ArticleJournal of the American Chemical Society2010
Unfolded-state dynamics and structure of protein L characterized by simulation and experiment.
Article in Journal of the American Chemical Society, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
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Who cites it
43 citing papers in PubMed, 88 citations in OpenAlex.
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- Oncogenic Mutations in the DNA-Binding Domain of FOXO1 that Disrupt Folding: Quantitative Insights from Experiments and Molecular Simulations.Biochemistry · 2022Article
- Scaffold Hopping Transformations Using Auxiliary Restraints for Calculating Accurate Relative Binding Free Energies.Journal of chemical theory and computation · 2021Article
- Single-Molecular Förster Resonance Energy Transfer Measurement on Structures and Interactions of Biomolecules.Micromachines · 2021Review
- N-Terminal Decarboxylation as a Probe for Intramolecular Contact Formation in γ-Glu-(Pro)The journal of physical chemistry. B · 2020Article
- Identification of an α-MoRF in the Intrinsically Disordered Region of the Escargot Transcription Factor.ACS omega · 2020Article
- Water as a Good Solvent for Unfolded Proteins: Folding and Collapse are Fundamentally Different.Journal of molecular biology · 2020Review
- Evaluating the strengths of salt bridges in the CutA1 protein using molecular dynamic simulations: a comparison of different force fields.FEBS open bio · 2019Article
- Commonly used FRET fluorophores promote collapse of an otherwise disordered protein.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- What DrivesBiophysical journal · 2018Article
- Validating Molecular Dynamics Simulations against Experimental Observables in Light of Underlying Conformational Ensembles.The journal of physical chemistry. B · 2018Article
- Ion-ion interactions in the denatured state contribute to the stabilization of CutA1 proteins.Scientific reports · 2018Article
- Equilibrium Ensembles for Insulin Folding from Bias-Exchange Metadynamics.Biophysical journal · 2017Article
- Prion protein dynamics before aggregation.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Atomistic structural ensemble refinement reveals non-native structure stabilizes a sub-millisecond folding intermediate of CheY.Scientific reports · 2017Article
- Integrated view of internal friction in unfolded proteins from single-molecule FRET, contact quenching, theory, and simulations.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- The effect of chirality and steric hindrance on intrinsic backbone conformational propensities: tools for protein design.Protein engineering, design & selection : PEDS · 2016Article
- Dodine as a transparent protein denaturant for circular dichroism and infrared studies.Protein science : a publication of the Protein Society · 2016Article
- Markov state models of protein misfolding.The Journal of chemical physics · 2016Article
- Quantitative assessments of the distinct contributions of polypeptide backbone amides versus side chain groups to chain expansion via chemical denaturation.Journal of the American Chemical Society · 2015Article
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
Abstract
While several experimental techniques now exist for characterizing protein unfolded states, all-atom simulation of unfolded states has been challenging due to the long time scales and conformational sampling required. We address this problem by using a combination of accelerated calculations on graphics processor units and distributed computing to simulate tens of thousands of molecular dynamics trajectories each up to approximately 10 mus (for a total aggregate simulation time of 127 ms). We used this approach in conjunction with Trp-Cys contact quenching experiments to characterize the unfolded structure and dynamics of protein L. We employed a polymer theory method to make quantitative comparisons between high-temperature simulated and chemically denatured experimental ensembles and find that reaction-limited quenching rates calculated from simulation agree remarkably well with experiment. In both experiment and simulation, we find that unfolded-state intramolecular diffusion rates are very slow compared to highly denatured chains and that a single-residue mutation can significantly alter unfolded-state dynamics and structure. This work suggests a view of the unfolded state in which surprisingly low diffusion rates could limit folding and opens the door for all-atom molecular simulation to be a useful predictive tool for characterizing protein unfolded states along with experiments that directly measure intramolecular diffusion.
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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.