Calculation of protein-ligand binding free energy by using a polarizable potential

Proceedings of the National Academy of Sciences of the United States of America

Volumn 105, Issue 17, 2008, Pages 6290-6295

  Jiao, Dian ^a   Golubkov, Pavel A ^a   Darden, Thomas A ^b   Ren, Pengyu ^a  

^a The University of Texas at Austin   (United States)

^b NATIONAL INSTITUTE OF ENVIRONMENTAL HEALTH SCIENCES   (United States)

Author keywords

Benzamidine; Force field; Molecular dynamics; Simulation; Trypsin

Indexed keywords

AMIDINE; BENZAMIDINE; DIAZAMIDINE; TRYPSIN; WATER; BENZAMIDINE DERIVATIVE; LIGAND; PROTEIN;

ARTICLE; CALCULATION; CHEMICAL STRUCTURE; ELECTRICITY; ENERGY; LIGAND BINDING; MOLECULAR DYNAMICS; POLARIZATION; PRIORITY JOURNAL; PROTEIN BINDING; SOLVATION; SUBSTITUTION REACTION; THERMODYNAMICS; CHEMISTRY; ENTROPY;

BENZAMIDINES; ELECTROSTATICS; ENTROPY; LIGANDS; MODELS, MOLECULAR; PROTEIN BINDING; PROTEINS; TRYPSIN; WATER;

EID: 44049091290     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0711686105     Document Type: Article

References (53)

1. Lamb ML, Jorgensen WL (1997) Computational approaches to molecular recognition. Curr Opin Chem Biol 1:449-457.
2. Kollman PA, et al. (2000) Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models. Acc Chem Res 33:889-897.
3. Brandsdal BO, et al. (2003) Free energy calculations and ligand binding. Protein Simul 66:123-158.
4. Jorgensen WL (2004) The many roles of computation in drug discovery. Science 303:1813-1818.
5. Gilson MK, Zhou HX (2007) Calculation of protein-ligand binding affinities. Annu Rev Biophys Biomol Struct 36:21-42.
6. Woo HJ, Roux B (2005) Calculation of absolute protein-ligand binding free energy from computer simulations. Proc Natl Acad Sci USA 102:6825-6830.
7. Burykin A, Schutz CN, Villa J, Warshel A (2002) Simulations of Ion current in realistic models of ion channels: The Kcsa potassium channel. Proteins 47:265-280.
8. Warshel A, Sharma PK, Kato M, Parson WW (2006) Modeling Electrostatic effects in proteins. Biochim Biophys Acta Proteins Proteom 1764:1647-1676.
9. Kato M, Warshel A (2005) Through the channel and around the channel: validating and comparing microscopic approaches for the evaluation of free energy profiles for ion penetration through ion channels. J Phys Chem B 109:19516-19522.
10. Lee FS, Chu ZT, Bolger MB, Warshel A (1992) Calculations of antibody Antigen interactions - Microscopic and semimicroscopic evaluation of the free-energies of binding of phosphorylcholine analogs to Mcpc603. Protein Eng 5:215-228.
11. Aqvist J, Medina C, Samuelsson JE (1994) New method for predicting binding-affinity in computer-aided drug design. Protein Eng 7:385-391.
12. Sham YY, Chu ZT, Tao H, Warshel A (2000) Examining methods for calculations of binding free energies: Lra, Lie, Pdld-Lra, and Pdld/S-Lra calculations of ligands binding to an Hiv protease. Proteins 39:393-407.
13. Warshel A, Kato M, Pisliakov AV (2007) Polarizable force fields: History, test cases, and prospects. J Chem Theory Comput 3:2034-2045.
14. Boresch S, Tettinger F, Leitgeb M, Karplus M (2003) Absolute binding free energies: A quantitative approach for their calculation. J Phys Chem B 107:9535-9551.
15. Deng YQ, Roux B (2006) Calculation of standard binding free energies: Aromatic molecules in the T4 lysozyme L99a mutant. J Chem Theory Comput 2:1255-1273.
16. Hermans J, Wang L (1997) Inclusion of loss of translational and rotational freedom in theoretical estimates of free energies of binding. Application to a complex of benzene and mutant T4 lysozyme. J Am Chem Soc 119:2707-2714.
17. Fujitani H, et al. (2005) Direct calculation of the binding free energies of Fkbp ligands. J Chem Phys 123:084108.
18. Wang JY, Deng YQ, Roux B (2006) Absolute binding free energy calculations using molecular dynamics simulations with restraining potentials. Biophys J 91:2798-2814.
19. Warshel A, Levitt M (1976) Theoretical studies of enzymic reactions - Dielectric, electrostatic and steric stabilization of carbonium-ion in reaction of lysozyme. J Mol Biol 103:227-249.
20. Warshel A, Sussman F, Hwang JK (1988) Evaluation of catalytic free-energies in genetically modified proteins. J Mol Biol 201:139-159.
21. Florian J, Goodman MF, Warshel A (2002) Theoretical Investigation of the binding free energies and key substrate-recognition components of the replication fidelity of human DNA polymerase beta. J Phys Chem B 106:5739-5753.
22. Ponder JW, Case DA (2003) Force fields for protein simulations. Adv Protein Chem 66:27-85.
23. Kato M, Braun-Sand S, Warshel A (2008) Computational and Structural Approaches to Drug Discovery:Ligand-Protein Interactions, eds Stroud R, Finer-Moore J (Royal Society of Chemistry, Cambridge, UK), pp 268-290.
24. Katz BA, et al. (2000) Structural basis for selectivity of a small molecule, S1-binding, submicromolar inhibitor of urokinase-type plasminogen activator. Chem Biol 7:299-312.
25. Katz BA, et al. (2001) A novel serine protease inhibition motif involving a multi-centered short hydrogen bonding network at the active site. J Mol Biol 307:1451-1486.
26. Mares-Guia M (1965) Studies on active center of trypsin - Binding of amidines and guanidines as models of substrate side chain. J Biol Chem 240:1579.
27. Schwarzl SM, Tschopp TB, Smith JC, Fischer S (2002) Can the calculation of ligand binding free energies be improved with continuum solvent electrostatics and an ideal-gas entropy correction? J Comput Chem 23:1143-1149.
28. Geerke DP, van Gunsteren WF (2007) Calculation of the free energy of polarization: Quantifying the effect of explicitly treating electronic polarization on the transferability of force-field parameters. J Phys Chem B 111:6425-6436.
29. Hensen C, et al. (2004) A combined Qm/Mm approach to protein-ligand interactions: Polarization effects of the Hiv-1 proteaseonselected high affinity inhibitors. J Med Chem 47:6673-6680.
30. Aqvist J (1996) Calculation of absolute binding free energies for charged ligands and effects of long-range electrostatic interactions. J Comput Chem 17:1587-1597.
31. Wang W, Wang J, Kollman PA (1999) What determines the van der Waals coefficient beta in the LIE (linear interaction energy) method to estimate binding free energies using molecular dynamics simulations? Proteins 34:395-402.
32. Leiros HKS, et al. (2004) Trypsin specificity as elucidated by lie calculations, x-ray structures, and association constant measurements. Protein Sci 13:1056-1070.
33. Grater F, Schwarzl SM, Dejaegere A, Fischer S, Smith JC (2005) Protein/ligand binding free energies calculated with quantum mechanics/molecular mechanics. J Phys Chem B 109:10474-10483.
34. Grossfield A, Ren PY, Ponder JW (2003) Ion solvation thermodynamics from simulation with a polarizable force field. J Am Chem Soc 125:15671-15682.
35. Ren PY, Ponder JW (2002) Consistent treatment of inter- and intramolecular polarization in molecular mechanics calculations. J Comput Chem 23:1497-1506.
36. Ren PY, Ponder JW (2003) Polarizable atomic multipole water model for molecular mechanics simulation. J Phys Chem B 107:5933-5947.
37. Halgren TA (1992) Representation of Van Der Waals (Vdw) interactions in molecular mechanics force fields: Potential form, combination rules, and Vdw parameters. J Am Chem Soc 114:7827-7843.
38. Allinger NL, Yuh YH, Lii J-H (1989) Molecular mechanics. The Mm3 force Field for hydrocarbons. J Am Chem Soc 111:8551-8566.
39. Ren PY, Ponder JW (2004) Temperature and pressure dependence of AMOEBA water model. J Phys Chem B 108:13427-13437.
40. 2+ solvation using polarizable atomic multipole potential. J Phys Chem B 110:18553-18559.
41. Piquemal JP, et al. (2006) Towards accurate solvation dynamics of divalent cations in water using the polarizable amoeba force field: From energetics to structure. J Chem Phys 125:054511.
42. Tuma L, Jenicek D, Jungwirth P (2005) Propensity of heavier halides for the water/vapor interface revisited using the amoeba force field. Chem Phys Lett 411:70-74.
43. Liang T, Walsh TR (2006) Molecular dynamics simulations of peptide carboxylate hydration. Phys Chem Chem Phys 8:4410-4419.
44. Liang T, Walsh TR (2007) Simulation of the hydration structure of glycyl-alanine. Mol Simul 33:337-342.
45. Jiang H, Jordan KD, Taylor CE (2007) Molecular dynamics simulations of methane hydrate using polarizable force fields. J Phys Chem B 111:6486-6492.
46. Ponder JW (2004) Tinker: Software Tools for Molecular Design (Washington Univ, Saint Louis, MO), Version 4.2. Available at: http://dasher.wustl.edu/ tinker/. Accessed on April 5, 2008.
47. Beutler TC, Mark AE, Vanschaik RC, Gerber PR, Vangunsteren WF (1994) Avoiding singularities and numerical instabilities in free-energy calculations based on mol simuls. Chem Phys Lett 222:529-539.
48. Case DA, et al. (2005) The amber biomolecular simulation programs. J Comput Chem 26:1668-1688.
49. Sagui C, Pedersen LG, Darden TA (2004) Towards an accurate representation of electrostatics in classical force fields: Efficient implementation of multipolar interactions in biomolecular simulations. J Chem Phys 120:73-87.
50. Hamelberg D, McCammon JA (2004) Standard free energy of releasing a localized water molecule from the binding pockets of proteins: Double-decoupling method. J Am Chem Soc 126:7683-7689.
51. Gilson MK, Given JA, Bush BL, McCammon JA (1997) The statistical- thermodynamic basis for computation of binding affinities: A critical review. Biophys J 72:1047-1069.
52. Bennett CH (1976) Efficient estimation of free-energy differences from monte-carlo data. J Comput Phys 22:245-268.
53. Maresguia M, Nelson DL, Rogana E (1977) Electronic effects in interaction of para-substituted benzamidines with trypsin - Involvement of pi-electronic density at central atom of substituent in binding. J Am Chem Soc 99:2331-2336.