Literature DB >> 29026044

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

Joshua A Riback1, Micayla A Bowman2, Adam M Zmyslowski3, Catherine R Knoverek2, John M Jumper3,4, James R Hinshaw4, Emily B Kaye2, Karl F Freed4, Patricia L Clark5, Tobin R Sosnick6,7.   

Abstract

A substantial fraction of the proteome is intrinsically disordered, and even well-folded proteins adopt non-native geometries during synthesis, folding, transport, and turnover. Characterization of intrinsically disordered proteins (IDPs) is challenging, in part because of a lack of accurate physical models and the difficulty of interpreting experimental results. We have developed a general method to extract the dimensions and solvent quality (self-interactions) of IDPs from a single small-angle x-ray scattering measurement. We applied this procedure to a variety of IDPs and found that even IDPs with low net charge and high hydrophobicity remain highly expanded in water, contrary to the general expectation that protein-like sequences collapse in water. Our results suggest that the unfolded state of most foldable sequences is expanded; we conjecture that this property was selected by evolution to minimize misfolding and aggregation.
Copyright © 2017 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

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Year:  2017        PMID: 29026044      PMCID: PMC5959285          DOI: 10.1126/science.aan5774

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


  28 in total

1.  Chain collapse can occur concomitantly with the rate-limiting step in protein folding.

Authors:  K W Plaxco; I S Millett; D J Segel; S Doniach; D Baker
Journal:  Nat Struct Biol       Date:  1999-06

2.  Random-coil behavior and the dimensions of chemically unfolded proteins.

Authors:  Jonathan E Kohn; Ian S Millett; Jaby Jacob; Bojan Zagrovic; Thomas M Dillon; Nikolina Cingel; Robin S Dothager; Soenke Seifert; P Thiyagarajan; Tobin R Sosnick; M Zahid Hasan; Vijay S Pande; Ingo Ruczinski; Sebastian Doniach; Kevin W Plaxco
Journal:  Proc Natl Acad Sci U S A       Date:  2004-08-16       Impact factor: 11.205

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.  Pertactin beta-helix folding mechanism suggests common themes for the secretion and folding of autotransporter proteins.

Authors:  Mirco Junker; Christopher C Schuster; Andrew V McDonnell; Kelli A Sorg; Mary C Finn; Bonnie Berger; Patricia L Clark
Journal:  Proc Natl Acad Sci U S A       Date:  2006-03-20       Impact factor: 11.205

Review 5.  Assessing the accuracy of physical models used in protein-folding simulations: quantitative evidence from long molecular dynamics simulations.

Authors:  Stefano Piana; John L Klepeis; David E Shaw
Journal:  Curr Opin Struct Biol       Date:  2014-01-24       Impact factor: 6.809

6.  Consistent View of Polypeptide Chain Expansion in Chemical Denaturants from Multiple Experimental Methods.

Authors:  Alessandro Borgia; Wenwei Zheng; Karin Buholzer; Madeleine B Borgia; Anja Schüler; Hagen Hofmann; Andrea Soranno; Daniel Nettels; Klaus Gast; Alexander Grishaev; Robert B Best; Benjamin Schuler
Journal:  J Am Chem Soc       Date:  2016-09-01       Impact factor: 15.419

7.  Stress-Triggered Phase Separation Is an Adaptive, Evolutionarily Tuned Response.

Authors:  Joshua A Riback; Christopher D Katanski; Jamie L Kear-Scott; Evgeny V Pilipenko; Alexandra E Rojek; Tobin R Sosnick; D Allan Drummond
Journal:  Cell       Date:  2017-03-09       Impact factor: 41.582

Review 8.  How, when and why proteins collapse: the relation to folding.

Authors:  Gilad Haran
Journal:  Curr Opin Struct Biol       Date:  2011-11-19       Impact factor: 6.809

9.  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

10.  TonB-dependent transporter FhuA in planar lipid bilayers: partial exit of its plug from the barrel.

Authors:  Eshwar Udho; Karen S Jakes; Alan Finkelstein
Journal:  Biochemistry       Date:  2012-08-15       Impact factor: 3.162

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  61 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

Review 3.  Advances in targeting 'undruggable' transcription factors with small molecules.

Authors:  Matthew J Henley; Angela N Koehler
Journal:  Nat Rev Drug Discov       Date:  2021-05-18       Impact factor: 84.694

4.  Relation between single-molecule properties and phase behavior of intrinsically disordered proteins.

Authors:  Gregory L Dignon; Wenwei Zheng; Robert B Best; Young C Kim; Jeetain Mittal
Journal:  Proc Natl Acad Sci U S A       Date:  2018-09-14       Impact factor: 11.205

Review 5.  Lessons from pressure denaturation of proteins.

Authors:  Julien Roche; Catherine A Royer
Journal:  J R Soc Interface       Date:  2018-10-03       Impact factor: 4.118

6.  Sequence Reversal Prevents Chain Collapse and Yields Heat-Sensitive Intrinsic Disorder.

Authors:  Lance R English; Alexander Tischer; Aysha K Demeler; Borries Demeler; Steven T Whitten
Journal:  Biophys J       Date:  2018-07-17       Impact factor: 4.033

7.  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

8.  Valence and patterning of aromatic residues determine the phase behavior of prion-like domains.

Authors:  Erik W Martin; Alex S Holehouse; Ivan Peran; Mina Farag; J Jeremias Incicco; Anne Bremer; Christy R Grace; Andrea Soranno; Rohit V Pappu; Tanja Mittag
Journal:  Science       Date:  2020-02-07       Impact factor: 47.728

9.  A Metastable Contact and Structural Disorder in the Estrogen Receptor Transactivation Domain.

Authors:  Yi Peng; Shufen Cao; Janna Kiselar; Xiangzhu Xiao; Zhanwen Du; An Hsieh; Soobin Ko; Yinghua Chen; Prashansa Agrawal; Wenwei Zheng; Wuxian Shi; Wei Jiang; Lin Yang; Mark R Chance; Witold K Surewicz; Matthias Buck; Sichun Yang
Journal:  Structure       Date:  2018-12-20       Impact factor: 5.006

10.  Origin of Internal Friction in Disordered Proteins Depends on Solvent Quality.

Authors:  Wenwei Zheng; Hagen Hofmann; Benjamin Schuler; Robert B Best
Journal:  J Phys Chem B       Date:  2018-10-02       Impact factor: 2.991

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