Steered Molecular Dynamics Simulation of the Rieske Subunit Motion in the Cytochrome bc1 Complex

Abrahams, 1994, Structure at 2.8Å resolution of F1-ATPase from bovine heart mitochondria, Nature, 370, 621, 10.1038/370621a0

Balsera, 1997, Reconstructing potential energy functions from simulated force-induced unbinding processes, Biophys. J., 73, 1281, 10.1016/S0006-3495(97)78161-X

Bernstein, 1977, The Protein Data Bank: a computer-based archival file for macromolecular structures, J. Mol. Biol., 112, 535, 10.1016/S0022-2836(77)80200-3

Besler, 1990, Atomic charges derived from semiempirical methods, J. Comp. Chem., 11, 431, 10.1002/jcc.540110404

Bishop, 1997, How hormone receptor-DNA binding affects nucleosomal DNA: the role of symmetry, Biophys. J., 72, 2056, 10.1016/S0006-3495(97)78849-0

Blume, 1983, Apparent molar heat capacities of phospholipids in aqueous dispersion: effects of chain length and headgroup structure, Biochemistry, 22, 5436, 10.1021/bi00292a027

Brandt, 1997, Proton-translocation by membrane-bound NADH-ubiquinone-oxidoreductase (complex I) through redox-gated ligand conduction, Biochim. Biophys. Acta. Bioenerget., 1318, 79, 10.1016/S0005-2728(96)00141-7

Brandt, 1998, The chemistry and mechanisms of ubihydroquinone oxidation at center P (Qo) of the cytochrome bc1 complex, Biochim. Biophys. Acta, 1365, 261, 10.1016/S0005-2728(98)00078-4

Brandt, 1994, The protonmotive Q cycle in mitochondria and bacteria, CRC Crit. Rev. Biochem., 29, 165, 10.3109/10409239409086800

Brünger, 1992

Connolly, 1983, Solvent-accessible surfaces or proteins and nucleic acids, Science, 221, 709, 10.1126/science.6879170

Crofts, 1985, The mechanism of ubiquinol:cytochrome c oxidoreductases of mitochondria and of Rhodopseudomonas sphaeroides, 4

Crofts, 1995, Structure and function in the bc1-complex of rb. sphaeroides

Crofts, 1998, Structure and function of the cytochrome bc1 complex of mitochondria and photosynthetic bacteria, Curr. Opin. Struct. Biol., 8, 501, 10.1016/S0959-440X(98)80129-2

Dalke, 1997, Using TCL for molecular visualization and analysis, Pac. Symp. Biocomp., 2, 85

Elston, 1997, Energy transduction in ATP synthase, Nature, 391, 510, 10.1038/35185

Frisch, 1995

Gennis, 1993, The bc1 complexes of Rhodobacter sphaeroides and Rhodobacter capsulatus, J. Bioenerg. Biomembr., 25, 195, 10.1007/BF00762582

Grubmüller, 1996, Ligand binding and molecular mechanics calculation of the streptavidin-biotin rupture force, Science, 271, 997, 10.1126/science.271.5251.997

Gullingsrud, 1999, Reconstructing potentials of mean force through time series analysis of steered molecular dynamics simulations, J. Comp. Phys., 151, 190, 10.1006/jcph.1999.6218

Hermans, 1998, Simulation studies of protein-ligand interactions, 4, 129

Humphrey, 1996, VMD: visual molecular dynamics, J. Mol. Graphics., 14, 33, 10.1016/0263-7855(96)00018-5

Isralewitz, 1997, Binding pathway of retinal to bacterio-opsin: A prediction by molecular dynamics simulations, Biophys. J., 73, 2972, 10.1016/S0006-3495(97)78326-7

Iwata, 1998, Complete structure of the 11-subunit bovine mitochondrial cytochrome bc1 complex, Science, 281, 64, 10.1126/science.281.5373.64

Iwata, 1996, Structure of a water soluble fragment of the “Rieske” iron-sulphur protein of the bovine heart mitochondrial cytochrome bc1 complex determined by MAD phasing at 1.5Å resolution, Structure, 4, 567, 10.1016/S0969-2126(96)00062-7

Izrailev, 1997, Molecular dynamics study of unbinding of the avidin-biotin complex, Biophys. J., 72, 1568, 10.1016/S0006-3495(97)78804-0

Izrailev, 1998, Steered molecular dynamics, 4, 39

Kim, 1998, Inhibitor binding changes domain mobility in the iron-sulfur protein of the mitochondrial bc1 complex from bovine heart, Proc. Natl. Acad. Sci. USA, 95, 8026, 10.1073/pnas.95.14.8026

Kosztin, 1997, Binding of the estrogen receptor to DNA: the role of waters, Biophys. J., 73, 557, 10.1016/S0006-3495(97)78093-7

Kosztin, 1999, Unbinding of retinoic acid from its receptor studied by steered molecular dynamics, Biophys. J., 76, 188, 10.1016/S0006-3495(99)77188-2

Lancaster, 1997, The coupling of light-induced electron transfer and proton uptake as derived from crystal structures of reaction centers from Rhodopseudomonas viridis modified at the binding site of the secondary quinone, QB, Structure, 5, 1339, 10.1016/S0969-2126(97)00285-2

Link, 1996, The role of the “Rieske” iron sulfur protein in the hydroquinone oxidation (Qp−) site of the cytochrome bc1 complex: the “proton-gated affinity change” mechanism, FEBS Lett., 412, 257, 10.1016/S0014-5793(97)00772-2

Lu, 1998, Unfolding of titin immunoglobulin domains by steered molecular dynamics simulation, Biophys. J., 75, 662, 10.1016/S0006-3495(98)77556-3

Lüdemann, 1997, Substrate access to cytochrome P450cam: a comparison of a thermal motion pathway analysis with molecular dynamics simulation data, J. Mol. Model., 3, 369, 10.1007/s008940050053

MacKerell, 1998, All-hydrogen empirical potential for molecular modeling and dynamics studies of proteins using the CHARMM22 force field, J. Phys. Chem. B, 102, 3586, 10.1021/jp973084f

MacKerell, 1992, Self-consistent parametrization of biomolecules for molecular modeling and condensed phase simulations, FASEB J., 6, 143a

MacKerell, 1995, An all-atom empirical energy function for the simulation of nucleic acids, J. Am. Chem. Soc., 117, 11946, 10.1021/ja00153a017

Mitchell, 1976, Possible molecular mechanisms of the protonmotive function of cytochrome systems, J. Theor. Biol., 62, 327, 10.1016/0022-5193(76)90124-7

MSI. 1994. QUANTA 4.0. Molecular Simulations Inc., Burlington, Massachusetts.

Nelson, 1996, NAMD: a parallel, object-oriented molecular dynamics program, Int. J. Supercomput. Appl. High Perform. Comput., 10, 251

Noji, 1997, Direct observation of the rotation of F1-ATPase, Nature, 386, 299, 10.1038/386299a0

Ousterhout, 1994

Powell, 1977, Restart procedures for the conjugate gradient method, Mathematical Programming, 12, 241, 10.1007/BF01593790

Schlenkrich, 1996, Empirical potential energy function for phospholipids: criteria for parameter optimization and applications, 31

Singh, 1984, An approach to computing electrostatic charges for molecules, J. Comp. Chem., 5, 129, 10.1002/jcc.540050204

Stepaniants, 1997, Extraction of lipids from phospholipid membranes by steered molecular dynamics, J. Mol. Model, 3, 473, 10.1007/s008940050065

Sutton, L.E. 1965. Table of Interatomic Distances and Configuration in Molecules and Ions. Supplement 1956–1959. Special Publication No. 18., Chemical Society, London.

Treutlein, 1988, Molecular dynamics simulation of the primary processes in the photosynthetic reaction center of Rhodopseudomonas viridis, 149, 139

Wang, 1998, Energy transduction ATP synthase, Nature, 391, 510, 10.1038/35185

Wriggers, 1997, Protein domain movements: detection of rigid domains and visualization of hinges in comparisons of atomic coordinates, Proteins: Struct., Funct., Genet., 29, 1, 10.1002/(SICI)1097-0134(199709)29:1<1::AID-PROT1>3.0.CO;2-J

Wriggers, 1999, Investigating a back door mechanism of actin phosphate release by steered molecular dynamics, Proteins: Struct., Funct., Genet., 35, 262, 10.1002/(SICI)1097-0134(19990501)35:2<262::AID-PROT11>3.0.CO;2-N

Xia, 1997, Crystal structure of the cytochrome bc1 complex from bovine heart mitochondria, Science, 277, 60, 10.1126/science.277.5322.60

Zhang, 1996, Hydrophilicity of cavities in proteins, Proteins: Struct., Funct., Genet., 24, 433, 10.1002/(SICI)1097-0134(199604)24:4<433::AID-PROT3>3.0.CO;2-F

Zhang, 1998, Electron transfer by domain movement in cytochrome bc1, Nature, 392, 677, 10.1038/33612

Zhou, 1995, Molecular dynamics study of a membrane-water interface, J. Phys. Chem., 99, 2194, 10.1021/j100007a059