Effective simulations of gas diffusion through kinetically accessible tunnels in multisubunit proteins: O 2 pathways and escape routes in T-state deoxyhemoglobin

Journal of the American Chemical Society

Volumn 134, Issue 27, 2012, Pages 11177-11184

  Shadrina, Maria S ^a   English, Ann M ^a   Peslherbe, Gilles H ^a  

^a Gina Cody School of Engineering and Computer Science   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ALTERNATIVE APPROACH; CONTROL ACCESS; DAMPENING EFFECTS; DEOXYHEMOGLOBIN; DISTAL HISTIDINE; ESCAPE ROUTE; GAS DIFFUSION; KINETIC DATA; LARGE SYSTEM; MD SIMULATION; MOLECULAR DYNAMICS SIMULATIONS; MULTISUBUNIT; POTENTIAL OF MEAN FORCE; REALISTIC SIMULATION; SIMULATION EFFICIENCY; SIMULATION TIME;

ACCESS CONTROL; AMINO ACIDS; BINDING SITES; HEMOGLOBIN; KINETICS; LIGANDS; MOLECULAR DYNAMICS; PORPHYRINS; PROTEINS;

DIFFUSION;

DEOXYHEMOGLOBIN; HISTIDINE; LIGAND; OXYGEN; PROTEIN;

ARTICLE; CALCULATION; CONTROLLED STUDY; CRYSTAL STRUCTURE; HUMAN; KINETICS; MOLECULAR DOCKING; MOLECULAR DYNAMICS; OXYGEN DIFFUSION; SIMULATION; TEMPERATURE;

ADULT; BINDING SITES; DIFFUSION; HEMOGLOBIN A; HEMOGLOBINS; HUMANS; KINETICS; MOLECULAR DYNAMICS SIMULATION; OXYGEN; PROTEIN MULTIMERIZATION;

EID: 84863814690     PISSN: 00027863     EISSN: 15205126     Source Type: Journal    
DOI: 10.1021/ja300903c     Document Type: Article

References (41)

1. Berg, O. G.; von Hippel, P. H. Annu. Rev. Biophys. Biophys. Chem. 1985, 14, 131-160
2. Cohen, J.; Schulten, K. Biophys. J. 2007, 93, 3591-3600
3. Elber, R. Curr. Opin. Struct. Biol. 2010, 20, 162-167
4. Tomita, A.; Kreutzer, U.; Adachi, S.; Koshihara, S. Y.; Jue, T. J. Exp. Biol. 2010, 213, 2748-2754
5. Elber, R.; Karplus, M. J. Am. Chem. Soc. 1990, 112, 9161-9175
6. Ruscio, J. Z.; Kumar, D.; Shukla, M.; Prisant, M. G.; Murali, T. M.; Onufriev, A. V. Proc. Natl. Acad. Sci. U.S.A. 2008, 105, 9204-9209
7. Cohen, J.; Arkhipov, A.; Braun, R.; Schulten, K. Biophys. J. 2006, 91, 1844-1857
8. Maragliano, L.; Cottone, G.; Ciccotti, G.; Vanden-Eijnden, E. J. Am. Chem. Soc. 2010, 132, 1010-1017
9. Bocahut, A.; Bernad, S.; Sebban, P.; Sacquin-Mora, S. J. Phys. Chem. B 2009, 113, 16257-16267
10. Orlowski, S.; Nowak, W. J. Mol. Model. 2007, 13, 715-723
11. Cohen, J.; Olsen, K. W.; Schulten, K. Methods Enzymol. 2008, 437, 439-57
12. Daigle, R.; Rousseau, J. A.; Guertin, M.; Lague, P. Biophys. J. 2009, 97, 2967-2977
13. Golden, S. D.; Olsen, K. W. Methods Enzymol. 2008, 437, 459-475
14. Czerminski, R.; Elber, R. Proteins: Struct., Funct., Bioinf. 1991, 10, 70-80
15. Schechter, A. N. Blood 2008, 112, 3927-3938
16. Savino, C.; Miele, A. E.; Draghi, F.; Johnson, K. A.; Sciara, G.; Brunori, M.; Vallone, B. Biopolymers 2009, 91, 1097-1107
17. Lepeshkevich, S. V.; Biziuk, S. A.; Lemeza, A. M.; Dzhagarov, B. M. Biochim. Biophys. Acta 2011, 1814, 1279-1288
18. Hub, J. S.; Kubitzki, M. B.; de Groot, B. L. PLoS Comput. Biol. 2010, 6, e1000774
19. Cohen, J.; Kim, K.; King, P.; Seibert, M.; Schulten, K. Structure (Cambridge) 2005, 13, 1321-1329
20. Tilton, R. F., Jr.; Kuntz, I. D., Jr.; Petsko, G. A. Biochemistry 1984, 23, 2849-2857
21. Gerber, R.; Buch, V.; Ratner, M. J. Chem. Phys. 1982, 94, 3022-3030
22. Straub, J.; Karplus, M. J. Chem. Phys. 1991, 94, 6737-6739
23. Das, B.; Helms, V.; Lounnas, V.; Wade, R. C. J. Inorg. Biochem. 2000, 81, 121-131
24. Phillips, J. C.; Braun, R.; Wang, W.; Gumbart, J.; Tajkhorshid, E.; Villa, E.; Chipot, C.; Skeel, R. D.; Kale, L.; Schulten, K. J. Comput. Chem. 2005, 26, 1781-1802
25. Chatake, T.; Shibayama, N.; Park, S. Y.; Kurihara, K.; Tamada, T.; Tanaka, I.; Niimura, N.; Kuroki, R.; Morimoto, Y. J. Am. Chem. Soc. 2007, 129, 14840-14841
26. Humphrey, W.; Dalke, A.; Schulten, K. J. Mol. Graphics 1996, 14, 27-28
27. Lukin, J. A.; Ho, C. Chem. Rev. 2004, 104, 1219-1230
28. Samuni, U.; Dantsker, D.; Ray, A.; Wittenberg, J. B.; Wittenberg, B. A.; Dewilde, S.; Moens, L.; Ouellet, Y.; Guertin, M.; Friedman, J. M. J. Biol. Chem. 2003, 278, 27241-27250
29. Scott, E. E.; Gibson, Q. H.; Olson, J. S. J. Biol. Chem. 2001, 276, 5177-5188
30. Pesce, A.; Nardini, M.; Dewilde, S.; Geuens, E.; Yamauchi, K.; Ascenzi, P.; Riggs, A. F.; Moens, L.; Bolognesi, M. Structure (Cambridge) 2002, 10, 725-735
31. Perutz, M. F.; Mathews, F. S. J. Mol. Biol. 1966, 21, 199-202
32. Birukou, I.; Schweers, R. L.; Olson, J. S. J. Biol. Chem. 2010, 285, 8840-8854
33. Birukou, I.; Soman, J.; Olson, J. S. J. Biol. Chem. 2011, 286, 10515-10529
34. Birukou, I.; Maillett, D. H.; Birukova, A.; Olson, J. S. Biochemistry 2011, 50, 7361-7374
35. Luisi, B.; Shibayama, N. J. Mol. Biol. 1989, 206, 723-736
36. Luisi, B.; Liddington, B.; Fermi, G.; Shibayama, N. J. Mol. Biol. 1990, 214, 7-14
37. Adachi, S.; Park, S. Y.; Tame, J. R.; Shiro, Y.; Shibayama, N. Proc. Natl. Acad. Sci. U.S.A 2003, 100, 7039-7044
38. Shibayama, N.; Yonetani, T.; Regan, R. M.; Gibson, Q. H. Biochemistry 1995, 34, 14658-14667
39. Ho, C. Adv. Protein Chem. 1992, 43, 153-312
40. Walder, J. A.; Chatterjee, R.; Steck, T. L.; Low, P. S.; Musso, G. F.; Kaiser, E. T.; Rogers, P. H.; Arnone, A. J. Biol. Chem. 1984, 259, 10238-10246
41. Esquerra, R. M.; Lopez-Pena, I.; Tipgunlakant, P.; Birukou, I.; Nguyen, R. L.; Soman, J.; Olson, J. S.; Kliger, D. S.; Goldbeck, R. A. Phys. Chem. Chem. Phys. 2010, 12, 10270-10278