Computational simulations of protein- protein and protein- nucleic acid association

Computational Protein-Protein Interactions

Volumn , Issue , 2009, Pages 109-128

  Pachov, Georgi V ^a   Gabdoulline, Razif R ^a,b   Wade, Rebecca C ^a  

^a EML Research gGmbH   (Germany)

^b UNIVERSITY OF HEIDELBERG   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 77954006075     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1201/9781420070071     Document Type: Chapter

References (86)

1. Allison, S. A., G. Ganti, and J. A. McCammon. 1985. Simulation of the diffusion-controlled reaction between superoxide and superoxide dismutase. I. Simple models. Biopolymers 24 (7):1323-1336.
2. Alsallaq, R., and H.-X. Zhou. 2007. Prediction of protein-protein association rates from a transition-state theory. Structure 15 (2):215-224.
3. Alsallaq, R., and H.-X. Zhou. 2008a. Electrostatic rate enhancement and transient complex of protein-protein association. Proteins 71 (1):320-335.
4. Alsallaq, R., and H.-X. Zhou. 2008b. Protein association with circular DNA: Rate enhancement by nonspecific binding. J Chem Phys 128 (11): 115108.
5. Altobelli, G., and S. Subramaniam. 2000. Kinetics of association of anti-lysozyme monoclonal antibody D44.1 and hen-egg lysozyme. Biophys J 79 (6):2954-2965.
6. Antosiewicz, J., J. M. Briggs, and J. A. McCammon. 1996. Orientational steering in enzymesubstrate association: Ionic strength dependence of hydrodynamic torque effects. Eur Biophys J 24 (3):137-141.
7. Arya, G., Q. Zhang, and T. Schlick. 2006. Flexible histone tails in a new mesoscopic oligonucleosome model. Biophys J 91 (1):133-150.
8. Bachut-Okrasinska, E., and J. M. Antosiewicz. 2007. Brownian dynamics simulations of binding mRNA cap analogues to eIF4E protein. J Phys Chem B 111 (45):13107-13115.
9. Berg, O. G., and P. H. von Hippel. 1985. Diffusion-controlled macromolecular interactions. Annu Rev Biophys Biophys Chem 14:131-160.
10. Brown, D. T., T. Izard, and T. Misteli. 2006. Mapping the interaction surface of linker histone H1(0) with the nucleosome of native chromatin in vivo. Nat Struct Mol Biol 13 (3):250-255.
11. Bui, J. M., and J. A. McCammon. 2006. Protein complex formation by acetylcholinesterase and the neurotoxin fasciculin-2 appears to involve an induced-fit mechanism. Proc Natl Acad Sci USA 103 (42):15451-15456.
12. Bui, J. M., Z. Radic, P. Taylor, and J. A. McCammon. 2006. Conformational transitions in protein-protein association: Binding of fasciculin-2 to acetylcholinesterase. Biophys J 90 (9):3280-3287.
13. Chebotareva, N. A. 2007. Effect of molecular crowding on the enzymes of glycogenolysis. Biochemistry (Mosc) 72 (13):1478-1490.
14. Cheng, Y., J. K. Suen, D. Zhang, S. D. Bond, Y. Zhang, Y. Song, N. A. Baker, C. L. Bajaj, M. J. Holst, and J. A. McCammon. 2007. Finite element analysis of the time-dependent Smoluchowski equation for acetylcholinesterase reaction rate calculations. Biophys J 92 (10):3397-3406.
15. Dix, J. A., and A. S. Verkman. 2008. Crowding effects on diffusion in solutions and cells. Annu Rev Biophys 37:247-263.
16. Djordjevic, M., and R. Bundschuh. 2008. Formation of the open complex by bacterial RNA polymerase—a quantitative model. Biophys J 94 (11):4233-4248.
17. Elcock, A. H., R. R. Gabdoulline, R. C. Wade, and J. A. McCammon. 1999. Computer simulation of protein-protein association kinetics: Acetylcholinesterase-fasciculin. J Mol Biol 291 (1):149-162.
18. Elf, J., G.-W. Li, and X. S. Xie. 2007. Probing transcription factor dynamics at the singlemolecule level in a living cell. Science 316 (5828):1191-1194.
19. Fan, L., and V. A. Roberts. 2006. Complex of linker histone H5 with the nucleosome and its implications for chromatin packing. Proc Natl Acad Sci USA 103 (22):8384-8389.
20. Fogolari, F., R. Ugolini, H. Molinari, P. Viglino, and G. Esposito. 2000. Simulation of electrostatic effects in Fab-antigen complex formation. Eur J Biochem 267 (15):4861-4869.
21. Frisch, C., A. R. Fersht, and G. Schreiber. 2001. Experimental assignment of the structure of the transition state for the association of barnase and barstar. J Mol Biol 308 (1):69-77.
22. Gabdoulline, R. R., and R. C. Wade. 1997. Simulation of the diffusional association of barnase and barstar. Biophys J 72 (5):1917-1929.
23. Gabdoulline, R. R., and R. C. Wade. 1999. On the protein-protein diffusional encounter complex. J Mol Recognit 12 (4):226-234.
24. Gabdoulline, R. R., and R. C. Wade. 2001. Protein-protein association: Investigation of factors influencing association rates by Brownian dynamics simulations. J Mol Biol 306 (5):1139-1155.
25. Gabdoulline, R. R., and R. C. Wade. 2002. Biomolecular diffusional association. Curr Opin Struct Biol 12 (2):204-213.
26. Gruenberg, R., J. Leckner, and M. Nilges. 2004. Complementarity of structure ensembles in protein-protein binding. Structure 12 (12):2125-2136.
27. Haddadian, E. J., and E. L. Gross. 2006. A Brownian dynamics study of the interactions of the luminal domains of the cytochrome b6f complex with plastocyanin and cytochrome c6: The effects of the Rieske FeS protein on the interactions. Biophys J 91 (7):2589-2600.
28. Halford, S. E., and J. F. Marko. 2004. How do site-specific DNA-binding proteins find their targets? Nucleic Acids Res 32 (10):3040-3052.
29. Harel, M., M. Cohen, and G. Schreiber. 2007. On the dynamic nature of the transition state for protein-protein association as determined by double-mutant cycle analysis and simulation. J Mol Biol 371 (1):180-196.
30. Hu, L., A. Y. Grosberg, and R. Bruinsma. 2008. Are DNA transcription factor proteins Maxwellian demons? Biophys J 95 (3):1151-1156.
31. Hu, T., and B. I. Shklovskii. 2007. How a protein searches for its specific site on DNA: The role of intersegment transfer. Phys Rev E Stat Nonlin Soft Matter Phys 76 (5 Pt 1): 051909.
32. Huber, G. A., and S. Kim. 1996. Weighted-ensemble Brownian dynamics simulations for protein association reactions. Biophys J 70 (1):97-110.
33. Jucovic, M., and R. W. Hartley. 1996. Protein-protein interaction: A genetic selection for compensating mutations at the barnase-barstar interface. Proc Natl Acad Sci USA 93 (6):2343-2347.
34. Kampmann, M. 2005. Facilitated diffusion in chromatin lattices: Mechanistic diversity and regulatory potential. Mol Microbiol 57 (4):889-899.
35. Kepper, N., D. Foethke, R. Stehr, G. Wedemann, and K. Rippe. 2008. Nucleosome geometry and internucleosomal interactions control the chromatin fiber conformation. Biophys J. 95 (8):3692-3705.
36. Kiel, C., T. Selzer, Y. Shaul, G. Schreiber, and C. Herrmann. 2004. Electrostatically optimized Ras-binding Ral guanine dissociation stimulator mutants increase the rate of association by stabilizing the encounter complex. Proc Natl Acad Sci USA 101 (25):9223-9228.
37. Kim, Y. C., C. Tang, G. M. Clore, and G. Hummer. 2008. Replica exchange simulations of transient encounter complexes in protein-protein association. Proc Natl Acad Sci USA 105 (35):12855-12860.
38. Kourentzi, K., M. Srinivasan, S. J. Smith-Gill, and R. C. Willson. 2008. Conformational flexibility and kinetic complexity in antibody-antigen interactions. J Mol Recognit 21 (2):114-121.
39. Kozer, N., Y. Y. Kuttner, G. Haran, and G. Schreiber. 2007. Protein-protein association in polymer solutions: From dilute to semidilute to concentrated. Biophys J 92 (6):2139-2149.
40. Kozer, N., and G. Schreiber. 2004. Effect of crowding on protein-protein association rates: Fundamental differences between low and high mass crowding agents. J Mol Biol 336 (3):763-774.
41. Langowski, J., and D. W. Heermann. 2007. Computational modeling of the chromatin fiber. Semin Cell Dev Biol 18 (5):659-667.
42. Lee, S., and M. Karplus. 1987. Kinetics of diffusion-influenced bimolecular reactions in solution. I. General formalism and relaxation kinetics of fast reversible reactions. J. Chem. Phys. 86:1883-1903.
43. Levy, Y., S. S. Cho, J. N. Onuchic, and P. G. Wolynes. 2005. A survey of flexible protein binding mechanisms and their transition states using native topology based energy landscapes. J Mol Biol 346 (4):1121-1145.
44. Levy, Y., J. N. Onuchic, and P. G. Wolynes. 2007. Fly-casting in protein-DNA binding: Frustration between protein folding and electrostatics facilitates target recognition. J Am Chem Soc 129 (4):738-739.
45. Long, H., C. H. Chang, P. W. King, M. L. Ghirardi, and K. Kim. 2008. Brownian dynamics and molecular dynamics study of the association between hydrogenase and ferredoxin from Chlamydomonas reinhardtii. Biophys 95 (8):3753-3766.
46. Merlitz, H., K. V. Klenin, C.-X. Wu, and J. Langowski. 2006. Facilitated diffusion of DNAbinding proteins: Simulation of large systems. J Chem Phys 125 (1): 014906.
47. Miyashita, O., J. N. Onuchic, and M. Y. Okamura. 2004. Transition state and encounter complex for fast association of cytochrome c2 with bacterial reaction center. Proc Natl Acad Sci USA 101 (46):16174-16179.
48. Motiejunas, D., and R. C. Wade. 2007. Structural, energetic, and dynamic aspects of ligand receptor interactions. In Comprehensive Medicinal Chemistry II (Vol. 4), edited by D. J. Triggle and J. B. Taylor. Elsevier, Oxford.
49. Murugan, R. 2007. Generalized theory of site-specific DNA-protein interactions. Phys Rev E Stat Nonlin Soft Matter Phys 76 (1 Pt 1): 011901.
50. Northrup, S. H., J. O. Boles, and J. C. Reynolds. 1988. Brownian dynamics of cytochrome c and cytochrome c peroxidase association. Science 241 (4861):67-70.
51. Northrup, S. H., and H. P. Erickson. 1992. Kinetics of protein-protein association explained by Brownian dynamics computer simulation. Proc Natl Acad Sci USA 89 (8):3338-3342.
52. Northrup, S. H., S. A. Allison, and J. A. McCammon. 1984. Brownian dynamics simulation of diffusion-influenced bimolecular reactions. J. Chem. Phys. 80:1517-1524.
53. Ouporov, I. V., H. R. Knull, S. L. Lowe, and K. A. Thomasson. 2001. Interactions of glyceraldehyde- 3-phosphate dehydrogenase with G- and F-actin predicted by Brownian dynamics. J Mol Recognit 14 (1):29-41.
54. Pachov, G. V., R. R. Gabdoulline, and R. C. Wade. 2007. Simulation of linker histone-chromatin interactions. NIC Series 36: 69-74.
55. Qin, S., and H.-X. Zhou. 2008. Prediction of salt and mutational effects on the association rate of U1A protein and U1 small nuclear RNA stem/loop II. J Phys Chem B 112 (19):5955-5960.
56. Quinn, D. M. 1987. Acetylcholinesterase: Enzyme structure, reaction dynamics, and virtual transition states. Chem Rev 87:955-979.
57. Rezania, V., J. Tuszynski, and M. Hendzel. 2007. Modeling transcription factor binding events to DNA using a random walker/jumper representation on a 1D/2D lattice with different affinity sites. Phys Biol 4 (4):256-267.
58. Ridgway, D., G. Broderick, A. Lopez-Campistrous, M. Ru’aini, P. Winter, M. Hamilton, P. Boulanger, A. Kovalenko, and M. J. Ellison. 2008. Coarse-grained molecular simulation of diffusion and reaction kinetics in a crowded virtual cytoplasm. Biophys J 94 (10):3748-3759.
59. Rienzo, F. De, R. R. Gabdoulline, M. C. Menziani, P. G. De Benedetti, and R. C. Wade. 2001. Electrostatic analysis and Brownian dynamics simulation of the association of plastocyanin and cytochrome f. Biophys J 81 (6):3090-3104.
60. Rojnuckarin, A., D. R. Livesay, and S. Subramaniam. 2000. Bimolecular reaction simulation using weighted ensemble Brownian dynamics and the University of Houston Brownian Dynamics program. Biophys J 79 (2):686-693.
61. Routh, A., S. Sandin, and D. Rhodes. 2008. Nucleosome repeat length and linker histone stoichiometry determine chromatin fiber structure. Proc Natl Acad Sci USA 105 (26):8872-8877.
62. Schlosshauer, M., and D. Baker. 2004. Realistic protein-protein association rates from a simple diffusional model neglecting long-range interactions, free energy barriers, and landscape ruggedness. Protein Sci 13 (6):1660-1669.
63. Schreiber, G. Y. S., and K. E. Gottschalk. 2006. Electrostatic design of protein-protein association rates. Methods Mol Biol 340:235-249.
64. Selzer, T., S. Albeck, and G. Schreiber. 2000. Rational design of faster associating and tighter binding protein complexes. Nat Struct Biol 7 (7):537-541.
65. Selzer, T., and G. Schreiber. 1999. Predicting the rate enhancement of protein complex formation from the electrostatic energy of interaction. J Mol Biol 287 (2):409-419.
66. Sept, D., and J. A. McCammon. 2001. Thermodynamics and kinetics of actin filament nucleation. Biophys J 81 (2):667-674.
67. Shaul, Y., and G. Schreiber. 2005. Exploring the charge space of protein-protein association: A proteomic study. Proteins 60 (3):341-352.
68. Slutsky, M., and L. A. Mirny. 2004. Kinetics of protein-DNA interaction: Facilitated target location in sequence-dependent potential. Biophys J 87 (6):4021-4035.
69. Smoluchowski, M. V. 1917. Versuch einer mathematischen Theorie der Koagulationskinetik kolloider Losungen. Z Phys Chem 92:129-168.
70. Sohn, J., G. Buhrman, and J. Rudolph. 2007. Kinetic and structural studies of specific protein-protein interactions in substrate catalysis by Cdc25B phosphatase. Biochemistry 46 (3):807-818.
71. Song, Y., Y. Zhang, T. Shen, C. L. Bajaj, J. A. McCammon, and N. A. Baker. 2004. Finite element solution of the steady-state Smoluchowski equation for rate constant calculations. Biophys J 86 (4):2017-2029.
72. Spaar, A., C. Dammer, R. R. Gabdoulline, R. C. Wade, and V. Helms. 2006. Diffusional encounter of barnase and barstar. Biophys J 90 (6):1913-1924.
73. Stehr, R., N. Kepper, K. Rippe, and G. Wedemann. 2008. The effect of the internucleosomal interaction on the folding of the chromatin fiber. Biophys J 95 (8):3677-3691.
74. Stroppolo, M. E., A. Pesce, M. Falconi, P. O’Neill, M. Bolognesi, and A. Desideri. 2000. Single mutation at the intersubunit interface confers extra efficiency to Cu, Zn superoxide dismutase. FEBS Lett 483 (1):17-20.
75. Tang, C., J. Iwahara, and G. M. Clore. 2006. Visualization of transient encounter complexes in protein-protein association. Nature 444 (7117):383-386.
76. van der Heijden, T., and C. Dekker. 2008. Monte Carlo simulations of protein assembly, disassembly, and linear motion on DNA. Biophys J 95 (10):4560-4569.
77. Volkov, A. N., J. A. R. Worrall, E. Holtzmann, and M. Ubbink. 2006. Solution structure and dynamics of the complex between cytochrome c and cytochrome c peroxidase determined by paramagnetic NMR. Proc Natl Acad Sci USA 103 (50):18945-18950.
78. Wade, R. C. 1996. Brownian dynamics simulations of enzyme-substrate encounter. Biochem Soc Trans 24 (1):254-259.
79. Wade, R. C., R. R. Gabdoulline, S. K. Luedemann, and V. Lounnas. 1998. Electrostatic steering and ionic tethering in enzyme-ligand binding: Insights from simulations. Proc Natl Acad Sci USA 95 (11):5942-5949.
80. Wang, Y., B. J. Shen, and W. Sebald. 1997. A mixed-charge pair in human interleukin 4 dominates high-affinity interaction with the receptor alpha chain. Proc Natl Acad Sci USA 94 (5):1657-1662.
81. Wedemeier, A., T. Zhang, H. Merlitz, C.-X. Wu, and J. Langowski. 2008. The role of chromatin conformations in diffusional transport of chromatin-binding proteins: Cartesian lattice simulations. J Chem Phys 128 (15): 155101.
82. Wong, H., J.-M. Victor, and J. Mozziconacci. 2007. An all-atom model of the chromatin fiber containing linker histones reveals a versatile structure tuned by the nucleosomal repeat length. PLoS ONE 2 (9):e877.
83. Zhou, H.-X. 1997. Enhancement of protein-protein association rate by interaction potential: Accuracy of prediction based on local Boltzmann factor. Biophys J 73 (5):2441-2445.
84. Zhou, H.-X. 2008. Effect of mixed macromolecular crowding agents on protein folding. Proteins 72 (4):1109-1113.
85. Zhou, H.-X., and A. Szabo. 1996. Theory and simulation of the time-dependent rate coefficients of diffusion-influenced reactions. Biophys J 71 (5):2440-2457.
86. Zhou, H.-X., K. Y. Wong, and M. Vijayakumar. 1997. Design of fast enzymes by optimizing interaction potential in active site. Proc Natl Acad Sci USA 94 (23):12372-12377.