Literature DB >> 15240492

Folding lambda-repressor at its speed limit.

Wei Yuan Yang1, Martin Gruebele.   

Abstract

We show that the five-helix bundle lambda(6-85) can be engineered and solvent-tuned to make the transition from activated two-state folding to downhill folding. The transition manifests itself as the appearance of additional dynamics faster than the activated kinetics, followed by the disappearance of the activated kinetics when the bias toward the native state is increased. Our fastest value of 1 micros for the "speed" limit of lambda(6-85) is measured at low concentrations of a denaturant that smooths the free-energy surface. Complete disappearance of the activated phase is obtained in stabilizing glucose buffer. Langevin dynamics on a rough free-energy surface with variable bias toward the native state provides a robust and quantitative description of the transition from activated to downhill folding. Based on our simulation, we estimate the residual energetic frustration of lambda(6-85) to be delta(2) G approximately 0.64 k(2)T(2). We show that lambda(6-86), as well as very fast folding proteins or folding intermediates estimated to lie near the speed limit, provide a better rate-topology correlation than proteins with larger energetic frustration. A limit of beta > or = 0.7 on any stretching of lambda(6-85) barrier-free dynamics suggests that a low-dimensional free-energy surface is sufficient to describe folding.

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Year:  2004        PMID: 15240492      PMCID: PMC1304381          DOI: 10.1529/biophysj.103.039040

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


  54 in total

1.  Direct observation of fast protein folding: the initial collapse of apomyoglobin.

Authors:  R M Ballew; J Sabelko; M Gruebele
Journal:  Proc Natl Acad Sci U S A       Date:  1996-06-11       Impact factor: 11.205

2.  Diffusion-limited contact formation in unfolded cytochrome c: estimating the maximum rate of protein folding.

Authors:  S J Hagen; J Hofrichter; A Szabo; W A Eaton
Journal:  Proc Natl Acad Sci U S A       Date:  1996-10-15       Impact factor: 11.205

3.  Protein folding dynamics: quantitative comparison between theory and experiment.

Authors:  R E Burton; J K Myers; T G Oas
Journal:  Biochemistry       Date:  1998-04-21       Impact factor: 3.162

4.  Contact order, transition state placement and the refolding rates of single domain proteins.

Authors:  K W Plaxco; K T Simons; D Baker
Journal:  J Mol Biol       Date:  1998-04-10       Impact factor: 5.469

5.  Diffusion control in an elementary protein folding reaction.

Authors:  M Jacob; T Schindler; J Balbach; F X Schmid
Journal:  Proc Natl Acad Sci U S A       Date:  1997-05-27       Impact factor: 11.205

6.  Submillisecond folding of monomeric lambda repressor.

Authors:  G S Huang; T G Oas
Journal:  Proc Natl Acad Sci U S A       Date:  1995-07-18       Impact factor: 11.205

7.  Structure of the hydrophobic core in the transition state for folding of chymotrypsin inhibitor 2: a critical test of the protein engineering method of analysis.

Authors:  S E Jackson; N elMasry; A R Fersht
Journal:  Biochemistry       Date:  1993-10-26       Impact factor: 3.162

8.  Laser temperature jump study of the helix<==>coil kinetics of an alanine peptide interpreted with a 'kinetic zipper' model.

Authors:  P A Thompson; W A Eaton; J Hofrichter
Journal:  Biochemistry       Date:  1997-07-29       Impact factor: 3.162

9.  Formation of a molten globule intermediate early in the kinetic folding pathway of apomyoglobin.

Authors:  P A Jennings; P E Wright
Journal:  Science       Date:  1993-11-05       Impact factor: 47.728

10.  The energy landscape of a fast-folding protein mapped by Ala-->Gly substitutions.

Authors:  R E Burton; G S Huang; M A Daugherty; T L Calderone; T G Oas
Journal:  Nat Struct Biol       Date:  1997-04
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  49 in total

1.  Variations in the fast folding rates of the lambda-repressor: a hybrid molecular dynamics study.

Authors:  Taras V Pogorelov; Zaida Luthey-Schulten
Journal:  Biophys J       Date:  2004-07       Impact factor: 4.033

2.  Equilibrium unfolding of the PDZ domain of β2-syntrophin.

Authors:  Gabriela María Torchio; Mario Roberto Ermácora; Mauricio Pablo Sica
Journal:  Biophys J       Date:  2012-06-19       Impact factor: 4.033

3.  Atomistic folding simulations of the five-helix bundle protein λ(6−85).

Authors:  Gregory R Bowman; Vincent A Voelz; Vijay S Pande
Journal:  J Am Chem Soc       Date:  2011-02-02       Impact factor: 15.419

4.  The fast and the slow: folding and trapping of λ6-85.

Authors:  Maxim B Prigozhin; Martin Gruebele
Journal:  J Am Chem Soc       Date:  2011-11-14       Impact factor: 15.419

5.  A natural missing link between activated and downhill protein folding scenarios.

Authors:  Feng Liu; Caroline Maynard; Gregory Scott; Artem Melnykov; Kathleen B Hall; Martin Gruebele
Journal:  Phys Chem Chem Phys       Date:  2010-02-11       Impact factor: 3.676

6.  Conformational changes during the nanosecond-to-millisecond unfolding of ubiquitin.

Authors:  Hoi Sung Chung; Munira Khalil; Adam W Smith; Ziad Ganim; Andrei Tokmakoff
Journal:  Proc Natl Acad Sci U S A       Date:  2005-01-03       Impact factor: 11.205

7.  Kinetics are probe-dependent during downhill folding of an engineered lambda6-85 protein.

Authors:  Hairong Ma; Martin Gruebele
Journal:  Proc Natl Acad Sci U S A       Date:  2005-02-07       Impact factor: 11.205

8.  Alpha-helix formation in a photoswitchable peptide tracked from picoseconds to microseconds by time-resolved IR spectroscopy.

Authors:  Jens Bredenbeck; Jan Helbing; Janet R Kumita; G Andrew Woolley; Peter Hamm
Journal:  Proc Natl Acad Sci U S A       Date:  2005-02-07       Impact factor: 11.205

9.  Exploring protein-folding ensembles: a variable-barrier model for the analysis of equilibrium unfolding experiments.

Authors:  Victor Muñoz; Jose M Sanchez-Ruiz
Journal:  Proc Natl Acad Sci U S A       Date:  2004-12-09       Impact factor: 11.205

10.  T-jump infrared study of the folding mechanism of coiled-coil GCN4-p1.

Authors:  Ting Wang; Wai Leung Lau; William F DeGrado; Feng Gai
Journal:  Biophys J       Date:  2005-09-08       Impact factor: 4.033

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