title: Determination of equilibrium free energy from nonequilibrium work measurements.
abstract: The fluctuation-dissipation theorem (FDT) of Brownian dynamics (BD) is applied to extract the equilibrium free-energy profile from the nonequilibrium, irreversible work measured in single-molecule pulling experiments. Two sets of in silico experiments are performed to explore the free-energy landscape of deca-alanine peptide as a function of its end-to-end distance and to determine the free-energy profile of water permeation through the channels of aquaglyceroporin GlpF. With a small number of pulling paths sampled, the BD-FDT is shown to produce accurate estimates of the free-energy profiles for both systems.
authors.affiliation: Department of Physics, University of Texas at San Antonio, One UTSA Circle, San Antonio, Texas 78249, USA.
authors.forename: L Y
authors.initials: LY
authors.lastname: Chen
authors.forename: D A
authors.initials: DA
authors.lastname: Bastien
authors.forename: H E
authors.initials: HE
authors.lastname: Espejel
mesh_terms: D000409:Alanine / Q000737:chemistry; D051397:Aquaglyceroporins / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D010455:Peptides / Q000737:chemistry; D013816:Thermodynamics; D014867:Water / Q000737:chemistry
chemical_list: D051397:Aquaglyceroporins; D010455:Peptides; D014867:Water; D000409:Alanine
references.citation: J Chem Phys. 2006 Nov 14;125(18):184114
references.pmid: 17115745
references.citation: Biophys J. 2008 Feb 1;94(3):832-9
references.pmid: 17921212
references.citation: Science. 2001 Dec 14;294(5550):2353-7
references.pmid: 11743202
references.citation: Phys Rev Lett. 2007 Aug 10;99(6):068101
references.pmid: 17930869
references.citation: J Comput Chem. 2005 Dec;26(16):1781-802
references.pmid: 16222654
references.citation: J Chem Phys. 2008 Oct 14;129(14):144113
references.pmid: 19045140
references.citation: Nat Methods. 2008 Jun;5(6):491-505
references.pmid: 18511917
references.citation: Adv Protein Chem. 2003;63:291-316
references.pmid: 12629974
references.citation: J Chem Phys. 2004 Apr 1;120(13):5946-61
references.pmid: 15267476
references.citation: Proc Natl Acad Sci U S A. 2001 Mar 27;98(7):3658-61
references.pmid: 11274384
references.citation: Curr Opin Struct Biol. 2003 Aug;13(4):424-31
references.pmid: 12948772
references.citation: J Chem Phys. 2008 Sep 7;129(9):091101
references.pmid: 19044857
references.citation: J Chem Phys. 2006 Feb 14;124(6):64106
references.pmid: 16483195
references.citation: J Bacteriol. 1980 Oct;144(1):274-8
references.pmid: 6998951
references.citation: Biopolymers. 2000-2001;56(4):257-65
references.pmid: 11754339
references.citation: Science. 2002 Jun 7;296(5574):1832-5
references.pmid: 12052949
references.citation: Curr Opin Struct Biol. 2007 Apr;17(2):181-6
references.pmid: 17395451
references.citation: J Chem Phys. 2006 Feb 14;124(6):64108
references.pmid: 16483197