Parameter effects on binding chemistry in crowded media using a two-dimensional stochastic off-lattice model

Physical Review E - Statistical, Nonlinear, and Soft Matter Physics

Volumn 80, Issue 4, 2009, Pages

  Lee, Byoungkoo ^a   Leduc, Philip R ^b   Schwartz, Russell ^a  

^a CARNEGIE MELLON UNIVERSITY   (United States)

^b CARNEGIE MELLON UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ASSEMBLY REACTIONS; ASSEMBLY SYSTEMS; BINDING REACTIONS; BIOCHEMICAL REACTIONS; CONCENTRATION OF; CRITICAL PARAMETER; CROWDING EFFECTS; DIFFUSION COEFFICIENTS; DISSOCIATION REACTIONS; GREEN'S FUNCTION REACTION DYNAMICS; IDEAL SOLUTIONS; INERT PARTICLE; LINEAR MODEL; MACROMOLECULAR CROWDING; MULTIPARAMETERS; NONLINEAR POLYNOMIALS; OFF-LATTICE MODELS; PARAMETER EFFECTS; PARAMETER RANGE; PARAMETER VARIATION; PREDICTIVE MODELS; REACTION SYSTEM; REGRESSION MODEL; SIMULATION ENVIRONMENT; THEORETICAL MODELS; THREE PARAMETERS;

BINDING SITES; CRYSTAL LATTICES; DIFFERENTIAL EQUATIONS; EQUILIBRIUM CONSTANTS; GREEN'S FUNCTION; REACTION RATES; REGRESSION ANALYSIS; SIMULATORS; THERMODYNAMIC STABILITY; TWO DIMENSIONAL;

STOCHASTIC MODELS;

EID: 70350244548     PISSN: 15393755     EISSN: 15502376     Source Type: Journal    
DOI: 10.1103/PhysRevE.80.041918     Document Type: Article

References (38)

1. A. P. Minton, J. Cell Sci. 119, 2863 (2006). 10.1242/jcs.03063
2. A. P. Minton, J. Biol. Chem. 276, 10577 (2001). 10.1074/jbc.R100005200
3. D. M. Hatters, A. P. Minton, and G. J. Howlett, J. Biol. Chem. 277, 7824 (2002). 10.1074/jbc.M110429200
4. M. del Alamo, G. Rivas, and M. G. Mateu, J. Virol. 79, 14271 (2005). 10.1128/JVI.79.22.14271-14281.2005
5. D. Drenckhahn and T. D. Pollard, J. Biol. Chem. 261, 12754 (1986).
6. R. A. Lindner and G. B. Ralston, Biophys. Chem. 66, 57 (1997). 10.1016/S0301-4622(97)00011-2
7. N. Tokuriki, M. Kinjo, S. Negi, M. Hoshino, Y. Goto, I. Urabe, and T. Yomo, Protein Sci. 13, 125 (2004). 10.1110/ps.03288104
8. P. McPhie, Y. Ni, and A. P. Minton, J. Mol. Biol. 361, 7 (2006). 10.1016/j.jmb.2006.05.075
9. M. Jiang and Z. Guo, J. Am. Chem. Soc. 129, 730 (2007). 10.1021/ja065064+
10. J. R. Wenner and V. A. Bloomfield, Biophys. J. 77, 3234 (1999). 10.1016/S0006-3495(99)77154-7
11. S. B. Zimmerman and A. P. Minton, Annu. Rev. Biophys. Biomol. Struct. 22, 27 (1993). 10.1146/annurev.bb.22.060193.000331
12. A. P. Minton, Curr. Opin. Biotechnol. 8, 65 (1997). 10.1016/S0958- 1669(97)80159-0
13. A. P. Minton, Mol. Cell. Biochem. 55, 119 (1983). 10.1007/BF00673707
14. D. Hall and A. P. Minton, Biochim. Biophys. Acta 1649, 127 (2003).
15. P. R. LeDuc and R. Schwartz, Cell Biochem. Biophys. 48, 16 (2007). 10.1007/s12013-007-0012-y
16. R. Kopelman, Science 241, 1620 (1988). 10.1126/science.241.4873.1620
17. S. Schnell and T. E. Turner, Prog. Biophys. Mol. Biol. 85, 235 (2004). 10.1016/j.pbiomolbio.2004.01.012
18. A. P. Minton, Biopolymers 20, 2093 (1981). 10.1002/bip.1981.360201006
19. J. L. Lebowitz, E. Helfand, and E. Praestgaard, J. Chem. Phys. 43, 774 (1965). 10.1063/1.1696842
20. R. M. Gibbons, Mol. Phys. 17, 81 (1969). 10.1080/00268976900100811
21. R. M. Gibbons, Mol. Phys. 18, 809 (1970). 10.1080/00268977000100871
22. D. Hall and A. P. Minton, Biophys. Chem. 98, 93 (2002). 10.1016/S0301-4622(02)00087-X
23. D. Hall and A. P. Minton, Biophys. Chem. 107, 299 (2004). 10.1016/j.bpc.2003.09.016
24. R. C. Chatelier and A. P. Minton, Biopolymers 26, 507 (1987). 10.1002/bip.360260405
25. Z. Hu, J. Jiang, and R. Rajagopalan, Biophys. J. 93, 1464 (2007). 10.1529/biophysj.107.104646
26. D. Ridgway, G. Broderick, and M. J. Ellison, Curr. Opin. Biotechnol. 17, 493 (2006). 10.1016/j.copbio.2006.08.004
27. L. Apeltsin, K. Puskar, P. R. LeDuc, and R. Schwartz, (unpublished).
28. K. Puskar, S. Ta'asan, R. Schwartz, and P. R. LeDuc, Cell Biochem. Biophys. 45, 195 (2006). 10.1385/CBB:45:2:195
29. K. Puskar, L. Apeltsin, S. Ta'asan, R. Schwartz, and P. R. LeDuc, Mech. Chem. Biosyst. 1, 123 (2004).
30. A. H. Elcock, Proc. Natl. Acad. Sci. U.S.A. 100, 2340 (2003). 10.1073/pnas.0535055100
31. S. Izvekov and G. A. Voth, J. Phys. Chem. B 109, 2469 (2005). 10.1021/jp044629q
32. B. Lee, P. R. LeDuc, and R. Schwartz, Phys. Rev. E 78, 031911 (2008). 10.1103/PhysRevE.78.031911
33. J. S. van Zon and P. R. ten Wolde, J. Chem. Phys. 123, 234910 (2005). 10.1063/1.2137716
34. P. Sheterline, J. Clayton, and J. C. Sparrow, Protein Profile: Actin, 4th ed. (Oxford University Press, New York, 1998), p. 14.
35. S. Bicknese, N. Periasamy, S. B. Shohet, and A. S. Verkman, Biophys. J. 65, 1272 (1993). 10.1016/S0006-3495(93)81179-2
36. J. V. Sengers and J. T. R. Watson, J. Phys. Chem. Ref. Data 15, 1291 (1986).
37. See EPAPS Document No. E-PLEEE8-80-038910 for the movie files in AVI format. High-resolution versions of the movies can be downloaded from: http://www.cs.cmu.edu/~russells/projects/crowding/crowding.html. For more information on EPAPS, see http://www.aip.org/pubservs/epaps.html.
38. B. Sweeney, T. Zhang, and R. Schwartz, Biophys. J. 94, 772 (2008). 10.1529/biophysj.107.107284