Literature DB >> 32642303

Critical phenomena in the temperature-pressure-crowding phase diagram of a protein.

Andrei G Gasic1,2, Mayank M Boob3, Maxim B Prigozhin4, Dirar Homouz1,2,5, Anna Jean Wirth4, Caleb M Daugherty1,2, Martin Gruebele3,4,6, Margaret S Cheung1,2.   

Abstract

In the cell, proteins fold and perform complex functions through global structural rearrangements. Function requires a protein to be at the brink of stability to be susceptible to small environmental fluctuations, yet stable enough to maintain structural integrity. These apparently conflicting behaviors are exhibited by systems near a critical point, where distinct phases merge-a concept beyond previous studies indicating proteins have a well-defined folded/unfolded phase boundary in the pressure-temperature plane. Here, by modeling the protein phosphoglycerate kinase (PGK) on the temperature (T), pressure (P), and crowding volume-fraction (ϕ) phase diagram, we demonstrate a critical transition where phases merge, and PGK exhibits large structural fluctuations. Above the critical point, the difference between the intermediate and unfolded phases disappears. When ϕ increases, the critical point moves to lower T c. We verify the calculations with experiments mapping the T-P-ϕ space, which likewise reveal a critical point at 305 K and 170 MPa that moves to lower T c as ϕ increases. Crowding places PGK near a critical line in its natural parameter space, where large conformational changes can occur without costly free energy barriers. Specific structures are proposed for each phase based on simulation.

Entities:  

Keywords:  Biological Physics; Soft Matter; Statistical Physics

Year:  2019        PMID: 32642303      PMCID: PMC7343146          DOI: 10.1103/physrevx.9.041035

Source DB:  PubMed          Journal:  Phys Rev X        ISSN: 2160-3308            Impact factor:   15.762


  39 in total

1.  Pressure-induced protein-folding/unfolding kinetics.

Authors:  N Hillson; J N Onuchic; A E García
Journal:  Proc Natl Acad Sci U S A       Date:  1999-12-21       Impact factor: 11.205

2.  Observation of strange kinetics in protein folding.

Authors:  J Sabelko; J Ervin; M Gruebele
Journal:  Proc Natl Acad Sci U S A       Date:  1999-05-25       Impact factor: 11.205

3.  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

4.  Nonlinear elasticity, proteinquakes, and the energy landscapes of functional transitions in proteins.

Authors:  O Miyashita; J N Onuchic; P G Wolynes
Journal:  Proc Natl Acad Sci U S A       Date:  2003-10-17       Impact factor: 11.205

5.  Force-dependent switch in protein unfolding pathways and transition-state movements.

Authors:  Pavel I Zhuravlev; Michael Hinczewski; Shaon Chakrabarti; Susan Marqusee; D Thirumalai
Journal:  Proc Natl Acad Sci U S A       Date:  2016-01-27       Impact factor: 11.205

6.  A critical comparison of coarse-grained structure-based approaches and atomic models of protein folding.

Authors:  Jie Hu; Tao Chen; Moye Wang; Hue Sun Chan; Zhuqing Zhang
Journal:  Phys Chem Chem Phys       Date:  2017-05-31       Impact factor: 3.676

7.  Critical Fluctuations in the Native State of Proteins.

Authors:  Qian-Yuan Tang; Yang-Yang Zhang; Jun Wang; Wei Wang; Dante R Chialvo
Journal:  Phys Rev Lett       Date:  2017-02-24       Impact factor: 9.161

8.  Reversible pressure--temperature denaturation of chymotrypsinogen.

Authors:  S A Hawley
Journal:  Biochemistry       Date:  1971-06-22       Impact factor: 3.162

9.  Challenges in protein folding simulations: Timescale, representation, and analysis.

Authors:  Peter L Freddolino; Christopher B Harrison; Yanxin Liu; Klaus Schulten
Journal:  Nat Phys       Date:  2010-10-01       Impact factor: 20.034

10.  Biomolecular dynamics: order-disorder transitions and energy landscapes.

Authors:  Paul C Whitford; Karissa Y Sanbonmatsu; José N Onuchic
Journal:  Rep Prog Phys       Date:  2012-06-28
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  3 in total

1.  A Tale of Two Desolvation Potentials: An Investigation of Protein Behavior under High Hydrostatic Pressure.

Authors:  Andrei G Gasic; Margaret S Cheung
Journal:  J Phys Chem B       Date:  2020-02-24       Impact factor: 2.991

Review 2.  Protein folding and surface interaction phase diagrams in vitro and in cells.

Authors:  Martin Gruebele
Journal:  FEBS Lett       Date:  2021-03-27       Impact factor: 4.124

3.  Density fluctuations, homeostasis, and reproduction effects in bacteria.

Authors:  Shahla Nemati; Abhyudai Singh; Scott D Dhuey; Armando McDonald; Daniel M Weinreich; Andreas E Vasdekis
Journal:  Commun Biol       Date:  2022-04-28
  3 in total

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