-
1
-
-
0033001692
-
Simulation of electron-proton coupling with a Monte Carlo method: Application to cytochrome C3 using continuum electrostatics
-
Baptista, A. M., P. J. Martel, and C. M. Soares. 1999. Simulation of electron-proton coupling with a Monte Carlo method: application to cytochrome C3 using continuum electrostatics. Biophys. J. 76:2978-2998.
-
(1999)
Biophys. J.
, vol.76
, pp. 2978-2998
-
-
Baptista, A.M.1
Martel, P.J.2
Soares, C.M.3
-
2
-
-
0035120969
-
Some theoretical and computational aspects of the inclusion of proton isomerism in the protonation equilibrium of proteins
-
Baptista, A. M., and C. M. Soares. 2001. Some theoretical and computational aspects of the inclusion of proton isomerism in the protonation equilibrium of proteins. J. Phys. Chem. B. 105:293-309.
-
(2001)
J. Phys. Chem. B
, vol.105
, pp. 293-309
-
-
Baptista, A.M.1
Soares, C.M.2
-
3
-
-
84957665033
-
-
Y. Ishikawa, R. R. Oldehoeft, J. V. W. Reynders, and M. Tholburn, editors. Springer, Berlin, Germany
-
Bashford, D. 1997. In Scientific Computing in Object-Oriented Parallel Environments, Vol. 1343. Y. Ishikawa, R. R. Oldehoeft, J. V. W. Reynders, and M. Tholburn, editors. Springer, Berlin, Germany. 233-240.
-
(1997)
Scientific Computing in Object-Oriented Parallel Environments
, vol.1343
, pp. 233-240
-
-
Bashford, D.1
-
4
-
-
0026612756
-
Electrostatic calculations of the pKa values of ionisable groups in bacteriorhodopsin
-
Bashford, D., and K. Gerwert. 1992. Electrostatic calculations of the pKa values of ionisable groups in bacteriorhodopsin. J. Mol. Biol. 224: 473-486.
-
(1992)
J. Mol. Biol.
, vol.224
, pp. 473-486
-
-
Bashford, D.1
Gerwert, K.2
-
5
-
-
0348047621
-
3 from Desulfovibrio desulfuricans ATCC 27774: Crystallographic and modelling studies of oxidised and reduced high resolution structures at pH 7.6
-
3 from Desulfovibrio desulfuricans ATCC 27774: crystallographic and modelling studies of oxidised and reduced high resolution structures at pH 7.6. Proteins. 54:135-152.
-
(2004)
Proteins
, vol.54
, pp. 135-152
-
-
Bento, I.1
Matias, P.M.2
Baptista, A.M.3
Da Costa, P.N.4
Van Dongen, W.M.A.M.5
Saraiva, L.M.6
Schneider, T.R.7
Soares, C.M.8
Carrondo, M.A.9
-
6
-
-
0141815636
-
Redox-Bohr and other cooperativity effects in the nine heme cytochrome c from Desulfovibrio desulfuricans ATCC 27774: Crystallographic and modeling studies
-
Bento, I., V. H. Teixeira, A. M. Baptista, C. M. Soares, P. M. Matias, and M. A. Carrondo. 2003. Redox-Bohr and other cooperativity effects in the nine heme cytochrome c from Desulfovibrio desulfuricans ATCC 27774: crystallographic and modeling studies. J. Biol. Chem. 278:36455-36469.
-
(2003)
J. Biol. Chem.
, vol.278
, pp. 36455-36469
-
-
Bento, I.1
Teixeira, V.H.2
Baptista, A.M.3
Soares, C.M.4
Matias, P.M.5
Carrondo, M.A.6
-
7
-
-
33750587438
-
Molecular dynamics with coupling to an external bath
-
Berendsen, H. J. C., J. P. M. Postma, W. F. Van Gunsteren, A. DiNola, and J. R. Haak. 1984. Molecular dynamics with coupling to an external bath. J. Chem. Phys. 81:3684-3690.
-
(1984)
J. Chem. Phys.
, vol.81
, pp. 3684-3690
-
-
Berendsen, H.J.C.1
Postma, J.P.M.2
Van Gunsteren, W.F.3
Dinola, A.4
Haak, J.R.5
-
8
-
-
0029129996
-
Control of the redox potential in c-type cytochromes: Importance of the entropic contribution
-
Bertrand, P., O. Mbarki, M, Asso, L. Blanchard, F. Guerlesquin, and M. Tegoni. 1995. Control of the redox potential in c-type cytochromes: importance of the entropic contribution. Biochemistry. 34:11071-11079.
-
(1995)
Biochemistry
, vol.34
, pp. 11071-11079
-
-
Bertrand, P.1
Mbarki, O.2
Asso, M.3
Blanchard, L.4
Guerlesquin, F.5
Tegoni, M.6
-
9
-
-
0034687810
-
The proton/ electron coupling ratio at heme a and Cu-A in bovine heart cytochrome c oxidase
-
Capitanio, N., G. Capitanio, D. Boffoli, and S. Papa. 2000. The proton/ electron coupling ratio at heme a and Cu-A in bovine heart cytochrome c oxidase. Biochemistry. 39:15454-15461.
-
(2000)
Biochemistry
, vol.39
, pp. 15454-15461
-
-
Capitanio, N.1
Capitanio, G.2
Boffoli, D.3
Papa, S.4
-
10
-
-
0032788471
-
Modelling of electron transfer complexes between flavodoxin and c-type cytochromes
-
Cunha, C. A., M. J. Romão, S. J. Sadeghi, F. Valetti, G. Gilardi, and C. M. Soares. 1999. Modelling of electron transfer complexes between flavodoxin and c-type cytochromes. Bioinorg. Chem. 4:360-374.
-
(1999)
Bioinorg. Chem.
, vol.4
, pp. 360-374
-
-
Cunha, C.A.1
Romão, M.J.2
Sadeghi, S.J.3
Valetti, F.4
Gilardi, G.5
Soares, C.M.6
-
11
-
-
0028099794
-
The protein moiety modulates the redox potential in cytochromes c
-
Dolla, A., L. Blanchard, F. Guerlesquin, and M. Bruschi. 1994. The protein moiety modulates the redox potential in cytochromes c. Biochimie. 76:471-479.
-
(1994)
Biochimie
, vol.76
, pp. 471-479
-
-
Dolla, A.1
Blanchard, L.2
Guerlesquin, F.3
Bruschi, M.4
-
14
-
-
33845379583
-
Control of heme protein redox potential and reduction rate: Linear free-energy relation between potential and ferric spin state equilibrium
-
Fisher, M. T., and S. G. Sugar. 1985. Control of heme protein redox potential and reduction rate: linear free-energy relation between potential and ferric spin state equilibrium. J. Am. Chem. Soc. 107:5018-5019.
-
(1985)
J. Am. Chem. Soc.
, vol.107
, pp. 5018-5019
-
-
Fisher, M.T.1
Sugar, S.G.2
-
16
-
-
9444219714
-
Active site structure and redox processes of cytochrome c oxidase immobilised in a novel biomimetic lipid membrane
-
Friedrich, M., F. Gieß, R. Naumann, W. Knoll, K. Ataka, J. Heberle, J. Hrabakova, D. H. Murgida, and P. Hildebrandt. 2004. Active site structure and redox processes of cytochrome c oxidase immobilised in a novel biomimetic lipid membrane. Chem. Commun. 2376-2377.
-
(2004)
Chem. Commun.
, pp. 2376-2377
-
-
Friedrich, M.1
Gieß, F.2
Naumann, R.3
Knoll, W.4
Ataka, K.5
Heberle, J.6
Hrabakova, J.7
Murgida, D.H.8
Hildebrandt, P.9
-
17
-
-
84988087911
-
Calculating the electrostatic potential of molecules in solution: Method and error assessment
-
Gilson, M. K., K. A. Sharp, and B. H. Honig. 1987. Calculating the electrostatic potential of molecules in solution: method and error assessment. J. Comput. Chem. 9:327-335.
-
(1987)
J. Comput. Chem.
, vol.9
, pp. 327-335
-
-
Gilson, M.K.1
Sharp, K.A.2
Honig, B.H.3
-
18
-
-
0027185516
-
Automated docking in crystallography: Analysis of the substrates of aconitase
-
Goodsell, D. S., H. Lauble, C. D. Stout, and A. J. Olson. 1993. Automated docking in crystallography: analysis of the substrates of aconitase. Proteins. 17:1-10.
-
(1993)
Proteins
, vol.17
, pp. 1-10
-
-
Goodsell, D.S.1
Lauble, H.2
Stout, C.D.3
Olson, A.J.4
-
19
-
-
0025135112
-
Automated docking of substrates to proteins by simulated annealing
-
Goodsell, D. S., and A. J. Olson. 1990. Automated docking of substrates to proteins by simulated annealing. Proteins. 8:195-202.
-
(1990)
Proteins
, vol.8
, pp. 195-202
-
-
Goodsell, D.S.1
Olson, A.J.2
-
20
-
-
84990424072
-
A consistent empirical potential for water-protein interactions
-
Hermans, J., H. J. C. Berendsen, W. F. Van Gunsteren, and J. P. M. Postma. 1984. A consistent empirical potential for water-protein interactions. Biopolymers. 23:1513-1518.
-
(1984)
Biopolymers
, vol.23
, pp. 1513-1518
-
-
Hermans, J.1
Berendsen, H.J.C.2
Van Gunsteren, W.F.3
Postma, J.P.M.4
-
21
-
-
0000388705
-
LINCS: A linear constraint solver for molecular simulations
-
Hess, B., H. Bekker, H. J. C. Berendsen, and J. G. E. M. Fraaije. 1997. LINCS: a linear constraint solver for molecular simulations. J. Comput. Chem. 18:1463-1472.
-
(1997)
J. Comput. Chem.
, vol.18
, pp. 1463-1472
-
-
Hess, B.1
Bekker, H.2
Berendsen, H.J.C.3
Fraaije, J.G.E.M.4
-
22
-
-
0027818118
-
Complete assignment of cytochrome c resonance Raman spectra via enzymatic reconstitution with isotopically labelled hemes
-
Hu, S., J. K. Morris, J. P. Singh, K. M. Smith, and T. G. Spiro. 1993. Complete assignment of cytochrome c resonance Raman spectra via enzymatic reconstitution with isotopically labelled hemes. J. Am. Chem. Soc. 115:12446-12458.
-
(1993)
J. Am. Chem. Soc.
, vol.115
, pp. 12446-12458
-
-
Hu, S.1
Morris, J.K.2
Singh, J.P.3
Smith, K.M.4
Spiro, T.G.5
-
23
-
-
0015385789
-
Effects of nonpolar environments on the redox potentials of heme complexes
-
Kassner, R. 1972. Effects of nonpolar environments on the redox potentials of heme complexes. Proc. Natl. Acad. Sci. USA. 69:2263-2267.
-
(1972)
Proc. Natl. Acad. Sci. USA
, vol.69
, pp. 2263-2267
-
-
Kassner, R.1
-
24
-
-
0035789518
-
GROMACS 3.0: A package for molecular simulation and trajectory analysis
-
Online
-
Lindahl, E., B. Hess, and D. van der Spoel. 2001. GROMACS 3.0: a package for molecular simulation and trajectory analysis. J. Mol. Model. [Online]. 7:306-317.
-
(2001)
J. Mol. Model.
, vol.7
, pp. 306-317
-
-
Lindahl, E.1
Hess, B.2
Van Der Spoel, D.3
-
25
-
-
0035941269
-
Conformational component in the coupled transfer of multiple electrons and protons in a monomeric tetraheme cytochrome
-
Louro, R. O., I. Bento, P. M. Matias, T. Catarino, A. M. Baptista, C. M. Soares, M. A. Carrondo, D. L. Turner, and A. V. Xavier. 2001. Conformational component in the coupled transfer of multiple electrons and protons in a monomeric tetraheme cytochrome. J. Biol. Chem. 276:44044-44051.
-
(2001)
J. Biol. Chem.
, vol.276
, pp. 44044-44051
-
-
Louro, R.O.1
Bento, I.2
Matias, P.M.3
Catarino, T.4
Baptista, A.M.5
Soares, C.M.6
Carrondo, M.A.7
Turner, D.L.8
Xavier, A.V.9
-
31
-
-
84986440341
-
SETTLE: An analytical version of the SHAKE and RATTLE algorithms for rigid water models
-
Miyamoto, S., and P. A. Kollman. 1992. SETTLE: an analytical version of the SHAKE and RATTLE algorithms for rigid water models. J. Comput. Chem. 13:952-962.
-
(1992)
J. Comput. Chem.
, vol.13
, pp. 952-962
-
-
Miyamoto, S.1
Kollman, P.A.2
-
32
-
-
0021108037
-
Control of redox properties of cytochrome c by special electrostatic interactions
-
Moore, G. R. 1983. Control of redox properties of cytochrome c by special electrostatic interactions. FEBS Lett. 161:171-175.
-
(1983)
FEBS Lett.
, vol.161
, pp. 171-175
-
-
Moore, G.R.1
-
33
-
-
0017406836
-
Structural basis for the variation in redox potential of cytochromes
-
Moore, G. R., and R. J. P. Williams. 1977. Structural basis for the variation in redox potential of cytochromes. FEBS Lett. 79:229-232.
-
(1977)
FEBS Lett.
, vol.79
, pp. 229-232
-
-
Moore, G.R.1
Williams, R.J.P.2
-
34
-
-
0000698565
-
Surface enhanced spectroscopy
-
Moskovits, M. 1985. Surface enhanced spectroscopy. Rev. Mod. Phys. 57:783-826.
-
(1985)
Rev. Mod. Phys.
, vol.57
, pp. 783-826
-
-
Moskovits, M.1
-
35
-
-
0035280932
-
Heterogeneous electron transfer of cytochrome c on coated silver electrodes. Electric field effects on structure and redox potential
-
Murgida, D. H., and P. Hildebrandt. 2001a. Heterogeneous electron transfer of cytochrome c on coated silver electrodes. Electric field effects on structure and redox potential. J. Phys. Chem. B. 105:1578-1586.
-
(2001)
J. Phys. Chem. B
, vol.105
, pp. 1578-1586
-
-
Murgida, D.H.1
Hildebrandt, P.2
-
36
-
-
0034795290
-
Proton-coupled electron transfer of cytochrome c
-
Murgida, D. H., and P. Hildebrandt. 2001b. Proton-coupled electron transfer of cytochrome c. J. Am. Chem. Soc. 123:4062-4068.
-
(2001)
J. Am. Chem. Soc.
, vol.123
, pp. 4062-4068
-
-
Murgida, D.H.1
Hildebrandt, P.2
-
37
-
-
9444232272
-
Electron transfer processes of cytochrome c at interfaces. New insights by surface-enhanced resonance Raman spectroscopy
-
In press
-
Murgida, D. H., and P. Hildebrandt. 2004. Electron transfer processes of cytochrome c at interfaces. New insights by surface-enhanced resonance Raman spectroscopy. Acc. Chem. Res. In press.
-
(2004)
Acc. Chem. Res.
-
-
Murgida, D.H.1
Hildebrandt, P.2
-
38
-
-
0036923706
-
Molecular dynamics simulations of a hydrated protein vectorially oriented on polar and nonpolar soft surfaces
-
Nordgren, C. E., D. J. Tobias, M. L. Klein, and J. K. Blasie. 2002. Molecular dynamics simulations of a hydrated protein vectorially oriented on polar and nonpolar soft surfaces. Biophys. J. 83:2906-2917.
-
(2002)
Biophys. J.
, vol.83
, pp. 2906-2917
-
-
Nordgren, C.E.1
Tobias, D.J.2
Klein, M.L.3
Blasie, J.K.4
-
39
-
-
0018792384
-
Redox Bohr-effects in the cytochrome system in mitochondria
-
Papa, S., F. Guerrieri, and G. Izzo. 1979. Redox Bohr-effects in the cytochrome system in mitochondria. FEBS Lett. 105:213-216.
-
(1979)
FEBS Lett.
, vol.105
, pp. 213-216
-
-
Papa, S.1
Guerrieri, F.2
Izzo, G.3
-
40
-
-
0008819754
-
The GROMOS biomolecular simulation program package
-
Scott, W. R. P., P. H. Hünenberger, I. G. Tironi, A. E. Mark, S. R. Billeter, J. Fennen, A. E. Torda, T. Huber, P. Krüger, and W. F. Van Gunsteren. 1999. The GROMOS biomolecular simulation program package. J. Phys. Chem. 103:3596-3607.
-
(1999)
J. Phys. Chem.
, vol.103
, pp. 3596-3607
-
-
Scott, W.R.P.1
Hünenberger, P.H.2
Tironi, I.G.3
Mark, A.E.4
Billeter, S.R.5
Fennen, J.6
Torda, A.E.7
Huber, T.8
Krüger, P.9
Van Gunsteren, W.F.10
-
42
-
-
0026315121
-
Electrostatic screening in molecular dynamics simulations
-
Solmajer, T., and E. L. Mehler. 1991. Electrostatic screening in molecular dynamics simulations. Protein Eng. 4:911-917.
-
(1991)
Protein Eng.
, vol.4
, pp. 911-917
-
-
Solmajer, T.1
Mehler, E.L.2
-
43
-
-
0037006983
-
A multigeneration analysis of cytochrome b(562) redox variants: Evolutionary strategies for modulating redox potential revealed using a library approach
-
Springs, S. L., S. E. Bass, G. Bowman, I. Nodelman, C. E. Schutt, and G. L. McLendon. 2002. A multigeneration analysis of cytochrome b(562) redox variants: evolutionary strategies for modulating redox potential revealed using a library approach. Biochemistry. 41:4321-4328.
-
(2002)
Biochemistry
, vol.41
, pp. 4321-4328
-
-
Springs, S.L.1
Bass, S.E.2
Bowman, G.3
Nodelman, I.4
Schutt, C.E.5
McLendon, G.L.6
-
44
-
-
0018129356
-
Haem exposure as the determinate of oxidation-reduction potential of haem proteins
-
Stellwagen, E. 1978. Haem exposure as the determinate of oxidation-reduction potential of haem proteins. Nature. 275:73-74.
-
(1978)
Nature
, vol.275
, pp. 73-74
-
-
Stellwagen, E.1
-
46
-
-
0036359052
-
Studies of the reduction and protonation behaviour of tetrahaem cytochromes using atomic detail
-
Teixeira, V. H., C. M. Soares, and A. M. Baptista. 2002. Studies of the reduction and protonation behaviour of tetrahaem cytochromes using atomic detail. Bioinorg. Chem. 7:200-216.
-
(2002)
Bioinorg. Chem.
, vol.7
, pp. 200-216
-
-
Teixeira, V.H.1
Soares, C.M.2
Baptista, A.M.3
-
47
-
-
0029769798
-
Molecular dynamics simulations of a protein on hydrophobic and hydrophilic surfaces
-
Tobias, D. J., W. Mar, J. K. Blasie, and M. L. Klein. 1996. Molecular dynamics simulations of a protein on hydrophobic and hydrophilic surfaces. Biophys. J. 71:2933-2941.
-
(1996)
Biophys. J.
, vol.71
, pp. 2933-2941
-
-
Tobias, D.J.1
Mar, W.2
Blasie, J.K.3
Klein, M.L.4
-
51
-
-
0018447734
-
Coupling between oxidation state and hydrogen bond conformation in heme proteins
-
Valentine, J., R. P. Sheridan, L. C. Allen, and P. C. Kahn. 1979. Coupling between oxidation state and hydrogen bond conformation in heme proteins. Proc. Natl. Acad. Sci. USA. 76:1009-1013.
-
(1979)
Proc. Natl. Acad. Sci. USA
, vol.76
, pp. 1009-1013
-
-
Valentine, J.1
Sheridan, R.P.2
Allen, L.C.3
Kahn, P.C.4
-
52
-
-
0003544049
-
-
BIOMOS, Zurich, Switzerland; Groningen, The Netherlands
-
Van Gunsteren, W. F., S. R. Billeter, A. A. Eising, P. H. Hunenberger. P. Kruger, A. M. Mark, W. R. P. Scott, and I. G. Tironi. (1996) Biomolecular simulation: the GROMOS96 manual and user guide. BIOMOS, Zurich, Switzerland; Groningen, The Netherlands.
-
(1996)
Biomolecular Simulation: The GROMOS96 Manual and User Guide
-
-
Van Gunsteren, W.F.1
Billeter, S.R.2
Eising, A.A.3
Hunenberger, P.H.4
Kruger, P.5
Mark, A.M.6
Scott, W.R.P.7
Tironi, I.G.8
-
53
-
-
0345658006
-
-
A. V. Xavier, editor. VCH Publishers, Weinheim, Germany
-
Xavier, A. V. 1985. In Frontiers in Bioinorganic Chemistry. A. V. Xavier, editor. VCH Publishers, Weinheim, Germany. 722-725.
-
(1985)
Frontiers in Bioinorganic Chemistry
, pp. 722-725
-
-
Xavier, A.V.1
-
54
-
-
3543041902
-
Thermodynamic and choreographic constraints for energy transduction by cytochrome c oxidase
-
Xavier, A. V. 2004. Thermodynamic and choreographic constraints for energy transduction by cytochrome c oxidase. Biochim. Biophys. Acta. 1658:23-30.
-
(2004)
Biochim. Biophys. Acta.
, vol.1658
, pp. 23-30
-
-
Xavier, A.V.1
-
55
-
-
9144237008
-
Molecular simulation studies of the orientation and conformation of cytochrome c adsorbed on self-assembled monolayers
-
Zhou, J., J. Zheng, and S. Jiang. 2004. Molecular simulation studies of the orientation and conformation of cytochrome c adsorbed on self-assembled monolayers. J. Phys. Chem. B. 108:17418-17424.
-
(2004)
J. Phys. Chem. B.
, vol.108
, pp. 17418-17424
-
-
Zhou, J.1
Zheng, J.2
Jiang, S.3
|