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Boubeta, F.M.; Contestín García, R.M.; Lorenzo, E.N.; Boechi, L.; Estrin, D.; Sued, M.; Arrar, M. "Lessons learned about steered molecular dynamics simulations and free energy calculations" (2019) Chemical Biology and Drug Design
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Abstract:

The calculation of free energy profiles is central in understanding differential enzymatic activity, for instance, involving chemical reactions that require QM-MM tools, ligand migration, and conformational rearrangements that can be modeled using classical potentials. The use of steered molecular dynamics (sMD) together with the Jarzynski equality is a popular approach in calculating free energy profiles. Here, we first briefly review the application of the Jarzynski equality to sMD simulations, then revisit the so-called stiff-spring approximation and the consequent expectation of Gaussian work distributions and, finally, reiterate the practical utility of the second-order cumulant expansion, as it coincides with the parametric maximum-likelihood estimator in this scenario. We illustrate this procedure using simulations of CO, both in aqueous solution and in a carbon nanotube as a model system for biologically relevant nanoheterogeneous environments. We conclude the use of the second-order cumulant expansion permits the use of faster pulling velocities in sMD simulations, without introducing bias due to large dispersion in the non-equilibrium work distribution. © 2019 John Wiley & Sons A/S

Registro:

Documento: Artículo
Título:Lessons learned about steered molecular dynamics simulations and free energy calculations
Autor:Boubeta, F.M.; Contestín García, R.M.; Lorenzo, E.N.; Boechi, L.; Estrin, D.; Sued, M.; Arrar, M.
Filiación:CONICET-Facultad de Ciencias Exactas y Naturales, Instituto de Química-Física de los Materiales, Medio Ambiente y Energía, Universidad de Buenos Aires, Buenos Aires, Argentina
Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
CONICET-Facultad de Ciencias Exactas y Naturales, Instituto de Cálculo, Universidad de Buenos Aires, Buenos Aires, Argentina
Palabras clave:free energy; Jarzynski; maximum likelihood; steered molecular dynamics
Año:2019
DOI: http://dx.doi.org/10.1111/cbdd.13485
Título revista:Chemical Biology and Drug Design
Título revista abreviado:Chem. Biol. Drug Des.
ISSN:17470277
CODEN:CBDDA
Registro:https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_17470277_v_n_p_Boubeta

Referencias:

  • Arrar, M., Boubeta, F.M., Szretter, M.E., Sued, M., Boechi, L., Rodriguez, D., On the accurate estimation of free energies using the Jarzynski equality (2018) The Journal of Computational Chemistry, 40, pp. 688-696. , https://doi.org/10.1002/jcc.25754
  • Bartels, C., Karplus, M., Multidimensional adaptive umbrella sampling: Applications to main chain and side chain peptide conformations (1997) Journal of Computational Chemistry, 18, pp. 1450-1462. , https://doi.org/10.1002/(ISSN)1096-987X
  • Bieza, S.A., Boubeta, F., Feis, A., Smulevich, G., Estrin, D.A., Boechi, L., Bari, S.E., Reactivity of inorganic sulfide species toward a heme protein model (2014) Inorganic Chemistry, 54, pp. 527-533
  • Boechi, L., Martí, M.A., Milani, M., Bolognesi, M., Luque, F.J., Estrin, D.A., Structural determinants of ligand migration in Mycobacterium tuberculosis truncated hemoglobin O (2008) Proteins Structure, Function, and Bioinformatics, 73, pp. 372-379. , https://doi.org/10.1002/prot.22072
  • Boubeta, F.M., Bari, S.E., Estrin, D.A., Boechi, L., Access and binding of H2S to hemeproteins: The case of HbI of Lucina pectinata (2016) The Journal of Physical Chemistry B, 120, pp. 9642-9653. , https://doi.org/10.1021/acs.jpcb.6b06686
  • Bringas, M., Petruk, A.A., Estrin, D.A., Capece, L., Martí, M.A., Tertiary and quaternary structural basis of oxygen affinity in human hemoglobin as revealed by multiscale simulations (2017) Scientific Reports, 7, p. 10926. , https://doi.org/10.1038/s41598-017-11259-0
  • Bucher, D., Walker, R.C., McCammon, J.A., Improved reweighting of accelerated molecular dynamics simulations for free energy calculation (2014) Journal of Chemical Theory and Computation, 10, pp. 2677-2689
  • Case, D.A., Darden, T.A., Cheatham, T.E.I.I.I., Simmerling, C.L., Wang, J., Duke, R.E., Kollman, P., (2010) Amber 11, , San Francisco, University of California
  • Chelli, R., Local sampling in steered Monte Carlo simulations decreases dissipation and enhances free energy estimates via nonequilibrium work theorems (2012) Journal of Chemical Theory and Computation, 8, pp. 4040-4052. , https://doi.org/10.1021/ct300348w
  • Chipot, C., Pohorille, A., (2007) Free energy calculations, , https://doi.org/10.1007/978-3-540-38448-9, New York, NY, Springer
  • Crespo, A., Martí, M.A., Estrin, D.A., Roitberg, A.E., Multiple-steering QM-MM calculation of the free energy profile in chorismate mutase (2005) Journal of the American Chemical Society, 127, pp. 6940-6941. , https://doi.org/10.1021/ja0452830
  • Echeverria, I., Amzel, L.M., Estimation of free-energy differences from computed work distributions: An application of jarzynski?s equality (2012) The Journal of Physical Chemistry B, 116, pp. 10986-10995. , https://doi.org/10.1021/jp300527q
  • Feller, S.E., Zhang, Y., Pastor, R.W., Brooks, B.R., Constant pressure molecular dynamics simulation: The Langevin piston method (1995) The Journal of Chemical Physics, 103, pp. 4613-4621. , https://doi.org/10.1063/1.470648
  • Ferrenberg, A.M., Swendsen, R.H., Optimized monte carlo data analysis (1989) Computers in Physics, 3, pp. 101-104. , https://doi.org/10.1063/1.4822862
  • Gohlke, H., Kiel, C., Case, D.A., Insights into protein–protein binding by binding free energy calculation and free energy decomposition for the Ras–Raf and Ras–RalGDS complexes (2003) Journal of Molecular Biology, 330, pp. 891-913. , https://doi.org/10.1016/S0022-2836(03)00610-7
  • Gore, J., Ritort, F., Bustamante, C., Bias and error in estimates of equilibrium free-energy differences from nonequilibrium measurements (2003) Proceedings of the National Academy of Sciences, 100, pp. 12564-12569. , https://doi.org/10.1073/pnas.1635159100
  • Hu, G., Xu, S., Wang, J., Characterizing the free-energy landscape of MDM2 protein–ligand interactions by steered molecular dynamics simulations (2015) Chemical Biology & Drug Design, 86, pp. 1351-1359. , https://doi.org/10.1111/cbdd.12598
  • Hummer, G., Fast-growth thermodynamic integration: Error and efficiency analysis (2001) The Journal of Chemical Physics, 114, pp. 7330-7337. , https://doi.org/10.1063/1.1363668
  • Hummer, G., (2007) Free energy calculations, pp. 171-198. , New York, NY, Springer
  • Humphrey, W., Dalke, A., Schulten, K., VMD – Visual molecular dynamics (1996) Journal of Molecular Graphics, 14, pp. 33-38. , https://doi.org/10.1016/0263-7855(96)00018-5
  • Isralewitz, B., Baudry, J., Gullingsrud, J., Kosztin, D., Schulten, K., Steered molecular dynamics investigations of protein function (2001) Journal of Molecular Graphics and Modelling, 19, pp. 13-25. , https://doi.org/10.1016/S1093-3263(00)00133-9
  • Isralewitz, B., Gao, M., Schulten, K., Steered molecular dynamics and mechanical functions of proteins (2001) Current Opinion in Structural Biology, 11, pp. 224-230. , https://doi.org/10.1016/S0959-440X(00)00194-9
  • Jarzynski, C., Nonequilibrium equality for free energy differences (1997) Physical Review Letters, 78, pp. 2690-2693. , https://doi.org/10.1103/PhysRevLett.78.2690
  • Jarzynski, C., Rare events and the convergence of exponentially averaged work values (2006) Physical Review E, 73, p. 046105. , https://doi.org/10.1103/PhysRevE.73.046105
  • Jarzynski, C., Equalities and inequalities: Irreversibility and the second law of thermodynamics at the nanoscale (2011) Annual Review of Condensed Matter Physics, 2, pp. 329-351. , https://doi.org/10.1146/annurev-conmatphys-062910-140506
  • Jorgensen, W.L., Chandrasekhar, J., Madura, J.D., Impey, R.W., Klein, M.L., Comparison of simple potential functions for simulating liquid water (1983) The Journal of Chemical Physics, 79, pp. 926-935. , https://doi.org/10.1063/1.445869
  • Kumar, S., Rosenberg, J.M., Bouzida, D., Swendsen, R.H., Kollman, P.A., The weighted histogram analysis method for free-energy calculations on biomolecules. I. The method (1992) Journal of Computational Chemistry, 13, pp. 1011-1021. , https://doi.org/10.1002/(ISSN)1096-987X
  • Marsico, F., Burastero, O., Defelipe, L.A., Lopez, E.D., Arrar, M., Turjanski, A.G., Marti, M.A., Multiscale approach to the activation and phosphotransfer mechanism of CpxA histidine kinase reveals a tight coupling between conformational and chemical steps (2018) Biochemical and Biophysical Research Communications, 498, pp. 305-312. , https://doi.org/10.1016/j.bbrc.2017.09.039
  • Martyna, G.J., Tobias, D.J., Klein, M.L., Constant pressure molecular dynamics algorithms (1994) The Journal of Chemical Physics, 101, pp. 4177-4189. , https://doi.org/10.1063/1.467468
  • Nicolini, P., Frezzato, D., Chelli, R., Exploiting configurational freezing in nonequilibrium Monte Carlo simulations (2011) Journal of Chemical Theory and Computation, 7, pp. 582-593. , https://doi.org/10.1021/ct100568n
  • Ozer, G., Valeev, E.F., Quirk, S., Hernandez, R., Adaptive steered molecular dynamics of the long-distance unfolding of neuropeptide Y (2010) Journal of Chemical Theory and Computation, 6, pp. 3026-3038. , https://doi.org/10.1021/ct100320g
  • Park, S., Schulten, K., Calculating potentials of mean force from steered molecular dynamics simulations (2004) Journal of Chemical Physics, 120, pp. 5946-5961. , https://doi.org/10.1063/1.1651473
  • Phillips, J.C., Braun, R., Wang, W., Gumbart, J., Tajkhorshid, E., Villa, E., Schulten, K., Scalable molecular dynamics with NAMD (2005) Journal of Computational Chemistry, 26, pp. 1781-1802. , https://doi.org/10.1002/(ISSN)1096-987X
  • Pohorille, A., Jarzynski, C., Chipot, C., Good practices in free-energy calculations (2010) Journal of Physical Chemistry B, 114, pp. 10235-10253. , https://doi.org/10.1021/jp102971x
  • Ramírez, C.L., Zeida, A., Jara, G.E., Roitberg, A.E., Martí, M.A., Improving Efficiency in SMD simulations through a hybrid differential relaxation algorithm (2014) Journal of Chemical Theory and Computation, 10, pp. 4609-4617. , https://doi.org/10.1021/ct500672d
  • Ryckaert, J., Ciccotti, G., ScienceDirect—choose organization (1977) Journal of Computational Physics, 23, pp. 327-341. , https://doi.org/10.1016/0021-9991(77)90098-5
  • Schmiedl, T., Seifert, U., Optimal finite-time processes in stochastic thermodynamics (2007) Physical Review Letters, 98, p. 108301. , https://doi.org/10.1103/PhysRevLett.98.108301
  • Selvam, B., Wereszczynski, J., Tikhonova, I.G., Comparison of dynamics of extracellular accesses to the β1 and β2 adrenoceptors binding sites uncovers the potential of kinetic basis of antagonist selectivity (2012) Chemical Biology & Drug Design, 80, pp. 215-226. , https://doi.org/10.1111/j.1747-0285.2012.01390.x
  • Shirts, M.R., Chodera, J.D., Statistically optimal analysis of samples from multiple equilibrium states (2008) The Journal of Chemical Physics, 129, p. 124105. , https://doi.org/10.1063/1.2978177
  • Shirts, M.R., Mobley, D.L., Brown, S.P., Free-energy calculations in structure-based drug design (2010) Drug Design: Structure-and Ligand-Based Approaches, pp. 61-86. , https://doi.org/10.1017/CBO9780511730412
  • Vaikuntanathan, S., Jarzynski, C., Escorted free energy simulations: Improving convergence by reducing dissipation (2008) Physical Review Letters, 100, p. 190601. , https://doi.org/10.1103/PhysRevLett.100.190601
  • Wu, D., Kofke, D.A., Phase-space overlap measures: I: Fail-safe bias detection in free energies calculated by molecular simulation (2005) The Journal of Chemical Physics, 123, p. 054103. , https://doi.org/10.1063/1.1992483
  • Wu, D., Kofke, D.A., Phase-space overlap measures. II. Design and implementation of staging methods for free-energy calculations (2005) The Journal of Chemical Physics, 123, p. 084109. , https://doi.org/10.1063/1.2011391
  • Xiong, H., Crespo, A., Marti, M., Estrin, D., Roitberg, A.E., Free energy calculations with non-equilibrium methods: Applications of the Jarzynski relationship (2006) Theoretical Chemistry Accounts, 116, pp. 338-346. , https://doi.org/10.1007/s00214-005-0072-2
  • Ytreberg, F.M., Zuckerman, D.M., Efficient use of nonequilibrium measurement to estimate free energy differences for molecular systems (2004) Journal of Computational Chemistry, 25, pp. 1749-1759. , https://doi.org/10.1002/(ISSN)1096-987X
  • Yunger Halpern, N., Jarzynski, C., Number of trials required to estimate a free-energy difference, using fluctuation relations (2016) Physical Review E, 93, p. 052144. , https://doi.org/10.1103/PhysRevE.93.052144
  • Zerbetto, M., Piserchia, A., Frezzato, D., Looking for some free energy? (2014) Journal of Computational Chemistry, 35, pp. 1865-1881. , https://doi.org/10.1002/jcc.23701
  • Zuckerman, D.M., Woolf, T.B., (2001) Extrapolative analysis of fast-switching free energy estimates in a molecular system
  • Zuckerman, D.M., Woolf, T.B., Overcoming finite-sampling errors in fast-switching free-energy estimates: Extrapolative analysis of a molecular system (2002) Chemical Physics Letters, 351, pp. 445-453

Citas:

---------- APA ----------
Boubeta, F.M., Contestín García, R.M., Lorenzo, E.N., Boechi, L., Estrin, D., Sued, M. & Arrar, M. (2019) . Lessons learned about steered molecular dynamics simulations and free energy calculations. Chemical Biology and Drug Design.
http://dx.doi.org/10.1111/cbdd.13485
---------- CHICAGO ----------
Boubeta, F.M., Contestín García, R.M., Lorenzo, E.N., Boechi, L., Estrin, D., Sued, M., et al. "Lessons learned about steered molecular dynamics simulations and free energy calculations" . Chemical Biology and Drug Design (2019).
http://dx.doi.org/10.1111/cbdd.13485
---------- MLA ----------
Boubeta, F.M., Contestín García, R.M., Lorenzo, E.N., Boechi, L., Estrin, D., Sued, M., et al. "Lessons learned about steered molecular dynamics simulations and free energy calculations" . Chemical Biology and Drug Design, 2019.
http://dx.doi.org/10.1111/cbdd.13485
---------- VANCOUVER ----------
Boubeta, F.M., Contestín García, R.M., Lorenzo, E.N., Boechi, L., Estrin, D., Sued, M., et al. Lessons learned about steered molecular dynamics simulations and free energy calculations. Chem. Biol. Drug Des. 2019.
http://dx.doi.org/10.1111/cbdd.13485