Design principles for high-pressure force fields: Aqueous TMAO solutions from ambient to kilobar pressures.

Accurate force fields are one of the major pillars on which successful molecular dynamics simulations of complex biomolecular processes rest. They have been optimized for ambient conditions, whereas high-pressure simulations become increasingly important in pressure perturbation studies, using pressure as an independent thermodynamic variable. Here, we explore the design of non-polarizable force fields tailored to work well in the realm of kilobar pressures--while avoiding complete reparameterization. Our key is to first compute the pressure-induced electronic and structural response of a solute by combining an integral equation approach to include pressure effects on solvent structure with a quantum-chemical treatment of the solute within the embedded cluster reference interaction site model (EC-RISM) framework. Next, the solute's response to compression is taken into account by introducing pressure-dependence into selected parameters of a well-established force field. In our proof-of-principle study, the full machinery is applied to N,N,N-trimethylamine-N-oxide (TMAO) in water being a potent osmolyte that counteracts pressure denaturation. EC-RISM theory is shown to describe well the charge redistribution upon compression of TMAO(aq) to 10 kbar, which is then embodied in force field molecular dynamics by pressure-dependent partial charges. The performance of the high pressure force field is assessed by comparing to experimental and ab initio molecular dynamics data. Beyond its broad usefulness for designing non-polarizable force fields for extreme thermodynamic conditions, a good description of the pressure-response of solutions is highly recommended when constructing and validating polarizable force fields.

[1]  D. Marx,et al.  Water structure and solvation of osmolytes at high hydrostatic pressure: pure water and TMAO solutions at 10 kbar versus 1 bar. , 2015, Physical chemistry chemical physics : PCCP.

[2]  Jochen Heil,et al.  Targeting Drug Resistance in EGFR with Covalent Inhibitors: A Structure-Based Design Approach. , 2015, Journal of medicinal chemistry.

[3]  Jochen Heil,et al.  3D RISM theory with fast reciprocal-space electrostatics. , 2015, The Journal of chemical physics.

[4]  Stefan M. Kast,et al.  Solvation effects on chemical shifts by embedded cluster integral equation theory. , 2014, The journal of physical chemistry. A.

[5]  Axel Groß,et al.  Dispersion corrected RPBE studies of liquid water. , 2014, The Journal of chemical physics.

[6]  S. Kast,et al.  Acidity in DMSO from the embedded cluster integral equation quantum solvation model , 2014, Journal of Molecular Modeling.

[7]  Joost VandeVondele,et al.  cp2k: atomistic simulations of condensed matter systems , 2014 .

[8]  Sandip Paul,et al.  Trimethylamine-N-oxide's effect on polypeptide solvation at high pressure: a molecular dynamics simulation study. , 2013, The journal of physical chemistry. B.

[9]  B. Berne,et al.  When does trimethylamine N-oxide fold a polymer chain and urea unfold it? , 2013, The journal of physical chemistry. B.

[10]  J. Shea,et al.  Double resolution model for studying TMAO/water effective interactions. , 2013, The journal of physical chemistry. B.

[11]  R. Netz,et al.  Insight into the molecular mechanisms of protein stabilizing osmolytes from global force-field variations. , 2013, The journal of physical chemistry. B.

[12]  S. Garde,et al.  Trimethylamine N-oxide (TMAO) and tert-butyl alcohol (TBA) at hydrophobic interfaces: insights from molecular dynamics simulations. , 2013, Langmuir : the ACS journal of surfaces and colloids.

[13]  Hirofumi Sato A modern solvation theory: quantum chemistry and statistical chemistry. , 2013, Physical chemistry chemical physics : PCCP.

[14]  T. Morawietz,et al.  A density-functional theory-based neural network potential for water clusters including van der Waals corrections. , 2013, The journal of physical chemistry. A.

[15]  K. Schulten,et al.  Misplaced helix slows down ultrafast pressure-jump protein folding , 2013, Proceedings of the National Academy of Sciences.

[16]  Pritam Ganguly,et al.  Convergence of Sampling Kirkwood-Buff Integrals of Aqueous Solutions with Molecular Dynamics Simulations. , 2013, Journal of chemical theory and computation.

[17]  P. McMillan,et al.  High-Pressure Biochemistry and Biophysics , 2013 .

[18]  S. Chong,et al.  Aqueous interaction site integral-equation theory that exactly takes into account intramolecular correlations. , 2012, The Journal of chemical physics.

[19]  J. Tomasi,et al.  Calculation and analysis of the harmonic vibrational frequencies in molecules at extreme pressure: methodology and diborane as a test case. , 2012, The Journal of chemical physics.

[20]  George I Makhatadze,et al.  Molecular mechanism for the preferential exclusion of TMAO from protein surfaces. , 2012, The journal of physical chemistry. B.

[21]  Sandip Paul,et al.  Effect of trimethylamine-N-oxide on pressure-induced dissolution of hydrophobic solute. , 2012, The Journal of chemical physics.

[22]  Miguel A. L. Marques,et al.  Libxc: A library of exchange and correlation functionals for density functional theory , 2012, Comput. Phys. Commun..

[23]  I. Vetter,et al.  Revealing conformational substates of lipidated N-Ras protein by pressure modulation , 2011, Proceedings of the National Academy of Sciences.

[24]  Carlos Vega,et al.  Simulating water with rigid non-polarizable models: a general perspective. , 2011, Physical chemistry chemical physics : PCCP.

[25]  Sandip Paul,et al.  Hydrophobic interactions in presence of osmolytes urea and trimethylamine-N-oxide. , 2011, The Journal of chemical physics.

[26]  A. Seitsonen,et al.  Van der Waals effects in ab initio water at ambient and supercritical conditions. , 2011, The Journal of chemical physics.

[27]  R. Netz,et al.  Can simulations quantitatively predict peptide transfer free energies to urea solutions? Thermodynamic concepts and force field limitations. , 2011, The journal of physical chemistry. A.

[28]  H. Kokubo,et al.  Peptide conformational preferences in osmolyte solutions: transfer free energies of decaalanine. , 2011, Journal of the American Chemical Society.

[29]  P. Oger,et al.  The many ways of coping with pressure. , 2010, Research in microbiology.

[30]  D. Marx,et al.  Glycine in aqueous solution: solvation shells, interfacial water, and vibrational spectroscopy from ab initio molecular dynamics. , 2010, The Journal of chemical physics.

[31]  A. Garcia,et al.  Studying pressure denaturation of a protein by molecular dynamics simulations , 2010, Proteins.

[32]  S. Grimme,et al.  A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu. , 2010, The Journal of chemical physics.

[33]  Stefan M. Kast,et al.  Prediction of tautomer ratios by embedded-cluster integral equation theory , 2010, J. Comput. Aided Mol. Des..

[34]  Y. Gao,et al.  Effects of urea, tetramethyl urea, and trimethylamine N-oxide on aqueous solution structure and solvation of protein backbones: a molecular dynamics simulation study. , 2010, The journal of physical chemistry. B.

[35]  Hans Robert Kalbitzer,et al.  Fundamental link between folding states and functional states of proteins. , 2009, Journal of the American Chemical Society.

[36]  Yuko Okamoto,et al.  Thermodynamic perspective on the dock-lock growth mechanism of amyloid fibrils. , 2009, The journal of physical chemistry. B.

[37]  S. Kast,et al.  Closed-form expressions of the chemical potential for integral equation closures with certain bridge functions. , 2008, The Journal of chemical physics.

[38]  A. Garcia,et al.  Computing the stability diagram of the Trp-cage miniprotein , 2008, Proceedings of the National Academy of Sciences.

[39]  R. Winter,et al.  Cold- and pressure-induced dissociation of protein aggregates and amyloid fibrils. , 2008, Angewandte Chemie.

[40]  Fumio Hirata,et al.  Combination of molecular dynamics method and 3D‐RISM theory for conformational sampling of large flexible molecules in solution , 2008, J. Comput. Chem..

[41]  Jochen Heil,et al.  Quantum chemistry in solution by combining 3D integral equation theory with a cluster embedding approach. , 2008, The journal of physical chemistry. B.

[42]  C. Vega,et al.  Determination of phase diagrams via computer simulation: methodology and applications to water, electrolytes and proteins , 2008, 0901.1823.

[43]  Ryan Day,et al.  Water penetration in the low and high pressure native states of ubiquitin , 2008, Proteins.

[44]  J. Tomasi,et al.  Towards the elaboration of a QM method to describe molecular solutes under the effect of a very high pressure , 2008 .

[45]  Carsten Kutzner,et al.  GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation. , 2008, Journal of chemical theory and computation.

[46]  Joost VandeVondele,et al.  Gaussian basis sets for accurate calculations on molecular systems in gas and condensed phases. , 2007, The Journal of chemical physics.

[47]  M. Parrinello,et al.  Canonical sampling through velocity rescaling. , 2007, The Journal of chemical physics.

[48]  W. V. van Gunsteren,et al.  Protein under pressure: Molecular dynamics simulation of the arc repressor , 2006, Proteins.

[49]  Roland Winter,et al.  Origins of life and biochemistry under high-pressure conditions. , 2006, Chemical Society reviews.

[50]  A. Kovalenko,et al.  Self-consistent combination of the three-dimensional RISM theory of molecular solvation with analytical gradients and the Amsterdam density functional package. , 2006 .

[51]  K. Akasaka Probing conformational fluctuation of proteins by pressure perturbation. , 2006, Chemical reviews.

[52]  Fumio Hirata,et al.  A new method to determine electrostatic potential around a macromolecule in solution from molecular wave functions , 2006, J. Comput. Chem..

[53]  Roland Winter,et al.  Solvation-assisted pressure tuning of insulin fibrillation: from novel aggregation pathways to biotechnological applications. , 2006, Journal of molecular biology.

[54]  C. Vega,et al.  A general purpose model for the condensed phases of water: TIP4P/2005. , 2005, The Journal of chemical physics.

[55]  P. Yancey,et al.  Organic osmolytes as compatible, metabolic and counteracting cytoprotectants in high osmolarity and other stresses , 2005, Journal of Experimental Biology.

[56]  Michele Parrinello,et al.  Quickstep: Fast and accurate density functional calculations using a mixed Gaussian and plane waves approach , 2005, Comput. Phys. Commun..

[57]  A. Garcia,et al.  Reversible temperature and pressure denaturation of a protein fragment: a replica exchange molecular dynamics simulation study. , 2004, Physical review letters.

[58]  Wely B. Floriano,et al.  Dielectric Constant and Density of Water as a Function of Pressure at Constant Temperature , 2004 .

[59]  A. Fornili,et al.  Molecular dynamics simulation of aqueous solutions of trimethylamine-N-oxide and tert-butyl alcohol , 2003 .

[60]  J. Brickmann,et al.  Binary phases of aliphatic N-oxides and water: Force field development and molecular dynamics simulation , 2003 .

[61]  S. Kast,et al.  Integral equation theory for correcting truncation errors in molecular simulations , 2003 .

[62]  E. Paci High pressure simulations of biomolecules. , 2002, Biochimica et biophysica acta.

[63]  D. Bartlett Pressure effects on in vivo microbial processes. , 2002, Biochimica et biophysica acta.

[64]  Valerie Daggett,et al.  The molecular mechanism of stabilization of proteins by TMAO and its ability to counteract the effects of urea. , 2002, Journal of the American Chemical Society.

[65]  C A Royer,et al.  Pressure provides new insights into protein folding, dynamics and structure. , 2001, Trends in biochemical sciences.

[66]  H. Geyer,et al.  Measurement of densities and excess molar volumes for (1,2-propanediol, or 1,2-butanediol + water) at the temperatures (288.15, 298.15, and 308.15) K and at the pressures (0.1, 20, 40, and 60) MPa , 2001 .

[67]  V. Uversky,et al.  Effect of environmental factors on the kinetics of insulin fibril formation: elucidation of the molecular mechanism. , 2001, Biochemistry.

[68]  C. Royer,et al.  Volume, expansivity and isothermal compressibility changes associated with temperature and pressure unfolding of Staphylococcal nuclease. , 2001, Journal of molecular biology.

[69]  Fumio Hirata,et al.  Potentials of mean force of simple ions in ambient aqueous solution. I. Three-dimensional reference interaction site model approach , 2000 .

[70]  Fumio Hirata,et al.  Potentials of mean force of simple ions in ambient aqueous solution. II. Solvation structure from the three-dimensional reference interaction site model approach, and comparison with simulations , 2000 .

[71]  M. Record,et al.  Vapor pressure osmometry studies of osmolyte-protein interactions: implications for the action of osmoprotectants in vivo and for the interpretation of "osmotic stress" experiments in vitro. , 2000, Biochemistry.

[72]  P. Yancey,et al.  Trimethylamine oxide stabilizes teleost and mammalian lactate dehydrogenases against inactivation by hydrostatic pressure and trypsinolysis. , 1999, The Journal of experimental biology.

[73]  Fumio Hirata,et al.  Solution of three‐dimensional reference interaction site model and hypernetted chain equations for simple point charge water by modified method of direct inversion in iterative subspace , 1999 .

[74]  Fumio Hirata,et al.  Self-consistent description of a metal–water interface by the Kohn–Sham density functional theory and the three-dimensional reference interaction site model , 1999 .

[75]  K. Heremans,et al.  Pressure effect on the temperature-induced unfolding and tendency to aggregate of myoglobin. , 1999, Biochemistry.

[76]  J. Nørskov,et al.  Improved adsorption energetics within density-functional theory using revised Perdew-Burke-Ernzerhof functionals , 1999 .

[77]  F. Hirata,et al.  Three-dimensional density profiles of water in contact with a solute of arbitrary shape: a RISM approach , 1998 .

[78]  J. Tomasi,et al.  Ab initio study of ionic solutions by a polarizable continuum dielectric model , 1998 .

[79]  S. Goedecker,et al.  Relativistic separable dual-space Gaussian pseudopotentials from H to Rn , 1998, cond-mat/9803286.

[80]  William D. Grant,et al.  Extremophiles : microbial life in extreme environments , 1998 .

[81]  Benoît Roux,et al.  An Integral Equation To Describe the Solvation of Polar Molecules in Liquid Water , 1997 .

[82]  Berk Hess,et al.  LINCS: A linear constraint solver for molecular simulations , 1997, J. Comput. Chem..

[83]  Jacopo Tomasi,et al.  A new integral equation formalism for the polarizable continuum model: Theoretical background and applications to isotropic and anisotropic dielectrics , 1997 .

[84]  D. W. Bolen,et al.  A naturally occurring protective system in urea-rich cells: mechanism of osmolyte protection of proteins against urea denaturation. , 1997, Biochemistry.

[85]  N. Marzari,et al.  Maximally localized generalized Wannier functions for composite energy bands , 1997, cond-mat/9707145.

[86]  Jacopo Tomasi,et al.  Continuum solvation models: A new approach to the problem of solute’s charge distribution and cavity boundaries , 1997 .

[87]  S. Prusiner,et al.  Chemical chaperones interfere with the formation of scrapie prion protein. , 1996, The EMBO journal.

[88]  K Schulten,et al.  VMD: visual molecular dynamics. , 1996, Journal of molecular graphics.

[89]  M. Teter,et al.  Separable dual-space Gaussian pseudopotentials. , 1995, Physical review. B, Condensed matter.

[90]  T. Darden,et al.  A smooth particle mesh Ewald method , 1995 .

[91]  Jean-Philippe Blaudeau,et al.  Extension of Gaussian-2 (G2) theory to molecules containing third-row atoms K and Ca , 1995 .

[92]  Jorge Nocedal,et al.  A Limited Memory Algorithm for Bound Constrained Optimization , 1995, SIAM J. Sci. Comput..

[93]  T. Lin,et al.  Why do some organisms use a urea-methylamine mixture as osmolyte? Thermodynamic compensation of urea and trimethylamine N-oxide interactions with protein. , 1994, Biochemistry.

[94]  B. Montgomery Pettitt,et al.  A site-site theory for finite concentration saline solutions , 1992 .

[95]  P. Kollman,et al.  Settle: An analytical version of the SHAKE and RATTLE algorithm for rigid water models , 1992 .

[96]  B. Montgomery Pettitt,et al.  A dielectrically consistent interaction site theory for solvent—electrolyte mixtures , 1992 .

[97]  C. Breneman,et al.  Determining atom‐centered monopoles from molecular electrostatic potentials. The need for high sampling density in formamide conformational analysis , 1990 .

[98]  A. Becke,et al.  Density-functional exchange-energy approximation with correct asymptotic behavior. , 1988, Physical review. A, General physics.

[99]  Parr,et al.  Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. , 1988, Physical review. B, Condensed matter.

[100]  David Chandler,et al.  Density functional theory of nonuniform polyatomic systems. I. General formulation , 1986 .

[101]  David Chandler,et al.  Density functional theory of nonuniform polyatomic systems. II: Rational closures for integral equations , 1986 .

[102]  M. E. Clark,et al.  Living with water stress: evolution of osmolyte systems. , 1982, Science.

[103]  P. Dierckx A Fast Algorithm for Smoothing Data on a Rectangular Grid while Using Spline Functions , 1982 .

[104]  M. Parrinello,et al.  Polymorphic transitions in single crystals: A new molecular dynamics method , 1981 .

[105]  A. D. McLean,et al.  Contracted Gaussian basis sets for molecular calculations. I. Second row atoms, Z=11–18 , 1980 .

[106]  J. Pople,et al.  Self‐consistent molecular orbital methods. XX. A basis set for correlated wave functions , 1980 .

[107]  P. Dierckx An algorithm for smoothing, differentiation and integration of experimental data using spline functions , 1975 .

[108]  K. Ng Hypernetted chain solutions for the classical one‐component plasma up to Γ=7000 , 1974 .

[109]  David Chandler,et al.  Optimized Cluster Expansions for Classical Fluids. II. Theory of Molecular Liquids , 1972 .

[110]  J. Kirkwood,et al.  The Statistical Mechanical Theory of Solutions. I , 1951 .