Literature DB >> 20167475

Models of macromolecular crowding effects and the need for quantitative comparisons with experiment.

Adrian H Elcock1.   

Abstract

In recent years significant effort has been devoted to exploring the potential effects of macromolecular crowding on protein folding and association phenomena. Theoretical calculations and molecular simulations have, in particular, been exploited to describe aspects of protein behavior in crowded and confined conditions and many aspects of the simulated behavior have reflected, at least at a qualitative level, the behavior observed in experiments. One major and immediate challenge for the theorists is to now produce models capable of making quantitatively accurate predictions of in vitro behavior. A second challenge is to derive models that explain results obtained from experiments performed in vivo, the results of which appear to call into question the assumed dominance of excluded-volume effects in vivo.

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Year:  2010        PMID: 20167475      PMCID: PMC2854290          DOI: 10.1016/j.sbi.2010.01.008

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


  78 in total

1.  Atomic-level observation of macromolecular crowding effects: escape of a protein from the GroEL cage.

Authors:  Adrian H Elcock
Journal:  Proc Natl Acad Sci U S A       Date:  2003-02-24       Impact factor: 11.205

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.  Unfolding of Green Fluorescent Protein mut2 in wet nanoporous silica gels.

Authors:  Barbara Campanini; Sara Bologna; Fabio Cannone; Giuseppe Chirico; Andrea Mozzarelli; Stefano Bettati
Journal:  Protein Sci       Date:  2005-03-31       Impact factor: 6.725

4.  Effect of macromolecular crowding on reaction rates: a computational and theoretical study.

Authors:  Jun Soo Kim; Arun Yethiraj
Journal:  Biophys J       Date:  2009-02-18       Impact factor: 4.033

5.  Side-chain recognition and gating in the ribosome exit tunnel.

Authors:  Paula M Petrone; Christopher D Snow; Del Lucent; Vijay S Pande
Journal:  Proc Natl Acad Sci U S A       Date:  2008-10-22       Impact factor: 11.205

6.  The effects of macromolecular crowding on the mechanical stability of protein molecules.

Authors:  Jian-Min Yuan; Chia-Lin Chyan; Huan-Xiang Zhou; Tse-Yu Chung; Haibo Peng; Guanghui Ping; Guoliang Yang
Journal:  Protein Sci       Date:  2008-09-09       Impact factor: 6.725

7.  Effect of mixed macromolecular crowding agents on protein folding.

Authors:  Huan-Xiang Zhou
Journal:  Proteins       Date:  2008-09

8.  Rapid, electrostatically assisted association of proteins.

Authors:  G Schreiber; A R Fersht
Journal:  Nat Struct Biol       Date:  1996-05

Review 9.  Ficoll and dextran vs. globular proteins as probes for testing glomerular permselectivity: effects of molecular size, shape, charge, and deformability.

Authors:  Daniele Venturoli; Bengt Rippe
Journal:  Am J Physiol Renal Physiol       Date:  2005-04

10.  Modulation of calmodulin plasticity by the effect of macromolecular crowding.

Authors:  Dirar Homouz; Hugo Sanabria; M Neal Waxham; Margaret S Cheung
Journal:  J Mol Biol       Date:  2009-07-03       Impact factor: 5.469

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  105 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.  Protein-binding dynamics imaged in a living cell.

Authors:  Yael Phillip; Vladimir Kiss; Gideon Schreiber
Journal:  Proc Natl Acad Sci U S A       Date:  2012-01-17       Impact factor: 11.205

Review 3.  Capturing the essence of folding and functions of biomolecules using coarse-grained models.

Authors:  Changbong Hyeon; D Thirumalai
Journal:  Nat Commun       Date:  2011-09-27       Impact factor: 14.919

4.  Brownian dynamics simulation of protein solutions: structural and dynamical properties.

Authors:  Paolo Mereghetti; Razif R Gabdoulline; Rebecca C Wade
Journal:  Biophys J       Date:  2010-12-01       Impact factor: 4.033

5.  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

Review 6.  Protein binding specificity versus promiscuity.

Authors:  Gideon Schreiber; Amy E Keating
Journal:  Curr Opin Struct Biol       Date:  2010-11-09       Impact factor: 6.809

7.  Enzyme localization, crowding, and buffers collectively modulate diffusion-influenced signal transduction: Insights from continuum diffusion modeling.

Authors:  Peter M Kekenes-Huskey; Changsun Eun; J A McCammon
Journal:  J Chem Phys       Date:  2015-09-07       Impact factor: 3.488

8.  Probing molecular choreography through single-molecule biochemistry.

Authors:  Antoine M van Oijen; Nicholas E Dixon
Journal:  Nat Struct Mol Biol       Date:  2015-12       Impact factor: 15.369

9.  A bulk water-dependent desolvation energy model for analyzing the effects of secondary solutes on biological equilibria.

Authors:  Daryl K Eggers
Journal:  Biochemistry       Date:  2011-02-21       Impact factor: 3.162

10.  Minimal effects of macromolecular crowding on an intrinsically disordered protein: a small-angle neutron scattering study.

Authors:  David P Goldenberg; Brian Argyle
Journal:  Biophys J       Date:  2014-02-18       Impact factor: 4.033

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