Computation of protein pK's values by an integrated density functional theory/Polarizable Continuum Model approach

Theoretical Chemistry Accounts

Volumn 111, Issue 2-6, 2004, Pages 237-245

  Barone, Vincenzo ^a   Improta, Roberto ^a,b   Rega, Nadia ^a  

^a UNIVERSITY OF NAPLES FEDERICO II   (Italy)

^b CNR   (Italy)

Author keywords

Human prion protein; pK calculation; Polarizable Continuum Model

Indexed keywords

HISTIDINE; PRION PROTEIN;

ARTICLE; CALCULATION; CONFORMATION; DENSITY FUNCTIONAL THEORY; POLARIZATION; PROTON TRANSPORT; QUANTUM MECHANICS; THEORETICAL MODEL; THEORETICAL STUDY;

EID: 2442521209     PISSN: 1432881X     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00214-003-0541-4     Document Type: Article

References (47)

1. (a) Hansch C, Sammes PG, Taylor JB (eds) (1990) Comprehensive medicinal chemistry Vol 4. Quantitative drug design. Pergamon, Oxford;
2. (b) Shuurmann G, (1998) In: Ecotoxicology. Shuurmann G, Marken B (eds) John Wiley, New York, pp 665-749
3. (a) Reeve W, Erikson CM, Aluotto PF (1979) Can J Chem 57: 2747;
4. (b) Bordwell FG (1988) Acc Chem Res 21: 456
5. (a) Li H, Hains AW, Everts JE, Robertson AD, Jensen JH (2002) J Phys Chem B 106: 3486;
6. (b) Jang YH, Goddard WA III, Noyes KT, Sowers LC, Hwang S, Chung DS (2003) J Phys Chem B 107: 344
7. (a) Shuurmann G (1997) In: Chen F, Shuurmann G (eds) Quantitative structure - activity relationship in environmental sciences Vol VII. SETAC, Pensacola, FL, p 225;
8. (b) Shuurmann G, Cossi M, Barone V, Tomasi J (1998) J Phys Chem A 102: 6706;
9. (c) Adzelm J, Kulmel C, Klamt A (1995) J Chem Phys 103: 9312;
10. (d) Cramer CJ, Truhlar D (1992) Science 256: 213;
11. (e) da Silva CO, da Silva EC, Nascimento MAC (2000) J Phys Chem A 104: 2402;
12. (f) Liptak MD, Shields GC (2001) J Am Chem Soc 123: 7314;
13. (g) Liptak MD, Gross KC, Seybold PG, Feldgus S, Shields GC (2002) J Am Chem Soc 124: 6421;
14. (h) Chipman DM (2002) J Phys Chem A 106: 7413
15. Piego JR Jr (2003) Chem Phys Lett 367: 145
16. Saracino GAA, Improta R, Barone V (2003) Chem Phys Lett 373: 411
17. Li H, Pomelli CS, Jensen JH (2003) Theor Chem Acc 109: 71
18. Scalmani G, Barone V, Kudin K, Pomelli C, Scuseria GE, Frisch M Theor Chem Acc (in press)
19. Bashford D, Gerwert K (1992) J Mol Biol 224: 473-486
20. Prusiner SB, DeArmond SJ (1994) Annu Rev Neurosci 17: 311
21. Weissmann C (1996) FEBS Lett 21: 482
22. Prusiner SB (1991) Science 252: 1515
23. Prusiner SB, McKinley MP, Bowman KA, Bolton DC, Bendheim PE, Groth DF, Glenner GG (1983) Cell 35: 349
24. Swietnicki W, Petersen R, Gambetti P, Surewicz WK (1997) J Biol Chem 272: 27517
25. Jackson GS, Hill AF, Joseph C, Hosszu L, Power A, Waltho JP, Clarke AR (1999) Collinge J Biochim Biophys Acta 1431: 1
26. Hornemann S, Glockshuber R (1998) Proc Natl Acad Sci USA 95: 6010
27. Alonso DOV, DeArmond SJ, Cohen FE, Daggett V (2001) Proc Natl Acad Sci USA 98: 2985
28. Alonso DOV, An C, Daggett V (2002) Philos Trans R Soc London Ser A 360: 1165
29. Langella E, Improta R, Barone V (submitted)
30. Topol IA, Tawa GJ, Burt SK, Rashin AA (1999) J Chem Phys 111: 10998
31. Tissandier MD, Cowen KA, Feng WY, Gundluach E, Cohen MH, Earhart AD, Coe JV, Tuttle TR (1998) J Phys Chem A 102: 7787
32. Lim C, Bashford D, Karplus M (1991) J Phys Chem 95: 5610
33. Cossi M, Rega N, Scalmani G, Barone V (2002) J Chem Phys 117: 43
34. Barone V, Cossi M, Tomasi J (1997) J Chem Phys 107: 3210
35. Cances E, Mennucci B, Tomasi J (1997) J Chem Phys 107: 3031
36. Cossi M, Rega N, Scalmani G, Barone V (2001) J Chem Phys 114: 5691
37. Cossi M, Rega N, Scalmani G, Barone V (2003) J Comput Chem 24: 669
38. Amovilli C, Barone V, Cammi R, Cances E, Cossi M, Mennucci B, Pomelli CS, Tomasi J (1998) Adv Quantum Chem 32: 227
39. Tomasi J, Persico M (1994) Chem Rev 94: 2027
40. Chipman DM (2000) J Chem Phys 112: 5558
41. Mennucci B, Tomasi J (1997) J Chem Phys 106: 5151
42. Adamo C, Barone V (1999) J Chem Phys 110: 6158
43. Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Montgomery JA Jr, Vreven T, Kudin KN, Burant JC, Millam JM, Iyengar SS, Tomasi J, Barone V, Mennucci B, Cossi M, Scalmani G, Rega N, Petersson GA, Nakatsuji H, Hada M, Ehara M, Toyota K, Fukuda R, Hasegawa J, Ishida M, Nakajima T, Honda Y, Kitao O, Nakai H, Klene M, Li X, Knox JE, Hratchian HP, Cross JB, Adamo C, Jaramillo J, Gomperts R, Stratmann RE, Yazyev O, Cammi R, Pomelli C, Ochterski J, Ayala PY, Morokuma K, Voth G, Salvador P, Dannenberg JJ, Zakrzewski VG, Dapprich S, Daniels AD, Strain MC, Farkas O, Malick DK, Rabuck AD, Raghavachari K, Foresman JB, Ortiz JV, Cui Q, Baboul AG, Clifford S, Cioslowski J, Stefanov BB, Liu G, Liashenko A, Piskorz P, Komaromi I, Martin RL, Fox DJ, Keith T, Al-Laham MA, Peng CY, Nanayakkara A, Challacombe M, Gill PMW, Johnson B, Chen W, Wong MW, Gonzalez C, Pople JA (2003) Gaussian, Pittsburgh, PA
44. Rappé AK, Casewit CJ, Colwell KS, Goddard WA III, Skiff WM (1992) J Am Chem Soc 114: 10024
45. Dapprich S, Komáromi I, Byun KS, Morokhma K, Frisch MJ (1999) J Mol Struc (Theochem) 461: 1
46. Zahn R, Liu A, Luhrs T, Riek R, von Schroetter C, Garcia F, Billeter M, Calzolai L, Wider G, Wüthrich K (2000) Proc Natl Acad Sci USA 97: 145-150
47. Beroza P, Fredkin DR, Okamura MY, Feher G (1991) J Mol Biol 224: 473