-
2
-
-
5344278362
-
Molecular dynamics simulations on HiPIP from Chromatium vinosum and comparison with NMR data
-
Banci, L., I. Bertini, P. Carloni, C. Luchinat, and P. L. Orioli. 1992. Molecular dynamics simulations on HiPIP from Chromatium vinosum and comparison with NMR data. J. Am. Chem. Soc. 114:10683-10689.
-
(1992)
J. Am. Chem. Soc.
, vol.114
, pp. 10683-10689
-
-
Banci, L.1
Bertini, I.2
Carloni, P.3
Luchinat, C.4
Orioli, P.L.5
-
3
-
-
4344606960
-
Multidimensional adaptive umbrella sampling: Applications to main chain and side chain peptide conformations
-
Bartels, C., and M. Karplus. 1997. Multidimensional adaptive umbrella sampling: applications to main chain and side chain peptide conformations. J. Comput. Chem. 18:1450-1462.
-
(1997)
J. Comput. Chem.
, vol.18
, pp. 1450-1462
-
-
Bartels, C.1
Karplus, M.2
-
4
-
-
0025743628
-
Computer simulation and analysis of the reaction pathway of triosephosphate isomerase
-
Bash, P. A., M. J. Field, R. C. Davenport, G. A. Petsko, D. Ringe, and M. Karplus. 1991. Computer simulation and analysis of the reaction pathway of triosephosphate isomerase. Biochemistry. 30:5826-5832.
-
(1991)
Biochemistry
, vol.30
, pp. 5826-5832
-
-
Bash, P.A.1
Field, M.J.2
Davenport, R.C.3
Petsko, G.A.4
Ringe, D.5
Karplus, M.6
-
5
-
-
0000989147
-
Aconitase as iron-sulfur protein, enzyme, and iron-regulatory protein
-
Beinert, H., M. C. Kennedy, and C. D. Stout. 1996. Aconitase as iron-sulfur protein, enzyme, and iron-regulatory protein. Chem. Rev. 96:2335-2373.
-
(1996)
Chem. Rev.
, vol.96
, pp. 2335-2373
-
-
Beinert, H.1
Kennedy, M.C.2
Stout, C.D.3
-
6
-
-
84986492477
-
Atomic charges derived from semiempirical methods
-
Besler, B. H., K. M. Merz, and P. A. Kollman. 1990. Atomic charges derived from semiempirical methods. J. Comp. Chem. 11:431-439.
-
(1990)
J. Comp. Chem.
, vol.11
, pp. 431-439
-
-
Besler, B.H.1
Merz, K.M.2
Kollman, P.A.3
-
7
-
-
84986512474
-
CHARMM, a program for macromolecular energy, minimization, and dynamics calculations
-
Brooks, B. R., R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, and M. Karplus. 1983. CHARMM, a program for macromolecular energy, minimization, and dynamics calculations. J. Comput. Chem. 4:187-217.
-
(1983)
J. Comput. Chem.
, vol.4
, pp. 187-217
-
-
Brooks, B.R.1
Bruccoleri, R.E.2
Olafson, B.D.3
States, D.J.4
Swaminathan, S.5
Karplus, M.6
-
8
-
-
36749119973
-
Deformable stochastic boundaries in molecular dynamics
-
Brooks III, C. L., and M. Karplus. 1983. Deformable stochastic boundaries in molecular dynamics. J. Chem. Phys. 79:6312-6325.
-
(1983)
J. Chem. Phys.
, vol.79
, pp. 6312-6325
-
-
Brooks III, C.L.1
Karplus, M.2
-
9
-
-
0024354001
-
Solvent effects on protein motion and protein effects on solvent motion: Dynamics of the active site region of lysozyme
-
Brooks III, C. L., and M. Karplus. 1989. Solvent effects on protein motion and protein effects on solvent motion: dynamics of the active site region of lysozyme. J. Mol. Biol. 208:159-181.
-
(1989)
J. Mol. Biol.
, vol.208
, pp. 159-181
-
-
Brooks III, C.L.1
Karplus, M.2
-
10
-
-
0024250301
-
Polar hydrogen positions in proteins: Empirical energy function placement and neutron diffraction comparison
-
Brünger, A. T., and M. Karplus. 1988. Polar hydrogen positions in proteins: empirical energy function placement and neutron diffraction comparison. Proteins. 4:148-156.
-
(1988)
Proteins
, vol.4
, pp. 148-156
-
-
Brünger, A.T.1
Karplus, M.2
-
11
-
-
0026684043
-
A 500 ps molecular dynamics simulation study of interleukin-1b in water: Correlation with nuclear magnetic resonance spectroscopy and crystallography
-
Chandrasekhar, I., G. M. Clore, A. Szabo, A. M. Gronenborn, and B. R. Brooks. 1992. A 500 ps molecular dynamics simulation study of interleukin-1b in water: correlation with nuclear magnetic resonance spectroscopy and crystallography. J. Mol. Biol. 226:239-250.
-
(1992)
J. Mol. Biol.
, vol.226
, pp. 239-250
-
-
Chandrasekhar, I.1
Clore, G.M.2
Szabo, A.3
Gronenborn, A.M.4
Brooks, B.R.5
-
12
-
-
0034659779
-
Atomically defined mechanism for proton transfer to a buried redox centre in a protein
-
Chen, K., J. Hirst, R. Camba, C. A. Bonagura, C. D. Stout, B. K. Burgess, and F. A. Armstrong. 2000. Atomically defined mechanism for proton transfer to a buried redox centre in a protein. Nature. 405:814-817.
-
(2000)
Nature
, vol.405
, pp. 814-817
-
-
Chen, K.1
Hirst, J.2
Camba, R.3
Bonagura, C.A.4
Stout, C.D.5
Burgess, B.K.6
Armstrong, F.A.7
-
16
-
-
33748381480
-
Proton-coupled electron transfer reactions: Evaluation of rate constants
-
Cukier, R. I. 1996. Proton-coupled electron transfer reactions: evaluation of rate constants. J. Phys. Chem. 100:15428-15443.
-
(1996)
J. Phys. Chem.
, vol.100
, pp. 15428-15443
-
-
Cukier, R.I.1
-
17
-
-
0000451307
-
The gas-phase acidity and the acidic site of acetohydroxamic acid: An FT-ICR study
-
Decouzon, M., O. Exner, J.-F. Gal, and P.-C. Maria. 1990. The gas-phase acidity and the acidic site of acetohydroxamic acid: an FT-ICR study. J. Org. Chem. 55:3980-3981.
-
(1990)
J. Org. Chem.
, vol.55
, pp. 3980-3981
-
-
Decouzon, M.1
Exner, O.2
Gal, J.-F.3
Maria, P.-C.4
-
18
-
-
0028921999
-
Demonstration of positionally disordered water within a protein hydrophobic cavity by NMR
-
Ernst, J. A., R. T. Clubb, H.-X. Zhou, A. M. Gronenborn, and G. M. Clore. 1995. Demonstration of positionally disordered water within a protein hydrophobic cavity by NMR. Science. 267:1813-1817.
-
(1995)
Science
, vol.267
, pp. 1813-1817
-
-
Ernst, J.A.1
Clubb, R.T.2
Zhou, H.-X.3
Gronenborn, A.M.4
Clore, G.M.5
-
19
-
-
0033578333
-
Binding of buried structural water increases the flexibility of proteins
-
Fischer, S., and C. S. Verma. 1999. Binding of buried structural water increases the flexibility of proteins. Proc. Natl. Acad. Sci. USA. 96:9613-9615.
-
(1999)
Proc. Natl. Acad. Sci. USA
, vol.96
, pp. 9613-9615
-
-
Fischer, S.1
Verma, C.S.2
-
20
-
-
84962357545
-
-
Gaussian, Inc., Pittsburgh, PA
-
Frisch, M. J., G. W. Trucks, H. B. Schlegel, P. M. W. Gill, B. G. Johnson, M. A. Robb, J. R. Cheeseman, T. Keith, G. A. Petersson, J. A. Montgomery, K. Raghavachari, M. A. Al-Laham, V. G. Zakrzewski, J. V. Ortiz, J. B. Foresman, J. Cioslowski, B. B. Stefanov, A. Nanayakkara, M. Challacombe, C. Y. Peng, P. Y. Ayala, W. Chen, M. W. Wong, J. L. Andres, E. S. Replogle, R. Gomperts, R. L. Martin, D. J. Fox, J. S. Binkley, D. J. Defrees, J. Baker, J. P. Stewart, M. Head-Gordon, C. Gonzalez, and J. A. Pople. 1998. Gaussian 94, Rev. e.2. Gaussian, Inc., Pittsburgh, PA.
-
(1998)
Gaussian 94, Rev. E.2
-
-
Frisch, M.J.1
Trucks, G.W.2
Schlegel, H.B.3
Gill, P.M.W.4
Johnson, B.G.5
Robb, M.A.6
Cheeseman, J.R.7
Keith, T.8
Petersson, G.A.9
Montgomery, J.A.10
Raghavachari, K.11
Al-Laham, M.A.12
Zakrzewski, V.G.13
Ortiz, J.V.14
Foresman, J.B.15
Cioslowski, J.16
Stefanov, B.B.17
Nanayakkara, A.18
Challacombe, M.19
Peng, C.Y.20
Ayala, P.Y.21
Chen, W.22
Wong, M.W.23
Andres, J.L.24
Replogle, E.S.25
Gomperts, R.26
Martin, R.L.27
Fox, D.J.28
Binkley, J.S.29
Defrees, D.J.30
Baker, J.31
Stewart, J.P.32
Head-Gordon, M.33
Gonzalez, C.34
Pople, J.A.35
more..
-
21
-
-
84946450438
-
Algorithms for macromolecular dynamics and constraint dynamics
-
Van Gunsteren, W. V., and H. J. C. Berendsen. 1977. Algorithms for macromolecular dynamics and constraint dynamics. Mol. Phys. 34:1311-1327.
-
(1977)
Mol. Phys.
, vol.34
, pp. 1311-1327
-
-
Van Gunsteren, W.V.1
Berendsen, H.J.C.2
-
22
-
-
0034859929
-
Theoretical perspectives on proton-coupled electron transfer reactions
-
Hammes-Schiffer, S. 2001. Theoretical perspectives on proton-coupled electron transfer reactions. Acc. Chem. Res. 34:273-283.
-
(2001)
Acc. Chem. Res.
, vol.34
, pp. 273-283
-
-
Hammes-Schiffer, S.1
-
23
-
-
0029758487
-
Molecular control of vertebrate iron metabolism: MRNA-based regulatory circuits operated by iron, nitric oxide and oxidative stress
-
Hentze, M. W., and L. C. Kühn. 1996. Molecular control of vertebrate iron metabolism: mRNA-based regulatory circuits operated by iron, nitric oxide and oxidative stress. Proc. Natl. Acad. Sci. USA. 93:8175-8182.
-
(1996)
Proc. Natl. Acad. Sci. USA
, vol.93
, pp. 8175-8182
-
-
Hentze, M.W.1
Kühn, L.C.2
-
24
-
-
0032558152
-
Kinetics and mechanism of redox-coupled, long-range proton transfer in an iron-sulfur protein. Investigation by fast-scan protein-film voltammetry
-
Hirst, J., J. L. C. Duff, G. N. L. Jameson, M. A. Kemper, B. K. Burgess, and F. A. Armstrong. 1998. Kinetics and mechanism of redox-coupled, long-range proton transfer in an iron-sulfur protein. Investigation by fast-scan protein-film voltammetry. J. Am. Chem. Soc. 120:7085-7094.
-
(1998)
J. Am. Chem. Soc.
, vol.120
, pp. 7085-7094
-
-
Hirst, J.1
Duff, J.L.C.2
Jameson, G.N.L.3
Kemper, M.A.4
Burgess, B.K.5
Armstrong, F.A.6
-
25
-
-
0032366914
-
Evaluated gas phase basicities and proton affinities of molecules: An update
-
Hunter, E. P., and S. G. Lias. 1998. Evaluated gas phase basicities and proton affinities of molecules: an update. J. Phys. Chem. Ref. Data. 27:413-656.
-
(1998)
J. Phys. Chem. Ref. Data
, vol.27
, pp. 413-656
-
-
Hunter, E.P.1
Lias, S.G.2
-
26
-
-
0019332456
-
Evidence for a three-iron center in a ferredoxin from Desulfovibrio gigas
-
Huynh, B. H., J. J. G. Moura, I. Moura, T. A. Kent, J. LeGall, A. V. Xavier, and E. Münck. 1980. Evidence for a three-iron center in a ferredoxin from Desulfovibrio gigas. J. Biol. Chem. 255:3242-3244.
-
(1980)
J. Biol. Chem.
, vol.255
, pp. 3242-3244
-
-
Huynh, B.H.1
Moura, J.J.G.2
Moura, I.3
Kent, T.A.4
LeGall, J.5
Xavier, A.V.6
Münck, E.7
-
27
-
-
0036570243
-
Theoretical investigation of large kinetic isotope effects for proton-coupled electron transfer in ruthenium polypyridil complexes
-
Iordanova, N., and S. Hammes-Schiffer. 2002. Theoretical investigation of large kinetic isotope effects for proton-coupled electron transfer in ruthenium polypyridil complexes. J. Am. Chem. Soc. 124:4848-4856.
-
(2002)
J. Am. Chem. Soc.
, vol.124
, pp. 4848-4856
-
-
Iordanova, N.1
Hammes-Schiffer, S.2
-
28
-
-
0035827120
-
Nonadiabatic instanton calculation of multistate electron transfer reaction rate: Interference effects in three- and four-states systems
-
Jang, S., and J. Cao. 2001. Nonadiabatic instanton calculation of multistate electron transfer reaction rate: interference effects in three- and four-states systems. J. Chem. Phys. 22:9959-9968.
-
(2001)
J. Chem. Phys.
, vol.22
, pp. 9959-9968
-
-
Jang, S.1
Cao, J.2
-
29
-
-
0032043449
-
Iron-sulfur proteins: New roles for old clusters
-
Johnson, M. K. 1998. Iron-sulfur proteins: new roles for old clusters. Curr. Opin. Chem. Biol. 2:173-181.
-
(1998)
Curr. Opin. Chem. Biol.
, vol.2
, pp. 173-181
-
-
Johnson, M.K.1
-
31
-
-
84962367570
-
Incorporating protein environments in density functional theory: A self-consistent reaction field calculation of redox potentials of [2Fe2S] clusters in ferredoxin and phthalate dioxygenase reductase
-
Li, J., M. R. Nelson, C. Y. Peng, D. Bashford, and L. Noodleman. 1998. Incorporating protein environments in density functional theory: a self-consistent reaction field calculation of redox potentials of [2Fe2S] clusters in ferredoxin and phthalate dioxygenase reductase. J. Phys. Chem. A. 102:6311-6324.
-
(1998)
J. Phys. Chem. A
, vol.102
, pp. 6311-6324
-
-
Li, J.1
Nelson, M.R.2
Peng, C.Y.3
Bashford, D.4
Noodleman, L.5
-
32
-
-
2442609830
-
Vectorial chemistry in bioenergetics: Cytochrome c oxidase as a redox-linked proton pump
-
Malmström, B. G. 1993. Vectorial chemistry in bioenergetics: cytochrome c oxidase as a redox-linked proton pump. Acc. Chem. Res. 26:332-338.
-
(1993)
Acc. Chem. Res.
, vol.26
, pp. 332-338
-
-
Malmström, B.G.1
-
33
-
-
0142212202
-
Theoretical investigations of Ferredoxin I: The possible role of internal water molecules on the coupled electron proton transfer reaction
-
Meuwly, M., and M. Karplus. 2003. Theoretical investigations of Ferredoxin I: the possible role of internal water molecules on the coupled electron proton transfer reaction. Faraday Discuss. 124:297-313.
-
(2003)
Faraday Discuss
, vol.124
, pp. 297-313
-
-
Meuwly, M.1
Karplus, M.2
-
34
-
-
0027082924
-
Internal water molecules and H-bonding in biological macromolecules: A review of structural features with functional implications
-
Meyer, E. 1992. Internal water molecules and H-bonding in biological macromolecules: a review of structural features with functional implications. Prot. Sci. 1:1542-1562.
-
(1992)
Prot. Sci.
, vol.1
, pp. 1542-1562
-
-
Meyer, E.1
-
35
-
-
0000318315
-
Density functional/Poisson-Boltzmann calculations of redox potentials for iron-sulfur clusters
-
Mouesca, J.-M., J. L. Chen, L. Noodleman, D. Bashford, and D. A. Case. 1994. Density functional/Poisson-Boltzmann calculations of redox potentials for iron-sulfur clusters. J. Am. Chem. Soc. 116:11898-11914.
-
(1994)
J. Am. Chem. Soc.
, vol.116
, pp. 11898-11914
-
-
Mouesca, J.-M.1
Chen, J.L.2
Noodleman, L.3
Bashford, D.4
Case, D.A.5
-
36
-
-
0019087876
-
Iron-sulfur proteins: Spin-coupling model for three-iron clusters
-
Kent, T. A., B. H. Huynh, and E. Münck. 1980. Iron-sulfur proteins: spin-coupling model for three-iron clusters. Proc. Natl. Acad. Sci. USA. 77:6574-6576.
-
(1980)
Proc. Natl. Acad. Sci. USA
, vol.77
, pp. 6574-6576
-
-
Kent, T.A.1
Huynh, B.H.2
Münck, E.3
-
37
-
-
0001379854
-
Broken symmetry analysis of spin coupling in iron-sulfur clusters
-
Noodleman, L., D. A. Case, and A. Aizman. 1988. Broken symmetry analysis of spin coupling in iron-sulfur clusters. J. Am. Chem. Soc. 110:1001-1005.
-
(1988)
J. Am. Chem. Soc.
, vol.110
, pp. 1001-1005
-
-
Noodleman, L.1
Case, D.A.2
Aizman, A.3
-
38
-
-
0031700045
-
Quantum chemical calculations of the reorganisation energy of blue copper proteins
-
Olsson, M. H. M., U. Ryde, and B. O. Roos. 1998. Quantum chemical calculations of the reorganisation energy of blue copper proteins. Prot. Sci. 7:2659-2668.
-
(1998)
Prot. Sci.
, vol.7
, pp. 2659-2668
-
-
Olsson, M.H.M.1
Ryde, U.2
Roos, B.O.3
-
40
-
-
0031076776
-
pH Dependence of protein stability: Absolute electrostatic free energy differences between conformations
-
Schaefer, M., M. Sommer, and M. Karplus. 1997. pH Dependence of protein stability: absolute electrostatic free energy differences between conformations. J. Phys. Chem. B. 101:1663-1683.
-
(1997)
J. Phys. Chem. B
, vol.101
, pp. 1663-1683
-
-
Schaefer, M.1
Sommer, M.2
Karplus, M.3
-
42
-
-
0027518193
-
Azotobacter vinelandii Ferredoxin I: Aspartate 15 facilitates proton transfer to the reduced [3Fe-4S] cluster
-
Shen, B., L. L. Martin, J. N. Butt, F. A. Armstrong, C. D. Stout, G. M. Jensen, P. J. Stephens, G. N. La Mar, C. M. Gorst, and B. K. Burgess. 1993. Azotobacter vinelandii Ferredoxin I: Aspartate 15 facilitates proton transfer to the reduced [3Fe-4S] cluster. J. Mol. Biol. 268:25928-25939.
-
(1993)
J. Mol. Biol.
, vol.268
, pp. 25928-25939
-
-
Shen, B.1
Martin, L.L.2
Butt, J.N.3
Armstrong, F.A.4
Stout, C.D.5
Jensen, G.M.6
Stephens, P.J.7
La Mar, G.N.8
Gorst, C.M.9
Burgess, B.K.10
-
43
-
-
84986468608
-
An approach to computing electrostatic charges for molecules
-
Singh, U. C., and P. A. Kollman. 1984. An approach to computing electrostatic charges for molecules. J. Comput. Chem. 5:129-145.
-
(1984)
J. Comput. Chem.
, vol.5
, pp. 129-145
-
-
Singh, U.C.1
Kollman, P.A.2
-
44
-
-
0034248772
-
Derivation of rate expressions for nonadiabatic proton-coupled electron transfer reactions in solution
-
Soudackov, A., and S. Hammes-Schiffer. 2000. Derivation of rate expressions for nonadiabatic proton-coupled electron transfer reactions in solution. J. Chem. Phys. 113:2385-2396.
-
(2000)
J. Chem. Phys.
, vol.113
, pp. 2385-2396
-
-
Soudackov, A.1
Hammes-Schiffer, S.2
-
46
-
-
0032496372
-
1.35 Å Structure of Azotobacter 7-Fe ferredoxin and determination of Fe-S cluster positions to 0.01 Å precision
-
Stout, C. D., E. A. Stura, and D. E. McRee. 1998. 1.35 Å Structure of Azotobacter 7-Fe ferredoxin and determination of Fe-S cluster positions to 0.01 Å precision. J. Mol. Biol. 278:629-639.
-
(1998)
J. Mol. Biol.
, vol.278
, pp. 629-639
-
-
Stout, C.D.1
Stura, E.A.2
McRee, D.E.3
-
47
-
-
84983035977
-
The nature and analysis of substituent effects
-
Taft, R. W., and R. D. Topsom. 1987. The nature and analysis of substituent effects. Prog. Phys. Org. Chem. 16:1.
-
(1987)
Prog. Phys. Org. Chem.
, vol.16
, pp. 1
-
-
Taft, R.W.1
Topsom, R.D.2
-
49
-
-
0028889166
-
Crystal structure of the nickel-iron hydrogenase from Desulfovibrio gigas
-
Volbeda, A., M.-H. Charon, C. Piras, E. C. Hatchiklan, M. Frey, and J. C. Fontecilla-Camps. 1995. Crystal structure of the nickel-iron hydrogenase from Desulfovibrio gigas. Nature. 373:580-587.
-
(1995)
Nature
, vol.373
, pp. 580-587
-
-
Volbeda, A.1
Charon, M.-H.2
Piras, C.3
Hatchiklan, E.C.4
Frey, M.5
Fontecilla-Camps, J.C.6
-
50
-
-
0029936755
-
4 cluster: Synthesis, stability, and geometric and electronic structures in a non-protein environment
-
4 cluster: synthesis, stability, and geometric and electronic structures in a non-protein environment. J. Am. Chem. Soc. 118:1966-1980.
-
(1996)
J. Am. Chem. Soc.
, vol.118
, pp. 1966-1980
-
-
Zhou, J.1
Hu, Z.2
Münck, E.3
Holm, R.H.4
|