Literature DB >> 17075136

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

Charles Dumont1, Yoshitaka Matsumura, Seung Joong Kim, Jinsong Li, Elena Kondrashkina, Hiroshi Kihara, Martin Gruebele.   

Abstract

The lambda(6-85)(*) pseudo-wild type of lambda repressor fragment is a fast two-state folder (k(f) approximately 35 microsec(-1) at 58 degrees C). Previously, highly stable lambda(6-85)(*) mutants with k(f) > 30 microsec(-1) have been engineered to fold nearly or fully downhill. Stabilization of the native state by solvent tuning might also tune lambda(6-85)(*) away from two-state folding. We test this prediction by examining the folding thermodynamics and kinetics of lambda(6-85)(*) in a stabilizing solvent, 45% by weight aqueous ethylene glycol at -28 degrees C. Detection of kinetics by circular dichroism at 222 nm (sensitive to helix content) and small angle X-ray scattering (measuring the radius of gyration) shows that refolding from guanidine hydrochloride denatured conditions exhibits very different time scales for collapse and secondary structure formation: the two processes become decoupled. Collapse remains a low-barrier activated process, while the fastest of several secondary structure formation time scales approaches the downhill folding limit. Two-state folding of lambda(6-85)(*) is not a robust process.

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Year:  2006        PMID: 17075136      PMCID: PMC2242409          DOI: 10.1110/ps.062257406

Source DB:  PubMed          Journal:  Protein Sci        ISSN: 0961-8368            Impact factor:   6.725


  46 in total

1.  Refolding of beta-lactoglobulin studied by stopped-flow circular dichroism at subzero temperatures.

Authors:  Z Qin; D Hu; L Shimada; T Nakagawa; M Arai; J M Zhou; H Kihara
Journal:  FEBS Lett       Date:  2001-11-02       Impact factor: 4.124

2.  Distinguishing between two-state and three-state models for ubiquitin folding.

Authors:  B A Krantz; T R Sosnick
Journal:  Biochemistry       Date:  2000-09-26       Impact factor: 3.162

3.  Kinetic equivalence of the heat and cold structural transitions of lambda6-85.

Authors:  Wei Y Yang; Martin Gruebele
Journal:  Philos Trans A Math Phys Eng Sci       Date:  2005-02-15       Impact factor: 4.226

4.  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

5.  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

Review 6.  Downhill protein folding: evolution meets physics.

Authors:  Martin Gruebele
Journal:  C R Biol       Date:  2005-04-01       Impact factor: 1.583

7.  Robustness of downhill folding: guidelines for the analysis of equilibrium folding experiments on small proteins.

Authors:  Athi N Naganathan; Raúl Perez-Jimenez; Jose M Sanchez-Ruiz; Victor Muñoz
Journal:  Biochemistry       Date:  2005-05-24       Impact factor: 3.162

8.  Engineering a beta-sheet protein toward the folding speed limit.

Authors:  Houbi Nguyen; Marcus Jäger; Jeffery W Kelly; Martin Gruebele
Journal:  J Phys Chem B       Date:  2005-08-18       Impact factor: 2.991

9.  Binary and ternary aggregation within tethered protein constructs.

Authors:  Wei Yuan Yang; Martin Gruebele
Journal:  Biophys J       Date:  2006-01-20       Impact factor: 4.033

10.  Structure-function-folding relationship in a WW domain.

Authors:  Marcus Jäger; Yan Zhang; Jan Bieschke; Houbi Nguyen; Maria Dendle; Marianne E Bowman; Joseph P Noel; Martin Gruebele; Jeffery W Kelly
Journal:  Proc Natl Acad Sci U S A       Date:  2006-06-28       Impact factor: 11.205

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  18 in total

1.  An extended dynamical hydration shell around proteins.

Authors:  Simon Ebbinghaus; Seung Joong Kim; Matthias Heyden; Xin Yu; Udo Heugen; Martin Gruebele; David M Leitner; Martina Havenith
Journal:  Proc Natl Acad Sci U S A       Date:  2007-12-19       Impact factor: 11.205

2.  Simulation-based fitting of protein-protein interaction potentials to SAXS experiments.

Authors:  Seung Joong Kim; Charles Dumont; Martin Gruebele
Journal:  Biophys J       Date:  2008-03-07       Impact factor: 4.033

3.  An experimental survey of the transition between two-state and downhill protein folding scenarios.

Authors:  Feng Liu; Deguo Du; Amelia A Fuller; Jennifer E Davoren; Peter Wipf; Jeffery W Kelly; Martin Gruebele
Journal:  Proc Natl Acad Sci U S A       Date:  2008-02-11       Impact factor: 11.205

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

Authors:  Charles Dumont; Tryggvi Emilsson; Martin Gruebele
Journal:  Nat Methods       Date:  2009-05-31       Impact factor: 28.547

5.  Slowing down downhill folding: a three-probe study.

Authors:  Seung Joong Kim; Yoshitaka Matsumura; Charles Dumont; Hiroshi Kihara; Martin Gruebele
Journal:  Biophys J       Date:  2009-07-08       Impact factor: 4.033

6.  Direct observation of downhill folding of lambda-repressor in a microfluidic mixer.

Authors:  Stephen J DeCamp; Athi N Naganathan; Steven A Waldauer; Olgica Bakajin; Lisa J Lapidus
Journal:  Biophys J       Date:  2009-09-16       Impact factor: 4.033

7.  Analysis of the free-energy surface of proteins from reversible folding simulations.

Authors:  Lucy R Allen; Sergei V Krivov; Emanuele Paci
Journal:  PLoS Comput Biol       Date:  2009-07-10       Impact factor: 4.475

8.  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

9.  Transient helical structure during PI3K and Fyn SH3 domain folding.

Authors:  Yoshitaka Matsumura; Masaji Shinjo; Seung Joong Kim; Nobuyuki Okishio; Martin Gruebele; Hiroshi Kihara
Journal:  J Phys Chem B       Date:  2013-04-18       Impact factor: 2.991

10.  Structural study of hNck2 SH3 domain protein in solution by circular dichroism and X-ray solution scattering.

Authors:  Yoshitaka Matsumura; Masaji Shinjo; Tsutomu Matsui; Kaoru Ichimura; Jianxing Song; Hiroshi Kihara
Journal:  Biophys Chem       Date:  2013-02-26       Impact factor: 2.352

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