Roles of boundary conditions in DNA simulations: Analysis of ion distributions with the finite-difference Poisson-Boltzmann method

Biophysical Journal

Volumn 97, Issue 2, 2009, Pages 554-562

  Ye, Xiang ^a   Cai, Qin ^a,b   Yang, Wei ^c,d   Luo, Ray ^a,b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b University of California at Irvine   (United States)

^c FLORIDA STATE UNIVERSITY   (United States)

^d NANKAI UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

COUNTERION; DNA BINDING PROTEIN; SODIUM CHLORIDE; TRANSFER RNA;

ARTICLE; CELL SURFACE; CELLULAR DISTRIBUTION; CONTROLLED STUDY; DIPOLE; ELECTRICITY; IONIC STRENGTH; MONTE CARLO METHOD; NUCLEIC ACID ANALYSIS; PERIODICITY; SEQUENCE ANALYSIS; SOLUTE; SOLVATION;

EID: 68949086437     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2009.05.012     Document Type: Article

References (43)

1. Neumann, M., O. Steinhauser, and G. S. Pawley. 1984. Consistent calculation of the static and frequency-dependent dielectric-constant in computer simulations. Mol. Phys. 52:97-113.
2. Brooks, C. L. 1987. The influence of long-range force truncation on the thermodynamics of aqueous ionic solutions. J. Chem. Phys. 86:5156-5162.
3. Madura, J. D., and B. M. Pettitt. 1988. Effects of truncating long-range interactions in aqueous ionic solution simulations. Chem. Phys. Lett. 150:105-108.
4. Pettitt, B. M., and P. J. Rossky. 1986. Alkali-halides in water - ion solvent correlations and ion-ion potentials of mean force at infinite dilution. J. Chem. Phys. 84:5836-5844.
5. Smith, P. E., and B. M. Pettitt. 1991. Peptides in ionic-solutions - a comparison of the Ewald and switching function techniques. J. Chem. Phys. 95:8430-8441.
6. Schreiber, H., and O. Steinhauser. 1992. Molecular-dynamics studies of solvated polypeptides - why the cutoff scheme does not work. Chem. Phys. 168:75-89.
7. Ewald, P. P. 1921. The calculation of optical and electrostatic grid potential. Ann. Phys. Berlin. 64:253-287.
8. Hockney, R. W., and J. W. Eastwood. 1981. Computer Simulation Using Particles. McGraw-Hill, New York.
9. Darden, T., D. York, and L. Pedersen. 1993. Particle mesh Ewald - an n.log(n) method for Ewald sums in large systems. J. Chem. Phys. 98:10089-10092.
10. Hünenberger, P. H. 2000. Optimal charge-shaping functions for the particle-particle-particle-mesh (P3M) method for computing electrostatic interactions in molecular simulations. J. Chem. Phys. 113:10464-10476.
11. Fox, T., and P. A. Kollman. 1996. The application of different solvation and electrostatic models in molecular dynamics simulations of ubiquitin: how well is the x-ray structure "maintained"? Proteins. 25:315-334.
12. Figueirido, F., G. S. Delbuono, and R. M. Levy. 1995. On finite-size effects in computer-simulations using the Ewald potential. J. Chem. Phys. 103:6133-6142.
13. Hünenberger, P. H., and J. A. McCammon. 1999. Ewald artifacts in computer simulations of ionic solvation and ion-ion interaction: a continuum electrostatics study. J. Chem. Phys. 110:1856-1872.
14. Hünenberger, P. H., and J. A. McCammon. 1999. Effect of artificial periodicity in simulations of biomolecules under Ewald boundary conditions: a continuum electrostatics study. Biophys. Chem. 78:69-88.
15. de Vries, A. H., I. Chandrasekhar, W. F. van Gunsteren, and P. H. Hünenberger. 2005. Molecular dynamics simulations of phospholipid bilayers: influence of artificial periodicity, system size, and simulation time. J. Phys. Chem. B. 109:11643-11652.
16. Kastenholz, M. A., and P. H. Hünenberger. 2006. Development of a lattice-sum method emulating nonperiodic boundary conditions for the treatment of electrostatic interactions in molecular simulations: a continuum- electrostatics study. J. Chem. Phys. 124:124106.
17. Kastenholz, M. A., and P. H. Hünenberger. 2004. Influence of artificial periodicity and ionic strength in molecular dynamics simulations of charged biomolecules employing lattice-sum methods. J. Phys. Chem. B. 108:774-788.
18. Bergdorf, M., C. Peter, and P. H. Hünenberger. 2003. Influence of cutoff truncation and artificial periodicity of electrostatic interactions in molecular simulations of solvated ions: a continuum electrostatics study. J. Chem. Phys. 119:9129-9144.
19. Luo, R., L. David, and M. K. Gilson. 2002. Accelerated Poisson-Boltzmann calculations for static and dynamic systems. J. Comput. Chem. 23:1244-1253.
20. Lu, Q., and R. Luo. 2003. A Poisson-Boltzmann dynamics method with nonperiodic boundary condition. J. Chem. Phys. 119:11035-11047.
21. Min, D. H., H. Z. Li, G. H. Li, B. A. Berg, M. O. Fenley, et al. 2008. Efficient sampling of ion motions in molecular dynamics simulations on DNA: variant Hamiltonian replica exchange method. Chem. Phys. Lett. 454:391-395.
22. Jayaram, B., S. Swaminathan, D. L. Beveridge, K. Sharp, and B. Honig. 1990. Monte-Carlo simulation studies on the structure of the counterion atmosphere of b-DNA - variations on the primitive dielectric model. Macromolecules. 23:3156-3165.
23. Hill, T. L. 1986. An Introduction to Statistical Thermo-Dynamics. Dover Publications, New York.
24. Sharp, K. A., and B. Honig. 1990. Calculating total electrostatic energies with the nonlinear Poisson-Boltzmann equation. J. Phys. Chem. 94:7684-7692.
25. Reiner, E. S., and C. J. Radke. 1990. Variational approach to the electrostatic free-energy in charged colloidal suspensions - general-theory for open systems. J. Chem. Soc., Faraday Trans. 86:3901-3912.
26. Nicholls, A., and B. Honig. 1991. A rapid finite-difference algorithm, utilizing successive over-relaxation to solve the Poisson-Boltzmann equation. J. Comput. Chem. 12:435-445.
27. Allen, M. P., and D. J. Tildesley. 1987. Computer Simulation of Liquids. Oxford University Press, New York.
28. Hockney, R. W., and J. W. Eastwood. 1981. Computer Simulation Using Particles. McGraw-Hill, New York.
29. Valleau, J. P., and L. K. Cohen. 1980. Primitive model electrolytes. 1. Grand canonical Monte-Carlo computations. J. Chem. Phys. 72:5935-5941.
30. Torrie, G. M., and J. P. Valleau. 1980. Electrical double-layers. 1. Monte-Carlo study of a uniformly charged surface. J. Chem. Phys. 73:5807-5816.
31. Fukunishi, H., O. Watanabe, and S. Takada. 2002. On the Hamiltonian replica exchange method for efficient sampling of biomolecular systems: application to protein structure prediction. J. Chem. Phys. 116:9058-9067.
32. Jang, S. M., S. Shin, and Y. Pak. 2003. Replica-exchange method using the generalized effective potential. Phys. Rev. Lett. 91:058305.
33. Kwak, W., and U. H. E. Hansmann. 2005. Efficient sampling of protein structures by model hopping. Phys. Rev. Lett. 95:138102.
34. Liu, P., X. H. Huang, R. H. Zhou, and B. J. Berne. 2006. Hydrophobic aided replica exchange: an efficient algorithm for protein folding in explicit solvent. J. Phys. Chem. B 36:19018-19022.
35. Liu, P., B. Kim, R. A. Friesner, and B. J. Berne. 2005. Replica exchange with solute tempering: a method for sampling biological systems in explicit water. Proc. Natl. Acad. Sci. USA. 102:13749-13754.
36. Sugita, Y., A. Kitao, and Y. Okamoto. 2000. Multidimensional replica-exchange method for free-energy calculations. J. Chem. Phys. 113:6042-6051.
37. Case, D. A., T. E. Cheatham, T. Darden, H. Gohlke, R. Luo, et al. 2005. The AMBER biomolecular simulation programs. J. Comput. Chem. 26:1668-1688.
38. Tan, C. H., L. J. Yang, and R. Luo. 2006. How well does Poisson-Boltzmann implicit solvent agree with explicit solvent? A quantitative analysis. J. Phys. Chem. B. 110:18680-18687.
39. Dong, F., M. Vijayakumar, and H. X. Zhou. 2003. Comparison of calculation and experiment implicates significant electrostatic contributions to the binding stability of barnase and barstar. Biophys. J. 85:49-60.
40. Talley, K., C. Ng, M. Shoppell, P. Kundrotas, and E. Alexov. 2008. On the electrostatic component of protein-protein binding free energy. PMC Biophys. 1:2. DOI: 10.1186/1757-5036-1-2.
41. Ponomarev, S. Y., K. M. Thayer, and D. L. Beveridge. 2004. Ion motions in molecular dynamics simulations on DNA. Proc. Natl. Acad. Sci. USA. 101:14771-14775.
42. Prabhu, N. V., M. Panda, Q. Y. Yang, and K. A. Sharp. 2008. Explicit ion, implicit water solvation for molecular dynamics of nucleic acids and highly charged molecules. J. Comput. Chem. 29:1113-1130.
43. Manning, G. S. 1969. Limiting laws and counterion condensation in polyelectrolyte solutions. I. Colligative properties. J. Chem. Phys. 51:924-933.