Literature DB >> 18305176

Solvent molecules bridge the mechanical unfolding transition state of a protein.

Lorna Dougan1, Gang Feng, Hui Lu, Julio M Fernandez.   

Abstract

We demonstrate a combination of single molecule force spectroscopy and solvent substitution that captures the presence of solvent molecules in the transition state structure. We measure the effect of solvent substitution on the rate of unfolding of the I27 titin module, placed under a constant stretching force. From the force dependency of the unfolding rate, we determine Deltax(u), the distance to the transition state. Unfolding the I27 protein in water gives a Deltax(u) = 2.5 A, a distance that compares well to the size of a water molecule. Although the height of the activation energy barrier to unfolding is greatly increased in both glycerol and deuterium oxide solutions, Deltax(u) depends on the size of the solvent molecules. Upon replacement of water by increasing amounts of the larger glycerol molecules, Deltax(u) increases rapidly and plateaus at its maximum value of 4.4 A. In contrast, replacement of water by the similarly sized deuterium oxide does not change the value of Deltax(u). From these results we estimate that six to eight water molecules form part of the unfolding transition state structure of the I27 protein, and that the presence of just one glycerol molecule in the transition state is enough to lengthen Deltax(u). Our results show that solvent composition is important for the mechanical function of proteins. Furthermore, given that solvent composition is actively regulated in vivo, it may represent an important modulatory pathway for the regulation of tissue elasticity and other important functions in cellular mechanics.

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Year:  2008        PMID: 18305176      PMCID: PMC2265161          DOI: 10.1073/pnas.0706075105

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  41 in total

1.  Reverse engineering of the giant muscle protein titin.

Authors:  Hongbin Li; Wolfgang A Linke; Andres F Oberhauser; Mariano Carrion-Vazquez; Jason G Kerkvliet; Hui Lu; Piotr E Marszalek; Julio M Fernandez
Journal:  Nature       Date:  2002-08-29       Impact factor: 49.962

2.  The unfolding kinetics of ubiquitin captured with single-molecule force-clamp techniques.

Authors:  Michael Schlierf; Hongbin Li; Julio M Fernandez
Journal:  Proc Natl Acad Sci U S A       Date:  2004-04-27       Impact factor: 11.205

3.  Temperature softening of a protein in single-molecule experiments.

Authors:  Michael Schlierf; Matthias Rief
Journal:  J Mol Biol       Date:  2005-10-10       Impact factor: 5.469

Review 4.  What makes an aquaporin a glycerol channel? A comparative study of AqpZ and GlpF.

Authors:  Yi Wang; Klaus Schulten; Emad Tajkhorshid
Journal:  Structure       Date:  2005-08       Impact factor: 5.006

5.  Force-dependent chemical kinetics of disulfide bond reduction observed with single-molecule techniques.

Authors:  Arun P Wiita; Sri Rama Koti Ainavarapu; Hector H Huang; Julio M Fernandez
Journal:  Proc Natl Acad Sci U S A       Date:  2006-04-27       Impact factor: 11.205

6.  Dwell-time distribution analysis of polyprotein unfolding using force-clamp spectroscopy.

Authors:  Jasna Brujic; Rodolfo I Z Hermans; Sergi Garcia-Manyes; Kirstin A Walther; Julio M Fernandez
Journal:  Biophys J       Date:  2007-01-26       Impact factor: 4.033

7.  Correct protein folding in glycerol.

Authors:  R V Rariy; A M Klibanov
Journal:  Proc Natl Acad Sci U S A       Date:  1997-12-09       Impact factor: 11.205

8.  The key event in force-induced unfolding of Titin's immunoglobulin domains.

Authors:  H Lu; K Schulten
Journal:  Biophys J       Date:  2000-07       Impact factor: 4.033

9.  Tandem repeating modular proteins avoid aggregation in single molecule force spectroscopy experiments.

Authors:  Lorna Dougan; Julio M Fernandez
Journal:  J Phys Chem A       Date:  2007-11-20       Impact factor: 2.781

10.  Stepwise unfolding of titin under force-clamp atomic force microscopy.

Authors:  A F Oberhauser; P K Hansma; M Carrion-Vazquez; J M Fernandez
Journal:  Proc Natl Acad Sci U S A       Date:  2001-01-09       Impact factor: 11.205

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  23 in total

1.  Probing static disorder in Arrhenius kinetics by single-molecule force spectroscopy.

Authors:  Tzu-Ling Kuo; Sergi Garcia-Manyes; Jingyuan Li; Itay Barel; Hui Lu; Bruce J Berne; Michael Urbakh; Joseph Klafter; Julio M Fernández
Journal:  Proc Natl Acad Sci U S A       Date:  2010-06-08       Impact factor: 11.205

2.  Full reconstruction of a vectorial protein folding pathway by atomic force microscopy and molecular dynamics simulations.

Authors:  Whasil Lee; Xiancheng Zeng; Huan-Xiang Zhou; Vann Bennett; Weitao Yang; Piotr E Marszalek
Journal:  J Biol Chem       Date:  2010-09-24       Impact factor: 5.157

3.  Water's role in the force-induced unfolding of ubiquitin.

Authors:  Jingyuan Li; Julio M Fernandez; B J Berne
Journal:  Proc Natl Acad Sci U S A       Date:  2010-10-25       Impact factor: 11.205

4.  An experimentally guided umbrella sampling protocol for biomolecules.

Authors:  Maria Mills; Ioan Andricioaei
Journal:  J Chem Phys       Date:  2008-09-21       Impact factor: 3.488

5.  Mechanical characterization of protein L in the low-force regime by electromagnetic tweezers/evanescent nanometry.

Authors:  Ruchuan Liu; Sergi Garcia-Manyes; Atom Sarkar; Carmen L Badilla; Julio M Fernández
Journal:  Biophys J       Date:  2009-05-06       Impact factor: 4.033

6.  Computational and single-molecule force studies of a macro domain protein reveal a key molecular determinant for mechanical stability.

Authors:  Dora L Guzmán; Arlo Randall; Pierre Baldi; Zhibin Guan
Journal:  Proc Natl Acad Sci U S A       Date:  2010-01-13       Impact factor: 11.205

7.  Membrane-based actuation for high-speed single molecule force spectroscopy studies using AFM.

Authors:  Krishna Sarangapani; Hamdi Torun; Ofer Finkler; Cheng Zhu; Levent Degertekin
Journal:  Eur Biophys J       Date:  2010-01-07       Impact factor: 1.733

8.  Osmolyte-induced separation of the mechanical folding phases of ubiquitin.

Authors:  Sergi Garcia-Manyes; Lorna Dougan; Julio M Fernández
Journal:  Proc Natl Acad Sci U S A       Date:  2009-06-16       Impact factor: 11.205

Review 9.  Discovery through the computational microscope.

Authors:  Eric H Lee; Jen Hsin; Marcos Sotomayor; Gemma Comellas; Klaus Schulten
Journal:  Structure       Date:  2009-10-14       Impact factor: 5.006

10.  Sequence-specific size, structure, and stability of tight protein knots.

Authors:  Joachim Dzubiella
Journal:  Biophys J       Date:  2009-02       Impact factor: 4.033

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