Comprehensive structural and dynamical view of an unfolded protein from the combination of single-molecule FRET, NMR, and SAXS.

scientific article published on 26 August 2016

Comprehensive structural and dynamical view of an unfolded protein from the combination of single-molecule FRET, NMR, and SAXS. is …
instance of (P31):
scholarly articleQ13442814

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P819ADS bibcode2016PNAS..113E5389A
P356DOI10.1073/PNAS.1607193113
P932PMC publication ID5027429
P698PubMed publication ID27566405

P50authorAndrea SorannoQ42316865
Benjamin SchulerQ42316868
Mikayel AznauryanQ42320745
Jie-rong HuangQ44885914
Stephan GrzesiekQ44958017
P2093author name stringDaniel Nettels
Alexander M Labhardt
Leonildo Delgado
P2860cites workIntrinsically unstructured proteins and their functionsQ22061731
Single-Molecule Studies of Intrinsically Disordered ProteinsQ22061737
Levinthal's paradoxQ24563507
The Xplor-NIH NMR molecular structure determination packageQ27860805
Some factors in the interpretation of protein denaturationQ28202994
Structural characterization of flexible proteins using small-angle X-ray scatteringQ29617289
The denatured state (the other half of the folding equation) and its role in protein stability.Q30423402
Single-molecule spectroscopy of protein folding dynamics--expanding scope and timescales.Q30425834
Mapping protein collapse with single-molecule fluorescence and kinetic synchrotron radiation circular dichroism spectroscopyQ30478703
Recovering a representative conformational ensemble from underdetermined macromolecular structural dataQ30671380
Quantitative comparison of the hydrogen bond network of A-state and native ubiquitin by hydrogen bond scalar couplingsQ30959012
Deciphering protein dynamics from NMR data using explicit structure sampling and selectionQ31115115
Data registration and selective single-molecule analysis using multi-parameter fluorescence detectionQ31882181
Probing structural heterogeneities and fluctuations of nucleic acids and denatured proteinsQ33227189
DOTA-M8: An extremely rigid, high-affinity lanthanide chelating tag for PCS NMR spectroscopyQ33507143
Ensemble calculations of unstructured proteins constrained by RDC and PRE data: a case study of urea-denatured ubiquitinQ33517739
Molecular origins of internal friction effects on protein-folding ratesQ34083277
From the Cover: Charge interactions can dominate the dimensions of intrinsically disordered proteins.Q34093140
Sequence-specific mapping of the interaction between urea and unfolded ubiquitin from ensemble analysis of NMR and small angle scattering dataQ34151812
Probing the free-energy surface for protein folding with single-molecule fluorescence spectroscopyQ34154877
Quantitative assessments of the distinct contributions of polypeptide backbone amides versus side chain groups to chain expansion via chemical denaturationQ34461896
Coil-globule transition in the denatured state of a small proteinQ34984407
Toward an accurate theoretical framework for describing ensembles for proteins under strongly denaturing conditionsQ34984722
Toward a taxonomy of the denatured state: small angle scattering studies of unfolded proteinsQ34989905
Distribution of end-to-end distances of oligopeptides in solution as estimated by energy transferQ35078720
Combining experiments and simulations using the maximum entropy principleQ35105556
Characterizing the unfolded states of proteins using single-molecule FRET spectroscopy and molecular simulationsQ35616340
Ultrafast dynamics of protein collapse from single-molecule photon statistics.Q35669661
Improving the quality of NMR and crystallographic protein structures by means of a conformational database potential derived from structure databasesQ36279917
Polymer scaling laws of unfolded and intrinsically disordered proteins quantified with single-molecule spectroscopyQ36342960
The conformational ensembles of α-synuclein and tau: combining single-molecule FRET and simulationsQ36379177
Quantifying internal friction in unfolded and intrinsically disordered proteins with single-molecule spectroscopy.Q36398007
Localizing internal friction along the reaction coordinate of protein folding by combining ensemble and single-molecule fluorescence spectroscopyQ36445621
Peptide chain dynamics in light and heavy water: zooming in on internal frictionQ45327991
Quantitative modelfree analysis of urea binding to unfolded ubiquitin using a combination of small angle X-ray and neutron scattering.Q45978446
Single-molecule fluorescence studies of intrinsically disordered proteins.Q46033026
Single-molecule spectroscopy of cold denaturation and the temperature-induced collapse of unfolded proteinsQ46440887
Single-molecule spectroscopy of the unexpected collapse of an unfolded protein at low pH.Q46791997
Interaction of urea with amino acids: implications for urea-induced protein denaturationQ46875424
Analysis of main chain torsion angles in proteins: prediction of NMR coupling constants for native and random coil conformationsQ47630147
Early collapse is not an obligate step in protein foldingQ47812546
Effect of urea on the β-hairpin conformational ensemble and protein denaturation mechanism.Q53088094
Fifty years of solvent denaturationQ53433405
Rouse Model with Internal Friction: A Coarse Grained Framework for Single Biopolymer DynamicsQ56829784
Conformational distributions of unfolded polypeptides from novel NMR techniquesQ57080193
Mapping the Conformational Landscape of Urea-Denatured Ubiquitin Using Residual Dipolar CouplingsQ57080200
Direct Observation of Dipolar Couplings and Hydrogen Bonds across a β-Hairpin in 8 M UreaQ57080206
Long-Range Correlated Dynamics in Intrinsically Disordered ProteinsQ57712515
Single-molecule spectroscopy of protein conformational dynamics in live eukaryotic cellsQ57831648
Motional properties of unfolded ubiquitin: a model for a random coil proteinQ58062241
Single-Molecule FRET Spectroscopy and the Polymer Physics of Unfolded and Intrinsically Disordered ProteinsQ59332370
Unfolded Protein and Peptide Dynamics Investigated with Single-Molecule FRET and Correlation Spectroscopy from Picoseconds to Seconds†Q59332561
Characterization of long-range structure in the denatured state of staphylococcal nuclease. I. Paramagnetic relaxation enhancement by nitroxide spin labelsQ73335302
Effect of denaturing agents of the urea-guanidinium class on the solubility of acetyltetraglycine ethyl ester and related compoundsQ79606668
NMR characterization of the dynamics of biomacromoleculesQ80435130
Concerted dihedral rotations give rise to internal friction in unfolded proteinsQ87912069
Small-Angle X-ray Scattering and Single-Molecule FRET Spectroscopy Produce Highly Divergent Views of the Low-Denaturant Unfolded StateQ36470871
Atomic-level characterization of disordered protein ensemblesQ36717589
Heteronuclear three-dimensional NMR spectroscopy of a partially denatured protein: the A-state of human ubiquitin.Q36772070
Backbone Dynamics and Structural Characterization of the Partially Folded A State of Ubiquitin by 1H, 13C, and 15N Nuclear Magnetic Resonance SpectroscopyQ36886625
Urea denaturation by stronger dispersion interactions with proteins than water implies a 2-stage unfoldingQ36964255
Complete 15N and 1H NMR assignments for the amino-terminal domain of the phage 434 repressor in the urea-unfolded formQ37007122
Collapse transition in proteinsQ37137234
Interplay of alpha-synuclein binding and conformational switching probed by single-molecule fluorescence.Q37153744
Protein dynamics from single-molecule fluorescence intensity correlation functionsQ37397645
Single-molecule spectroscopy of the temperature-induced collapse of unfolded proteinsQ37469603
Reassessing random-coil statistics in unfolded proteinsQ37487200
Random-coil behavior and the dimensions of chemically unfolded proteinsQ37493905
Temperature-dependent solvation modulates the dimensions of disordered proteinsQ37702019
Structural analysis of intrinsically disordered proteins by small-angle X-ray scatteringQ37938727
How, when and why proteins collapse: the relation to foldingQ37959224
Exploring free-energy landscapes of intrinsically disordered proteins at atomic resolution using NMR spectroscopyQ38203952
Introducing protein intrinsic disorderQ38205058
Progress in studying intrinsically disordered proteins with atomistic simulations.Q38392991
Consistent View of Polypeptide Chain Expansion in Chemical Denaturants from Multiple Experimental MethodsQ39432831
Exploring the role of internal friction in the dynamics of unfolded proteins using simple polymer modelsQ39460391
Probing the Action of Chemical Denaturant on an Intrinsically Disordered Protein by Simulation and Experiment.Q41110746
Pulsed interleaved excitationQ42251940
Side-chain chi(1) conformations in urea-denatured ubiquitin and protein G from (3)J coupling constants and residual dipolar couplingsQ43162003
Quantitative description of backbone conformational sampling of unfolded proteins at amino acid resolution from NMR residual dipolar couplings.Q43243601
Persistence of native-like topology in a denatured protein in 8 M ureaQ43682045
Long-range interactions within a nonnative proteinQ43901723
Demonstration by NMR of folding domains in lysozymeQ44308247
Multiple probes reveal a native-like intermediate during low-temperature refolding of ubiquitinQ44926880
P433issue37
P407language of work or nameEnglishQ1860
P304page(s)E5389-98
P577publication date2016-08-26
P1433published inProceedings of the National Academy of Sciences of the United States of AmericaQ1146531
P1476titleComprehensive structural and dynamical view of an unfolded protein from the combination of single-molecule FRET, NMR, and SAXS.
P478volume113

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cites work (P2860)
Q896578201H-NMR Determination of Organic Compounds in Municipal Wastewaters and the Receiving Surface Waters in Eastern Cape Province of South Africa
Q50989054A critical comparison of coarse-grained structure-based approaches and atomic models of protein folding.
Q47972812An Efficient Method for Estimating the Hydrodynamic Radius of Disordered Protein Conformations
Q49424214Characterization of the multimeric structure of poly(A)-binding protein on a poly(A) tail
Q89741263Characterizing Single-Molecule Conformational Changes Under Shear Flow with Fluorescence Microscopy
Q41359094Combining NMR and small angle X-ray scattering for the study of biomolecular structure and dynamics.
Q47621056Combining short- and long-range fluorescence reporters with simulations to explore the intramolecular dynamics of an intrinsically disordered protein.
Q93137829Commonly used FRET fluorophores promote collapse of an otherwise disordered protein
Q57180326Conformational Ensemble of Disordered Proteins Probed by Solvent Paramagnetic Relaxation Enhancement (sPRE)
Q41293169Decoupling of size and shape fluctuations in heteropolymeric sequences reconciles discrepancies in SAXS vs. FRET measurements
Q34546157DisProt 7.0: a major update of the database of disordered proteins.
Q47236838Folding of maltose binding protein outside of and in GroEL.
Q90459885Friction-Limited Folding of Disulfide-Reduced Monomeric SOD1
Q87910173Highly Disordered Amyloid-β Monomer Probed by Single-Molecule FRET and MD Simulation
Q49990719Hypothesis: structural heterogeneity of the unfolded proteins originating from the coupling of the local clusters and the long-range distance distribution.
Q52329881Idiosyncrasies of hnRNP A1-RNA recognition: Can binding mode influence function
Q59332309Inferring properties of disordered chains from FRET transfer efficiencies
Q57751774Local and non-local topological information in the denatured state ensemble of a β-barrel protein
Q89542344Molecular dynamics-derived rotamer libraries for d-amino acids within homochiral and heterochiral polypeptides
Q47106499Monomeric Huntingtin Exon 1 Has Similar Overall Structural Features for Wild-Type and Pathological Polyglutamine Lengths.
Q64869800Multi-Pronged Interactions Underlie Inhibition of α-Synuclein Aggregation by β-Synuclein
Q89952853Protein structural changes characterized by high-pressure, pulsed field gradient diffusion NMR spectroscopy
Q47778340SAXS versus FRET: A Matter of Heterogeneity?
Q52616567Simulation of FRET dyes allows quantitative comparison against experimental data.
Q58575706Single Molecule FRET: A Powerful Tool to Study Intrinsically Disordered Proteins
Q50577647Slow Interconversion in a Heterogeneous Unfolded-State Ensemble of Outer-Membrane Phospholipase A.
Q55164334Study of protein folding under native conditions by rapidly switching the hydrostatic pressure inside an NMR sample cell.
Q96687783The SARS-CoV-2 nucleocapsid protein is dynamic, disordered, and phase separates with RNA
Q107112189The SARS-CoV-2 nucleocapsid protein is dynamic, disordered, and phase separates with RNA
Q92397223The combined force field-sampling problem in simulations of disordered amyloid-β peptides
Q39371374To be disordered or not to be disordered: is that still a question for proteins in the cell?
Q92547425Unfolded states under folding conditions accommodate sequence-specific conformational preferences with random coil-like dimensions
Q47213644Using a FRET Library with Multiple Probe Pairs To Drive Monte Carlo Simulations of α-Synuclein.

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