Energetics and mechanism of the normal-to-amyloidogenic isomerization of β2-microglobulin: On-the-fly string method calculations

Journal of Physical Chemistry B

Volumn 116, Issue 31, 2012, Pages 9371-9375

  Stober, Spencer T ^a   Abrams, Cameron F ^a  

^a Drexel University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; DIALYSIS; ISOMERS; PROTONATION;

CIS-TRANS; CIS-TRANS ISOMERIZATION; COLLECTIVE VARIABLES; ELECTROSTATIC ATTRACTIONS; FINITE TEMPERATURE STRING METHODS; HISTIDINE RESIDUES; HYDROPHOBIC POCKETS; IN-VITRO; MUTAGENESIS EXPERIMENT; N-TERMINALS; ON-THE-FLY; PROTONATED; PROTONATING; PROTONATION STATE; SIDE-CHAINS; STRING METHODS;

ISOMERIZATION;

EID: 84864913316     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp304805v     Document Type: Article

References (24)

1. Gidalevitz, T.; Ben-Zvi, A.; Ho, K. H.; Brignull, H. R.; Morimoto, R. I. Science 2006, 311, 1471-4
2. Rubin, E.; Gorstein, F.; Schwarting, R.; Strayer, D., Eds. Rubin's Pathology: Clinicopathologic Foundations of Medicine, 4 th ed.; Lippincott Williams & Wilkins: Boston, 2004.
3. Gussow, D.; Rein, R.; Ginjaar, I.; Hochstenbach, F.; Seemann, G.; Kottman, A.; Ploegh, H. J. Immunol. 1987, 139, 3132-3138
4. Gorevic, P. D.; Munoz, P. C.; Casey, T. T.; DiRaimondo, C. R.; Stone, W. J.; Prelli, F. C.; Rodrigues, M. M.; Poulik, M. D.; Frangione, B. Proc. Natl. Acad. Sci. U. S. A. 1986, 83, 7908-12
5. Padrini, R.; Canova, C.; Conz, P.; Mancini, E.; Rizzioli, E.; Santoro, A. Kidney Int. 2005, 68, 2331-7
6. Eichner, T.; Kalverda, A. P.; Thompson, G. S.; Homans, S. W.; Radford, S. E. Mol. Cell 2011, 41, 161-72
7. Esposito, G.; Ricagno, S.; Corazza, A.; Rennella, E.; Gümral, D.; Mimmi, M.; Betto, E.; Pucillo, C.; Fogolari, F.; Viglino, P. J. Mol. Biol. 2008, 378, 887-97
8. Trinh, C. H.; Smith, D. P.; Kalverda, A. P.; Phillips, S. E. V.; Radford, S. E. Proc. Natl. Acad. Sci. U. S. A. 2002, 99, 9771-6
9. Maragliano, L.; Vanden-Eijnden, E. Chem. Phys. Lett. 2007, 446, 182-190
10. Maragliano, L.; Fischer, A.; Vanden-Eijnden, E.; Ciccotti, G. J. Chem. Phys. 2006, 125, 24106
11. E, W.; Ren, W.; Vanden-Eijnden, E. J. Phys. Chem. B 2005, 109, 6688-93
12. Eichner, T.; Radford, S. E. J. Mol. Biol. 2009, 386, 1312-1326
13. Cheng, H. N.; Bovey, F. A.; Laboratories, B.; Murray, H. Biopolymers 1977, 16, 1465-1472
14. Vanden-Eijnden, E.; Venturoli, M. J. Chem. Phys. 2009, 130, 194103
15. Ovchinnikov, V.; Karplus, M.; Vanden-Eijnden, E. J. Chem. Phys. 2011, 134, 085103
16. Zhu, F.; Hummer, G. Proc. Natl. Acad. Sci. U. S. A. 2010, 107, 19814
17. Vashisth, H.; Maragliano, L.; Abrams, C. F. Biophys. J. 2012, 102, 1979-1987
18. Stober, S.; Abrams, C. F. Protein Sci. 2012, 21, 307-317
19. Jorgensen, W.; Chandrasekhar, J.; Madura, J.; Impey, R.; Klein, M. J. Chem. Phys. 1983, 79, 926
20. Humphrey, W.; Dalke, A.; Schulten, K. J. Mol. Graph. 1996, 14, 33-38
21. MacKerell, A., Jr.; Bashford, D.; Bellott, M.; Dunbrack, R., Jr.; Evanseck, J.; Field, M.; Fischer, S.; Gao, J.; Guo, H.; Ha, S. J. Phys. Chem. B 1998, 102, 3586-3616
22. Mackerell, A. D.; Feig, M.; Brooks, C. L. J. Comput. Chem. 2004, 25, 1400-15
23. Phillips, J. C.; Braun, R.; Wang, W.; Gumbart, J.; Tajkhorshid, E.; Villa, E.; Chipot, C.; Skeel, R. D.; Kalé, L.; Schulten, K. J. Comput. Chem. 2005, 26, 1781-802
24. Bonomi, M.; Branduardi, D.; Bussi, G.; Camilloni, C.; Provasi, D.; Raiteri, P.; Donadio, D.; Marinelli, F.; Pietrucci, F.; Broglia, R. A. Comput. Phys. Commun. 2009, 180, 1961-1972