Brownian dynamics simulation of protein solutions: Structural and dynamical properties

Biophysical Journal

Volumn 99, Issue 11, 2010, Pages 3782-3791

  Mereghetti, Paolo ^a,b   Gabdoulline, Razif R ^c   Wade, Rebecca C ^a  

^a HEIDELBERG INSTITUTE FOR THEORETICAL STUDIES   (Germany)

^b UNIVERSITY OF HEIDELBERG   (Germany)

^c BIOBASE GMBH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 78649859456     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2010.10.035     Document Type: Article

References (72)

1. Minton, A. P. 2001. The influence of macromolecular crowding and macromolecular confinement on biochemical reactions in physiological media. J. Biol. Chem. 276:10577-10580.
2. Ellis, R. J. 2001. Macromolecular crowding: obvious but underappreciated. Trends Biochem. Sci. 26:597-604.
3. Homouz, D., L. Stagg, M. S. Cheung. 2009. Macromolecular crowding modulates folding mechanism of α/β protein apoflavodoxin. Biophys. J. 96:671-680.
4. Zhou, H.-X., G. Rivas, and A. P. Minton. 2008. Macromolecular crowding and confinement: biochemical, biophysical, and potential physiological consequences. Annu. Rev. Biophys. 37:375-397.
5. Kim, J. S., and A. Yethiraj. 2009. Effect of macromolecular crowding on reaction rates: a computational and theoretical study. Biophys. J. 96:1333-1340.
6. Batra, J., K. Xu, H. X. Zhou. 2009. Effect of macromolecular crowding on protein binding stability: modest stabilization and significant biological consequences. Biophys. J. 97:906-911.
7. Mittal, J., and R. B. Best. 2010. Dependence of protein folding stability and dynamics on the density and composition of macromolecular crowders. Biophys. J. 98:315-320.
8. Huppa, J. B., M. Axmann, M. M. Davis. 2010. TCR-peptide-MHC interactions in situ show accelerated kinetics and increased affinity. Nature. 463:963-967.
9. Batra, J., K. Xu, and H.-X. Zhou. 2009. Nonadditive effects of mixed crowding on protein stability. Proteins. 77:133-138.
10. Elcock, A. H., D. Sept, and J. A. McCammon. 2001. Computer simulation of protein-protein interactions. J. Phys. Chem. B. 105:1504-1518. (Pubitemid 32252337)
11. McGuffee, S. R., and A. H. Elcock. 2006. Atomically detailed simulations of concentrated protein solutions: the effects of salt, pH, point mutations, and protein concentration in simulations of 1000-molecule systems. J.Am. Chem. Soc. 128:12098-12110.
12. Klein, M. L., and W. Shinoda. 2008. Large-scale molecular dynamics simulations of self-assembling systems. Science. 321:798-800.
13. McGuffee, S. R., and A. H. Elcock. 2010. Diffusion, crowding & protein stability in a dynamic molecular model of the bacterial cytoplasm. PLOS Comput. Biol. 6:e1000694.
14. Gabdoulline, R. R., and R. C. Wade. 1997. Simulation of the diffusional association of barnase and barstar. Biophys. J. 72:1917-1929.
15. Elcock, A. H. 2010. Models of macromolecular crowding effects and the need for quantitative comparisons with experiment. Curr. Opin. Struct. Biol. 20:196-206.
16. Gabdoulline, R. R., and R. C. Wade. 2009. On the contributions of diffusion and thermal activation to electron transfer between Phormidium laminosum plastocyanin and cytochrome f: Brownian dynamics simulations with explicit modeling of nonpolar desolvation interactions and electron transfer events. J. Am. Chem. Soc. 131:9230-9238.
17. Gabdoulline, R. R., and R. C. Wade. 1996. Effective charges for macro-molecules in solvent. J. Phys. Chem. 100:3868-3878.
18. Elcock, A. H., R. R. Gabdoulline, J. A. McCammon. 1999. Computer simulation of protein-protein association kinetics: acetyl-cholinesterase- fasciculin. J. Mol. Biol. 291:149-162.
19. Gabdoulline, R. R., and R. C. Wade. 1998. Brownian dynamics simulation of protein-protein diffusional encounter. Methods. 14:329-341.
20. Madura, J. D., J. M. Briggs, J. A. McCammon. 1995. Electrostatics and diffusion of molecules in solution: simulations with the University of Houston Brownian Dynamics program. Comput. Phys. Commun. 91:57-95.
21. McMillan, W. G., and J. E. Mayer. 1945. The statistical thermodynamics of multicomponent systems. J. Chem. Phys. 13:276-305.
22. Velev, O. D., E. W. Kaler, and A. M. Lenhoff. 1998. Protein interactions in solution characterized by light and neutron scattering: comparison of lysozyme and chymotrypsinogen. Biophys. J. 75:2682-2697.
23. Zimm, B. H. 1948. The scattering of light and the radial distribution function of high polymer solutions. J. Chem. Phys. 16:1093-1099.
24. Asthagiri, D., A. Paliwal, M. E. Paulaitis. 2005. A consistent experimental and modeling approach to light-scattering studies of protein-protein interactions in solution. Biophys. J. 88:3300-3309.
25. Hill, T. L. 1986. An Introduction to Statistical Thermodynamics. Dover, Mineola, NY.
26. Allen, M. P., and D. J. Tildesley. 1989. Computer Simulations of Liquids. Oxford University Press, New York.
27. Han, J., and J. Herzfeld. 1993. Macromolecular diffusion in crowded solutions. Biophys. J. 65:1155-1161.
28. Reiss, H., H. L. Frisch, and J. L. Lebowitz. 1959. Statistical mechanics of rigid spheres. J. Chem. Phys. 31:369-380.
29. Tokuyama, M., and I. Oppenheim, I. 1994. Dynamics of hard-sphere suspensions. Phys. Rev. E. 50:R16-R19.
30. Berman, H. M., J. Westbrook, P. E. Bourne. 2000. The Protein DataBank. Nucleic Acids Res. 28:235-242.
31. Wilson, K. P., B. A. Malcolm, and B. W. Matthews. 1992. Structural and thermodynamic analysis of compensating mutations within the core of chicken egg white lysozyme. J. Biol. Chem. 267:10842-10849.
32. Lubkowski, J., and A. Wlodawer. 1999. Decamers observed in the crystals of bovine pancreatic trypsin inhibitor. Acta Crystallogr. D Biol. Crystallogr. 55:335-337.
33. Eriksson, A. E., W. A. Baase, and B. W. Matthews. 1993. Similar hydrophobic replacements of Leu99 and Phe153 within the core of T4 lysozyme have different structural and thermodynamic consequences. J. Mol. Biol. 229:747-769.
34. Gordon, J. C., J. B. Myers, A. Onufriev. 2005. HPP: a server for estimating pKas and adding missing hydrogens to macromolecules. Nucleic Acids Res. 33:368-371.
35. Abe, Y., T. Ueda, T. Imoto. 1995. Effect of salt concentration on the pKa of acidic residues in lysozyme. J. Biochem. 118:946-952.
36. Demchuk, E., and R. C. Wade. 1996. Improving the continuum dielectric approach to calculating pKas of ionizable groups in proteins. J. Phys. Chem. 100:17373-17387.
37. Kuhn, B., P. A. Kollman, and M. Stahl. 2004. Prediction of pKa shifts in proteins using a combination of molecular mechanical and continuum solvent calculations. J. Comput. Chem. 25:1865-1872.
38. Kuehner, D. E., J. Engmann, J. M. Prausnitz. 1999. Lysozyme net charge and ion binding in concentrated aqueous electrolyte solutions. J. Phys. Chem. B. 103:1368-1374.
39. Jorgensen, W. L., and J. Tirado-Rives. 1988. The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin. J. Am. Chem. Soc. 110:1657-1666.
40. Sali, A., and T. L. Blundell. 1993. Comparative protein modeling by satisfaction of spatial restraints. J. Mol. Biol. 234:779-815.
41. McQuarrie, D. A. 1976. Statistical Mechanics. Harper and Row, New York.
42. Neal, B. L., D. Asthagiri, and A. M. Lenhoff. 1998. Molecular origins of osmotic second virial coefficients of proteins. Biophys. J. 75:2469-2477.
43. Elcock, A. H., and J. A. McCammon. 2001. Calculation of weak protein-protein interactions: the pH dependence of the second virial coefficient. Biophys. J. 80:613-625.
44. Carlsson, F., M. Malmsten, and P. Linse. 2001. Monte Carlo simulations of lysozyme self-association in aqueous solution. J. Phys. Chem. B. 105:12189-12195.
45. Lund, M., and B. Jonsson. 2003. A mesoscopic model for protein-protein interactions in solution. Biophys. J. 85:2940-2947.
46. Teraoka, I. 2002. Polymer Solutions: An Introduction to Physical Properties. Wiley, New York.
47. Farnum, M., and C. Zukoski. 1999. Effect of glycerol on the interactions and solubility of bovine pancreatic trypsin inhibitor. Biophys. J. 76:2716-2726.
48. Appavou, M. S., G. Gibrat, and M.-C. Bellissent-Funel. 2009. Temperature dependence on structure and dynamics of Bovine Pancreatic Trypsin Inhibitor (BPTI): a neutron scattering study. Biochim. Biophys. Acta. 1794:1398-1406.
49. Chang, R. C., D. Asthagiri, and A. M. Lenhoff. 2000. Measured and calculated effects of mutations in bacteriophage T4 lysozyme on interactions in solution. Proteins. 41:123-132.
50. Stradner, A., F. Cardinaux, and P. Schurtenberger. 2006. A small-angle scattering study on equilibrium clusters in lysozyme solutions. J. Phys. Chem. B. 110:21222-21231.
51. Shukla, A., E. Mylonas, D. I. Svergun. 2008. Absence of equilibrium cluster phase in concentrated lysozyme solutions. Proc. Natl. Acad. Sci. USA. 105:5075-5080.
52. Porcar, L., P. Falus, Y. Liu. 2009. Formation ofthe dynamic clusters in concentrated lysozyme protein solutions. J. Phys. Chem. Lett. 1: 126-129.
53. Price, W. S., F. Tsuchiya, and Y. Arata. 1999. Lysozyme aggregation and solution properties studied using PGSE NMR diffusion measurements. J. Am. Chem. Soc. 121:11503-11512.
54. Gallagher, W. H., and C. K. Woodward. 1989. The concentration dependence of the diffusion coefficient for bovine pancreatic trypsin inhibitor: a dynamic light scattering study of a small protein. Biopolymers. 28:2001-2024.
55. Veesler, S., S. Lafont, R. Boistelle. 1996. Prenucleation, crystalgrowth and polymorphism of some proteins. J. Cryst. Growth. 168:124-129.
56. Lafont, S., S. Veesler, R. Boistelle. 1997. Comparison of solubilities and molecular interactions of BPTI molecules giving different polymorphs. J. Cryst. Growth. 173:132-140.
57. Hamiaux, C., J. Pérez, P. Vachette. 2000. The BPTI decamer observed in acidic pH crystal forms pre-exists as a stable species in solution. J. Mol. Biol. 297:697-712.
58. Grouazel, S., F. Bonneté, S. Veesler. 2006. Exploring bovine pancreatic trypsin inhibitor phase transitions. J. Phys. Chem. B. 110:19664-19670.
59. Ilyina, E., V. Roongta, K. H. Mayo. 1997. A pulsed-field gradient NMR study of bovine pancreatic trypsin inhibitor self-association. Biochemistry. 36:3383-3388.
60. Hamiaux, C., T. Prangé, S. Veesler. 1999. The decameric structure of bovine pancreatic trypsin inhibitor (BPTI) crystallized from thiocy-anate at 2.7 Å resolution. Acta Crystallogr. D Biol. Crystallogr. 55:103-113.
61. Gottschalk, M., and B. Halle. 2003. Self-association of lysozyme as seen by magnetic relaxation dispersion. J. Phys. Chem. B. 107:7914-7922.
62. Deisenhofer, J., and W. Steigemann. 1975. Crystallographic refinement of the structure of bovine pancreatic trypsin inhibitor at 1.5 A resolution. Acta Crystallogr. B. 31:238-250.
63. Wlodawer, A., J. Walter, L. Sjölin. 1984. Structure of bovine pancreatic trypsin inhibitor. Results of joint neutron and x-ray refinement of crystal form II. J. Mol. Biol. 180:301-329.
64. Tanaka, S., M. Ataka, S. Veesler. 2002. pH-dependent oligomerization of BPTI in undersaturated and supersaturated solutions studied by dynamic light scattering. J. Cryst. Growth. 237:289-294.
65. Vekilov, P. G., B. R. Monaco, F. Rosenberger. 1996. Repartitioning of NaCl and protein impurities in lysozyme crystallization. Acta Crystallogr. D Biol. Crystallogr. 52:785-798.
66. Thomas, B. R., P. G. Vekilov, and F. Rosenberger. 1998. Effects of microheterogeneity in hen egg-white lysozyme crystallization. Acta Crystallogr. D Biol. Crystallogr. 54:226-236.
67. Forsythe, E. L., A. Nadarajah, and M. L. Pusey. 1999. Growth of (101) faces of tetragonal lysozyme crystals: measured growth-rate trends. Acta Crystallogr. D Biol. Crystallogr. 55:1005-1011.
68. Zhang, J., and X. Y. Liu. 2003. Effect ofprotein-protein interactions on protein aggregation kinetics. J. Chem. Phys. 119:10972-10976.
69. Makhatadze, G. I., K. S. Kim, P. L. Privalov. 1993. Thermodynamics of BPTI folding. Protein Sci. 2:2028-2036.
70. Antosiewicz, J., and J. A. McCammon. 1995. Electrostatic and hydro-dynamic orientational steering effects in enzyme-substrate association. Biophys. J. 69:57-65.
71. Wieczorek, G., and P. Zielenkiewicz. 2008. Inluence of macromolecular crowding on protein-protein association rates - a Brownian dynamics study. Biophys. J. 95:5030-5036.
72. Li, X., I. H. Moal, and P. A. Bates. 2010. Detection and refinement of encounter complexes for protein-protein docking: taking account of macromolecular crowding. Proteins: Struct. Funct. Bioinform. 78:3189-3196.