Determination of equilibrium free energy from nonequilibrium work measurements.
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.
Chen
L Y
LY
Department of Physics, University of Texas at San Antonio, One UTSA Circle, San Antonio, Texas 78249, USA.
Bastien
D A
DA
Espejel
H E
HE
D000409:Alanine / Q000737:chemistry; D051397:Aquaglyceroporins / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D010455:Peptides / Q000737:chemistry; D013816:Thermodynamics; D014867:Water / Q000737:chemistry
D051397:Aquaglyceroporins; D010455:Peptides; D014867:Water; D000409:Alanine
J Chem Phys. 2006 Nov 14;125(18):184114
17115745
Biophys J. 2008 Feb 1;94(3):832-9
17921212
Science. 2001 Dec 14;294(5550):2353-7
11743202
Phys Rev Lett. 2007 Aug 10;99(6):068101
17930869
J Comput Chem. 2005 Dec;26(16):1781-802
16222654
J Chem Phys. 2008 Oct 14;129(14):144113
19045140
Nat Methods. 2008 Jun;5(6):491-505
18511917
Adv Protein Chem. 2003;63:291-316
12629974
J Chem Phys. 2004 Apr 1;120(13):5946-61
15267476
Proc Natl Acad Sci U S A. 2001 Mar 27;98(7):3658-61
11274384
Curr Opin Struct Biol. 2003 Aug;13(4):424-31
12948772
J Chem Phys. 2008 Sep 7;129(9):091101
19044857
J Chem Phys. 2006 Feb 14;124(6):64106
16483195
J Bacteriol. 1980 Oct;144(1):274-8
6998951
Biopolymers. 2000-2001;56(4):257-65
11754339
Science. 2002 Jun 7;296(5574):1832-5
12052949
Curr Opin Struct Biol. 2007 Apr;17(2):181-6
17395451
J Chem Phys. 2006 Feb 14;124(6):64108
16483197