Literature DB >> 19483692

Reaching the protein folding speed limit with large, sub-microsecond pressure jumps.

Charles Dumont1, Tryggvi Emilsson, Martin Gruebele.   

Abstract

Biomolecules are highly pressure-sensitive, but their dynamics upon return to ambient pressure are often too fast to observe with existing approaches. We describe a sample-efficient method capable of large and very fast pressure drops (<1 nanomole, >2,500 atmospheres and <0.7 microseconds). We validated the method by fluorescence-detected refolding of a genetically engineered lambda repressor mutant from its pressure-denatured state. We resolved barrierless structure formation upon return to ambient pressure; we observed a 2.1 +/- 0.7 microsecond refolding time, which is very close to the 'speed limit' for proteins and much faster than the corresponding temperature-jump refolding of the same protein. The ability to experimentally perform a large and very fast pressure drop opens up a new region of the biomolecular energy landscape for atomic-level simulation.

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Year:  2009        PMID: 19483692     DOI: 10.1038/nmeth.1336

Source DB:  PubMed          Journal:  Nat Methods        ISSN: 1548-7091            Impact factor:   28.547


  26 in total

1.  Microsecond folding of the cold shock protein measured by a pressure-jump technique.

Authors:  M Jacob; G Holtermann; D Perl; J Reinstein; T Schindler; M A Geeves; F X Schmid
Journal:  Biochemistry       Date:  1999-03-09       Impact factor: 3.162

2.  Pressure-jump X-ray studies of liquid crystal transitions in lipids.

Authors:  John M Seddon; Adam M Squires; Charlotte E Conn; Oscar Ces; Andrew J Heron; Xavier Mulet; Gemma C Shearman; Richard H Templer
Journal:  Philos Trans A Math Phys Eng Sci       Date:  2006-10-15       Impact factor: 4.226

3.  Microfilaments are involved in renal cell responses to sustained hydrostatic pressure.

Authors:  Julie S Martin; Lauren S Brown; Karen M Haberstroh
Journal:  J Urol       Date:  2005-04       Impact factor: 7.450

Review 4.  How well can simulation predict protein folding kinetics and thermodynamics?

Authors:  Christopher D Snow; Eric J Sorin; Young Min Rhee; Vijay S Pande
Journal:  Annu Rev Biophys Biomol Struct       Date:  2005

5.  Solvent-tuning the collapse and helix formation time scales of lambda(6-85)*.

Authors:  Charles Dumont; Yoshitaka Matsumura; Seung Joong Kim; Jinsong Li; Elena Kondrashkina; Hiroshi Kihara; Martin Gruebele
Journal:  Protein Sci       Date:  2006-11       Impact factor: 6.725

6.  V(i)-value analysis: a pressure-based method for mapping the folding transition state ensemble of proteins.

Authors:  Lally Mitra; Kazumi Hata; Ryohei Kono; Akihiro Maeno; Daniel Isom; Jean-Baptiste Rouget; Roland Winter; Kazuyuki Akasaka; Bertrand García-Moreno; Catherine A Royer
Journal:  J Am Chem Soc       Date:  2007-10-26       Impact factor: 15.419

7.  Computing the stability diagram of the Trp-cage miniprotein.

Authors:  Dietmar Paschek; Sascha Hempel; Angel E García
Journal:  Proc Natl Acad Sci U S A       Date:  2008-11-12       Impact factor: 11.205

Review 8.  The nature of the transition state ensemble and the mechanisms of protein folding: a review.

Authors:  Catherine A Royer
Journal:  Arch Biochem Biophys       Date:  2007-08-30       Impact factor: 4.013

9.  Ultrafast thermally induced unfolding of RNase A.

Authors:  C M Phillips; Y Mizutani; R M Hochstrasser
Journal:  Proc Natl Acad Sci U S A       Date:  1995-08-01       Impact factor: 11.205

10.  Urea and guanidinium chloride denature protein L in different ways in molecular dynamics simulations.

Authors:  C Camilloni; A Guerini Rocco; I Eberini; E Gianazza; R A Broglia; G Tiana
Journal:  Biophys J       Date:  2008-03-13       Impact factor: 4.033

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  21 in total

1.  Downhill protein folding under pressure.

Authors:  Victor Muñoz
Journal:  Nat Methods       Date:  2009-07       Impact factor: 28.547

2.  Dynamical fingerprints for probing individual relaxation processes in biomolecular dynamics with simulations and kinetic experiments.

Authors:  Frank Noé; Sören Doose; Isabella Daidone; Marc Löllmann; Markus Sauer; John D Chodera; Jeremy C Smith
Journal:  Proc Natl Acad Sci U S A       Date:  2011-03-02       Impact factor: 11.205

3.  Role of solvation in pressure-induced helix stabilization.

Authors:  Robert B Best; Cayla Miller; Jeetain Mittal
Journal:  J Chem Phys       Date:  2014-12-14       Impact factor: 3.488

4.  Misplaced helix slows down ultrafast pressure-jump protein folding.

Authors:  Maxim B Prigozhin; Yanxin Liu; Anna Jean Wirth; Shobhna Kapoor; Roland Winter; Klaus Schulten; Martin Gruebele
Journal:  Proc Natl Acad Sci U S A       Date:  2013-04-25       Impact factor: 11.205

5.  Fast pressure-jump all-atom simulations and experiments reveal site-specific protein dehydration-folding dynamics.

Authors:  Maxim B Prigozhin; Yi Zhang; Klaus Schulten; Martin Gruebele; Taras V Pogorelov
Journal:  Proc Natl Acad Sci U S A       Date:  2019-03-05       Impact factor: 11.205

6.  Nanopore Sensing of Protein Folding.

Authors:  Wei Si; Aleksei Aksimentiev
Journal:  ACS Nano       Date:  2017-07-13       Impact factor: 15.881

7.  Single-Molecule Protein Folding Experiments Using High-Precision Optical Tweezers.

Authors:  Junyi Jiao; Aleksander A Rebane; Lu Ma; Yongli Zhang
Journal:  Methods Mol Biol       Date:  2017

8.  Monitoring 15N Chemical Shifts During Protein Folding by Pressure-Jump NMR.

Authors:  Cyril Charlier; Joseph M Courtney; T Reid Alderson; Philip Anfinrud; Ad Bax
Journal:  J Am Chem Soc       Date:  2018-06-25       Impact factor: 15.419

9.  Crowding effects on the small, fast-folding protein lambda6-85.

Authors:  Sharlene Denos; Apratim Dhar; Martin Gruebele
Journal:  Faraday Discuss       Date:  2012       Impact factor: 4.008

10.  Ultrafast hydrogen exchange reveals specific structural events during the initial stages of folding of cytochrome c.

Authors:  Hossein Fazelinia; Ming Xu; Hong Cheng; Heinrich Roder
Journal:  J Am Chem Soc       Date:  2013-12-31       Impact factor: 15.419

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