Literature DB >> 28510157

Soft interactions and crowding.

Mohona Sarkar1, Conggang Li2, Gary J Pielak3,4,5.   

Abstract

The intracellular milieu is complex, heterogeneous and crowded-an environment vastly different from dilute solutions in which most biophysical studies are performed. The crowded cytoplasm excludes about a third of the volume available to macromolecules in dilute solution. This excluded volume is the sum of two parts: steric repulsions and chemical interactions, also called soft interactions. Until recently, most efforts to understand crowding have focused on steric repulsions. Here, we summarize the results and conclusions from recent studies on macromolecular crowding, emphasizing the contribution of soft interactions to the equilibrium thermodynamics of protein stability. Despite their non-specific and weak nature, the large number of soft interactions present under many crowded conditions can sometimes overcome the stabilizing steric, excluded volume effect.

Keywords:  Crowding; Excluded volume; Osmolytes; Protein stability; Second virial coefficient; Synthetic polymers

Year:  2013        PMID: 28510157      PMCID: PMC5418433          DOI: 10.1007/s12551-013-0104-4

Source DB:  PubMed          Journal:  Biophys Rev        ISSN: 1867-2450


  55 in total

1.  Second virial coefficients as a measure of protein--osmolyte interactions.

Authors:  G T Weatherly; G J Pielak
Journal:  Protein Sci       Date:  2001-01       Impact factor: 6.725

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.  Enthalpically driven peptide stabilization by protective osmolytes.

Authors:  Regina Politi; Daniel Harries
Journal:  Chem Commun (Camb)       Date:  2010-07-26       Impact factor: 6.222

4.  Internal and global protein motion assessed with a fusion construct and in-cell NMR spectroscopy.

Authors:  Christopher O Barnes; William B Monteith; Gary J Pielak
Journal:  Chembiochem       Date:  2010-12-15       Impact factor: 3.164

5.  Protein stability and folding kinetics in the nucleus and endoplasmic reticulum of eucaryotic cells.

Authors:  A Dhar; K Girdhar; D Singh; H Gelman; S Ebbinghaus; M Gruebele
Journal:  Biophys J       Date:  2011-07-20       Impact factor: 4.033

6.  Unexpected effects of macromolecular crowding on protein stability.

Authors:  Laura A Benton; Austin E Smith; Gregory B Young; Gary J Pielak
Journal:  Biochemistry       Date:  2012-11-27       Impact factor: 3.162

7.  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

8.  Exploring weak, transient protein--protein interactions in crowded in vivo environments by in-cell nuclear magnetic resonance spectroscopy.

Authors:  Qinghua Wang; Anastasia Zhuravleva; Lila M Gierasch
Journal:  Biochemistry       Date:  2011-10-05       Impact factor: 3.162

9.  Macromolecular crowding fails to fold a globular protein in cells.

Authors:  Alexander P Schlesinger; Yaqiang Wang; Xavier Tadeo; Oscar Millet; Gary J Pielak
Journal:  J Am Chem Soc       Date:  2011-05-10       Impact factor: 15.419

10.  Protein nuclear magnetic resonance under physiological conditions.

Authors:  Gary J Pielak; Conggang Li; Andrew C Miklos; Alexander P Schlesinger; Kristin M Slade; Gui-Fang Wang; Imola G Zigoneanu
Journal:  Biochemistry       Date:  2009-01-20       Impact factor: 3.162

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  43 in total

1.  Osmotic Shock Induced Protein Destabilization in Living Cells and Its Reversal by Glycine Betaine.

Authors:  Samantha S Stadmiller; Annelise H Gorensek-Benitez; Alex J Guseman; Gary J Pielak
Journal:  J Mol Biol       Date:  2017-03-03       Impact factor: 5.469

2.  Molecular crowding and early evolution.

Authors:  Ranajay Saha; Andrew Pohorille; Irene A Chen
Journal:  Orig Life Evol Biosph       Date:  2015-01-14       Impact factor: 1.950

3.  Quinary interactions with an unfolded state ensemble.

Authors:  Rachel D Cohen; Gary J Pielak
Journal:  Protein Sci       Date:  2017-06-12       Impact factor: 6.725

4.  Protein shape modulates crowding effects.

Authors:  Alex J Guseman; Gerardo M Perez Goncalves; Shannon L Speer; Gregory B Young; Gary J Pielak
Journal:  Proc Natl Acad Sci U S A       Date:  2018-10-09       Impact factor: 11.205

Review 5.  Recent progress of in-cell NMR of nucleic acids in living human cells.

Authors:  Yudai Yamaoki; Takashi Nagata; Tomoki Sakamoto; Masato Katahira
Journal:  Biophys Rev       Date:  2020-03-06

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

Authors:  David Moses; Feng Yu; Garrett M Ginell; Nora M Shamoon; Patrick S Koenig; Alex S Holehouse; Shahar Sukenik
Journal:  J Phys Chem Lett       Date:  2020-11-16       Impact factor: 6.475

7.  Thermostabilization of viruses via complex coacervation.

Authors:  Xue Mi; Whitney C Blocher McTigue; Pratik U Joshi; Mallory K Bunker; Caryn L Heldt; Sarah L Perry
Journal:  Biomater Sci       Date:  2020-12-15       Impact factor: 6.843

8.  Soft Interactions with Model Crowders and Non-canonical Interactions with Cellular Proteins Stabilize RNA Folding.

Authors:  May Daher; Julia R Widom; Wendy Tay; Nils G Walter
Journal:  J Mol Biol       Date:  2017-11-08       Impact factor: 5.469

9.  Controlling and quantifying protein concentration in Escherichia coli.

Authors:  Shannon L Speer; Alex J Guseman; Jon B Patteson; Brandie M Ehrmann; Gary J Pielak
Journal:  Protein Sci       Date:  2019-05-22       Impact factor: 6.725

10.  Crowder-Induced Conformational Ensemble Shift in Escherichia coli Prolyl-tRNA Synthetase.

Authors:  Lauren M Adams; Ryan J Andrews; Quin H Hu; Heidi L Schmit; Sanchita Hati; Sudeep Bhattacharyya
Journal:  Biophys J       Date:  2019-08-31       Impact factor: 4.033

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