Literature DB >> 31805437

Emerging consensus on the collapse of unfolded and intrinsically disordered proteins in water.

Robert B Best1.   

Abstract

Establishing the degree of collapse of unfolded or disordered proteins is a fundamental problem in biophysics, because of its relation to protein folding and to the function of intrinsically disordered proteins. However, until recently, different experiments gave qualitatively different results on collapse and there were large discrepancies between experiments and all-atom simulations. New methodology introduced in the past three years has helped to resolve the differences between experiments, and improvements in simulations have closed the gap between experiment and simulation. These advances have led to an emerging consensus on the collapse of disordered proteins in water. Published by Elsevier Ltd.

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Year:  2019        PMID: 31805437      PMCID: PMC7472963          DOI: 10.1016/j.sbi.2019.10.009

Source DB:  PubMed          Journal:  Curr Opin Struct Biol        ISSN: 0959-440X            Impact factor:   6.809


  76 in total

1.  Specific and nonspecific collapse in protein folding funnels.

Authors:  Jorge Chahine; Hugh Nymeyer; Vitor B P Leite; Nicholas D Socci; José Nelson Onuchic
Journal:  Phys Rev Lett       Date:  2002-04-05       Impact factor: 9.161

2.  Temperature-dependent structural changes in intrinsically disordered proteins: formation of alpha-helices or loss of polyproline II?

Authors:  Magnus Kjaergaard; Ann-Beth Nørholm; Ruth Hendus-Altenburger; Stine F Pedersen; Flemming M Poulsen; Birthe B Kragelund
Journal:  Protein Sci       Date:  2010-08       Impact factor: 6.725

3.  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

4.  Dynamic equilibrium engagement of a polyvalent ligand with a single-site receptor.

Authors:  Tanja Mittag; Stephen Orlicky; Wing-Yiu Choy; Xiaojing Tang; Hong Lin; Frank Sicheri; Lewis E Kay; Mike Tyers; Julie D Forman-Kay
Journal:  Proc Natl Acad Sci U S A       Date:  2008-11-13       Impact factor: 11.205

5.  Conformations of intrinsically disordered proteins are influenced by linear sequence distributions of oppositely charged residues.

Authors:  Rahul K Das; Rohit V Pappu
Journal:  Proc Natl Acad Sci U S A       Date:  2013-07-30       Impact factor: 11.205

6.  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

7.  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

8.  Temperature-dependent solvation modulates the dimensions of disordered proteins.

Authors:  René Wuttke; Hagen Hofmann; Daniel Nettels; Madeleine B Borgia; Jeetain Mittal; Robert B Best; Benjamin Schuler
Journal:  Proc Natl Acad Sci U S A       Date:  2014-03-21       Impact factor: 11.205

9.  Kinetics and thermodynamics of folding in model proteins.

Authors:  C J Camacho; D Thirumalai
Journal:  Proc Natl Acad Sci U S A       Date:  1993-07-01       Impact factor: 11.205

10.  Mapping protein collapse with single-molecule fluorescence and kinetic synchrotron radiation circular dichroism spectroscopy.

Authors:  Armin Hoffmann; Avinash Kane; Daniel Nettels; David E Hertzog; Peter Baumgärtel; Jan Lengefeld; Gerd Reichardt; David A Horsley; Robert Seckler; Olgica Bakajin; Benjamin Schuler
Journal:  Proc Natl Acad Sci U S A       Date:  2006-12-21       Impact factor: 11.205

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  10 in total

1.  Crowding-induced protein destabilization in the absence of soft attractions.

Authors:  Saman Bazmi; Stefan Wallin
Journal:  Biophys J       Date:  2022-06-07       Impact factor: 3.699

2.  Molecular Details of Protein Condensates Probed by Microsecond Long Atomistic Simulations.

Authors:  Wenwei Zheng; Gregory L Dignon; Nina Jovic; Xichen Xu; Roshan M Regy; Nicolas L Fawzi; Young C Kim; Robert B Best; Jeetain Mittal
Journal:  J Phys Chem B       Date:  2020-12-10       Impact factor: 2.991

3.  Visualizing and trapping transient oligomers in amyloid assembly pathways.

Authors:  Emma E Cawood; Theodoros K Karamanos; Andrew J Wilson; Sheena E Radford
Journal:  Biophys Chem       Date:  2020-11-10       Impact factor: 2.352

Review 4.  The Protein Folding Problem: The Role of Theory.

Authors:  Roy Nassar; Gregory L Dignon; Rostam M Razban; Ken A Dill
Journal:  J Mol Biol       Date:  2021-07-03       Impact factor: 6.151

5.  Denatured State Conformational Biases in Three-Helix Bundles Containing Divergent Sequences Localize near Turns and Helix Capping Residues.

Authors:  Moses J Leavens; Lisa E Spang; Melisa M Cherney; Bruce E Bowler
Journal:  Biochemistry       Date:  2021-10-04       Impact factor: 3.321

6.  Lipid bilayer induces contraction of the denatured state ensemble of a helical-bundle membrane protein.

Authors:  Kristen A Gaffney; Ruiqiong Guo; Michael D Bridges; Shaima Muhammednazaar; Daoyang Chen; Miyeon Kim; Zhongyu Yang; Anthony L Schilmiller; Nabil F Faruk; Xiangda Peng; A Daniel Jones; Kelly H Kim; Liangliang Sun; Wayne L Hubbell; Tobin R Sosnick; Heedeok Hong
Journal:  Proc Natl Acad Sci U S A       Date:  2022-01-04       Impact factor: 12.779

7.  Integrative structural dynamics probing of the conformational heterogeneity in synaptosomal-associated protein 25.

Authors:  Nabanita Saikia; Inna S Yanez-Orozco; Ruoyi Qiu; Pengyu Hao; Sergey Milikisiyants; Erkang Ou; George L Hamilton; Keith R Weninger; Tatyana I Smirnova; Hugo Sanabria; Feng Ding
Journal:  Cell Rep Phys Sci       Date:  2021-10-15

8.  Rate-limiting transport of positively charged arginine residues through the Sec-machinery is integral to the mechanism of protein secretion.

Authors:  William J Allen; Robin A Corey; Daniel W Watkins; A Sofia F Oliveira; Kiel Hards; Gregory M Cook; Ian Collinson
Journal:  Elife       Date:  2022-04-29       Impact factor: 8.713

9.  Full structural ensembles of intrinsically disordered proteins from unbiased molecular dynamics simulations.

Authors:  Utsab R Shrestha; Jeremy C Smith; Loukas Petridis
Journal:  Commun Biol       Date:  2021-02-23

10.  Integrating single-molecule spectroscopy and simulations for the study of intrinsically disordered proteins.

Authors:  Jhullian J Alston; Andrea Soranno; Alex S Holehouse
Journal:  Methods       Date:  2021-04-06       Impact factor: 3.608

  10 in total

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