics and protein conformations utilizing red edge excitation shift approach.Emerging topics in life sciences · 2021Review
- Advanced Methods for Accessing Protein Shape-Shifting Present New Therapeutic Opportunities.Trends in biochemical sciences · 2019Review
- A Dynamic Hydrophobic Core and Surface Salt Bridges Thermostabilize a Designed Three-Helix Bundle.Biophysical journal · 2019Article
- Modulation of allosteric coupling by mutations: from protein dynamics and packing to altered native ensembles and function.Current opinion in structural biology · 2019Review
- Enspara: Modeling molecular ensembles with scalable data structures and parallel computing.The Journal of chemical physics · 2019Article
- Cryptic binding sites on proteins: definition, detection, and druggability.Current opinion in chemical biology · 2018Review
- Quantifying Allosteric Communication via Both Concerted Structural Changes and Conformational Disorder with CARDS.Journal of chemical theory and computation · 2017Article
- A dynamic hydrophobic core orchestrates allostery in protein kinases.Science advances · 2017Article
- Capturing Invisible Motions in the Transition from Ground to Rare Excited States of T4 Lysozyme L99A.Biophysical journal · 2016Article
- Modelling proteins' hidden conformations to predict antibiotic resistance.Nature communications · 2016Article
- Protein Ensembles: How Does Nature Harness Thermodynamic Fluctuations for Life? The Diverse Functional Roles of Conformational Ensembles in the Cell.Chemical reviews · 2016Review
- Conformational heterogeneity of the calmodulin binding interface.Nature communications · 2016Article
- Flexible CDOCKER: Development and application of a pseudo-explicit structure-based docking method within CHARMM.Journal of computational chemistry · 2016Article
- Modeling molecular kinetics with tICA and the kernel trick.Journal of chemical theory and computation · 2015Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
Basic principles of statistical mechanics require that proteins sample an ensemble of conformations at any nonzero temperature. However, it is still common to treat the crystallographic structure of a protein as the structure of its native state, largely because high-resolution structural characterization of protein flexibility remains a profound challenge. To assess the typical degree of conformational heterogeneity within folded proteins, we construct Markov state models describing the thermodynamics and kinetics of proteins ranging from 72 to 263 residues in length. Each of these models is built from hundreds of microseconds of atomically detailed molecular dynamics simulations. Examination of the side-chain degrees of freedom reveals that almost every residue visits at least two rotameric states over this time frame, with rotamer transition rates spanning a wide range of time scales (from nanoseconds to tens of microseconds). We also report substantial backbone dynamics on time scales longer than are typically addressed by experimental measures of protein flexibility, such as NMR order parameters. Finally, we demonstrate that these extensive rearrangements are consistent with NMR and crystallographic data, which supports the validity of our models. Altogether, these results depict the interior of proteins not as well-ordered solids, as is often imagined, but instead as dense fluids, which undergo substantial structural fluctuations despite their high packing fraction.
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Registered trials
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.