New polarizable atomic force fields for calculation of non-bonded interactions in explicit and implicit aqueous surrounding

A. V. Finkelstein ; L. B. Pereyaslavets

Matematičeskaâ biologiâ i bioinformatika, Tome 5 (2010) no. 2, pp. 138-149.

Résumé

A new functional form is developed for the force field of non-bonded interactions. Apart from the traditional terms, this new form takes into account the molecular partial charge-induced polarization of all atoms of the interacting molecules and the surrounding solvent. In the frames of this unified functional form of the force field, the parameters of all non-bonded interactions are optimized for both explicit (in the force field PFFsubl) and implicit (in the force field PFFsol) presentation of the aqueous surrounding. With optimized parameters of the both developed fields, the correlation coefficient between calculated and experimentally determined strengths of cohesion of molecules in crystals is 93 – 95%, both in the vacuum and in the implicitly determined aqueous surrounding.

Bibliographie

[1] Shaw D. E., Maragakis P., Lindorff-Larsen K., Piana S., Dror R. O., Eastwood M. P., Bank J. A., Jumper J. M., Salmon J. K., Shah Y., Wriggers W., “Atom-level characterization of structural dynamics of proteins”, Science, 330 (2010), 341–346 | DOI

[2] Lindorff-Larsen K., Piana S., Palmo K., Maragakis P., Klepeis J. L., Dror R. O., Shaw D. E., “Improved side-chain torsion potentials for the Amber ff99SB protein force field”, Proteins, 78 (2010), 1950–1958

[3] Warshel A., Lifson S., “Consistent force field calculations. II. Crystal structures, sublimation energies, molecular and lattice vibrations, molecular conformations, and enthalpies of alkanes”, J. Chem. Phys., 53 (1970), 582–594 | DOI

[4] Hagler A. T., Huler E., Lifson S., “Energy functions for peptides and proteins. I. Derivation of a consistent force fields including the hydrogen bond from amide crystals”, J. Am. Chem. Soc., 96 (1974), 5319–5327 | DOI

[5] Hagler A. T., Lifson S., “Energy functions for peptides and proteins. II. The amide hydrogen bond and calculation of amide crystal properties”, J. Am. Chem. Soc., 96 (1974), 5327–5335 | DOI

[6] Levitt M., Hirshberg M., Sharon R., Daggett V., “Potential energy function and parameters for simulations of the molecular dynamics of proteins and nucleic acids in solution”, Comput. Phys. Commun., 91 (1995), 215–231 | DOI

[7] MacKerell A. D., Jr., Bashford D., Bellott M., Dunbrack R. L., Jr., Evanseck J. D., Field M. J., Fischer S., Gao J., Guo H., Ha S., Joseph-McCarthy D., Kuchnir L., Kuczera K., Lau F. T. K., Mattos C., Michnick S., Ngo T., Nguyen D. T., Prodhom B., Reiher W. E., III, Roux B., Schlenkrich M., Smith J. C., Stote R., Straub J., Watanabe M., Wiorkiewicz-Kuczera J., Yin D., Karplus M., “All-atom empirical potential for molecular modeling and dynamics studies of proteins”, J. Phys. Chem. B, 102 (1998), 3586–3616 | DOI

[8] Jorgensen W. L., Maxwell D. S., Tirado-Rives J., “Development and testing of the opls allatom force field on conformational energetics and properties of organic liquids”, J. Am. Chem. Soc., 118 (1996), 11225–11236 | DOI

[9] Halgren T. A., “Merck Molecular Force Field. I. Basis, form, parameterization and performance of MMFF94”, J. Comput. Chem., 17 (1995), 490–519 | 3.0.CO;2-P class='badge bg-secondary rounded-pill ref-badge extid-badge'>DOI

[10] Wang J., Wolf R. M., Caldwell J. W., Kollman P. A., Case D. A., “Development and testing of a general Amber force fields”, J. Comput. Chem., 25 (2004), 1157–1174 | DOI

[11] Kollman P. A., “Free energy calculations: Applications to chemical and biochemical phenomena”, Chem. Rev., 93 (1993), 2395–2417 | DOI

[12] Onufriev A., Bashford D., Case D., “Exploring protein native states and large-scale conformational changes with a modified generalized born model”, Proteins, 55 (2004), 383–394 | DOI

[13] Khoruzhii O. V., Donchev A. G., Galkin N. G., Illarionov A. A., Olevanov M. A., Ozrin V. D., Queen C., Tarasov V. I., “Application of a polarizable force field to calculations of relative protein-ligand binding affinities”, Proc. Natl. Acad. Sci. USA, 105 (2008), 10378–10383 | DOI

[14] Roux B., Simonson T., “Implicit solvent models”, Biophys. Chem., 78 (1999), 1–20 | DOI | MR

[15] Cramer C. J., Truhlar D. G., “Implicit solvation models: Equilibria, structure, spectra, and dynamics”, Chem. Rev., 99 (1999), 2161–2200 | DOI

[16] Ponder J. W., Case D. A., “Force fields for protein simulations”, Adv. Prot. Chem., 66 (2003), 27–85 | DOI

[17] Chothia C., “Hydrophobic bonding and accessible surface area in proteins”, Nature, 248 (1974), 338–339 | DOI

[18] Wesson L., Eisenberg D., “Atomic solvation parameters applied to molecular dynamics of proteins in solution”, Prot. Sci., 1 (1992), 227–235 | DOI

[19] Gallicchio E., Zhang L. Y., Levy R. M., “The SGB/NP hydration free energy model based on the surface generalized Born solvent reaction field and novel nonpolar hydration free energy estimators”, J. Comput. Chem., 23 (2002), 517–529 | DOI

[20] Simonson T., “Electrostatics and dynamics of proteins”, Rep. Prog. Phys., 66 (2003), 737–787 | DOI

[21] Baker N. A., “Improving implicit solvent simulations: a Poisson-centric view”, Curr. Opin. Struct. Biol., 15 (2005), 137–143 | DOI

[22] Shi X., Koehl P., “The geometry behind numerical solvers of the poisson-boltzmann equation”, Commun. Comput. Phys., 3 (2008), 1032–1050 | MR | Zbl

[23] Wang J., Tan C., Tan Y.-H., Lu Q., Luo R., “Poisson–Boltzmann solvents in molecular dynamics simulations”, Commun. Comput. Phys., 3 (2008), 1010–1031

[24] Still W. C., Tempczyk A., Hawley R. C., Hendrickson T., “Semianalytical treatment of solvation for molecular mechanics and dynamics”, J. Am. Chem. Soc., 112 (1990), 6127–6129 | DOI

[25] Ghosh A., Rapp C. S., Friesner R. A., “Generalized Born model based on a surface integral formulation”, J. Phys. Chem. B, 102 (1998), 10983–10990 | DOI

[26] Lide D. R., CRC Handbook of chemistry and physics on CD, CRC-press, Boca Raton, 2005 | Zbl

[27] Chickos J. S., Acree W. E. Jr., “Enthalpies of sublimation of organic and organometallic compounds. 1910–2001”, J. Phys. Chem. Ref. Data, 31 (2002), 537–698 | DOI

[28] Allen F. H., “The Cambridge Structural Database: a quarter of a million crystal structures and rising”, Acta Cryst. B, 58 (2002), 380–388 | DOI

[29] Sander R., Compilation of Henry's law constants for inorganic and organic species of potential importance in environmental chemistry (Version 3), , 1999 http://www.mpch-mainz.mpg.de/~sander/res/henry.html

[30] Pereyaslavets L. B., Finkelshtein A. V., “Silovoe pole FFSol dlya rascheta vzaimodeistvii molekul v vodnom okruzhenii”, Mol. biol., 44 (2010), 340–354

[31] Landau L. D., Lifshits E. M., Elektrodinamika sploshnykh sred, izd. 2, Nauka, M., 1982 | MR

[32] Finkelshtein A. V., Ptitsyn O. B., Fizika belka, izd. 3, Knizhnyi dom “Universitet”, M., 2005

[33] Halgren T. A., Damm W., “Polarizable force fields”, Curr. Opin. Struct. Biol., 11 (2001), 236–242 | DOI

[34] Finkelstein A. V., “Average and extreme multi-atom Van der Waals interactions: Strong coupling of multi-atom Van der Waals interactions with covalent bonding”, Chem. Central J., 1 (2007), 21 | DOI

[35] Landau L. D., Lifshits E. M., Kvantovaya mekhanika, chast I, OGIZ, M., L., 1948

[36] Bayly C. I., Cieplak P., Cornell W., Kollman P. A., “A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESP model”, J. Phys. Chem., 97 (1993), 10269–10280 | DOI

[37] Cornell W. D., Cieplak P., Bayly C. I., Kollman P. A., “Application of RESP charges to calculate conformational energies, hydrogen bond energies, and free energies of solvation”, J. Am. Chem. Soc., 115 (1993), 9620–9631 | DOI

[38] Granovsky A. A., PC GAMESS/Firefly 7.1.E, , 2008, (data obrascheniya: 11.05.2009–06.09.2010) http://classic.chem.msu.su/ gran/gamess/index.html

[39] Schmidt M. W., Baldridge K. K., Boatz J. A., Elbert S. T., Gordon M. S., Jensen J. H., Koseki S., Matsunaga N., Nguyen K. A., Su S., Windus T. L., Dupuis M., Montgomery J. A., “General atomic and molecular electronic structure system”, J. Comput. Chem., 14 (1993), 1347–1363 | DOI

[40] Wang J., Wang W., Kollman P. A., Case D. A., “Automatic atom type and bond type perception in molecular mechanical calculations”, J. Mol. Graph. Model., 25 (2006), 247–260 | DOI

[41] Ewig C. S., Thacher T. S., Hagler A. T., “Derivation of Class II force fields. 7. Nonbonded force field parameters for organic compounds”, J. Phys. Chem. B, 103 (1999), 6998–7014 | DOI

[42] Donchev A. G., Galkin N. G., Illarionov A. A., Khoruzhii O. V., Olevanov M. A., Ozrin V. D., Pereyaslavets L. B., Tarasov V. I., “Assessment of performance of the general purpose polarizable force field QMPFF3 in condensed phase”, J. Comput. Chem., 29 (2008), 1242–1249 | DOI