Studies of the reduction and protonation behavior of tetraheme cytochromes using atomic detail

Journal of Biological Inorganic Chemistry

Volumn 7, Issue 1-2, 2002, Pages 200-216

  Teixeira, Vitor H ^a   Soares, Cláudio M ^a   Baptista, António M ^a  

^a INSTITUTO DE TECNOLOGIA QUÍMICA E BIOLÓGICA   (Portugal)

Author keywords

Binding equilibrium; Continuum electrostatics; Electron proton coupling; Redox Bohr effect; Sulfate reducing bacteria

Indexed keywords

CYTOCHROME C3; HEME; HISTIDINE; PROPIONIC ACID; PROPIONIC ACID D; PROTON; UNCLASSIFIED DRUG; CYTOCHROME C; CYTOCHROME C(3); PROPIONIC ACID DERIVATIVE;

ACCURACY; ACIDITY; ARTICLE; BINDING AFFINITY; BOHR EFFECT; COMPARATIVE STUDY; CORRELATION ANALYSIS; DESULFOVIBRIO AFRICANUS; ELECTRICITY; ELECTRON; MATHEMATICAL COMPUTING; MICROSCOPY; OXIDATION REDUCTION REACTION; PH MEASUREMENT; PRIORITY JOURNAL; PROTON TRANSPORT; REDUCTION; SIMULATION; THEORY; THERMODYNAMICS; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; ENZYME STABILITY; ENZYMOLOGY; METABOLISM; MONTE CARLO METHOD; PROTEOBACTERIA;

DESULFOVIBRIO AFRICANUS;

COMPUTER SIMULATION; CYTOCHROME C GROUP; ELECTRONS; ELECTROSTATICS; ENZYME STABILITY; HEME; HISTIDINE; MODELS, MOLECULAR; MONTE CARLO METHOD; OXIDATION-REDUCTION; PROPIONATES; PROTEOBACTERIA; PROTONS; THERMODYNAMICS;

EID: 0036359052     PISSN: 09498257     EISSN: None     Source Type: Journal    
DOI: 10.1007/s007750100287     Document Type: Article

References (112)

1. Coutinho IB, Xavier AV (1994) Methods Enzymol 243:119-140
2. Pereira IAC, Romão CV, Xavier AV, LeGall J, Teixeira M (1998) JBIC 3:494-498
3. Pereira IC, Teixeira M, Xavier AV (1998) Struct Bonding 91:65-89
4. Yagi T, Honya M, Tamiya N (1968) Biochim Biophys Acta 153:699-705
5. Aubert C, Brugna M, Dolla A, Bruschi M, Giudici-Orticoni MT (2000) Biochim Biophys Acta 1476:85-92
6. Matias PM, Coelho R, Pereira IAC, Coelho AV, Thompson AW, Sieker LC, Le Gall J, Carrondo MA (1999) Structure 7:119-130
7. Matias PM, Soares CM, Saraiva LM, Coelho R, Morais J, LeGall J, Carrondo MA (2001) JBIC 6:63-81
8. Matias PM, Saraiva LM, Soares CM, Coelho AV, LeGall J, Carrondo MA (1999) JBIC 4:478-494
9. Papa S, Guerrieri F, Izzo G (1979) FEBS Lett 105:213-216
10. Santos H, Moura JJG, Moura I, LeGall J, Xavier AV (1984) Eur J Biochem 141:283-296
11. Coletta M, Catarino T, LeGall J, Xavier AV (1991) Eur J Biochem 202:1101-1106
12. Turner DL, Salgueiro CA, Catarino T, LeGall J, Xavier AV (1994) Biochim Biophys Acta 1187:232-235
13. Park JS, Ohmura T, Kano K, Sagara T, Niki K, Kyogoku Y, Akutsu H (1996) Biochim Biophys Acta 1293:45-54
14. Louro RO, Pacheco I, Turner DL, LeGall J, Xavier AV (1996) FEBS Lett 390:59-62
15. Turner DL, Salgueiro CA, Catarino T, LeGall J, Xavier AV (1996) Eur J Biochem 241:723-731
16. Louro RO, Catarino T, LeGall J, Xavier AV (1997) JBIC 2:488-491
17. Salgueiro CA, Turner DL, LeGall J, Xavier AV (1997) JBIC 2:343-349
18. Louro RO, Catarino T, Turner DL, Pi,carra-Pereira MA, Pacheco I, LeGall J, Xavier AV (1998) Biochemistry 37:15808-15815
19. Saraiva LM, Salgueiro CA, da Costa PN, Messias AC, LeGall J, van Dongen WMAM, Xavier AV (1998) Biochemistry 37:12160-12165
20. Soares CM, Martel PJ, Carrondo MA (1997) JBIC 2:714-727
21. Soares CM, Martel PJ, Mendes J, Carrondo MA (1998) Biophys J 74:1708-1721
22. Martel PJ, Soares CM, Baptista AM, Fuxreiter M, Náray-Szabó G, Louro RO, Carrondo MA (1999) JBIC 4:73-86
23. Baptista AM, Martel PJ, Soares CM (1999) Biophys J 76:2978-2998
24. Karplus M, Petsko GA (1990) Nature 347:631-639
25. van Gunsteren WF, Berendsen HJC (1990) Angew Chem Int Ed Engl 29:992-1023
26. Sharp KA, Honig B (1990) Annu Rev Biophys Biophys Chem 19:301-332
27. Honig B, Nicholls A (1995) Science 268:1144-1149
28. Martel PJ, Baptista A, Petersen SB (1996) Biotechnol Annu Rev 2:315-372
29. Churg AK, Warshel A (1986) Biochemistry 25:1675-1681
30. Cutler RL, Davies AM, Creighton S, Warshel A, Moore GR, Smith M, Mauk AG (1989) Biochemistry 28:3188-3197
31. Langen R, Jensen GM, Jacob U, Stephens PJ, Warshel A (1992) J Biol Chem 267:25625-25627
32. Langen R, Brayer GD, Berghuis AM, McLendon G, Sherman F, Warshel A (1992) J Mol Biol 224:589-600
33. Mark AE, van Gunsteren WF (1994) J Mol Biol 240:167-176
34. Alden RG, Parson WW, Chu ZT, Warshel A (1995) J Am Chem Soc 117:12284-12298
35. Apostolakis J, Muegge I, Ermler U, Fritzsch G, Knapp EW (1996) J Am Chem Soc 118:3743-3752
36. Muegge I, Qi PX, Wand AJ, Chu ZT, Warshel A (1997) J Phys Chem B 101:825-836
37. Warshel A (1981) Biochemistry 20:3167-3177
38. Russell ST, Warshel A (1985) J Mol Biol 185:389-404
39. Warshel A, Sussman F, King G (1986) Biochemistry 25:8368-8372
40. Lee FS, Chu ZT, Warshel A (1993) J Comput Chem 14:161-185
41. Del Buono GS, Figueirido FE, Levy RM (1994) Proteins Struct Funct Genet 20: 85-97
42. Warshel A, Russell ST (1984) Q Rev Biophys 17:283-422
43. Levy RM, Belhadj M, Kitchen DB (1991) J Chem Phys 95:3627-3633
44. Baptista AM, Martel PJ, Petersen SB (1997) Proteins Struct Funct Genet 27:523-544
45. Bashford D, Karplus M, Canters GW (1988) J Mol Biol 203:507-510
46. Gunner MR, Honig B (1991) Proc Natl Acad Sci USA 88:9151-9155
47. Bashford D, Karplus M (1990) Biochemistry 29:10219-10225
48. Bashford D, Gerwert K (1992) J Mol Biol 224:473-486
49. Bashford D, Case DA, Dalvit C, Tennant L, Wright PE (1993) Biochemistry 32:8045-8056
50. Yang AS, Gunner MR, Sampogna R, Sharp K, Honig B (1993) Proteins Struct Funct Genet 15:252-265
51. Demchuk E, Wade RC (1996) J Phys Chem 100:17373-17387
52. Warshel A, Aqvist J (1991) Annu Rev Biophys Biophys Chem 20:267-298
53. Simonson T, Brooks CL III (1996) J Am Chem Soc 118:8452-8458
54. Sham YY, Chu ZT, Warshel A (1997) J Phys Chem 101:4458-4472
55. Sham YY, Muegge I, Warshel A (1998) Biophys J 74:1744-1753
56. Warshel A, Papazyan A (1998) Curr Opin Struct Biol 8:211-217
57. Simonson T, Archontis G, Karplus M (1999) J Phys Chem B 103:6142-6156
58. Baptista AM, Soares CM (2001) J Phys Chem B 105:293-309
59. Beroza P, Case DA (1996) J Phys Chem 100:20156-20163
60. Spassov V, Bashford D (1999) J Comput Chem 20:1091-1111
61. Alexov EG, Gunner MR (1999) Biochemistry 38:8253-8270
62. Beroza P, Fredkin DR, Okamura MY, Feher G (1995) Biophys J 68:2233-2250
63. Lancaster CRD, Michel H, Honig B, Gunner MR (1996) Biophys J 70:2469-2492
64. Kannt A, Lancaster CRD, Michel H (1998) Biophys J 74:708-721
65. Ullmann GM (2000) J Phys Chem B 104:6293-6301
66. Antosiewicz J, McCammon JA, Gilson MK (1994) J Mol Biol 238:415-436
67. Oberoi H, Allewell NM (1993) Biophys J 65:48-55
68. Antosiewicz J, McCammon JA, Gilson MK (1996) Biochemistry 35:7819-7833
69. Zhou HX, Vijayakumar M (1997) J Mol Biol 267:1002-1011
70. Nielsen JE, Andersen KV, Honig B, Hooft RWW, Klebe G, Vriend G, Wade RC (1999) Protein Eng 12:657-662
71. Alexov EG, Gunner MR (1997) Biophys J 72:2075-2093
72. Haser R, Pierrot M, Frey M, Payan F, Astier J, Bruschi M, Le Gall J (1979) Nature 282:806-810
73. Higuchi Y, Kusunoki M, Matsuura Y, Yasuoka N, Kakudo M (1984) J Mol Biol 172:109-139
74. Matias PM, Frazão C, Morais J, Coll M, Carrondo MA (1993) J Mol Biol 234:680-699
75. Czjzek M, Payan F, Guerlesquin F, Bruschi M, Haser R (1994) J Mol Biol 243:653-667
76. Morais J, Palma PN, Frazão C, Caldeira J, LeGall J, Moura I, Moura JJ, Carrondo MA (1995) Biochemistry 34:12830-12841
77. Matias PM, Morais J, Coelho R, Carrondo MA, Wilson K, Dauter Z, Sieker L (1996) Protein Sci 5:1342-1354
78. Simões P, Matias PM, Morais J, Wilson K, Dauter Z, Carrondo MA (1998) Inorg Chim Acta 273:213-224
79. Messias AC, Kastrau DHW, Costa HS, LeGall J, Turner DL, Santos H, Xavier AV (1998) J Mol Biol 281:719-739
80. Norager S, Legrand P, Pieulle L, Hatchikian EC, Roth M (1999) J Mol Biol 290:881-902
81. Brennan L, Turner DL, Messias AC, Teodoro ML, LeGall J, Santos H, Xavier AV (2000) J Mol Biol 298:61-82
82. Pieulle L, Haladjian J, Bonicel J, Hatchikian EC (1996) Biochim Biophys Acta 1273:51-61
83. Magro V, Pieulle L, Forget N, Guigliarelli B, Petillot Y, Hatchikian EC (1997) Biochim Biophys Acta 1342:149-163
84. Valente AF, Saraiva LM, LeGall J, Xavier AV, Teixeira M, Pereira IAC (2001) Submitted;
85. Wyman J, Gill SJ (1990) Binding and linkage: functional chemistry of biological macromolecules. University Science Books, Mill Valley, Calif
86. Gilson MK (1993) Proteins Struct Funct Genet 15:266-282
87. Schaefer M, Sommer M, Karplus M (1997) J Phys Chem B 101:1663-1683
88. Bashford D, Karplus M (1991) J Phys Chem 95:9956-9561
89. Antosiewicz J, Porschke D (1989) Biochemistry 28:10072-10078
90. Beroza P, Fredkin DR, Okamura MY, Feher G (1991) Proc Natl Acad Sci USA 88:5804-5808
91. Vriend G (1990) J Mol Graph 8:52-56
92. Hooft RWW, Sander C, Vriend G (1996) Proteins Struct Funct Genet 26:363-376
93. Collaborative Computational Project, number 4 (1994) Acta Crystallogr Sect D 50:760-763
94. Eisenhaber F, Argos P (1993) J Comput Chem 14:1272-1280
95. Eisenhaber F, Lijnzaad P, Argos P, Sander C, Scharf M (1995) J Comput Chem 16:273-284
96. van Gunsteren WF, Berendsen HJC (1987) Groningen molecular simulation (GROMOS) library manual. Biomos, Groningen, The Netherlands
97. Smith LJ, Mark AE, Dobson CM, van Gunsteren WF (1995) Biochemistry 34:10918-10931
98. Bashford D (1997) In: Ishikawa Y, Oldehoeft RR, Reynders JVW, Tholburn M (eds) Scientific computing in object oriented parallel environments (ISCOPE97). (Lecture notes in computer science, vol. 1343) Springer, Berlin, pp 233-240
99. Gilson MK, Sharp KA, Honig B (1987) J Comput Chem 9:327-335
100. Harvey SC (1989) Proteins Struct Funct Genet 5:78-92
101. King G, Lee FS, Warshel A (1991) J Chem Phys 95:4366-4377
102. Simonson T, Perahia D (1995) Proc Natl Acad Sci USA 92:1082-1086
103. Tanford C, Kirkwood JG (1957) J Am Chem Soc 79:5333-5339
104. Sharp KA (1998) Biophys J 73:1241-1250
105. Gayda J, Benosman H, Bertrand P, More C, Asso M (1988) Eur J Biochem 177:199-206
106. Louro RO, Catarino T, Salgueiro CA, LeGall J, Xavier AV (1996) JBIC 1:34-38
107. Yang AS, Honig B (1993) J Mol Biol 231:459-474
108. You TJ, Bashford D (1995) Biophys J 69:1721-1733
109. Gibas CJ, Subramanian S (1996) Biophys J 71:138-147
110. Salgueiro CA, Turner DL, Xavier AV (1997) Eur J Biochem 244:721-734
111. Pavlov M, Siegbahn PEM, Blomberg MRA, Crabtree RH (1998) J Am Chem Soc 120:548-555
112. Kraulis PJ (1991) J Appl Crystallogr 24:946-950