Thermodynamic analysis of protegrin-1 insertion and permeation through a lipid bilayer

Journal of Physical Chemistry B

Volumn 115, Issue 49, 2011, Pages 14704-14712

  Vivcharuk, Victor ^a   Kaznessis, Yiannis N ^a  

^a University of Minnesota   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACTIVATION ENERGY; ADSORPTION; DIFFERENTIAL EQUATIONS; DYNAMICS; ENERGY BARRIERS; FREE ENERGY; MOLECULAR DYNAMICS; PEPTIDES; PERMEATION; RATE CONSTANTS; SURFACE DIFFUSION; THERMOANALYSIS;

ACTIVATION FREE ENERGY; ADAPTIVE BIASING; AQUEOUS PHASE; CATIONIC ANTIMICROBIAL PEPTIDES; ENERGY MINIMA; GENERALIZED LANGEVIN EQUATION; INSERTION PROCESS; KRAMERS THEORY; LANGEVIN EQUATION; MEMBRANE SURFACE; MOLECULAR DYNAMICS SIMULATIONS; POTENTIAL BARRIERS; POTENTIAL OF MEAN FORCE; PROTEGRIN-1; THERMO DYNAMIC ANALYSIS; TIME CORRELATION FUNCTIONS; TRANSMEMBRANES; TRANSMISSION COEFFICIENTS;

LIPID BILAYERS;

EID: 83455219504     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp205153y     Document Type: Article

References (50)

1. Fahrner, R. L.; Dieckmann, T.; Harwig, S. S.; Lehrer, R. I.; Eisenberg, D.; Feigon, J. Chem. Biol. 1996, 3, 543-550
2. Jenssen, H.; Hammil, P.; Hancock, R. E. Clin. Microbiol. Rev. 2006, 19, 491-511
3. Bolintineanu, D.; Sayyed-Ahmad, A.; Davis, H. T.; Kaznessis, Y. N. PLoS Comput. Biol. 2009, 5, e1000277
4. Bolintineanu, D.; Hazrati, E.; Davis, H. T.; Lahrer, R. I.; Kaznessis, Y. N. Peptides 2009, 31 (1) 1-8
5. Mani, R.; Tang, M.; Wu, X.; Buffy, I. J.; Waring, A. J.; Sherman, M. A.; Hong, M. Biochemistry 2006, 45, 8341-8349
6. Langham, A. A.; Sayyed-Ahmad, A.; Kaznessis, Y. N. J. Am. Chem. Soc. 2008, 130, 4338-4346
7. Ostberg, N.; Khandelia, H.; Kaznessis, Y. N. Peptides 2005, 26 (2) 297-306
8. Langham, A. A.; Khandelia, H.; Kaznessis, Y. N. Biopolymers 2006, 84 (2) 219-231
9. Langham, A. A.; Waring, A. J.; Kaznessis, Y. N. BMC Biochem. 2007, 8 (11) 1-13
10. Khandelia, H.; Kaznessis, Y. N. Peptides 2005, 26 (11) 2037-2049
11. Khandelia, H.; Langham, A. A.; Kaznessis, Y. N. Biochim. Biophys. Acta 2006, 1758 (9) 1224-1234
12. Khandelia, H.; Kaznessis, Y. N. Biochim. Biophys. Acta, Biomembr. 2007, 1768, 509-520
13. Jang, H.; Ma, B.; Lal, R.; Nussinov, R. Biophys. J. 2008, 95, 4631-4642
14. Lee, J.; Im, W. J. Comput. Chem. 2009, 30, 1334-1343
15. Vivcharuk, V.; Kaznessis, Y. J. Phys. Chem B 2010, 114 (8) 2790-2797
16. Sayyed-Ahmad, A.; Kaznessis, Y. N. PLoS One 2009, 4 (3) e4799
17. Jang, H.; Arce, F. T.; Mustata, M.; Ramachandran, S.; Capone, R.; Nussinov, R.; Lal, R. Biophys. J. 2011, 100, 1775-1783
18. Darve, E. In Free Energy Calculations; Chipot, C.; Pohorille, A., Eds.; Springer: Berlin, Germany, 2007; p 119.
19. Henin, J.; Chipot, C. J. Chem. Phys. 2004, 121, 2904-2914
20. Phillips, J. C.; Braun, R.; Wang, W.; Gumbart, J.; Tajkhorshid, E.; Villa, E.; Chipot, C.; Skeel, R. D.; Kalle, L.; Schulten, K. J. Comput. Chem. 2005, 26, 1781-1802
21. Henin, J.; Fiorin, G.; Klein, M. J. Chem. Theory Comput. 2010, 6, 35-47
22. Gorfe, A. A.; Babakhani, A.; McCammon, J. A. Angew. Chem., Int. Ed. 2007, 46, 8234-8237
23. Ulmschneider, M. B.; Doux, J. P. F.; Killian, J. A.; Smith, J. C.; Ulmschneider, P. J. Am. Chem. Soc. 2010, 132, 3452-3460
24. Bemporad, D.; Essex, J. W. J. Phys. Chem B 2004, 108, 4875-4884
25. Vivcharuk, V.; Tomberli, B.; Tolokh, I. S.; Gray, C. G. Phys. Rev. E 2008, 77, 031913
26. Allen, M. P.; Tildesley, D. Computer Simulation of Liquids; Oxford University Press: New York, 2005; p 385.
27. Shin, J. Y.; Abbot, N. L. Langmuir 2001, 17, 8434-8443
28. Roux, B.; Karplus, M. Annu. Rev. Biophys. Biomol. Struct. 1994, 23, 731-761 and references therein
29. White, G. W. N.; Goldman, S.; Gray, C. G. Mol. Phys. 2000, 98 (22) 1871-1885
30. Hu, J.; Goldman, S.; Gray, C. G.; Guy, H. R. Mol. Phys. 2000, 98 (8) 535-547
31. Kramers, H. A. Phys. 1940, 7, 284-304
32. Hanggi, P.; Talkner, P.; Berkovec, M. Rev. Mod. Phys. 1990, 62, 251-341
33. Carter, E. A.; Ciccotti, G.; Hynes, J. T.; Kapral, R. Chem. Phys. Lett. 1989, 156, 472-477
34. Chipot, C.; Pohorille, A. J. Am. Chem. Soc. 1998, 120, 11912-11924
35. Grote, R. F.; Hynes, J. T. J. Chem. Phys. 1980, 73, 2715-2732
36. Huston, S. E.; Zichi, P. J. R. D. A. J. Am. Chem. Soc. 1989, 111, 5680-5687
37. Tolokh, I. S.; White, G. W. N.; Goldman, S.; Gray, C. G. Mol. Phys. 2002, 100, 2511-2359
38. Jo, S.; Kim, T.; Iyer, V. G.; Im, W. J. Comput. Chem. 2008, 29, 1859-1865
39. Brooks, B. R.; Brucolleri, R. E.; Olafson, B. D.; States, D. J.; Swaminathan, S.; Karplus, M. J. Comput. Chem. 1983, 4, 187-217
40. MacKerell, A. D. J. Phys. Chem. B 1998, 102, 3586-3616
41. MacKerell, A. D.; Feig, M.; Brooks, C. L. J. Chem. Soc. 2004, 126, 698-699
42. Martyna, G. J.; Tobias, D. J.; Klein, M. L. J. Chem. Phys. 1994, 101, 4177-4189
43. Feller, S. E.; Zhang, Y.; Pastor, R. W.; Brooks, B. R. J. Chem. Phys. 1995, 103, 4613-4621
44. Tang, M.; Waring, J.; Hong, M. ChemBioChem 2008, 9, 1487-1482
45. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. J. Chem. Phys. 1983, 79, 926-935
46. Darden, T.; Perera, L.; Li, L.; Pedersen, L. Structure 1999, 7, R55-R60
47. den Otter, W. K. J. Chem. Phys. 2000, 112 (17) 7283-7293
48. Chipot, C.; Henin, J. J. Chem. Phys. 2005, 123, 244906
49. Walter, A.; Gutknecht, J. J. Membr. Biol. 1986, 90, 207-217
50. Vivcharuk, V.; Kaznessis, Y. To be submitted for publication.