Syddansk Universitet Atomistic determinants of coenzyme Q reduction at the Qi-site of the cytochrome bc 1 complex

[1]  Pekka A. Postila,et al.  Identifying involvement of Lys251/Asp252 pair in electron transfer and associated proton transfer at the quinone reduction site of Rhodobacter capsulatus cytochrome bc1 , 2016, Biochimica et biophysica acta.

[2]  Vivek Sharma,et al.  Role of subunit III and its lipids in the molecular mechanism of cytochrome c oxidase. , 2015, Biochimica et biophysica acta.

[3]  Vivek Sharma,et al.  Proton-coupled electron transfer and the role of water molecules in proton pumping by cytochrome c oxidase , 2015, Proceedings of the National Academy of Sciences.

[4]  Klaus Schulten,et al.  Identification of Ubiquinol Binding Motifs at the Qo-Site of the Cytochrome bc1 Complex , 2014, The journal of physical chemistry. B.

[5]  A. Crofts,et al.  The Semiquinone at the Qi Site of the bc1 Complex Explored Using HYSCORE Spectroscopy and Specific Isotopic Labeling of Ubiquinone in Rhodobacter sphaeroides via 13C Methionine and Construction of a Methionine Auxotroph , 2014, Biochemistry.

[6]  Keisuke Saito,et al.  Proton transfer reactions and hydrogen-bond networks in protein environments , 2014, Journal of The Royal Society Interface.

[7]  Pekka A. Postila,et al.  Atomistic simulations indicate cardiolipin to have an integral role in the structure of the cytochrome bc1 complex. , 2013, Biochimica et biophysica acta.

[8]  Pekka A. Postila,et al.  Key role of water in proton transfer at the Qo-site of the cytochrome bc1 complex predicted by atomistic molecular dynamics simulations. , 2013, Biochimica et biophysica acta.

[9]  Pekka A. Postila,et al.  Parameterization of the prosthetic redox centers of the bacterial cytochrome bc1 complex for atomistic molecular dynamics simulations , 2013, Theoretical Chemistry Accounts.

[10]  Jan H. Jensen,et al.  Improved Treatment of Ligands and Coupling Effects in Empirical Calculation and Rationalization of pKa Values. , 2011, Journal of chemical theory and computation.

[11]  Pekka A. Postila,et al.  Pharmacological activity of C10-substituted analogs of the high-affinity kainate receptor agonist dysiherbaine , 2010, Neuropharmacology.

[12]  Pekka A. Postila,et al.  Exploring kainate receptor pharmacology using molecular dynamics simulations , 2010, Neuropharmacology.

[13]  R. Sakai,et al.  Full Domain Closure of the Ligand-binding Core of the Ionotropic Glutamate Receptor iGluR5 Induced by the High Affinity Agonist Dysiherbaine and the Functional Antagonist 8,9-Dideoxyneodysiherbaine* , 2009, Journal of Biological Chemistry.

[14]  Nava Whiteford,et al.  Validation of all-atom phosphatidylcholine lipid force fields in the tensionless NPT ensemble. , 2009, Biochimica et biophysica acta.

[15]  Sozanne R. Solmaz,et al.  Structure of Complex III with Bound Cytochrome c in Reduced State and Definition of a Minimal Core Interface for Electron Transfer* , 2008, Journal of Biological Chemistry.

[16]  Pekka A. Postila,et al.  Novel Analogs and Stereoisomers of the Marine Toxin Neodysiherbaine with Specificity for Kainate Receptors , 2008, Journal of Pharmacology and Experimental Therapeutics.

[17]  P. Dutton,et al.  Exposing the complex III Qo semiquinone radical. , 2007, Biochimica et biophysica acta.

[18]  David M Kramer,et al.  A semiquinone intermediate generated at the Qo site of the cytochrome bc1 complex: Importance for the Q-cycle and superoxide production , 2007, Proceedings of the National Academy of Sciences.

[19]  C. Hunte,et al.  Redox-linked protonation state changes in cytochrome bc1 identified by Poisson-Boltzmann electrostatics calculations. , 2007, Biochimica et biophysica acta.

[20]  L. Esser,et al.  Surface-modulated motion switch: Capture and release of iron–sulfur protein in the cytochrome bc1 complex , 2006, Proceedings of the National Academy of Sciences.

[21]  C. Wraight,et al.  Chance and design--proton transfer in water, channels and bioenergetic proteins. , 2006, Biochimica et biophysica acta.

[22]  Laxmikant V. Kalé,et al.  Scalable molecular dynamics with NAMD , 2005, J. Comput. Chem..

[23]  E. Berry,et al.  Binding of the respiratory chain inhibitor antimycin to the mitochondrial bc1 complex: a new crystal structure reveals an altered intramolecular hydrogen-bonding pattern. , 2005, Journal of molecular biology.

[24]  Alexander D. MacKerell,et al.  Extending the treatment of backbone energetics in protein force fields: Limitations of gas‐phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations , 2004, J. Comput. Chem..

[25]  Mats Gyllenberg,et al.  BODIL: a molecular modeling environment for structure-function analysis and drug design , 2004, J. Comput. Aided Mol. Des..

[26]  A. Crofts,et al.  Exploration of Ligands to the Qi Site Semiquinone in the bc1 Complex Using High-resolution EPR* , 2003, Journal of Biological Chemistry.

[27]  G. Hummer,et al.  Water-gated mechanism of proton translocation by cytochrome c oxidase. , 2003, Biochimica et biophysica acta.

[28]  B. Trumpower,et al.  Specific roles of protein–phospholipid interactions in the yeast cytochrome bc1 complex structure , 2001, The EMBO journal.

[29]  P. Rich,et al.  On the Mechanism of Quinol Oxidation in thebc 1 Complex* , 1998, The Journal of Biological Chemistry.

[30]  T. Darden,et al.  A smooth particle mesh Ewald method , 1995 .

[31]  A. Crofts,et al.  Characterization of mutations in the cytochrome b subunit of the bc1 complex of Rhodobacter sphaeroides that affect the quinone reductase site (Qc). , 1993, Biochemistry.

[32]  P. Dutton,et al.  Thermodynamic properties of the semiquinone and its binding site in the ubiquinol-cytochrome c (c2) oxidoreductase of respiratory and photosynthetic systems. , 1984, The Journal of biological chemistry.

[33]  P. Mitchell Protonmotive redox mechanism of the cytochrome b‐c 1 complex in the respiratory chain: Protonmotive ubiquinone cycle , 1975, FEBS letters.

[34]  F. Daldal,et al.  X-Ray Structure of Rhodobacter Capsulatus Cytochrome bc1: Comparison with its Mitochondrial and Chloroplast Counterparts , 2004, Photosynthesis Research.

[35]  A. Crofts,et al.  Structure and function of cytochrome bc complexes. , 2000, Annual review of biochemistry.

[36]  B. Trumpower,et al.  The protonmotive Q cycle in mitochondria and bacteria. , 1994, Critical reviews in biochemistry and molecular biology.

[37]  F. Daldal,et al.  Comparison with its mitochondrial and chloroplast counterparts , 2022 .