Incorporation of solvation effects into the fragment molecular orbital calculations with the Poisson–Boltzmann equation

We developed FMO-PB method, which incorporates solvation effects into the Fragment Molecular Orbital calculation with the Poisson–Boltzmann equation. This method retains good accuracy in energy calculations with reduced computational time. We calculated the solvation free energies for polyalanines, Alpha-1 peptide, tryptophan cage, and complex of estrogen receptor and 17β-estradiol to show the applicability of this method for practical systems. From the calculated results, it has been confirmed that the FMO-PB method is useful for large biomolecules in solution. We also discussed the electric charges which are used in solving the Poisson–Boltzmann equation.

[1]  Emil Alexov,et al.  Rapid grid‐based construction of the molecular surface and the use of induced surface charge to calculate reaction field energies: Applications to the molecular systems and geometric objects , 2002, J. Comput. Chem..

[2]  P. Kollman,et al.  Application of RESP charges to calculate conformational energies, hydrogen bond energies, and free energies of solvation , 1993 .

[3]  B. Honig,et al.  Accurate First Principles Calculation of Molecular Charge Distributions and Solvation Energies from Ab Initio Quantum Mechanics and Continuum Dielectric Theory , 1994 .

[4]  Zhihai Liu,et al.  Evaluation of the performance of four molecular docking programs on a diverse set of protein‐ligand complexes , 2010, J. Comput. Chem..

[5]  M. Gordon,et al.  A combined effective fragment potential-fragment molecular orbital method. I. The energy expression and initial applications. , 2009, The Journal of chemical physics.

[6]  Barry Honig,et al.  Extending the Applicability of the Nonlinear Poisson−Boltzmann Equation: Multiple Dielectric Constants and Multivalent Ions† , 2001 .

[7]  C. Cramer,et al.  A universal approach to solvation modeling. , 2008, Accounts of chemical research.

[8]  Hui Li,et al.  The polarizable continuum model (PCM) interfaced with the fragment molecular orbital method (FMO) , 2006, J. Comput. Chem..

[9]  Kenneth M. Merz,et al.  Fully Quantum Mechanical Description of Proteins in Solution. Combining Linear Scaling Quantum Mechanical Methodologies with the Poisson−Boltzmann Equation , 1999 .

[10]  S. L. Dixon,et al.  Semiempirical molecular orbital calculations with linear system size scaling , 1996 .

[11]  P. Kollman,et al.  An approach to computing electrostatic charges for molecules , 1984 .

[12]  Kaori Fukuzawa,et al.  Application of the fragment molecular orbital method for determination of atomic charges on polypeptides , 2007 .

[13]  Alan R. Katritzky,et al.  Reconsideration of solvent effects calculated by semiempirical quantum chemical methods , 1993, J. Comput. Chem..

[14]  Fumio Hirata,et al.  Molecular Theory of Solvation , 2004 .

[15]  A. Klamt,et al.  COSMO : a new approach to dielectric screening in solvents with explicit expressions for the screening energy and its gradient , 1993 .

[16]  U. Ryde,et al.  QM/MM-PBSA method to estimate free energies for reactions in proteins. , 2008, The journal of physical chemistry. B.

[17]  Ye Mei,et al.  A new quantum method for electrostatic solvation energy of protein. , 2006, The Journal of chemical physics.

[18]  Nathan A. Baker,et al.  Improving implicit solvent simulations: a Poisson-centric view. , 2005, Current opinion in structural biology.

[19]  Kaori Fukuzawa,et al.  Application of the fragment molecular orbital method for determination of atomic charges on polypeptides. II. Towards an improvement of force fields used for classical molecular dynamics simulations , 2009 .

[20]  K. Kitaura,et al.  Fragment molecular orbital method: an approximate computational method for large molecules , 1999 .

[21]  B. Honig,et al.  New Model for Calculation of Solvation Free Energies: Correction of Self-Consistent Reaction Field Continuum Dielectric Theory for Short-Range Hydrogen-Bonding Effects , 1996 .

[22]  J. Tomasi,et al.  Quantum mechanical continuum solvation models. , 2005, Chemical reviews.

[23]  P A Kollman,et al.  Continuum solvent studies of the stability of RNA hairpin loops and helices. , 1998, Journal of biomolecular structure & dynamics.

[24]  Hui Li,et al.  Energy gradients in combined fragment molecular orbital and polarizable continuum model (FMO/PCM) calculation , 2009, J. Comput. Chem..

[25]  P. Kollman,et al.  A well-behaved electrostatic potential-based method using charge restraints for deriving atomic char , 1993 .

[26]  P. Koehl.  Electrostatics calculations: latest methodological advances. , 2006, Current opinion in structural biology.

[27]  Richard A. Friesner,et al.  Quantum mechanical geometry optimization in solution using a finite element continuum electrostatics method , 1996 .

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

[29]  D. Eisenberg,et al.  Centrosymmetric bilayers in the 0.75 å resolution structure of a designed alpha‐helical peptide, D, L‐Alpha‐1 , 1999, Protein science : a publication of the Protein Society.

[30]  Yutaka Akiyama,et al.  Fragment molecular orbital method: application to polypeptides , 2000 .