Literature DB >> 18697933

Crowded, cell-like environment induces shape changes in aspherical protein.

Dirar Homouz1, Michael Perham, Antonios Samiotakis, Margaret S Cheung, Pernilla Wittung-Stafshede.   

Abstract

How the crowded environment inside cells affects the structures of proteins with aspherical shapes is a vital question because many proteins and protein-protein complexes in vivo adopt anisotropic shapes. Here we address this question by combining computational and experimental studies of a football-shaped protein (i.e., Borrelia burgdorferi VlsE) in crowded, cell-like conditions. The results show that macromolecular crowding affects protein-folding dynamics as well as overall protein shape. In crowded milieus, distinct conformational changes in VlsE are accompanied by secondary structure alterations that lead to exposure of a hidden antigenic region. Our work demonstrates the malleability of "native" proteins and implies that crowding-induced shape changes may be important for protein function and malfunction in vivo.

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Year:  2008        PMID: 18697933      PMCID: PMC2515223          DOI: 10.1073/pnas.0803672105

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


  39 in total

1.  Structure of Met-enkephalin in explicit aqueous solution using replica exchange molecular dynamics.

Authors:  K Y Sanbonmatsu; A E García
Journal:  Proteins       Date:  2002-02-01

2.  Effect of dextran on protein stability and conformation attributed to macromolecular crowding.

Authors:  Kenji Sasahara; Peter McPhie; Allen P Minton
Journal:  J Mol Biol       Date:  2003-02-28       Impact factor: 5.469

3.  Simulations of beta-hairpin folding confined to spherical pores using distributed computing.

Authors:  D K Klimov; D Newfield; D Thirumalai
Journal:  Proc Natl Acad Sci U S A       Date:  2002-06-11       Impact factor: 11.205

4.  Life in a crowded world.

Authors:  Germán Rivas; Frank Ferrone; Judith Herzfeld
Journal:  EMBO Rep       Date:  2004-01       Impact factor: 8.807

Review 5.  Macromolecular crowding: qualitative and semiquantitative successes, quantitative challenges.

Authors:  Damien Hall; Allen P Minton
Journal:  Biochim Biophys Acta       Date:  2003-07-30

6.  Cell biology: join the crowd.

Authors:  R John Ellis; Allen P Minton
Journal:  Nature       Date:  2003-09-04       Impact factor: 49.962

7.  The largest protein observed to fold by two-state kinetic mechanism does not obey contact-order correlation.

Authors:  Kathryn Jones; Pernilla Wittung-Stafshede
Journal:  J Am Chem Soc       Date:  2003-08-13       Impact factor: 15.419

8.  Efficacy of macromolecular crowding in forcing proteins to fold.

Authors:  Youxing Qu; D W Bolen
Journal:  Biophys Chem       Date:  2002-12-10       Impact factor: 2.352

9.  Accelerated alpha-synuclein fibrillation in crowded milieu.

Authors:  Vladimir N Uversky; Elisa M Cooper; Kiowa S Bower; Jie Li; Anthony L Fink
Journal:  FEBS Lett       Date:  2002-03-27       Impact factor: 4.124

10.  Protein folding by the effects of macromolecular crowding.

Authors:  Nobuhiko Tokuriki; Masataka Kinjo; Shigeru Negi; Masaru Hoshino; Yuji Goto; Itaru Urabe; Tetsuya Yomo
Journal:  Protein Sci       Date:  2004-01       Impact factor: 6.725

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  69 in total

1.  Structure, function, and folding of phosphoglycerate kinase are strongly perturbed by macromolecular crowding.

Authors:  Apratim Dhar; Antonios Samiotakis; Simon Ebbinghaus; Lea Nienhaus; Dirar Homouz; Martin Gruebele; Margaret S Cheung
Journal:  Proc Natl Acad Sci U S A       Date:  2010-10-04       Impact factor: 11.205

2.  Generalized fundamental measure theory for atomistic modeling of macromolecular crowding.

Authors:  Sanbo Qin; Huan-Xiang Zhou
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2010-03-26

3.  Crowding and function reunite.

Authors:  Gary J Pielak; Andrew C Miklos
Journal:  Proc Natl Acad Sci U S A       Date:  2010-10-06       Impact factor: 11.205

4.  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

Review 5.  An expanding arsenal of experimental methods yields an explosion of insights into protein folding mechanisms.

Authors:  Alice I Bartlett; Sheena E Radford
Journal:  Nat Struct Mol Biol       Date:  2009-06       Impact factor: 15.369

6.  Macromolecular crowding in vitro as means of emulating cellular interiors: when less might be more.

Authors:  K S Harve; R Vigneshwar; R Rajagopalan; M Raghunath
Journal:  Proc Natl Acad Sci U S A       Date:  2008-12-05       Impact factor: 11.205

7.  Macromolecular crowding modulates folding mechanism of alpha/beta protein apoflavodoxin.

Authors:  Dirar Homouz; Loren Stagg; Pernilla Wittung-Stafshede; Margaret S Cheung
Journal:  Biophys J       Date:  2009-01       Impact factor: 4.033

8.  Quantification of excluded volume effects on the folding landscape of Pseudomonas aeruginosa apoazurin in vitro.

Authors:  Alexander Christiansen; Pernilla Wittung-Stafshede
Journal:  Biophys J       Date:  2013-10-01       Impact factor: 4.033

9.  Macromolecular crowding induces polypeptide compaction and decreases folding cooperativity.

Authors:  Douglas Tsao; Nikolay V Dokholyan
Journal:  Phys Chem Chem Phys       Date:  2010-04-14       Impact factor: 3.676

10.  Crowding effects on the mechanical stability and unfolding pathways of ubiquitin.

Authors:  David L Pincus; D Thirumalai
Journal:  J Phys Chem B       Date:  2009-01-08       Impact factor: 2.991

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