Analysis of biomolecular solvation sites by 3D-RISM theory

Journal of Physical Chemistry B

Volumn 117, Issue 22, 2013, Pages 6718-6723

  Sindhikara, Daniel J ^a   Hirata, Fumio ^a  

^a RITSUMEIKAN UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

SOLVENTS;

ACTIVE SITE; ANALYSIS METHOD; BIO-MOLECULAR; HIV-1 PROTEASE; SOLVATION FREE ENERGIES; THERMODYNAMIC DATA; VIRTUAL SCREENING; VISUAL ANALYSIS;

SOLVATION;

EID: 84879163438     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp4046116     Document Type: Article

References (44)

1. Lazaridis, T. Inhomogeneous Fluid Approach to Solvation Thermodynamics. 1. Theory J. Phys. Chem. B 1998, 102, 3531-3541
2. Lazaridis, T. Inhomogeneous Fluid Approach to Solvation Thermodynamics. 2. Applications to Simple Fluids J. Phys. Chem. B 1998, 102, 3542-3550
3. Young, T. T.; Abel, R. R.; Kim, B. B.; Berne, B. J. B.; Friesner, R. A. R. Motifs for Molecular Recognition Exploiting Hydrophobic Enclosure in Protein-Ligand Binding Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 808-813
4. Abel, R.; Young, T.; Farid, R.; Berne, B. J.; Friesner, R. A. Role of the Active-Site Solvent in the Thermodynamics of Factor Xa Ligand Binding J. Am. Chem. Soc. 2008, 130, 2817-2831
5. Nguyen, C. N.; Kurtzman Young, T.; Gilson, M. K. Grid Inhomogeneous Solvation Theory: Hydration Structure and Thermodynamics of the Miniature Receptor Cucurbit[7]Uril J. Chem. Phys. 2012, 137, 044101-044118
6. Deng, Y.; Roux, B. Computation of Binding Free Energy with Molecular Dynamics and Grand Canonical Monte Carlo Simulations J. Chem. Phys. 2008, 128, 115103-115111
7. Michel, J.; Essex, J. W. Prediction of Protein-Ligand Binding Affinity by Free Energy Simulations: Assumptions, Pitfalls and Expectations J. Comput.-Aided Mol. Des. 2010, 24, 639-658
8. Luccarelli, J.; Michel, J.; Tirado-Rives, J.; Jorgensen, W. L. Effects of Water Placement on Predictions of Binding Affinities for p38α MAP Kinase Inhibitors J. Chem. Theory Comput. 2010, 6, 3850-3856
9. Mobley, D. L. Let's Get Honest About Sampling J. Comput.-Aided Mol. Des. 2012, 26, 93-95
10. Beglov, D.; Roux, B. An Integral Equation to Describe the Solvation of Polar Molecules in Liquid Water J. Phys. Chem. B 1997, 101, 7821-7826
11. Kovalenko, A.; Hirata, F. Three-Dimensional Density Profiles of Water in Contact with a Solute of Arbitrary Shape: a RISM Approach Chem. Phys. Lett. 1998, 290, 237-244
12. Imai, T.; Hiraoka, R.; Kovalenko, A.; Hirata, F. Water Molecules in a Protein Cavity Detected by a Statistical-Mechanical Theory J. Am. Chem. Soc. 2005, 127, 15334-15335
13. Imai, T.; Hiraoka, R.; Kovalenko, A.; Hirata, F. Locating Missing Water Molecules in Protein Cavities by the Three-Dimensional Reference Interaction Site Model Theory of Molecular Solvation Proteins 2006, 66, 804-813
14. Yokogawa, D.; Sato, H.; Sakaki, S. The Position of Water Molecules in Bacteriorhodopsin: a Three-Dimensional Distribution Function Study Biophys. J. 2009, 147, 112-116
15. Sindhikara, D. J.; Yoshida, N.; Hirata, F. Placevent: an Algorithm for Prediction of Explicit Solvent Atom Distribution-Application to HIV-1 Protease and F-ATP Synthase J. Comput. Chem. 2012, 33, 1536-1543
16. Stumpe, M. C.; Blinov, N.; Wishart, D.; Kovalenko, A.; Pande, V. S. Calculation of Local Water Densities in Biological Systems: a Comparison of Molecular Dynamics Simulations and the 3D-RISM-KH Molecular Theory of Solvation J. Phys. Chem. B 2010, 115, 319-328
17. Watanabe, H. C.; Welke, K.; Sindhikara, D. J.; Hegemann, P.; Elstner, M. Towards an Understanding of Channelrhodopsin Function: Simulations Lead to Novel Insights of the Channel Mechanism J. Mol. Biol. 2013, 425, 1795-1814
18. Phongphanphanee, S.; Yoshida, N.; Hirata, F. The Potential of Mean Force of Water and Ions in Aquaporin Channels Investigated by the 3D-RISM Method Biophys. J. 2009, 147, 107-111
19. Yoshida, N.; Phongphanphanee, S.; Maruyama, Y.; Imai, T.; Hirata, F. Selective Ion-Binding by Protein Probed with the 3D-RISM Theory J. Am. Chem. Soc. 2006, 128, 12042-12043
20. Sindhikara, D. J.; Yoshida, N.; Kataoka, M.; Hirata, F. Solvent Penetration in Photoactive Yellow Protein R52Q Mutant: a Theoretical Study J. Mol. Liq. 2011, 164, 120-122
21. Palmer, D. S.; Frolov, A. I.; Ratkova, E. L.; Fedorov, M. V. Towards a Universal Method for Calculating Hydration Free Energies: a 3D Reference Interaction Site Model with Partial Molar Volume Correction J. Phys.: Condens. Matter 2010, 22, 492101
22. Imai, T.; Oda, K.; Kovalenko, A.; Hirata, F.; Kidera, A. Ligand Mapping on Protein Surfaces by the 3D-RISM Theory: Toward Computational Fragment-Based Drug Design J. Am. Chem. Soc. 2009, 131, 12430-12440
23. Imai, T.; Miyashita, N.; Sugita, Y.; Kovalenko, A.; Hirata, F.; Kidera, A. Functionality Mapping on Internal Surfaces of Multidrug Transporter AcrB Based on Molecular Theory of Solvation: Implications for Drug Efflux Pathway J. Phys. Chem. B 2011, 115, 8288-8295
24. Nikolic, D.; Blinov, N.; Wishart, D. S.; Kovalenko, A. 3D-RISM-Dock: a New Fragment-Based Drug Design Protocol. J. Chem. Theory Comput. 2012, not supplied.
25. Kiyota, Y.; Yoshida, N.; Hirata, F. A New Approach for Investigating the Molecular Recognition of Protein: Toward Structure-Based Drug Design Based on the 3D-RISM Theory J. Chem. Theory Comput. 2011, 7, 3803-3815
26. Gusarov, S.; Pujari, B. S.; Kovalenko, A. Efficient Treatment of Solvation Shells in 3D Molecular Theory of Solvation J. Comput. Chem. 2012, 33, 1478-1494
27. Maruyama, Y.; Hirata, F. Modified Anderson Method for Accelerating 3D-RISM Calculations Using Graphics Processing Unit J. Chem. Theory Comput. 2012, 8, 3015-3021
28. Hirano, K.; Yokogawa, D.; Sato, H.; Sakaki, S. An Analysis of 3D Solvation Structure in Biomolecules: Application to Coiled Coil Serine and Bacteriorhodopsin J. Phys. Chem. B 2010, 114, 7935-7941
29. Wodak, S. J.; Janin, J. Computer Analysis of Protein-Protein Interaction J. Mol. Biol. 1978, 124, 323-342
30. Mitchell, J. C. Sampling Rotation Groups by Successive Orthogonal Images SIAM J. Sci. Comput. 2008, 30, 525-547
31. Yershova, A.; Jain, S.; LaValle, S. M.; Mitchell, J. C. Generating Uniform Incremental Grids on SO(3) Using the Hopf Fibration Int. J. Robot. Res. 2010, 29, 801-812
32. Hirata, F. In Molecular Theory of Solvation; Fumio, H., Ed.; Kluwer Academic Publishers: Dordrecht, 2003.
33. Imai, T.; Kovalenko, A.; Hirata, F. Partial Molar Volume of Proteins Studied by the Three-Dimensional Reference Interaction Site Model Theory J. Phys. Chem. B 2005, 109, 6658-6665
34. Lazaridis, T.; Karplus, M. Orientational Correlations and Entropy in Liquid Water J. Chem. Phys. 1996, 105, 4294-4316
35. Case, D. A.; Darden, T. A.; Cheatham, T. E., III; Simmerling, C. L.; Wang, J.; Duke, R. E.; Luo, R.; Walker, R. C.; Zhang, W.; Merz, K. M.; et al. AMBER 12; University of California: CA, 2012.
36. Adachi, M.; Ohhara, T.; Kurihara, K.; Tamada, T.; Honjo, E.; Okazaki, N.; Arai, S.; Shoyama, Y.; Kimura, K.; Matsumura, H. Structure of HIV-1 Protease in Complex with Potent Inhibitor KNI-272 Determined by High-Resolution X-Ray and Neutron Crystallography Proc. Natl. Acad. Sci. U.S.A. 2009, 106, 4641-4646
37. Hornak, V.; Abel, R.; Okur, A.; Strockbine, B.; Roitberg, A.; Simmerling, C. Comparison of Multiple Amber Force Fields and Development of Improved Protein Backbone Parameters J. Comput. Chem. 2006, 65, 712-725
38. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Scalmani, G.; Barone, V.; Mennucci, B.; Petersson, G. A.; et al. Gaussian 09; Gaussian, Inc.: Wallingford, CT, 2009; Vol. 2, p 4.
39. Wang, J.; Wolf, R. M.; Caldwell, J. W.; Kollman, P. A.; Case, D. A. Development and Testing of a General Amber Force Field J. Comput. Chem. 2004, 25, 1157-1174
40. Word, J. M.; Lovell, S. C.; Richardson, J. S.; Richardson, D. C. Asparagine and Glutamine: Using Hydrogen Atom Contacts in the Choice of Side-Chain Amide Orientation J. Mol. Biol. 1999, 285, 1735-1747
41. Dupradeau, F.-Y.; Pigache, A.; Zaffran, T.; Savineau, C.; Lelong, R.; Grivel, N.; Lelong, D.; Rosanski, W.; Cieplak, P. The R.E.D. Tools: Advances in RESP and ESP Charge Derivation and Force Field Library Building Phys. Chem. Chem. Phys. 2010, 12, 7821
42. Luchko, T.; Gusarov, S.; Roe, D. R.; Simmerling, C.; Case, D. A.; Tuszynski, J.; Kovalenko, A. Three-Dimensional Molecular Theory of Solvation Coupled with Molecular Dynamics in Amber J. Chem. Theory Comput. 2010, 6, 607-624
43. Li, Z.; Lazaridis, T. Thermodynamic Contributions of the Ordered Water Molecule in HIV-1 Protease J. Am. Chem. Soc. 2003, 125, 6636-6637
44. Baldwin, E. T.; Bhat, T. N.; Gulnik, S.; Liu, B.; Topol, I. A.; Kiso, Y.; Mimoto, T.; Mitsuya, H.; Erickson, J. W. Structure of HIV-1 Protease with KNI-272, a Tight-Binding Transition-State Analog Containing Allophenylnorstatine Biophys. J. 1995, 3, 581-590