ArticleProceedings of the National Academy of Sciences of the United States of America2013
Defining a length scale for millisecond-timescale protein conformational exchange.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
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- QMrebind: incorporating quantum mechanical force field reparameterization at the ligand binding site for improved drug-target kinetics through milestoning simulations.Chemical science · 2023Article
- Profiling Enzyme Activity of l-Asparaginase II by NMR-Based Methyl Fingerprinting at Natural Abundance.Journal of the American Chemical Society · 2023Article
- NMR Provides Unique Insight into the Functional Dynamics and Interactions of Intrinsically Disordered Proteins.Chemical reviews · 2022Review
- Structure-Function Relationships in the Human P-Glycoprotein (ABCB1): Insights from Molecular Dynamics Simulations.International journal of molecular sciences · 2021Article
- Protons Are Fast and Smart; Proteins Are Slow and Dumb: On the Relationship of Electrospray Ionization Charge States and Conformations.Journal of the American Society for Mass Spectrometry · 2021Article
- Theoretical insights on helix repacking as the origin of P-glycoprotein promiscuity.Scientific reports · 2020Article
- Computational Nanoscopy of Tight Junctions at the Blood-Brain Barrier Interface.International journal of molecular sciences · 2019Review
- The Structure of Melanoregulin Reveals a Role for Cholesterol Recognition in the Protein's Ability to Promote Dynein Function.Structure (London, England : 1993) · 2018Article
- Structural and hydrodynamic properties of an intrinsically disordered region of a germ cell-specific protein on phase separation.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- How cooperative are protein folding and unfolding transitions?Protein science : a publication of the Protein Society · 2016Review
- "Invisible" conformers of an antifungal disulfide protein revealed by constrained cold and heat unfolding, CEST-NMR experiments, and molecular dynamics calculations.Chemistry (Weinheim an der Bergstrasse, Germany) · 2015Article
- Article
- An exact solution for R2,eff in CPMG experiments in the case of two site chemical exchange.Journal of magnetic resonance (San Diego, Calif. : 1997) · 2014Article
- Understanding the mechanism of proteasome 20S core particle gating.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- Assessment of local friction in protein folding dynamics using a helix cross-linker.The journal of physical chemistry. B · 2013Article
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3 authors.
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Abstract
Although atomic resolution 3D structures of protein native states and some folding intermediates are available, the mechanism of interconversion between such states remains poorly understood. Here we study the four-helix bundle FF module, which folds via a transiently formed and sparsely populated compact on-pathway intermediate, I. Relaxation dispersion NMR spectroscopy has previously been used to elucidate the 3D structure of this intermediate and to establish that the conformational exchange between the I and the native, N, states of the FF domain is driven predominantly by water dynamics. In the present study we use NMR methods to define a length scale for the FF I-N transition, namely the effective hydrodynamic radius (EHR) that provides an average measure of the size of the structural units participating in the transition at any given time. Our experiments establish that the EHR is less than 4 Å, on the order of the size of one to two amino acid side chains, much smaller than the FF domain hydrodynamic radius (13 Å). The small magnitude of the EHR provides strong evidence that the I-N interconversion does not proceed via the synchronous motion of large clusters of amino acid residues, but rather by the exposure/burial of one or two side chains from solvent at any given time. Because the hydration of small hydrophobic solutes (< 4 Å) does not involve considerable dewetting or disruption of the water-hydrogen bonding network, the FF domain I-N transition does not require appreciable changes to the structure of the surrounding water.
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