Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Decoupling of size and shape fluctuations in heteropolymeric sequences reconciles discrepancies in SAXS vs. FRET measurements.
Journal, issue, pages	Proc Natl Acad Sci U S A, Vol. 114, Issue 31, Page E6342-E6351, Year 2017
Publish date	Aug 1, 2017
Authors	Gustavo Fuertes / Niccolò Banterle / Kiersten M Ruff / Aritra Chowdhury / Davide Mercadante / Christine Koehler / Michael Kachala / Gemma Estrada Girona / Sigrid Milles / Ankur Mishra / Patrick R Onck / Frauke Gräter / Santiago Esteban-Martín / Rohit V Pappu / Dmitri I Svergun / Edward A Lemke /
PubMed Abstract	Unfolded states of proteins and native states of intrinsically disordered proteins (IDPs) populate heterogeneous conformational ensembles in solution. The average sizes of these heterogeneous ...Unfolded states of proteins and native states of intrinsically disordered proteins (IDPs) populate heterogeneous conformational ensembles in solution. The average sizes of these heterogeneous systems, quantified by the radius of gyration ( ), can be measured by small-angle X-ray scattering (SAXS). Another parameter, the mean dye-to-dye distance ( ) for proteins with fluorescently labeled termini, can be estimated using single-molecule Förster resonance energy transfer (smFRET). A number of studies have reported inconsistencies in inferences drawn from the two sets of measurements for the dimensions of unfolded proteins and IDPs in the absence of chemical denaturants. These differences are typically attributed to the influence of fluorescent labels used in smFRET and to the impact of high concentrations and averaging features of SAXS. By measuring the dimensions of a collection of labeled and unlabeled polypeptides using smFRET and SAXS, we directly assessed the contributions of dyes to the experimental values and For chemically denatured proteins we obtain mutual consistency in our inferences based on and , whereas for IDPs under native conditions, we find substantial deviations. Using computations, we show that discrepant inferences are neither due to methodological shortcomings of specific measurements nor due to artifacts of dyes. Instead, our analysis suggests that chemical heterogeneity in heteropolymeric systems leads to a decoupling between and that is amplified in the absence of denaturants. Therefore, joint assessments of and combined with measurements of polymer shapes should provide a consistent and complete picture of the underlying ensembles.
External links	Proc Natl Acad Sci U S A / PubMed:28716919 / PubMed Central
Methods	SAS (X-ray synchrotron)
Structure data	SASDE23: Labeled nuclear pore complex protein Nup153 (NUL-Alexa488/Alexa594) without denaturant Method: SAXS/SANS SASDE33: Unlabeled nuclear pore complex protein Nup153 (NUL) with denaturant Method: SAXS/SANS SASDE43: Labeled nuclear pore complex protein Nup153 (NUL-Alexa488/Alexa594) with denaturant Method: SAXS/SANS SASDE53: Unlabeled dihydrolipoyllysine-residue succinyltransferase component (BBL) with denaturant Method: SAXS/SANS SASDE63: Labeled dihydrolipoyllysine-residue succinyltransferase component (BBL-Alexa488/Alexa594) with denaturant Method: SAXS/SANS SASDE73: Unlabeled cold shock protein (CSP) with denaturant Method: SAXS/SANS SASDE83: Labeled cold shock protein (CSP-Alexa488/Alexa594) with denaturant Method: SAXS/SANS SASDE93: Unlabeled thioredoxin (TRX) with denaturant (Thioredoxin 1, TRX) Method: SAXS/SANS SASDEA3: Labeled thioredoxin (TRX-Alexa488/Alexa594) with denaturant Method: SAXS/SANS SASDEB3: Unlabeled nuclear pore complex protein Nup98-Nup96 (N98) without denaturant Method: SAXS/SANS SASDEC3: Unlabeled nucleoporin NSP1 (NSP) without denaturant Method: SAXS/SANS SASDEH2: Unlabeled nucleoporin NUP49/NSP49 (N49) without denaturant Method: SAXS/SANS SASDEJ2: Labeled nucleoporin NUP49/NSP49 (N49-Alexa488/Alexa594) without denaturant Method: SAXS/SANS SASDEK2: Unlabeled nucleoporin NUP49/NSP49 (N49) with denaturant Method: SAXS/SANS SASDEL2: Labeled nucleoporin NUP49/NSP49 (N49-Alexa488/Alexa594) with denaturant Method: SAXS/SANS SASDEM2: Unlabeled Nuclear Localization Signal (NLS) from the inner nuclear membrane protein HEH2 without denaturant Method: SAXS/SANS SASDEN2: Labeled Nuclear Localization Signal from the inner nuclear membrane protein HEH2 (NLS-Alexa488/Alexa594) without denaturant Method: SAXS/SANS SASDEP2: Unlabeled Nuclear Localization Signal (NLS) from the inner nuclear membrane protein HEH2 with denaturant Method: SAXS/SANS SASDEQ2: Labeled Nuclear Localization Signal from the inner nuclear membrane protein HEH2 (NLS-Alexa488/Alexa594) with denaturant Method: SAXS/SANS SASDER2: Unlabeled Importin Beta Binding domain (IBB) from importin subunit alpha-1 without denaturant Method: SAXS/SANS SASDES2: Labeled Importin Beta Binding Domain (IBB-Alexa488/Alexa594) from importin subunit alpha-1 without denaturant Method: SAXS/SANS SASDET2: Unlabeled Importin Beta Binding Domain (IBB) from importin subunit alpha-1 with denaturant Method: SAXS/SANS SASDEU2: Labeled Importin Beta Binding Domain from importin subunit alpha-1 (IBB-Alexa488/Alexa594) with denaturant Method: SAXS/SANS SASDEV2: Unlabeled nuclear pore complex protein Nup153 (NUS) without denaturant Method: SAXS/SANS SASDEW2: Labeled nuclear pore complex protein Nup153 (NUS-Alexa488/Alexa594) without denaturant Method: SAXS/SANS SASDEX2: Unlabeled nuclear pore complex protein Nup153 (NUS) with denaturant Method: SAXS/SANS SASDEY2: Labeled nuclear pore complex protein Nup153 (NUS-Alexa488/Alexa594) with denaturant Method: SAXS/SANS SASDEZ2: Unlabeled nuclear pore complex protein Nup153 (NUL) without denaturant Method: SAXS/SANS
Source	Homo sapiens (human) Escherichia coli (strain k12) (bacteria) Thermotoga maritima (strain atcc 43589 / msb8 / dsm 3109 / jcm 10099) (bacteria) Saccharomyces cerevisiae (strain atcc 204508 / s288c) (yeast)