The impact of protonation equilibria on protein structure

Journal of Physics Condensed Matter

Volumn 17, Issue 18, 2005, Pages

  Długosz, Maciej ^a   Antosiewicz, Jan M ^a  

^a UNIVERSITY OF WARSAW   (Poland)

Author keywords

[No Author keywords available]

Indexed keywords

CHARGE TRANSFER; COMPUTER SIMULATION; CONFORMATIONS; FUNCTIONS; IONIZATION; MOLECULAR DYNAMICS; MOLECULAR STRUCTURE; PROTONS;

PROTEIN STRUCTURES; PROTON EXCHANGE; PROTON TRANSFER; PROTONATION EQUILIBRIUM;

PROTEINS;

EID: 23144444735     PISSN: 09538984     EISSN: None     Source Type: Journal    
DOI: 10.1088/0953-8984/17/18/016     Document Type: Article

References (46)

1. Stryer L 1995 Biochemistry 4th edn (New York: Freeman)
2. Pace C N, Laurents D V and Thomson J A 1990 Biochemistry 29 2564
3. Pace C N, Laurents D V and Erickson R E 1992 Biochemistry 31 2728
4. Tollinger M, Crowhurst K A, Kay L E and Forman-Kay J D 2003 Proc. Natl Acad. Sci. USA 100 4545
5. Huang Q, Opitz R, Knapp E-W and Herrmann A 2002 Biophys. J. 82 1050
6. Ripoll D R, Vorobjev Y N, Li wo A, Vila J A and Scheraga H A 1996 J. Mol. Biol. 264 770
7. Muth G W, Chem L, Kosek A B and Strobel S A 2001 RNA 7 1403
8. Saksmerprome V and Burke D H 2004 J. Mol. Biol. 341 685
9. Martinez R E and Bowler B E 2004 J. Am. Chem. Soc. 126 6751
10. Wüthrich K 1986 NMR of Proteins and Nucleic Acids (New York: Wiley)
11. Bartik K, Redfield C and Dobson C M 1994 Biophys. J. 66 1180
12. Schaller W and Robertson A D 1995 Biochemistry 34 4714
13. Bashford D and Karplus M 1990 Biochemistry 29 10219
14. Bashford D, Case D A, Dalvit C, Tennant L and Wright P E 1993 Biochemistry 32 8045
15. Yang A S, Gunner M R, Sampogna R, Sharp K and Honig B 1993 Proteins: Struct. Funct. Genet. 15 252
16. Antosiewicz J, McCammon J A and Gilson M K 1994 J. Mol. Biol. 238 415
17. Antosiewicz J, Briggs J M, Elcock A E, Gilson M K and McCammon J A 1996 J. Comput. Chem. 17 1633
18. Alexov E G and Gunner M R 1997 Biophys. J. 74 2075
19. Warshel A 1981 Biochemistry 20 3167
20. Warshel A and Russell S 1984 Q. Rev. Biophys. 17 283
21. Sham Y Y, Chu Z T and Warshel A 1997 J. Phys. Chem. 101 4458
22. Warshel A and Papazyan A 1998 Curr. Opin. Struct. Biol. 8 211
23. Briggs J M and Antosiewicz J 1999 Rev. Comput. Chem. 13 249
24. Schutz C N and Warshel A 2001 Proteins: Struct. Funct. Genet. 44 400
25. Simonson T, Carlsson J and Case D A 2004 J. Am. Chem. Soc. 126 4167
26. McCammon J A and Harvey S C 1987 Dynamics of Proteins and Nucleic Acids (Cambridge: Cambridge University Press)
27. Lim C, Bashford D and Karplus M 1991 J. Phys. Chem. 95 5610
28. Chipman D M 2002 J. Phys. Chem. A 106 7413
29. Li H, Robertson A D and Jensen J H 2002 J. Phys. Chem. B 106 3486
30. Li H, Robertson A D and Jensen J H 2004 Proteins: Struct. Funct. Bioinf. 55 689
31. Baptista A M, Martel P J and Petersen S B 1997 Proteins: Struct. Funct. Genet. 27 523
32. Börjesson U and Hünenberger P H 2001 J. Chem. Phys. 114 9706
33. Börjesson U and Hünenberger H 2004 J. Phys. Chem. B 108 13551
34. Lee M S, Salsburyy F R Jr and Brooks C L III 2004 Proteins: Struct. Funct. Genet. 56 738
35. Bürgi R, Kollman P A and van Gunsteren W F 2002 Proteins: Struct. Funct. Genet. 47 469
36. Baptista A M, Teixeira V H and Soares C M 2002 J. Chem. Phys. 117 4184
37. Mongan J, Case D A and McCammon J A 2004 J. Comput. Chem. 25 2038
38. Walczak A M and Antosiewicz J M 2002 Phys. Rev. E 60 051911
39. Dlugosz M, Antosiewicz J M and Robertson A D 2004 Phys. Rev. E 69 021915
40. Dlugosz M and Antosiewicz J M 2004 Chem. Phys. 302 161
41. Read R J, Fujinaga M, Sielecki A R and James M N G 1983 Biochemistry 22 4420
42. Antosiewicz J 1995 Biophys. J. 69 1344
43. Lill M A and Helms V 2001 J. Chem. Phys. 115 7993
44. Spörlein S, Carstens H, Satzger H, Renner C, Berrendt R, Moroder L, Tavan P, Zinth Z and Wachtveitl J 2002 Proc. Natl Acad. Sci. USA 99 7998
45. Hummer G, Garcia A E and Garde S 2001 Proteins: Struct. Funct. Genet. 42 77
46. Humphrey W, Dalke A and Schulten K 1996 J. Mol. Graph. 14 33