TRIFORCE: Tessellated Semianalytical Solvent Exposed Surface Areas and Derivatives

We present a new approach to the calculation of solvent-accessible surface areas of molecules with potential application to surface area based methods for determination of solvation free energies. As in traditional analytical and statistical approaches, this new algorithm, called TRIFORCE, reports both component areas and derivatives as a function of the atomic coordinates and radii. Unique to TRIFORCE are the rapid and scalable approaches for the determination of sphere intersection points and numerical estimation of the surface areas, derivatives, and other properties that can be associated with the surface area facets. The algorithm performs a special tessellation and semianalytical integration that uses a precomputed look-up table. This provides a simple way to balance numerical accuracy and memory usage. TRIFORCE calculates derivatives in the same manner, enabling application in force-dependent activities such as molecular geometry minimization. TRIFORCE is available free of charge for academic purposes as both a C++ library, which can be directly interfaced to existing molecular simulation packages, and a web-accessible application.

[1]  A. D. McLachlan,et al.  Solvation energy in protein folding and binding , 1986, Nature.

[2]  R Samudrala,et al.  Decoys ‘R’ Us: A database of incorrect conformations to improve protein structure prediction , 2000, Protein science : a publication of the Protein Society.

[3]  B. Lee,et al.  The interpretation of protein structures: estimation of static accessibility. , 1971, Journal of molecular biology.

[4]  G. Hummer,et al.  HYDROPHOBIC FORCE FIELD AS A MOLECULAR ALTERNATIVE TO SURFACE-AREA MODELS , 1999 .

[5]  Bernard R. Brooks,et al.  New spherical‐cutoff methods for long‐range forces in macromolecular simulation , 1994, J. Comput. Chem..

[6]  Robert B. Hermann,et al.  Theory of hydrophobic bonding. II. Correlation of hydrocarbon solubility in water with solvent cavity surface area , 1972 .

[7]  宁北芳,et al.  疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A , 2005 .

[8]  Ronald M. Levy,et al.  The SGB/NP hydration free energy model based on the surface generalized born solvent reaction field and novel nonpolar hydration free energy estimators , 2002, J. Comput. Chem..

[9]  Wolfgang Wenzel,et al.  Derivatives of molecular surface area and volume: Simple and exact analytical formulas , 2011, J. Comput. Chem..

[10]  Nathan A. Baker,et al.  Assessing implicit models for nonpolar mean solvation forces: the importance of dispersion and volume terms. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[11]  K. Sharp,et al.  Protein folding and association: Insights from the interfacial and thermodynamic properties of hydrocarbons , 1991, Proteins.

[12]  Modesto Orozco,et al.  A consensus view of protein dynamics , 2007, Proceedings of the National Academy of Sciences.

[13]  P. Kollman,et al.  Solvation Model Based on Weighted Solvent Accessible Surface Area , 2001 .

[14]  Ray Luo,et al.  Implicit nonpolar solvent models. , 2007, The journal of physical chemistry. B.

[15]  Akbar Nayeem,et al.  MSEED: A program for the rapid analytical determination of accessible surface areas and their derivatives , 1992 .

[16]  Emilio Gallicchio,et al.  The AGBNP2 Implicit Solvation Model. , 2009, Journal of chemical theory and computation.

[17]  J. Janin,et al.  Analytical approximation to the accessible surface area of proteins. , 1980, Proceedings of the National Academy of Sciences of the United States of America.

[18]  Gregory D. Hawkins,et al.  Parametrized Models of Aqueous Free Energies of Solvation Based on Pairwise Descreening of Solute Atomic Charges from a Dielectric Medium , 1996 .

[19]  Werner Braun,et al.  Exact and efficient analytical calculation of the accessible surface areas and their gradients for macromolecules , 1998 .

[20]  M. L. Connolly.  Analytical molecular surface calculation , 1983 .

[21]  R. Rosenfeld.  Nature , 2009, Otolaryngology--head and neck surgery : official journal of American Academy of Otolaryngology-Head and Neck Surgery.

[22]  Charles W. Kehoe,et al.  Modeling aqueous solvation with semi-explicit assembly , 2011, Proceedings of the National Academy of Sciences.

[23]  R. Levy,et al.  Enthalpy−Entropy and Cavity Decomposition of Alkane Hydration Free Energies: Numerical Results and Implications for Theories of Hydrophobic Solvation , 2000 .

[24]  A. Pohorille,et al.  An information theory model of hydrophobic interactions. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[25]  Shura Hayryan,et al.  A new analytical method for computing solvent‐accessible surface area of macromolecules and its gradients , 2005, J. Comput. Chem..

[26]  H. Uhlig.  The Solubilities of Gases and Surface Tension , 1937 .

[27]  T. Richmond,et al.  Solvent accessible surface area and excluded volume in proteins. Analytical equations for overlapping spheres and implications for the hydrophobic effect. , 1984, Journal of molecular biology.

[28]  W. C. Still,et al.  Approximate atomic surfaces from linear combinations of pairwise overlaps (LCPO) , 1999 .

[29]  M. Karplus,et al.  Effective energy function for proteins in solution , 1999, Proteins.

[30]  Charles W. Kehoe,et al.  Oil/water transfer is partly driven by molecular shape, not just size. , 2010, Journal of the American Chemical Society.

[31]  Michael Petukhov,et al.  Joint neighbors approximation of macromolecular solvent accessible surface area , 2007, J. Comput. Chem..

[32]  S. Sridharan,et al.  A rapid method for calculating derivatives of solvent accessible surface areas of molecules , 1995, J. Comput. Chem..

[33]  Donald G. Truhlar,et al.  PARAMETRIZED MODEL FOR AQUEOUS FREE ENERGIES OF SOLVATION USING GEOMETRY-DEPENDENT ATOMIC SURFACE TENSIONS WITH IMPLICIT ELECTROSTATICS , 1997 .