Related ArticlesConformational ensembles of an intrinsically disordered protein consistent with NMR, SAXS and single-molecule FRET.
J Am Chem Soc. 2020 Aug 25;:
Authors: Gomes GW, Krzeminski M, Namini A, Martin EW, Mittag T, Head-Gordon T, Forman-Kay JD, Gradinaru CC
Abstract
Intrinsically disordered proteins (IDPs) have fluctuating heterogeneous conformations, which makes structural characterization challenging, but of great interest, since their conformational ensembles are the link between their sequences and functions. An accurate description of IDP conformational ensembles depends crucially on the amount and quality of the experimental data, how it is integrated, and if it mutually supports a consistent structural picture. We used integrative modelling and validation to apply conformational restraints and assess agreement with the most common structural techniques for IDPs: Nuclear Magnetic Resonance (NMR) spectroscopy, Small-angle X-ray Scattering (SAXS), and single-molecule Förster Resonance Energy Transfer (smFRET) reach concordance on structural ensembles for Sic1 and phosphorylated Sic1 (pSic1). To resolve apparent discrepancies between smFRET and SAXS, we integrated SAXS data with non-smFRET (NMR) data and reserved the new smFRET data for Sic1 and pSic1, as an independent validation. Given the consistency of the SAXS/PRE restrained ensembles with smFRET, which was not guaranteed a priori, indicates that the perturbative effects of NMR or smFRET labels on the Sic1 and pSic1 ensemble are minimal. Furthermore , the mutual agreement with such a diverse set of experimental data suggests that details of the generated ensembles can now be examined with a high degree of confidence, such as overall compactness and end-to-end distance fluctuations, to reveal distinguishing features of Sic1 vs. pSic1. From the experimentally well supported ensembles, we find they are consistent with independent biophysical models of Sic1's ultrasensitive binding to its partner Cdc4. Our results underscore the importance of integrative modelling and validation in calculating and drawing biological conclusions from IDP conformational ensembles.
PMID: 32840111 [PubMed - as supplied by publisher]
[NMR paper] Obtaining Hydrodynamic Radii of Intrinsically Disordered Protein Ensembles by Pulsed Field Gradient NMR Measurements.
Obtaining Hydrodynamic Radii of Intrinsically Disordered Protein Ensembles by Pulsed Field Gradient NMR Measurements.
Related Articles Obtaining Hydrodynamic Radii of Intrinsically Disordered Protein Ensembles by Pulsed Field Gradient NMR Measurements.
Methods Mol Biol. 2020;2141:285-302
Authors: Leeb S, Danielsson J
Abstract
In the disordered state, a protein exhibits a high degree of structural freedom, in both space and time. For an ensemble of disordered or unfolded proteins, this means that the ensemble comprises a high...
[ASAP] Single-Molecule Imaging Reveals Conformational Manipulation of Holliday Junction DNA by the Junction Processing Protein RuvA
Single-Molecule Imaging Reveals Conformational Manipulation of Holliday Junction DNA by the Junction Processing Protein RuvA
https://pubs.acs.org/appl/literatum/publisher/achs/journals/content/bichaw/0/bichaw.ahead-of-print/acs.biochem.8b00404/20180524/images/medium/bi-2018-00404a_0006.gif
Biochemistry
DOI: 10.1021/acs.biochem.8b00404
http://feeds.feedburner.com/~ff/acs/bichaw?d=yIl2AUoC8zA
http://feeds.feedburner.com/~r/acs/bichaw/~4/oGSxR5_mdcw
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05-25-2018 12:07 PM
[NMR paper] Revealing Conformational Variants of Solution-Phase Intrinsically Disordered Tau Protein at the Single-Molecule Level
Revealing Conformational Variants of Solution-Phase Intrinsically Disordered Tau Protein at the Single-Molecule Level
Intrinsically disordered proteins, such as tau protein, adopt a variety of conformations in solution, complicating solution-phase structural studies. We employ an anti-Brownian electrokinetic (ABEL) trap to prolong measurements of single tau proteins in solution. Once trapped, we record the fluorescence anisotropy to investigate the diversity of conformations sampled by the single molecules. A distribution of anisotropy values obtained from trapped tau protein is...
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10-24-2017 05:09 PM
A J-modulated protonless NMR experiment characterizes the conformational ensemble of the intrinsically disordered protein WIP
A J-modulated protonless NMR experiment characterizes the conformational ensemble of the intrinsically disordered protein WIP
Abstract
Intrinsically disordered proteins (IDPs) are multi-conformational polypeptides that lack a single stable three-dimensional structure. It has become increasingly clear that the versatile IDPs play key roles in a multitude of biological processes, and, given their flexible nature, NMR is a leading method to investigate IDP behavior on the molecular level. Here we present an IDP-tailored J-modulated experiment designed to...
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11-19-2016 08:35 PM
[NMR paper] Comprehensive structural and dynamical view of an unfolded protein from the combination of single-molecule FRET, NMR, and SAXS.
Comprehensive structural and dynamical view of an unfolded protein from the combination of single-molecule FRET, NMR, and SAXS.
Comprehensive structural and dynamical view of an unfolded protein from the combination of single-molecule FRET, NMR, and SAXS.
Proc Natl Acad Sci U S A. 2016 Aug 26;
Authors: Aznauryan M, Delgado L, Soranno A, Nettels D, Huang JR, Labhardt AM, Grzesiek S, Schuler B
Abstract
The properties of unfolded proteins are essential both for the mechanisms of protein folding and for the function of the large...
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08-28-2016 11:03 AM
[NMR paper] NMR Spectroscopic Studies of the Conformational Ensembles of Intrinsically Disordered Proteins.
NMR Spectroscopic Studies of the Conformational Ensembles of Intrinsically Disordered Proteins.
Related Articles NMR Spectroscopic Studies of the Conformational Ensembles of Intrinsically Disordered Proteins.
Adv Exp Med Biol. 2015;870:149-185
Authors: Kurzbach D, Kontaxis G, Coudevylle N, Konrat R
Abstract
Intrinsically disordered proteins (IDPs) are characterized by substantial conformational flexibility and thus not amenable to conventional structural biology techniques. Given their inherent structural flexibility NMR...
Conformational ensembles of an intrinsically disordered protein consistent with NMR, SAXS and single-molecule FRET.
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