Models for recovering the energy landscape of conformational transitions from single-molecule pulling experiments

References

• Wales D. Energy landscapes: Applications to clusters, biomolecules and glasses. Cambridge: Cambridge University Press; 2003.
   Google Scholar
• Bolhuis PG, Chandler D, Dellago C, et al. Transition path sampling: Throwing ropes over rough mountain passes, in the dark. Ann Rev Phys Chem. 2002;53:291–318.
   PubMed Web of Science ®Google Scholar
• Roux B. The calculation of the potential of mean force using computer simulations. Comput Phys Commun. 1995;91:275–282.
   Web of Science ®Google Scholar
• Woodside MT, Block SM. Reconstructing folding energy landscapes by single-molecule force spectroscopy. Ann Rev Biophys. 2014;43:19–39.
   PubMed Web of Science ®Google Scholar
• Neuman KC, Nagy A. Single-molecule force spectroscopy: optical tweezers, magnetic tweezers and atomic force microscopy. Nat Methods. 2008;5:491–505.
   PubMed Web of Science ®Google Scholar
• Hummer G, Szabo A. Free energy reconstruction from nonequilibrium single-molecule pulling experiments. Proc Natl Acad Sci. 2001;98:3658–3661.
   PubMed Web of Science ®Google Scholar
• Collin D, Ritort F, Jarzynski C, et al. Verification of the crooks fluctuation theorem and recovery of RNA folding free energies. Nature. 2005;437:231–234.
   PubMed Web of Science ®Google Scholar
• Jarzynski C. Nonequilibrium equality for free energy differences. Phys Rev Lett. 1997;78:2690–2693.
   Web of Science ®Google Scholar
• Crooks GE. Entropy production fluctuation theorem and the nonequilibrium work relation for free energy differences. Phys Rev E. 1999;60:2721–2726.
   PubMed Web of Science ®Google Scholar
• Bell GI. Models for the specific adhesion of cells to cells. Science. 1978;200:618–627.
   PubMed Web of Science ®Google Scholar
• Zhurkov SN. Kinetic concept of the strength of solids. Int J Fract Mech. 1965;1:311–323.
   Web of Science ®Google Scholar
• Schlierf M, Li H, Fernandez JM. The unfolding kinetics of ubiquitin captured with single-molecule force-clamp techniques. Proc Natl Acad Sci. 2004;101:7299–7304.
   PubMed Web of Science ®Google Scholar
• Marshall BT, Long M, Piper JW, et al. Direct observation of catch bonds involving cell-adhesion molecules. Nature. 2003;423:190–193.
   PubMed Web of Science ®Google Scholar
• Evans E, Berk D, Leung A. Detachment of agglutinin-bonded red blood cells. I. Forces to rupture molecular-point attachments. Biophys J. 1991;59:838–848.
   PubMed Web of Science ®Google Scholar
• Evans E, Ritchie K. Dynamic strength of molecular adhesion bonds. Biophys J. 1997;72:1541–1555.
   PubMed Web of Science ®Google Scholar
• Hummer G, Szabo A. Kinetics from nonequilibrium single-molecule pulling experiments. Biophys J. 2003;85:5–15.
   PubMed Web of Science ®Google Scholar
• Gergely C, Voegel JC, Schaaf P, et al. Unbinding process of adsorbed proteins under external stress studied by atomic force microscopy spectroscopy. Proc Natl Acad Sci. 2000;97:10802–10807.
   PubMed Web of Science ®Google Scholar
• Dietz H, Rief M. Exploring the energy landscape of GFP by single-molecule mechanical experiments. Proc Natl Acad Sci. 2004;101:16192–16197.
   PubMed Web of Science ®Google Scholar
• Kramers HA. Brownian motion in a field of force and the diffusion model of chemical reactions. Physica. 1940;7:284–304.
   Google Scholar
• Hänggi P, Talkner P, Borkovec M. Reaction-rate theory: fifty years after Kramers. Rev Mod Phys. 1990;62:251–341.
   Web of Science ®Google Scholar
• McQuarrie DA. Statistical mechanics. Sausalito (CA): University Science Books; 2000.
   Google Scholar
• Smoluchowski M. Brownian molecular movement under the action of external forces and its connection with the generalized diffusion equation. Ann Phys (Leipzig). 1915;48:1103–1112.
   Google Scholar
• Welty JR, Wicks CE, Rorrer G, et al. Fundamentals of momentum, heat, and mass transfer. Hoboken (NJ): John Wiley & Sons; 2009.
   Google Scholar
• Dudko O, Filippov A, Klafter J, et al. Beyond the conventional description of dynamic force spectroscopy of adhesion bonds. Proc Natl Acad Sci. 2003;100:11378–11381.
   PubMed Web of Science ®Google Scholar
• Dudko OK, Hummer G, Szabo A. Intrinsic rates and activation free energies from single-molecule pulling experiments. Phys Rev Lett. 2006;96:108101.
   PubMed Web of Science ®Google Scholar
• Freund L. Characterizing the resistance generated by a molecular bond as it is forcibly separated. Proc Natl Acad Sci. 2009;106:8818–8823.
   PubMed Web of Science ®Google Scholar
• Li D, Ji B. Predicted rupture force of a single molecular bond becomes rate independent at ultralow loading rates. Phys Rev Lett. 2014;112:078302.
   Web of Science ®Google Scholar
• Bullerjahn JT, Sturm S, Kroy K. Theory of rapid force spectroscopy. Nat Commun. 2014;5:4463.
   PubMed Web of Science ®Google Scholar
• Friddle RW. Unified model of dynamic forced barrier crossing in single molecules. Phys Rev Lett. 2008;100:138302.
   PubMed Web of Science ®Google Scholar
• Li PC, Makarov DE. Simulation of the mechanical unfolding of ubiquitin: Probing different unfolding 19 December 14, 2015 Molecular Simulation Manuscript reaction coordinates by changing the pulling geometry. J Chem Phys. 2004;121:4826–4832.
   PubMed Web of Science ®Google Scholar
• Best RB, Paci E, Hummer G, et al. Pulling direction as a reaction coordinate for the mechanical unfolding of single molecules. J Phys Chem B. 2008;112:5968–5976.
   PubMed Web of Science ®Google Scholar
• Suzuki Y, Dudko OK. Single-molecule rupture dynamics on multidimensional landscapes. Phys Rev Lett. 2010;104:048101.
   Web of Science ®Google Scholar
• Zwanzig R. Diffusion a rough potential. Proc Natl Acad Sci. 1988;85:2029–2030.
   PubMed Web of Science ®Google Scholar
• Hyeon C, Thirumalai D. Can energy landscape roughness of proteins and RNA be measured by using mechanical unfolding experiments? Proc Natl Acad Sci. 2003;100:10249–10253.
   PubMed Web of Science ®Google Scholar
• Maitra A, Arya G. Model accounting for the effects of pulling-device Stiffness in the analyses of singlemolecule force measurements. Phys Rev Lett. 2010;104:108301.
   PubMed Web of Science ®Google Scholar
• Evstigneev M, Reimann P. Refined force-velocity relation in atomic friction experiments. Phys Rev B. 2006;73:113401.
   Web of Science ®Google Scholar
• Walton EB, Lee S, Van Vliet KJ. Extending Bell’s model: how force transducer stiffness alters measured unbinding forces and kinetics of molecular complexes. Biophys J. 2008;94:2621–2630.
   PubMed Web of Science ®Google Scholar
• Friedsam C, Wehle AK, Kühner F, et al. Dynamic single-molecule force spectroscopy: bond rupture analysis with variable spacer length. J Phys Condens Matter. 2003;15:S1709–S1723.
   Web of Science ®Google Scholar
• Ratto TV, Langry KC, Rudd RE, et al. Force spectroscopy of the double-tethered concanavalin-A mannose bond. Biophys J. 2004;86:2430–2437.
   PubMed Web of Science ®Google Scholar
• Hyeon C, Thirumalai D. Forced-unfolding and force-quench refolding of RNA hairpins. Biophys J. 2006;90:3410–3427.
   PubMed Web of Science ®Google Scholar
• Evans E, Ritchie K. Strength of a weak bond connecting flexible polymer chains. Biophys J. 1999;76:2439–2447.
   PubMed Web of Science ®Google Scholar
• Ray C, Brown JR, Akhremitchev BB. Correction of systematic errors in single-molecule force spectroscopy with polymeric tethers by atomic force microscopy. J Phys Chem B. 2007;111:1963–1974.
   PubMed Web of Science ®Google Scholar
• Maitra A, Arya G. Influence of pulling handles and device stiffness in single-molecule force spectroscopy. Phys Chem Chem Phys. 2011;13:1836–1842.
   PubMed Web of Science ®Google Scholar
• Marko JF, Siggia ED. Stretching DNA. Macromolecules. 1995;28:8759–8770.
   Web of Science ®Google Scholar
• Dudko OK, Hummer G, Szabo A. Theory, analysis, and interpretation of single-molecule force spectroscopy experiments. Proc Natl Acad Sci. 2008;105:15755–15760.
   PubMed Web of Science ®Google Scholar
• Allen MP, Tildesley DJ. Computer simulation of liquids. Oxford: Oxford University Press; 1989.
   Google Scholar
• Frenkel D, Smit B. Understanding molecular simulation: from algorithms to applications. Vol. 1. San Diego (CA): Academic press; 2001.
   Google Scholar
• Leach AR. Molecular modelling: principles and applications. Harlow: Pearson Education; 2001.
   Google Scholar
• Lu H, Isralewitz B, Krammer A, et al. Unfolding of titin immunoglobulin domains by steered molecular dynamics simulation. Biophys J. 1998;75:662–671.
   PubMed Web of Science ®Google Scholar
• Gao M, Craig D, Lequin O, et al. Structure and functional significance of mechanically unfolded fibronectin type III1 intermediates. Proc Natl Acad Sci. 2003;100:14784–14789.
   PubMed Web of Science ®Google Scholar
• Izrailev S, Stepaniants S, Balsera M, et al. Molecular dynamics study of unbinding of the avidin-biotin complex. Biophys J. 1997;72:1568–1581.
   PubMed Web of Science ®Google Scholar
• Grubmüller H, Heymann B, Tavan P. Ligand binding: molecular mechanics calculation of the streptavidin-biotin rupture force. 1996;271:997–999.
   Google Scholar
• Schlierf M, Rief M, Paci E. Complex unfolding kinetics of single-domain proteins in the presence of force. Biophys J. 2010;99:1620–1627.
   PubMed Web of Science ®Google Scholar
• Sun L, Noel JK, Sulkowska JI, et al. Connecting thermal and mechanical protein (un) folding landscapes. Biophys J. 2014;107:2941–2952.
   PubMed Web of Science ®Google Scholar
• Lindor-Larsen K, Piana S, Dror RO, et al. How fast-folding proteins fold. Science. 2011;334:517–520.
   Google Scholar
• Paturej J, Dubbeldam JL, Rostiashvili VG, et al. Force spectroscopy of polymer desorption: Theory and molecular dynamics simulations. Soft Matter. 2014;10:2785–2799.
   PubMed Web of Science ®Google Scholar
• Chang JC, Fok PW, Chou T. Bayesian uncertainty quantification for bond energies and mobilities using path integral analysis. Biophys J. 2015;109:966–974.
   PubMed Web of Science ®Google Scholar