Literature DB >> 24639500

Single-molecule spectroscopy reveals polymer effects of disordered proteins in crowded environments.

Andrea Soranno1, Iwo Koenig, Madeleine B Borgia, Hagen Hofmann, Franziska Zosel, Daniel Nettels, Benjamin Schuler.   

Abstract

Intrinsically disordered proteins (IDPs) are involved in a wide range of regulatory processes in the cell. Owing to their flexibility, their conformations are expected to be particularly sensitive to the crowded cellular environment. Here we use single-molecule Förster resonance energy transfer to quantify the effect of crowding as mimicked by commonly used biocompatible polymers. We observe a compaction of IDPs not only with increasing concentration, but also with increasing size of the crowding agents, at variance with the predictions from scaled-particle theory, the prevalent paradigm in the field. However, the observed behavior can be explained quantitatively if the polymeric nature of both the IDPs and the crowding molecules is taken into account explicitly. Our results suggest that excluded volume interactions between overlapping biopolymers and the resulting criticality of the system can be essential contributions to the physics governing the crowded cellular milieu.

Entities:  

Keywords:  Flory–Huggins theory; excluded volume screening; single-molecule FRET; unfolded state collapse

Mesh:

Substances:

Year:  2014        PMID: 24639500      PMCID: PMC3977265          DOI: 10.1073/pnas.1322611111

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  46 in total

1.  Dependence of protein folding stability and dynamics on the density and composition of macromolecular crowders.

Authors:  Jeetain Mittal; Robert B Best
Journal:  Biophys J       Date:  2010-01-20       Impact factor: 4.033

2.  Models for excluded volume interaction between an unfolded protein and rigid macromolecular cosolutes: macromolecular crowding and protein stability revisited.

Authors:  Allen P Minton
Journal:  Biophys J       Date:  2004-12-13       Impact factor: 4.033

3.  Toward an accurate theoretical framework for describing ensembles for proteins under strongly denaturing conditions.

Authors:  Hoang T Tran; Rohit V Pappu
Journal:  Biophys J       Date:  2006-06-09       Impact factor: 4.033

4.  Mobility within the nucleus and neighboring cytosol is a key feature of prothymosin-alpha.

Authors:  S A Enkemann; R D Ward; S L Berger
Journal:  J Histochem Cytochem       Date:  2000-10       Impact factor: 2.479

5.  Capillarity theory for the fly-casting mechanism.

Authors:  Emmanuel Trizac; Yaakov Levy; Peter G Wolynes
Journal:  Proc Natl Acad Sci U S A       Date:  2010-01-28       Impact factor: 11.205

6.  Quantitative assessment of the relative contributions of steric repulsion and chemical interactions to macromolecular crowding.

Authors:  Allen P Minton
Journal:  Biopolymers       Date:  2013-04       Impact factor: 2.505

7.  Macromolecular crowding remodels the energy landscape of a protein by favoring a more compact unfolded state.

Authors:  Jiang Hong; Lila M Gierasch
Journal:  J Am Chem Soc       Date:  2010-08-04       Impact factor: 15.419

8.  Protein folding, protein collapse, and tanford's transfer model: lessons from single-molecule FRET.

Authors:  Guy Ziv; Gilad Haran
Journal:  J Am Chem Soc       Date:  2009-03-04       Impact factor: 15.419

9.  The effect of macromolecular crowding on protein aggregation and amyloid fibril formation.

Authors:  Larissa A Munishkina; Elisa M Cooper; Vladimir N Uversky; Anthony L Fink
Journal:  J Mol Recognit       Date:  2004 Sep-Oct       Impact factor: 2.137

Review 10.  Fundamental aspects of protein-protein association kinetics.

Authors:  G Schreiber; G Haran; H-X Zhou
Journal:  Chem Rev       Date:  2009-03-11       Impact factor: 60.622

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  71 in total

1.  Crowding-Induced Elongated Conformation of Urea-Unfolded Apoazurin: Investigating the Role of Crowder Shape in Silico.

Authors:  Fabio C Zegarra; Dirar Homouz; Andrei G Gasic; Lucas Babel; Michael Kovermann; Pernilla Wittung-Stafshede; Margaret S Cheung
Journal:  J Phys Chem B       Date:  2019-04-23       Impact factor: 2.991

2.  The Hsp90 ensemble: coordinated Hsp90-cochaperone complexes regulate diverse cellular processes.

Authors:  Serena Schwenkert; Thorsten Hugel; Marc B Cox
Journal:  Nat Struct Mol Biol       Date:  2014-12       Impact factor: 15.369

3.  Single-molecule spectroscopy of protein conformational dynamics in live eukaryotic cells.

Authors:  Iwo König; Arash Zarrine-Afsar; Mikayel Aznauryan; Andrea Soranno; Bengt Wunderlich; Fabian Dingfelder; Jakob C Stüber; Andreas Plückthun; Daniel Nettels; Benjamin Schuler
Journal:  Nat Methods       Date:  2015-07-06       Impact factor: 28.547

Review 4.  Understanding biochemical processes in the presence of sub-diffusive behavior of biomolecules in solution and living cells.

Authors:  Sujit Basak; Sombuddha Sengupta; Krishnananda Chattopadhyay
Journal:  Biophys Rev       Date:  2019-08-23

Review 5.  Features of molecular recognition of intrinsically disordered proteins via coupled folding and binding.

Authors:  Jing Yang; Meng Gao; Junwen Xiong; Zhengding Su; Yongqi Huang
Journal:  Protein Sci       Date:  2019-09-04       Impact factor: 6.725

Review 6.  Microorganisms maintain crowding homeostasis.

Authors:  Jonas van den Berg; Arnold J Boersma; Bert Poolman
Journal:  Nat Rev Microbiol       Date:  2017-03-27       Impact factor: 60.633

7.  Design and Properties of Genetically Encoded Probes for Sensing Macromolecular Crowding.

Authors:  Boqun Liu; Christoffer Åberg; Floris J van Eerden; Siewert J Marrink; Bert Poolman; Arnold J Boersma
Journal:  Biophys J       Date:  2017-05-09       Impact factor: 4.033

Review 8.  To be disordered or not to be disordered: is that still a question for proteins in the cell?

Authors:  Kris Pauwels; Pierre Lebrun; Peter Tompa
Journal:  Cell Mol Life Sci       Date:  2017-06-13       Impact factor: 9.261

Review 9.  Single-molecule fluorescence studies of intrinsically disordered proteins and liquid phase separation.

Authors:  Irem Nasir; Paulo L Onuchic; Sergio R Labra; Ashok A Deniz
Journal:  Biochim Biophys Acta Proteins Proteom       Date:  2019-05-02       Impact factor: 3.036

10.  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
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