Warning: Undefined array key "mm" in /www/wwwroot/www.ai-bt.com/si.php on line 10 Deprecated: trim(): Passing null to parameter #1 ($string) of type string is deprecated in /www/wwwroot/www.ai-bt.com/si.php on line 10 Comment on "Innovative scattering analysis shows that hydrophobic disordered proteins are expanded in water".

Literature DB >> 30166459

Comment on "Innovative scattering analysis shows that hydrophobic disordered proteins are expanded in water".

Robert B Best¹, Wenwei Zheng², Alessandro Borgia³, Karin Buholzer³, Madeleine B Borgia³, Hagen Hofmann⁴, Andrea Soranno⁵, Daniel Nettels³, Klaus Gast⁶, Alexander Grishaev⁷, Benjamin Schuler^8,9.

Abstract

Riback et al (Reports, 13 October 2017, p. 238) used small-angle x-ray scattering (SAXS) experiments to infer a degree of compaction for unfolded proteins in water versus chemical denaturant that is highly consistent with the results from Förster resonance energy transfer (FRET) experiments. There is thus no "contradiction" between the two methods, nor evidence to support their claim that commonly used FRET fluorophores cause protein compaction.

Entities: Chemical Disease Gene

Mesh：

Substances：
Water

Year: 2018 PMID： 30166459 PMCID： PMC7507683 DOI： 10.1126/science.aar7101

Source DB: PubMed Journal: Science ISSN： 0036-8075 Impact factor: 47.728

14 in total

1. Small-angle X-ray scattering and single-molecule FRET spectroscopy produce highly divergent views of the low-denaturant unfolded state.

Authors: Tae Yeon Yoo; Steve P Meisburger; James Hinshaw; Lois Pollack; Gilad Haran; Tobin R Sosnick; Kevin Plaxco
Journal: J Mol Biol Date: 2012-01-27 Impact factor: 5.469

2. Bayesian ensemble refinement by replica simulations and reweighting.

Authors: Gerhard Hummer; Jürgen Köfinger
Journal: J Chem Phys Date: 2015-12-28 Impact factor: 3.488

3. Characterizing the unfolded states of proteins using single-molecule FRET spectroscopy and molecular simulations.

Authors: Kusai A Merchant; Robert B Best; John M Louis; Irina V Gopich; William A Eaton
Journal: Proc Natl Acad Sci U S A Date: 2007-01-24 Impact factor: 11.205

4. Decoupling of size and shape fluctuations in heteropolymeric sequences reconciles discrepancies in SAXS vs. FRET measurements.

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
Journal: Proc Natl Acad Sci U S A Date: 2017-07-17 Impact factor: 11.205

5. Probing the Action of Chemical Denaturant on an Intrinsically Disordered Protein by Simulation and Experiment.

Authors: Wenwei Zheng; Alessandro Borgia; Karin Buholzer; Alexander Grishaev; Benjamin Schuler; Robert B Best
Journal: J Am Chem Soc Date: 2016-09-01 Impact factor: 15.419

6. A simple method for displaying the hydropathic character of a protein.

Authors: J Kyte; R F Doolittle
Journal: J Mol Biol Date: 1982-05-05 Impact factor: 5.469

7. Random coil negative control reproduces the discrepancy between scattering and FRET measurements of denatured protein dimensions.

Authors: Herschel M Watkins; Anna J Simon; Tobin R Sosnick; Everett A Lipman; Rex P Hjelm; Kevin W Plaxco
Journal: Proc Natl Acad Sci U S A Date: 2015-05-11 Impact factor: 11.205

8. An Adequate Account of Excluded Volume Is Necessary To Infer Compactness and Asphericity of Disordered Proteins by Förster Resonance Energy Transfer.

Authors: Jianhui Song; Gregory-Neal Gomes; Claudiu C Gradinaru; Hue Sun Chan
Journal: J Phys Chem B Date: 2015-12-01 Impact factor: 2.991

9. How accurate are polymer models in the analysis of Förster resonance energy transfer experiments on proteins?

Authors: Edward P O'Brien; Greg Morrison; Bernard R Brooks; D Thirumalai
Journal: J Chem Phys Date: 2009-03-28 Impact factor: 3.488

10. Innovative scattering analysis shows that hydrophobic disordered proteins are expanded in water.

Authors: Joshua A Riback; Micayla A Bowman; Adam M Zmyslowski; Catherine R Knoverek; John M Jumper; James R Hinshaw; Emily B Kaye; Karl F Freed; Patricia L Clark; Tobin R Sosnick
Journal: Science Date: 2017-10-13 Impact factor: 47.728

15 in total

1. The combined force field-sampling problem in simulations of disordered amyloid-β peptides.

Authors: James Lincoff; Sukanya Sasmal; Teresa Head-Gordon
Journal: J Chem Phys Date: 2019-03-14 Impact factor: 3.488

2. Commonly used FRET fluorophores promote collapse of an otherwise disordered protein.

Authors: Joshua A Riback; Micayla A Bowman; Adam M Zmyslowski; Kevin W Plaxco; Patricia L Clark; Tobin R Sosnick
Journal: Proc Natl Acad Sci U S A Date: 2019-04-16 Impact factor: 11.205

3. Binding Affinity and Function of the Extremely Disordered Protein Complex Containing Human Linker Histone H1.0 and Its Chaperone ProTα.

Authors: Hanqiao Feng; Bing-Rui Zhou; Yawen Bai
Journal: Biochemistry Date: 2018-11-19 Impact factor: 3.162

4. Generation of the configurational ensemble of an intrinsically disordered protein from unbiased molecular dynamics simulation.

Authors: Utsab R Shrestha; Puneet Juneja; Qiu Zhang; Viswanathan Gurumoorthy; Jose M Borreguero; Volker Urban; Xiaolin Cheng; Sai Venkatesh Pingali; Jeremy C Smith; Hugh M O'Neill; Loukas Petridis
Journal: Proc Natl Acad Sci U S A Date: 2019-09-23 Impact factor: 11.205

5. Accurate Transfer Efficiencies, Distance Distributions, and Ensembles of Unfolded and Intrinsically Disordered Proteins From Single-Molecule FRET.

Authors: Erik D Holmstrom; Andrea Holla; Wenwei Zheng; Daniel Nettels; Robert B Best; Benjamin Schuler
Journal: Methods Enzymol Date: 2018-11-16 Impact factor: 1.600