Molecular simulation of protein dynamics in nanopores. I. Stability and folding

Journal of Chemical Physics

Volumn 128, Issue 11, 2008, Pages

  Javidpour, Leili ^a   Tabar, M Reza Rahimi ^a,b   Sahimi, Muhammad ^c  

^a SHARIF UNIVERSITY OF TECHNOLOGY   (Iran)

^b UNIVERSITY OF OLDENBURG   (Germany)

^c University of Southern California ^*  (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER SIMULATION; MATHEMATICAL MODELS; MOLECULAR DYNAMICS; NANOPORES; PORE SIZE;

FOLDING TRANSITION; MOLECULAR SIMULATION; REPULSIVE INTERACTION POTENTIALS;

PROTEINS;

PROTEIN;

ARTICLE; CHEMICAL STRUCTURE; COMPUTER SIMULATION; ENTROPY; METABOLISM; PHYSICAL CHEMISTRY; PROTEIN CONFORMATION; PROTEIN FOLDING; THERMODYNAMICS;

CHEMISTRY, PHYSICAL; COMPUTER SIMULATION; ENTROPY; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEINS; THERMODYNAMICS;

EID: 41049107127     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.2894299     Document Type: Article

References (43)

1. C. Branden and J. Tooze, Introduction to Protein Structure, 2nd ed. (Garland, New York, 1998).
2. C. B. Anfinsen, Science SCIEAS 0036-8075 10.1126/science.181.4096.223 181, 223 (1973).
3. D. K. Klimov and D. Thirumalai, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.76.4070 76, 4070 (1996).
4. L. Mirny and E. Shakhnovich, Annu. Rev. Biophys. Biomol. Struct. ABBSE4 1056-8700 10.1146/annurev.biophys.30.1.361 30, 361 (2001); H.-X. Zhou, Acc. Chem. Res. ACHRE4 0001-4842 10.1021/ar0302282 37, 123 (2004); J. Kubelka, J. Hofrichter, and W. A. Eaton, Curr. Opin. Struct. Biol. COSBEF 0959-440X 10.1016/j.sbi.2004.01.013 14, 76 (2004).
5. D. N. Lu, Z. Liu, and J. Z. Wu, Biophys. J. BIOJAU 0006-3495 10.1529/biophysj.105.071761 90, 3224 (2006).
6. D. A. Kirschner, C. Abraham, and D. J. Selkoe, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.83.2.503 83, 503 (1986); E. H. Koo, P. T. J. Lansbury, and J. W. Kelly, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.96.18.9989 96, 9989 (1999).
7. K. A. Conway, S.-J. Lee, J.-C. Rochet, T. T. Ding, R. E. Williamson, and P. T. Lansbury, Jr., Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.97.2.571 97, 571 (2000).
8. D. G. Lynn and S. C. Meredith, J. Struct. Biol. JSBIEM 1047-8477 10.1006/jsbi.2000.4287 130, 153 (2000).
9. A. P. J. Midelberg, J Microbiol. Biotechnol. ZZZZZZ 1017-7825 6, 225 (1996); A. D. Guise, S. M. West, and J. B. Chaudhuri, Mol. Biotechnol. MLBOEO 1073-6085 10.1007/BF02762323 6, 53 (1996); J. G. Thomas, A. Ayling, and F. Baneyx, Appl. Biochem. Biotechnol. ABIBDL 0273-2289 66, 197 (1997).
10. D. K. Eggers and J. S. Valentine, Protein Sci. PRCIEI 0961-8368 10.1110/ps.36201 10, 250 (2001).
11. A. Brinker, G. Pfeifer, M. J. Kemer, D. J. Naylor, F.-U. Hartl, and M. Hayer-Hartl, Cell CELLB5 0092-8674 10.1016/S0092-8674(01)00517-7 107, 223 (2001).
12. E. E. Borrero and F. A. Escobedo, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.2357944 125, 164904 (2006); M. Hayer-Hartl and A. P. Minton, Biochemistry BICHAW 0006-2960 10.1021/bi061597j 45, 13356 (2006); Y. C. Tang and H.-C. Chang, Cell CELLB5 0092-8674 10.1016/j.cell.2006.04.027 125, 903 (2006); G. Ziv, G. Haran, and D. Thirumalai, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.0508234102 102, 18956 (2005); H. X. Zhou, J. Mol. Recognit. JMORE4 0952-3499 10.1002/jmr.711 17, 368 (2004); H. X. Zhou and K. A. Dill, Biochemistry BICHAW 0006-2960 10.1021/bi0155504 40, 11289 (2001); R. J. Ellis, Curr. Biol. CUBLE2 0960-9822 10.1016/j.cub.2003.10.051 13, R881 (2003); F. Tagaki, N. Koga, and S. Takada, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.1831920100 100, 11367 (2003).
13. G. F. Bickerstaff, Immobilization of Enzymes and Cells (Humana, Totowa, NJ, 1997); J. Livage, T. Coradin, and C. Roux, J. Phys.: Condens. Matter JCOMEL 0953-8984 10.1088/0953-8984/13/33/202 13, R673 (2001).
14. C. Lei, Y. Shin, J. Liu, and J. Ackerman, J. Am. Chem. Soc. JACSAT 0002-7863 10.1021/ja026855o 124, 11242 (2002).
15. M. Dadvar and M. Sahimi, Chem. Eng. Sci. CESCAC 0009-2509 10.1016/S0009-2509(00)00207-4 56, 1 (2000); M. Dadvar and M. Sahimi, Chem. Eng. Sci. CESCAC 0009-2509 10.1016/j.ces.2003.07.006 58, 4935 (2003).
16. M.-E. Avramescu, Z. Borneman, and M. Wessling, Biotechnol. Bioeng. BIBIAU 0006-3592 10.1002/bit.10807 84, 564 (2003).
17. R. J. Ciora, B. Fayyaz, P. K. T. Liu, V. Suwanmethanond, R. Mallada, M. Sahimi, and T. T. Tsotsis, Chem. Eng. Sci. CESCAC 0009-2509 10.1016/j.ces.2004. 07.015 59, 4957 (2004); B. Elyassi, M. Sahimi, and T. T. Tsotsis, J. Membr. Sci. JMESDO 0376-7388 288, 290 (2007).
18. A. J. Rosenbloom, D. M. Sipe, Y. Shishkin, Y. Ke, R. P. Devaty, and W. J. Choyke, Biomed. Microdevices ZZZZZZ 1387-2176 6, 261 (2004).
19. A. P. Minton, J. Cell. Sci. JNCSAI 0021-9533 10.1242/jcs.03063 119, 2863 (2006).
20. G. Ping, J. Yuan, M. Vallieres, H. Dong, Z. Sun, Y. Wei, F. Y. Li, and S. H. Lin, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1564053 118, 8042 (2003); H. C. Loebl and C. C. Matthai, Physica A PHYADX 0378-4371 10.1016/j.physa.2004.05. 039 342, 612 (2004).
21. M. S. Cheung, D. Klimov, and D. Thirumalai, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.0409630102 102, 4753 (2005).
22. J. Lendermann and R. Winter, Phys. Chem. Chem. Phys. PPCPFQ 1463-9076 10.1039/b209825n 5, 1440 (2003); C. H. Lee, J. Lang, C. W. Yen, P. C. Shih, T. S. Lin, and C. Y. Mou, J. Phys. Chem. B JPCBFK 1089-5647 10.1021/jp050535k 109, 12277 (2005); E. Rossinsky and S. Srebnik, Biopolymers BIPMAA 0006-3525 10.1002/bip.20365 79, 259 (2005); W. X. Xu, J. Wang, and W. Wang, Proteins 18PLAF 0887-3585 10.1002/prot.20689 61, 777 (2005); M. S. Cheung and D. Thirumalai, J. Mol. Biol. JMOBAK 0022-2836 10.1016/j.jmb.2005.12.048 357, 632 (2006).
23. L. Regan and W. F. DeGrado, Science SCIEAS 0036-8075 10.1126/science. 3043666 241, 976 (1988).
24. Z. Guo and D. Thirumalai, J. Mol. Biol. JMOBAK 0022-2836 10.1006/jmbi.1996.0578 263, 323 (1996).
25. S. Sun, Protein Sci. PRCIEI 0961-8368 2, 762 (1993); S. Sun, P. D. Thomas, and K. A. Dill, Protein Eng. PRENE9 0269-2139 10.1093/protein/8.8.769 8, 769 (1995); S. Takada, Z. Luthey-Schulten, and P. G. Wolynes, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.479101 110, 11616 (1999).
26. A. V. Smith and C. K. Hall, Proteins 18PLAF 0887-3585 10.1002/prot.1103 44, 376 (2001); A. V. Smith and C. K. Hall, J. Mol. Biol. JMOBAK 0022-2836 10.1006/jmbi.2001.4845 312, 187 (2001); H. D. Nguyen, A. J. Marchut, and C. K. Hall, Protein Sci. PRCIEI 0961-8368 10.1110/ps.04701304 13, 2909 (2004); H. D. Nguyen, A. J. Marchut, and C. K. Hall, Comput. Biol. Chem. ZZZZZZ 1476-9271 30, 215 (2006).
27. B. J. Alder and T. E. Wainwright, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1730376 31, 459 (1959); D. C. Rapaport, J. Phys. A JPHAC5 0305-4470 10.1088/0305-4470/11/8/008 11, L213 (1978); D. C. Rapaport, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.438770 71, 3299 (1979); A. Bellemans, J. Orban, and D. V. Belle, Mol. Phys. MOPHAM 0026-8976 10.1080/00268978000100671 39, 781 (1980); S. W. Smith, C. K. Hall, and B. D. Freeman, J. Comput. Phys. JCTPAH 0021-9991 10.1006/jcph.1996.5510 134, 16 (1997).
28. C. Bartels and M. Karplus, J. Comput. Chem. 18, 1450 (1997);
29. C. Bartels and M. Karplus, J. Phys. Chem. B 102, 865 (1998).
30. B. A. Berg and T. Neuhaus, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.68.9 68, 9 (1992); U. H. E. Hansmann and Y. Okomoto, J. Comput. Chem. JCCHDD 0192-8651 10.1002/jcc.540141110 14, 1333 (1993).
31. C. Jarzynski, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.78. 2690 78, 2690 (1997); C. Jarzynski, Phys. Rev. E PLEEE8 1063-651X 10.1103/PhysRevE.56.5018 56, 5018 (1997).
32. A. M. Ferrenberg and R. H. Swendsen, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.63.1195 63, 1195 (1989); S. Kumar, D. Bouzida, R. H. Swendsen, P. A. Kollman, and J. M. Rosenberg, J. Comput. Chem. JCCHDD 0192-8651 10.1002/jcc.540130812 13, 1011 (1992); S. Kumar, J. M. Rosenberg, D. Bouzida, R. H. Swendsen, and P. A. Kollman, J. Comput. Chem. JCCHDD 0192-8651 10.1002/jcc.540161104 16, 1339 (1995).
33. B. Roux, Comput. Phys. Commun. 91, 275 (1995);
34. S. Kumar, P. W. Payne, and M. Vasquez, J. Comput. Chem. 17, 1269 (1996).
35. Y. Zhou, M. Karplus, J. M. Wichert, and C. K. Hall, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.474186 107, 10691 (1997); E. Gallicchio, M. Andrec, A. K. Felts, and R. M. Levy, J. Phys. Chem. B JPCBFK 1089-5647 10.1021/jp045294f 109, 6722 (2005); J. D. Chodera, W. C. Swope, J. W. Pitera, C. Seok, and K. A. Dill, J. Chem. Theory Comput. JCTCCE 1549-9618 10.1021/ct0502864 3, 26 (2007).
36. S. Schnabel, M. Bachmann, and W. Janke, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.98.048103 98, 048103 (2007).
37. P. G. de Gennes, Scaling Concepts in Polymer Physics (Cornell University Press, Ithaca, NY, 1979).
38. N. Alexandrov, Protein Sci. PRCIEI 0961-8368 2, 1989 (1993).
39. M. Mallela, G. Krishna, and S. W. Wanglander, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.0409114102 102, 1053 (2005).
40. E. Jacob and R. Unger, Bioinformatics BOINFP 1367-4803 10.1093/bioinformatics/btl318 23, E225 (2007).
41. J. Cellitti, R. Bernstein, and S. Marqusee, Protein Sci. PRCIEI 0961-8368 10.1110/ps.062632807 16, 852 (2007).
42. C. C. Chow, C. Chow, V. Raghunathan, T. J. Huppert, E. B. Kimball, and S. Cavagnero, Biochemistry BICHAW 0006-2960 10.1021/bi0273056 42, 7090 (2003).
43. U. H. E. Hansmanna and Y. Okamoto, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.478169 110, 1267 (1999).