Literature DB >> 21156142

Cellular proteomes have broad distributions of protein stability.

Kingshuk Ghosh1, Ken Dill.   

Abstract

Biological cells are extremely sensitive to temperature. What is the mechanism? We compute the thermal stabilities of the whole proteomes of Escherichia coli, yeast, and Caenorhabditis elegans using an analytical model and an extensive database of stabilities of individual proteins. Our results support the hypothesis that a cell's thermal sensitivities arise from the collective instability of its proteins. This model shows a denaturation catastrophe at temperatures of 49-55°C, roughly the thermal death point of mesophiles. Cells live on the edge of a proteostasis catastrophe. According to the model, it is not that the average protein is problematic; it is the tail of the distribution. About 650 of E. coli's 4300 proteins are less than 4 kcal mol(-1) stable to denaturation. And upshifting by only 4° from 37° to 41°C is estimated to destabilize an average protein by nearly 20%. This model also treats effects of denaturants, osmolytes, and other physical stressors. In addition, it predicts the dependence of cellular growth rates on temperature. This approach may be useful for studying physical forces in biological evolution and the role of climate change on biology.
Copyright © 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved.

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Year:  2010        PMID: 21156142      PMCID: PMC3000515          DOI: 10.1016/j.bpj.2010.10.036

Source DB:  PubMed          Journal:  Biophys J        ISSN: 0006-3495            Impact factor:   4.033


  37 in total

1.  Protein-length distributions for the three domains of life.

Authors:  J Zhang
Journal:  Trends Genet       Date:  2000-03       Impact factor: 11.639

Review 2.  Protein folding and misfolding.

Authors:  Christopher M Dobson
Journal:  Nature       Date:  2003-12-18       Impact factor: 49.962

Review 3.  Structure, function and evolution of multidomain proteins.

Authors:  Christine Vogel; Matthew Bashton; Nicola D Kerrison; Cyrus Chothia; Sarah A Teichmann
Journal:  Curr Opin Struct Biol       Date:  2004-04       Impact factor: 6.809

4.  Unifying temperature effects on the growth rate of bacteria and the stability of globular proteins.

Authors:  David A Ratkowsky; June Olley; Tom Ross
Journal:  J Theor Biol       Date:  2004-11-30       Impact factor: 2.691

Review 5.  Hyperthermic biology and cancer therapies: a hypothesis for the "Lance Armstrong effect".

Authors:  Donald S Coffey; Robert H Getzenberg; Theodore L DeWeese
Journal:  JAMA       Date:  2006-07-26       Impact factor: 56.272

6.  Predicting melting temperature directly from protein sequences.

Authors:  Tienhsiung Ku; Peiyu Lu; Chenhsiung Chan; Tsusheng Wang; Szuming Lai; Pingchiang Lyu; Naiwan Hsiao
Journal:  Comput Biol Chem       Date:  2009-10-20       Impact factor: 2.877

7.  Temperature of egg incubation determines sex in Alligator mississippiensis.

Authors:  M W Ferguson; T Joanen
Journal:  Nature       Date:  1982-04-29       Impact factor: 49.962

8.  Global analysis of protein expression in yeast.

Authors:  Sina Ghaemmaghami; Won-Ki Huh; Kiowa Bower; Russell W Howson; Archana Belle; Noah Dephoure; Erin K O'Shea; Jonathan S Weissman
Journal:  Nature       Date:  2003-10-16       Impact factor: 49.962

9.  Protein disorder is positively correlated with gene expression in Escherichia coli.

Authors:  Oleg Paliy; Shawn M Gargac; Yugong Cheng; Vladimir N Uversky; A Keith Dunker
Journal:  J Proteome Res       Date:  2008-05-09       Impact factor: 4.466

10.  ProTherm and ProNIT: thermodynamic databases for proteins and protein-nucleic acid interactions.

Authors:  M D Shaji Kumar; K Abdulla Bava; M Michael Gromiha; Ponraj Prabakaran; Koji Kitajima; Hatsuho Uedaira; Akinori Sarai
Journal:  Nucleic Acids Res       Date:  2006-01-01       Impact factor: 16.971

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  37 in total

1.  FoldEco: a model for proteostasis in E. coli.

Authors:  Evan T Powers; David L Powers; Lila M Gierasch
Journal:  Cell Rep       Date:  2012-03-29       Impact factor: 9.423

2.  Physical limits of cells and proteomes.

Authors:  Ken A Dill; Kingshuk Ghosh; Jeremy D Schmit
Journal:  Proc Natl Acad Sci U S A       Date:  2011-10-17       Impact factor: 11.205

3.  How do thermophilic proteins and proteomes withstand high temperature?

Authors:  Lucas Sawle; Kingshuk Ghosh
Journal:  Biophys J       Date:  2011-07-06       Impact factor: 4.033

4.  Highly abundant proteins favor more stable 3D structures in yeast.

Authors:  Adrian W R Serohijos; S Y Ryan Lee; Eugene I Shakhnovich
Journal:  Biophys J       Date:  2013-02-05       Impact factor: 4.033

5.  Hypertonic stress induces rapid and widespread protein damage in C. elegans.

Authors:  Kris Burkewitz; Keith Choe; Kevin Strange
Journal:  Am J Physiol Cell Physiol       Date:  2011-05-25       Impact factor: 4.249

6.  Foldamer hypothesis for the growth and sequence differentiation of prebiotic polymers.

Authors:  Elizaveta Guseva; Ronald N Zuckermann; Ken A Dill
Journal:  Proc Natl Acad Sci U S A       Date:  2017-08-22       Impact factor: 11.205

7.  Yeasts collectively extend the limits of habitable temperatures by secreting glutathione.

Authors:  Diederik S Laman Trip; Hyun Youk
Journal:  Nat Microbiol       Date:  2020-04-20       Impact factor: 17.745

8.  Changes in translation rate modulate stress-induced damage of diverse proteins.

Authors:  Heejung Kim; Kevin Strange
Journal:  Am J Physiol Cell Physiol       Date:  2013-10-23       Impact factor: 4.249

9.  The safety dance: biophysics of membrane protein folding and misfolding in a cellular context.

Authors:  Jonathan P Schlebach; Charles R Sanders
Journal:  Q Rev Biophys       Date:  2014-11-25       Impact factor: 5.318

Review 10.  On the design of broad based screening assays to identify potential pharmacological chaperones of protein misfolding diseases.

Authors:  Subhashchandra Naik; Na Zhang; Phillip Gao; Mark T Fisher
Journal:  Curr Top Med Chem       Date:  2012       Impact factor: 3.295

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