Experimental validation of free-energy-landscape reconstruction from non-equilibrium single-molecule force spectroscopy measurements

The energy-landscape theory is an important tool for investigating how proteins fold. Hummer and Szabo conceived a simple method for constructing folding-energy landscapes from single-molecule pulling experiments. But are these non-equilibrium measurements a valid approach to equilibrium landscapes? The Hummer–Szabo formalism is now experimentally validated for the first time.

[1]  F. Ritort,et al.  Nonequilibrium fluctuations in small systems: From physics to biology , 2007, 0705.0455.

[2]  B. Honig,et al.  Protein structure prediction: inroads to biology. , 2005, Molecular cell.

[3]  I. Tinoco,et al.  Equilibrium Information from Nonequilibrium Measurements in an Experimental Test of Jarzynski's Equality , 2002, Science.

[4]  P. Bradley,et al.  Toward High-Resolution de Novo Structure Prediction for Small Proteins , 2005, Science.

[5]  Michelle D. Wang,et al.  Stretching DNA with optical tweezers. , 1997, Biophysical journal.

[6]  C. Jarzynski.  Nonequilibrium Equality for Free Energy Differences , 1996, cond-mat/9610209.

[7]  K. Schulten,et al.  Calculating potentials of mean force from steered molecular dynamics simulations. , 2004, The Journal of chemical physics.

[8]  Kirsten L. Frieda,et al.  Direct Observation of Hierarchical Folding in Single Riboswitch Aptamers , 2008, Science.

[9]  J. Liphardt,et al.  Reversible Unfolding of Single RNA Molecules by Mechanical Force , 2001, Science.

[10]  Steven M Block,et al.  Passive all-optical force clamp for high-resolution laser trapping. , 2005, Physical review letters.

[11]  C. Dobson.  Protein folding and misfolding , 2003, Nature.

[12]  Matthias Rief,et al.  Full distance-resolved folding energy landscape of one single protein molecule , 2010, Proceedings of the National Academy of Sciences.

[13]  Felix Ritort,et al.  Measurement of work in single-molecule pulling experiments. , 2009, The Journal of chemical physics.

[14]  G. Hummer,et al.  Free energy reconstruction from nonequilibrium single-molecule pulling experiments , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[15]  A. Fersht,et al.  Is there a unifying mechanism for protein folding? , 2003, Trends in biochemical sciences.

[16]  J. Onuchic,et al.  Theory of protein folding: the energy landscape perspective. , 1997, Annual review of physical chemistry.

[17]  G. Crooks.  Entropy production fluctuation theorem and the nonequilibrium work relation for free energy differences. , 1999, Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics.

[18]  P. Wolynes,et al.  Spin glasses and the statistical mechanics of protein folding. , 1987, Proceedings of the National Academy of Sciences of the United States of America.

[19]  A. Fersht.  Structure and mechanism in protein science , 1998 .

[20]  H. Eisenberg,et al.  The physics of biology , 1979, Nature.

[21]  P. S. Kim,et al.  Intermediates in the folding reactions of small proteins. , 1990, Annual review of biochemistry.

[22]  Changbong Hyeon,et al.  Can energy landscape roughness of proteins and RNA be measured by using mechanical unfolding experiments? , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[23]  D. Herschlag,et al.  Direct Measurement of the Full, Sequence-Dependent Folding Landscape of a Nucleic Acid , 2006, Science.

[24]  Joshua W Shaevitz,et al.  An automated two-dimensional optical force clamp for single molecule studies. , 2002, Biophysical journal.

[25]  Steven M Block,et al.  Folding and unfolding single RNA molecules under tension. , 2008, Current opinion in chemical biology.

[26]  D. Herschlag,et al.  Nanomechanical measurements of the sequence-dependent folding landscapes of single nucleic acid hairpins. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[27]  Johannes Buchner,et al.  Protein folding handbook , 2005 .

[28]  C. Bustamante,et al.  Overstretching B-DNA: The Elastic Response of Individual Double-Stranded and Single-Stranded DNA Molecules , 1996, Science.

[29]  C. Jarzynski,et al.  Verification of the Crooks fluctuation theorem and recovery of RNA folding free energies , 2005, Nature.

[30]  C. Kiang,et al.  Experimental free energy surface reconstruction from single-molecule force spectroscopy using Jarzynski's equality. , 2007, Physical review letters.

[31]  David D. L. Minh.  Free-energy reconstruction from experiments performed under different biasing programs. , 2006, Physical review. E, Statistical, nonlinear, and soft matter physics.