Molecular thermodynamics for charged biomacromolecules

Fluid Phase Equilibria

Volumn 241, Issue 1-2, 2006, Pages 317-333

  Wu, Jianzhong ^a   Morikis, Dimitrios ^a  

^a University of California Riverside   (United States)

Author keywords

Biomacromolecular stability; Computational biology; Electrostatics; Protein association; Protein protein interactions

Indexed keywords

AMINO ACIDS; BIOLOGICAL MEMBRANES; CHARGE TRANSFER; ELECTROSTATICS; LIPIDS; NUCLEIC ACIDS; PROTEINS;

BIOMACROMOLECULAR STABILITY; COMPUTATIONAL BIOLOGY; PROTEIN ASSOCIATION; PROTEIN-PROTEIN INTERACTIONS;

MACROMOLECULES;

AMINO ACIDS; BIOLOGICAL MEMBRANES; CHARGE TRANSFER; ELECTROSTATICS; LIPIDS; MACROMOLECULES; NUCLEIC ACIDS; PROTEINS;

EID: 33644680587     PISSN: 03783812     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.fluid.2005.12.044     Document Type: Article

References (138)

1. J.M. Prausnitz, R.N. Lichtenthaler, and E.G.D. Azevedo Molecular Thermodynamics of Fluid-Phase Equilibria 1999 Prentice-Hall PTR Upper Saddle River, NJ
2. M.K. Gilson, Biophysics Textbook Online, 2000.
3. J.A. McCammon, and S.C. Harvey Dynamics of Proteins and Nucleic Acids 1987 Cambridge University Press Cambridge, UK
4. C.L.I. Brooks, M. Karplus, and B. Montgomery Pettitt Protiens, A Theoretical Perspective of Dynamics, Structure, and Thermodynamics 1988 John Wiley & Sons New York
5. R. Cotterill Biophysics: An Introduction 2002 Wiley Chichester
6. M.E. Davis, and J.A. McCammon Chem. Rev. 90 1990 509 521
7. J.N. Israelachvili Intermolecular and Surface Forces 1992 Academic Press London
8. R.R. Netz, and H. Orland Eur. Phys. J. E 1 2000 203 214
9. V. Vlachy Annu. Rev. Phys. Chem. 50 1999 145 165
10. J.E. Sader, and D.Y.C. Chan Langmuir 16 2000 324 331
11. Y. Levin Rep. Prog. Phys. 65 2002 1577 1632
12. F. Fogolari, A. Brigo, and H. Molinari J. Mol. Recogn. 15 2002 377 392
13. W.B. Russel, D.A. Saville, and W.R. Schowalter Colloidal Dispersions 1999 Cambridge University Press Cambridge, UK
14. H. Boroudjerdi, and R.R. Netz J. Phys.: Conden. Matter 17 2005 S1137 S1151
15. A. Naji, S. Jungblut, A.G. Moreira, and R.R. Netz Phys. A: Stat. Mech. Appl. 352 2005 131 170
16. J.P. Hansen, and H. Lowen Annu. Rev. Phys. Chem. 51 2000 209 242
17. K. Besteman, M.A.G. Zevenbergen, H.A. Heering, and S.G. Lemay Phys. Rev. Lett. 93 2004
18. S. Ravindran, and J.Z. Wu Langmuir 20 2004 7333 7338
19. M. Quesada-Perez, E. Gonzalez-Tovar, A. Martin-Molina, M. Lozada-Cassou, and R. Hidalgo-Alvarez Chem. Phys. Chem. 4 2003 235 248
20. A.Y. Grosberg, T.T. Nguyen, and B.I. Shklovskii Rev. Modern Phys. 74 2002 329 345
21. C.W. Outhwaite, M. Molero, and L.B. Bhuiyan J. Chem. Soc., Faraday Trans. 89 1993 1315 1320
22. D. Henderson, and L. Blum J. Chem. Phys. 69 1978 5441 5449
23. Z.D. Li, and J.Z. Wu Macromol. Symp. 219 2005 51 57
24. Z.D. Li, and J.Z. Wu Phys. Rev. E 70 2004 (Art. No. 031109)
25. Y.X. Yu, J.Z. Wu, and G.H. Gao J. Chem. Phys. 120 2004 7223 7233
26. Y.X. Yu, J.Z. Wu, and G.H. Gao Chin. J. Chem. Eng. 12 2004 688 695
27. K. Wang, Y.X. Yu, and G.H. Gao Phys. Rev. E 70 2004
28. M. Bostrom, D.R.M. Williams, and B.W. Ninham Europhys. Lett. 63 2003 610 615
29. M. Karplus, and J.A. McCammon Nat. Struct. Biol. 9 2002 646 652
30. J.Z. Wu, AIChE J., 2006, in press.
31. R.M. Fuoss, S. Lifson, and A. Katchalsky PNAS 37 1951 579 589
32. A. Katchalsky Pure Appl. Chem. 26 1971 327 373
33. S. Nilsson, and L. Piculell Macromolecules 24 1991 3804 3811
34. S. Nilsson, and L. Piculell Macromolecules 23 1990 2776 2780
35. S. Nilsson, and L. Piculell Macromolecules 22 1989 3011 3017
36. S. Nilsson, L. Piculell, and B. Jonsson Macromolecules 22 1989 2367 2375
37. N. Korolev, A.P. Lyubartsev, and L. Nordenskiold Biophys. J. 75 1998 3041 3056
38. N. Korolev, A.P. Lyubartsev, A. Rupprecht, and L. Nordenskiold Biophys. J. 77 1999 2736 2749
39. G.S. Manning J. Chem. Phys. 51 1969 924 933
40. P.L. Hansen, R. Podgornik, and V.A. Parsegian Phys. Rev. E 6402 2001 (Art. No. 021907)
41. C.H. Spink, and S.E. Wellman Drug: Nucl. Acid Interactions 340 2001 193 211
42. N. Korolev, A.P. Lyubartsev, and L. Nordenskiold Biophys. Chem. 104 2003 55 66
43. F. Fogolari, P. Zuccato, G. Esposito, and P. Viglino Biophys. J. 76 1999 1 16
44. B. Honig, and A. Nicholls Science 268 1995 1144 1149
45. K.A. Sharp, and B. Honig J. Phys. Chem. 94 1990 7684 7692
46. B. Honig, K. Sharp, and A.S. Yang J. Phys. Chem. 97 1993 1101 1109
47. J.D. Madura, M.E. Davis, M.K. Gilson, R.C. Wade, B.A. Luty, and J.A. McCammon D.B. Boyd Reviews in Computational Chemistry vol. V 1994 VCH Publishers, Inc. New York 229 267
48. N.A. Baker, D. Sept, M.J. Hoist, and J.A. McCammon Ibm J. Res. Dev. 45 2001 427 438
49. N.A. Baker Meth. Enzymol. 383 2004 94 118
50. N.A. Baker, D. Sept, S. Joseph, M.J. Hoist, and J.A. McCammon Proc. Natl. Acad. Sci. U.S.A. 98 2001 10037 10041
51. J.D. Madura, J.M. Briggs, R.C. Wade, M.E. Davis, B.A. Luty, A. Ilin, J. Antosiewicz, M.K. Gilson, B. Bagheri, L.R. Scott, and J.A. McCammon Comput. Phys. Commun. 91 1995 57 95
52. A. Nicholls, and B. Honig J. Comput. Chem. 12 1991 435 445
53. D. Bashford M. Tholburn An object-oriented programming suite for electrostatic effects in biological molecules vol. 1343 1997 Springer-Verlag Berlin 233 240
54. G. Vriend J. Mol. Graph. 8 1990 52
55. B.R. Brooks, R.E. Bruccoleri, B.D. Olafson, D.J. States, S. Swaminathan, and M. Karplus J. Comput. Chem. 4 1983 187 217
56. A. Nicholls, K.A. Sharp, and B. Honig Proteins: Struct. Funct. Genet. 11 1991 281 296
57. R. Koradi, M. Billeter, and K. Wuthrich J. Mol. Graph. 14 1996 51 55
58. N. Guex, and M.C. Peitsch Electrophoresis 18 1997 2714 2723
59. M.K. Gilson, T.P. Straatsma, J.A. McCammon, D.R. Ripoll, C.H. Faerman, P.H. Axelsen, I. Silman, and J.L. Sussman Science 263 1994 1276 1278
60. D. Morikis, and J.D. Lambris J. Immunol. 172 2004 7537 7547
61. G. Sfyroera, M. Katragadda, D. Morikis, S.N. Isaacs, and J.D. Lambris J. Immunol. 174 2005 2143 2151
62. L. Zhang, D. Morikis, Biophys. J. (2006), in press.
63. D. Murray, and B. Honig Mol. Cell 9 2002 145 154
64. R.C. Wade, R.R. Gabdoulline, and F. De Rienzo Int. J. Quant. Chem. 83 2001 122 127
65. N. Blomberg, R.R. Gabdoulline, M. Nilges, and R.C. Wade Proteins: Struct. Funct. Genet. 37 1999 379 387
66. F. De Rienzo, R.R. Gabdoulline, M.C. Menziani, and R.C. Wade Protein Sci. 9 2000 1439 1454
67. D.R. Livesay, P. Jambeck, A. Rojnuckarin, and S. Subramaniam Biochemistry 42 2003 3464 3473
68. K. Sharp E. Di Cera Thermodynamics in Biology 2000 Oxford University Press New York
69. G.M. Ullmann, and E.W. Knapp Eur. Biophys. J. Biophys. Lett. 28 1999 533 551
70. G.M. Ullmann J. Phys. Chem. B 104 2000 6293 6301
71. J. Antosiewicz, J.A. McCammon, and M.K. Gilson J. Mol. Biol. 238 1994 415 436
72. J. Antosiewicz, J.A. McCammon, and M.K. Gilson Biochemistry 35 1996 7819 7833
73. D. Bashford, and M. Karplus Biochemistry 29 1990 10219 10225
74. D. Bashford, and M. Karplus J. Phys. Chem. 95 1991 9556 9561
75. M.K. Gilson Proteins: Struct. Funct. Genet. 15 1993 266 282
76. P. Beroza, D.R. Fredkin, M.Y. Okamura, and G. Feher Proc. Natl. Acad. Sci. U.S.A. 88 1991 5804 5808
77. A.S. Yang, M.R. Gunner, R. Sampogna, K. Sharp, and B. Honig Proteins: Struct. Funct. Genet. 15 1993 252 265
78. C. Tanford, and J.G. Kirkwood J. Am. Chem. Soc. 79 1957 5333 5339
79. D. Bashford, D.A. Case, C. Dalvit, L. Tennant, and P.E. Wright Biochemistry 32 1993 8045 8056
80. W.R. Forsyth, J.M. Antosiewiez, and A.D. Robertson Proteins: Struct. Funct. Genet. 48 2002 388 403
81. R.E. Georgescu, E.G. Alexov, and M.R. Gunner Biophys. J. 83 2002 1731 1748
82. J.E. Nielsen, and J.A. McCammon Protein Sci. 12 2003 1894 1901
83. J.E. Nielsen, and G. Vriend Proteins: Struct. Funct. Genet. 43 2001 403 412
84. D. Morikis, M. Roy, M.G. Newlon, J.D. Scott, and P.A. Jennings Eur. J. Biochem. 269 2002 2040 2051
85. D. Morikis, A.H. Elcock, P.A. Jennings, and J.A. McCammon Protein Sci. 10 2001 2379 2392
86. D. Morikis, A.H. Elcock, P.A. Jennings, and J.A. McCammon Protein Sci. 10 2001 2363 2378
87. M.J. Ondrechen, J.G. Clifton, and D. Ringe Proc. Natl. Acad. Sci. U.S.A. 98 2001 12473 12478
88. D. Bashford, and K. Gerwert J. Mol. Biol. 224 1992 473 486
89. V.Z. Spassov, H. Luecke, K. Gerwert, and D. Bashford J. Mol. Biol. 312 2001 203 219
90. R.V. Sampogna, A.S. Yang, and B.H. Honig Biophys. J. 66 1994 A45
91. A.S. Yang, and B. Honig J. Mol. Biol. 231 1993 459 474
92. C. Tanford Adv. Protein Chem. 24 1970 1 95
93. J.A. Schellman Biopolymers 14 1975 999 1018
94. A.H. Elcock J. Mol. Biol. 294 1999 1051 1062
95. A.H. Elcock J. Mol. Biol. 284 1998 489 502
96. L. Xiao, and B. Honig J. Mol. Biol. 289 1999 1435 1444
97. Y.N. Vorobjev, H.A. Scheraga, and B. Honig J. Phys. Chem. 99 1995 7180 7187
98. A.S. Yang, and B. Honig J. Mol. Biol. 237 1994 602 614
99. E. Alexov Eur. J. Biochem. 271 2004 173 185
100. T. Selzer, and G. Schreiber Proteins: Struct. Funct. Genet. 45 2001 190 198
101. T. Selzer, S. Albeck, and G. Schreiber Nat. Struct. Biol. 7 2000 537 541
102. A.H. Elcock, D. Sept, and J.A. McCammon J. Phys. Chem. B 105 2001 1504 1518
103. D. Sitkoff, K.A. Sharp, and B. Honig J. Phys. Chem. 98 1994 1978 1988
104. N. Froloff, A. Windemuth, and B. Honig Protein Sci. 6 1997 1293 1301
105. Z.S. Hendsch, and B. Tidor Protein Sci. 8 1999 1381 1392
106. V. Zoete, O. Michielin, and M. Karplus J. Comput. Aided Mol. Design 17 2003 861 880
107. G. Archontis, T. Simonson, D. Moras, and M. Karplus J. Mol. Biol. 275 1998 823 846
108. G. Archontis, T. Simonson, and M. Karplus J. Mol. Biol. 306 2001 307 327
109. F.B. Sheinerman, and B. Honig J. Mol. Biol. 318 2002 161 177
110. V.K. Misra, K.A. Sharp, R.A. Friedman, and B. Honig J. Mol. Biol. 238 1994 245 263
111. V.K. Misra, J.L. Hecht, K.A. Sharp, R.A. Friedman, and B. Honig J. Mol. Biol. 238 1994 264 280
112. A.H. Elcock, and J.A. McCammon J. Mol. Biol. 280 1998 731 748
113. L. Zhang, B. Mallik, D. Morikis, submitted for publication.
114. D.A. Doyle, J.M. Cabral, R.A. Pfuetzner, A.L. Kuo, J.M. Gulbis, S.L. Cohen, B.T. Chait, and R. MacKinnon Science 280 1998 69 77
115. B. Roux Annu. Rev. Biophys. Biomol. Struct. 34 2005 153 171
116. M. LeMasurier, L. Heginbotham, and C. Miller J. Gen. Physiol. 118 2001 303 313
117. J. Aqvist, and V. Luzhkov Nature 404 2000 881 884
118. D.J. Tobias Curr. Opin. Struct. Biol. 11 2001 253 261
119. J.U. Bowie Nature 438 2005 581 589
120. G.D. Cymes, Y. Ni, and C. Grosman Nature 438 2005 975 980
121. A.H. Elcock Curr. Opin. Struct. Biol. 12 2002 154 160
122. R. Mendez, R. Leplae, L. De Maria, and S.J. Wodak Proteins: Struct. Funct. Genet. 52 2003 51 67
123. R. Mendez, R. Leplae, M.F. Lensink, and S.J. Wodak Proteins: Struct. Funct. Bioinform. 60 2005 150 169
124. B. Parker, J. Sohn, G. Buhrman, P. Brown, K. Kristjansdottir, A. Safi, H. Edelsbrunner, W. Yang, and J. Rudolph Biochemistry 44 2005 16563 16573
125. R.R. Gabdoulline, and R.C. Wade Curr. Opin. Struct. Biol. 12 2002 204 213
126. L. Degreve, and M. Lozada-Cassou Mol. Phys. 86 1995 759 768
127. L. Degreve, M. Lozada-Cassou, E. Sanchez, and E. Gonzalez-Tovar J. Chem. Phys. 98 1993 8905 8909
128. B.J. Yoon, and S. Kim J. Colloid Interface Sci. 128 1989 275 288
129. J.P. Hsu, and B.T. Liu J. Colloid Interface Sci. 178 1996 785 788
130. R.E. Rice J. Chem. Phys. 82 1985 4337 4340
131. K.S. Pitzer Acc. Chem. Res. 10 1977 371 377
132. F. Oosawa Polyelectrolytes 1971 Marcel Dekker New York
133. M. Muthukumar J. Chem. Phys. 120 2004 9343 9350
134. U. Mohanty, B.W. Ninham, and I. Oppenheim Proc. Natl. Acad. Sci. U.S.A. 93 1996 4342 4344
135. M. Deserno, C. Holm, and S. May Macromolecules 33 2000 199 206
136. B. O'Shaughnessy, and Q. Yang Phys. Rev. Lett. 94 2005 (Art. No. 048302)
137. M.T. Record Jr., W. Zhang, and C.F. Anderson Adv. Protein Chem. 51 1998 281 353
138. D.E. Draper RNA 10 2004 335 343