Literature DB >> 33191750

Revealing the Hidden Sensitivity of Intrinsically Disordered Proteins to their Chemical Environment.

David Moses1,2, Feng Yu2,3, Garrett M Ginell4, Nora M Shamoon5, Patrick S Koenig3, Alex S Holehouse4,6, Shahar Sukenik1,2,3.   

Abstract

Intrinsically disordered protein-regions (IDRs) make up roughly 30% of the human proteome and are central to a wide range of biological processes. Given a lack of persistent tertiary structure, all residues in IDRs are, to some extent, solvent exposed. This extensive surface area, coupled with the absence of strong intramolecular contacts, makes IDRs inherently sensitive to their chemical environment. We report a combined experimental, computational, and analytical framework for high-throughput characterization of IDR sensitivity. Our framework reveals that IDRs can expand or compact in response to changes in their solution environment. Importantly, the direction and magnitude of conformational change depend on both protein sequence and cosolute identity. For example, some solutes such as short polyethylene glycol chains exert an expanding effect on some IDRs and a compacting effect on others. Despite this complex behavior, we can rationally interpret IDR responsiveness to solution composition changes using relatively simple polymer models. Our results imply that solution-responsive IDRs are ubiquitous and can provide an additional layer of regulation to biological systems.

Entities:  

Year:  2020        PMID: 33191750      PMCID: PMC8092420          DOI: 10.1021/acs.jpclett.0c02822

Source DB:  PubMed          Journal:  J Phys Chem Lett        ISSN: 1948-7185            Impact factor:   6.475


  43 in total

1.  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

Review 2.  How does solvation in the cell affect protein folding and binding?

Authors:  Caitlin M Davis; Martin Gruebele; Shahar Sukenik
Journal:  Curr Opin Struct Biol       Date:  2017-10-13       Impact factor: 6.809

3.  Controlling Structural Bias in Intrinsically Disordered Proteins Using Solution Space Scanning.

Authors:  Alex S Holehouse; Shahar Sukenik
Journal:  J Chem Theory Comput       Date:  2020-02-17       Impact factor: 6.006

4.  Effective concentrations enforced by intrinsically disordered linkers are governed by polymer physics.

Authors:  Charlotte S Sørensen; Magnus Kjaergaard
Journal:  Proc Natl Acad Sci U S A       Date:  2019-10-28       Impact factor: 11.205

5.  Folding propensity of intrinsically disordered proteins by osmotic stress.

Authors:  Amanda L Mansouri; Laura N Grese; Erica L Rowe; James C Pino; S Chakra Chennubhotla; Arvind Ramanathan; Hugh M O'Neill; Valerie Berthelier; Christopher B Stanley
Journal:  Mol Biosyst       Date:  2016-11-15

6.  Effects of denaturants and osmolytes on proteins are accurately predicted by the molecular transfer model.

Authors:  Edward P O'Brien; Guy Ziv; Gilad Haran; Bernard R Brooks; D Thirumalai
Journal:  Proc Natl Acad Sci U S A       Date:  2008-08-29       Impact factor: 11.205

7.  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

Review 8.  Classification of intrinsically disordered regions and proteins.

Authors:  Robin van der Lee; Marija Buljan; Benjamin Lang; Robert J Weatheritt; Gary W Daughdrill; A Keith Dunker; Monika Fuxreiter; Julian Gough; Joerg Gsponer; David T Jones; Philip M Kim; Richard W Kriwacki; Christopher J Oldfield; Rohit V Pappu; Peter Tompa; Vladimir N Uversky; Peter E Wright; M Madan Babu
Journal:  Chem Rev       Date:  2014-04-29       Impact factor: 60.622

9.  DisProt 7.0: a major update of the database of disordered proteins.

Authors:  Damiano Piovesan; Francesco Tabaro; Ivan Mičetić; Marco Necci; Federica Quaglia; Christopher J Oldfield; Maria Cristina Aspromonte; Norman E Davey; Radoslav Davidović; Zsuzsanna Dosztányi; Arne Elofsson; Alessandra Gasparini; András Hatos; Andrey V Kajava; Lajos Kalmar; Emanuela Leonardi; Tamas Lazar; Sandra Macedo-Ribeiro; Mauricio Macossay-Castillo; Attila Meszaros; Giovanni Minervini; Nikoletta Murvai; Jordi Pujols; Daniel B Roche; Edoardo Salladini; Eva Schad; Antoine Schramm; Beata Szabo; Agnes Tantos; Fiorella Tonello; Konstantinos D Tsirigos; Nevena Veljković; Salvador Ventura; Wim Vranken; Per Warholm; Vladimir N Uversky; A Keith Dunker; Sonia Longhi; Peter Tompa; Silvio C E Tosatto
Journal:  Nucleic Acids Res       Date:  2016-11-28       Impact factor: 16.971

10.  Modulation of allostery by protein intrinsic disorder.

Authors:  Allan Chris M Ferreon; Josephine C Ferreon; Peter E Wright; Ashok A Deniz
Journal:  Nature       Date:  2013-06-20       Impact factor: 49.962

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  12 in total

1.  An Introduction to the Stickers-and-Spacers Framework as Applied to Biomolecular Condensates.

Authors:  Garrett M Ginell; Alex S Holehouse
Journal:  Methods Mol Biol       Date:  2023

2.  SWI/SNF senses carbon starvation with a pH-sensitive low-complexity sequence.

Authors:  J Ignacio Gutierrez; Gregory P Brittingham; Yonca Karadeniz; Kathleen D Tran; Arnob Dutta; Alex S Holehouse; Craig L Peterson; Liam J Holt
Journal:  Elife       Date:  2022-02-07       Impact factor: 8.713

Review 3.  Fifteen compelling open questions in plant cell biology.

Authors:  Adrienne H K Roeder; Marisa S Otegui; Ram Dixit; Charles T Anderson; Christine Faulkner; Yan Zhang; Maria J Harrison; Charlotte Kirchhelle; Gohta Goshima; Jeremy E Coate; Jeff J Doyle; Olivier Hamant; Keiko Sugimoto; Liam Dolan; Heather Meyer; David W Ehrhardt; Arezki Boudaoud; Carlos Messina
Journal:  Plant Cell       Date:  2022-01-20       Impact factor: 12.085

4.  Clustering of Aromatic Residues in Prion-like Domains Can Tune the Formation, State, and Organization of Biomolecular Condensates.

Authors:  Alex S Holehouse; Garrett M Ginell; Daniel Griffith; Elvan Böke
Journal:  Biochemistry       Date:  2021-11-16       Impact factor: 3.162

5.  Intrinsically disordered signaling proteins: Essential hub players in the control of stress responses in Saccharomyces cerevisiae.

Authors:  Leidys French-Pacheco; Omar Rosas-Bringas; Lorenzo Segovia; Alejandra A Covarrubias
Journal:  PLoS One       Date:  2022-03-15       Impact factor: 3.240

6.  Probing Interdomain Linkers and Protein Supertertiary Structure In Vitro and in Live Cells with Fluorescent Protein Resonance Energy Transfer.

Authors:  Sujit Basak; Nabanita Sakia; Laura Dougherty; Zhuojun Guo; Fang Wu; Frank Mindlin; Jeffrey W Lary; James L Cole; Feng Ding; Mark E Bowen
Journal:  J Mol Biol       Date:  2021-01-01       Impact factor: 5.469

7.  Sequence determinants of in cell condensate morphology, dynamics, and oligomerization as measured by number and brightness analysis.

Authors:  Ryan J Emenecker; Alex S Holehouse; Lucia C Strader
Journal:  Cell Commun Signal       Date:  2021-06-05       Impact factor: 5.712

Review 8.  Viewing SARS-CoV-2 Nucleocapsid Protein in Terms of Molecular Flexibility.

Authors:  Tatsuhito Matsuo
Journal:  Biology (Basel)       Date:  2021-05-21

9.  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.  Self-Diffusive Properties of the Intrinsically Disordered Protein Histatin 5 and the Impact of Crowding Thereon: A Combined Neutron Spectroscopy and Molecular Dynamics Simulation Study.

Authors:  Eric Fagerberg; Samuel Lenton; Tommy Nylander; Tilo Seydel; Marie Skepö
Journal:  J Phys Chem B       Date:  2022-01-19       Impact factor: 2.991

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