- Email: [email protected]
Computational investigation of the redox-coupled proton pumping in respiratory complex I
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Abstracts
References: 1. M. Sarewicz and A. Osyczka, Electronic connection between the quinone and cytochrome c redox pools and its role in regulation of mitochondrial electron transport and redox signaling, Physiol Rev. 95 (2015) 219-243 2. S. Pintscher, P. Kuleta, E. Cieluch, A. Borek, M. Sarewicz, A. Osyczka, Tuning of hemes b equilibrium redox potential is not required for crossmembrane electron transfer, .J. Biol. Chem. 291 (2016) 6872-6881.
4. M. Wikström, V. Sharma, V. R. I. Kaila, J. P. Hosler, G. Hummer, New perspective on proton pumping in cellular respiration, Chem. Rev. 115 (2015) 2196-2221.
doi:10.1016/j.bbabio.2016.04.315
03.30
03.29 Computational investigation of the redox-coupled proton pumping in respiratory complex I Vivek Sharmaa,b, Judith Warnauc,d, Ana P. Gamiz-Hernandezc, Outi Haapanena, Andrea di Lucac, Ilpo Vattulainena,b,e, Mårten Wikströmf, Gerhard Hummerd, Ville R.I. Kailac a Department of Physics, Tampere University of Technology, Tampere, Finland b Department of Physics, University of Helsinki, Helsinki, Finland c Department of Chemistry, Technische Universität München, Munich, Germany d Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main,Germany e MEMPHYS – Center for Biomembrane Physics, Department of Physics, University of Southern Denmark, Odense, Denmark. f Institute of Biotechnology, University of Helsinki, Helsinki, Finland Corresponding author at: Department of Physics, Tampere University of Technology, Tampere, Finland. E-mail address: vivek.sharma@tut.fi (V. Sharma) Mitochondrial respiratory chain comprises Complex I (NADH:quinone oxidoreductase) as the first electron acceptor. It catalyzes the two-electron reduction of quinone (from NADH) to quinol, and couples it to proton pumping across the inner mitochondrial membrane. Recently solved crystal structures of mitochondrial and bacterial complexes have established the electron transfer path from NADH to quinone that binds in a tight tunnel-like cavity [1,2]. The structural data have also provided insights into the putative proton transfer pathways in the membrane bound subunits [1,2]. However, due to large spatial separation between the most distant proton pumping module and the electron transfer path, it remains entirely unclear how the two reactions (proton and electron transfer) are coupled. To shed light on the early reactions of the catalytic cycle and the molecular mechanism of proton pumping, we performed state-of-the-art fully-atomistic classical molecular dynamics (MD) simulations in different redox/ protonation states. Results from simulations show that both electrostatic and conformational transitions play a key role in redox-coupled proton pumping [3], and support our recent mechanistic models [4]. References 1. R. Baradaran, J. M. Berrisford, G. S. Minhas, L. A. Sazanov, Crystal structure of the entire respiratory complex I, Nature 494 (2013) 443-448 2. V. Zickermann, C. Wirth, H. Nasiri, K. Siegmund, H. Schwalbe, C. Hunte, U. Brandt, Mechanistic insight from the crystal structure of mitochondrial complex I, Science 347 (2015) 44-49 3. V. Sharma, G. Belevich, Ana P. Gamiz-Hernandez, T. Rog, I. Vattulainen, M. L. Verkhovskaya, M. Wikström, G. Hummer, V. R. I. Kaila, Redox-induced activation of the proton pump in the respiratory complex I, Proc. Natl. Acad. Sci. USA 112 (2015) 11571-11576
doi:10.1016/j.bbabio.2016.04.316
Extraction of native cytochrome c oxidase nanodiscs from yeast mitochondria using a styrene-maleic acid co-polymer Irina A. Smirnova, Dan Sjöstrand, Markus Björk, Christoph von Ballmoos, Pia Ädelroth, Peter Brzezinski Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden E-mail address: [email protected] (I.A. Smirnova) Functional studies of pure membrane proteins in a lipid environment typically involves detergent solubilization followed by reconstitution e.g. in liposomes. However, the use of detergent may alter the protein structure and/or function. Here, we have used poly(styrene-altmaleic acid) (SMA) co-polymer [1] to co-extract the S. cerevisiae cytochrome c oxidase (CytcO) together with a disc of the native lipids without the use of detergents. The SMA-embedded CytcO-containing native nanodiscs were purified using affinity chromatography and the purity of the CytcO was confirmed using optical absorption spectroscopy and SDS-PAGE. The lipid composition of the native nanodiscs was the same as that of the mitochondrial inner membranes. The native nanodiscs remained in solution after removal of the excess SMA. The CytcO displayed a steady-state activity similar to that in the mitochondrial membranes. The kinetics of CO-ligand binding to heme a3 in the catalytic site of CytcO was similar to that in mitochondria. All kinetic components seen during reaction of the reduced CytcO-native nanodiscs with O2 were observed. References 1. J.M. Dörr, S. Scheidelaar, M.C. Koorengevel, J.J. Dominguez, M. Schäfer, C.A. van Walree, J.A. Killian, The styrene–maleic acid copolymer: a versatile tool in membrane research, European Biophysics Journal, 45 (2016) 3-21. doi:10.1016/j.bbabio.2016.04.317
03.31 Human mitochondrial cytochrome b variants studied in yeast: not all are silent polymorphisms Zehua Songa, Anaïs Lalevea, Cindy Vallièresa, John E. McGeehanb, Rhiannon E. Lloydc, Brigitte Meuniera a Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris‐Sud, Université Paris‐Saclay, Gif‐sur‐Yvette, France b Molecular Biophysics Laboratories, University of Portsmouth, Portsmouth, UK c Brain Tumour Research Centre, University of Portsmouth, Portsmouth, UK E-mail address: [email protected] (B. Meunier) Variations in the mitochondrial cytochrome b gene, encoding the core subunit of the bc1 complex are frequently found within the healthy population, but also occur within a spectrum of mitochondrial and common disease cohorts. Despite significant efforts, most
Abstracts
References: 1. M. Sarewicz and A. Osyczka, Electronic connection between the quinone and cytochrome c redox pools and its role in regulation of mitochondrial electron transport and redox signaling, Physiol Rev. 95 (2015) 219-243 2. S. Pintscher, P. Kuleta, E. Cieluch, A. Borek, M. Sarewicz, A. Osyczka, Tuning of hemes b equilibrium redox potential is not required for crossmembrane electron transfer, .J. Biol. Chem. 291 (2016) 6872-6881.
4. M. Wikström, V. Sharma, V. R. I. Kaila, J. P. Hosler, G. Hummer, New perspective on proton pumping in cellular respiration, Chem. Rev. 115 (2015) 2196-2221.
doi:10.1016/j.bbabio.2016.04.315
03.30
03.29 Computational investigation of the redox-coupled proton pumping in respiratory complex I Vivek Sharmaa,b, Judith Warnauc,d, Ana P. Gamiz-Hernandezc, Outi Haapanena, Andrea di Lucac, Ilpo Vattulainena,b,e, Mårten Wikströmf, Gerhard Hummerd, Ville R.I. Kailac a Department of Physics, Tampere University of Technology, Tampere, Finland b Department of Physics, University of Helsinki, Helsinki, Finland c Department of Chemistry, Technische Universität München, Munich, Germany d Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main,Germany e MEMPHYS – Center for Biomembrane Physics, Department of Physics, University of Southern Denmark, Odense, Denmark. f Institute of Biotechnology, University of Helsinki, Helsinki, Finland Corresponding author at: Department of Physics, Tampere University of Technology, Tampere, Finland. E-mail address: vivek.sharma@tut.fi (V. Sharma) Mitochondrial respiratory chain comprises Complex I (NADH:quinone oxidoreductase) as the first electron acceptor. It catalyzes the two-electron reduction of quinone (from NADH) to quinol, and couples it to proton pumping across the inner mitochondrial membrane. Recently solved crystal structures of mitochondrial and bacterial complexes have established the electron transfer path from NADH to quinone that binds in a tight tunnel-like cavity [1,2]. The structural data have also provided insights into the putative proton transfer pathways in the membrane bound subunits [1,2]. However, due to large spatial separation between the most distant proton pumping module and the electron transfer path, it remains entirely unclear how the two reactions (proton and electron transfer) are coupled. To shed light on the early reactions of the catalytic cycle and the molecular mechanism of proton pumping, we performed state-of-the-art fully-atomistic classical molecular dynamics (MD) simulations in different redox/ protonation states. Results from simulations show that both electrostatic and conformational transitions play a key role in redox-coupled proton pumping [3], and support our recent mechanistic models [4]. References 1. R. Baradaran, J. M. Berrisford, G. S. Minhas, L. A. Sazanov, Crystal structure of the entire respiratory complex I, Nature 494 (2013) 443-448 2. V. Zickermann, C. Wirth, H. Nasiri, K. Siegmund, H. Schwalbe, C. Hunte, U. Brandt, Mechanistic insight from the crystal structure of mitochondrial complex I, Science 347 (2015) 44-49 3. V. Sharma, G. Belevich, Ana P. Gamiz-Hernandez, T. Rog, I. Vattulainen, M. L. Verkhovskaya, M. Wikström, G. Hummer, V. R. I. Kaila, Redox-induced activation of the proton pump in the respiratory complex I, Proc. Natl. Acad. Sci. USA 112 (2015) 11571-11576
doi:10.1016/j.bbabio.2016.04.316
Extraction of native cytochrome c oxidase nanodiscs from yeast mitochondria using a styrene-maleic acid co-polymer Irina A. Smirnova, Dan Sjöstrand, Markus Björk, Christoph von Ballmoos, Pia Ädelroth, Peter Brzezinski Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden E-mail address: [email protected] (I.A. Smirnova) Functional studies of pure membrane proteins in a lipid environment typically involves detergent solubilization followed by reconstitution e.g. in liposomes. However, the use of detergent may alter the protein structure and/or function. Here, we have used poly(styrene-altmaleic acid) (SMA) co-polymer [1] to co-extract the S. cerevisiae cytochrome c oxidase (CytcO) together with a disc of the native lipids without the use of detergents. The SMA-embedded CytcO-containing native nanodiscs were purified using affinity chromatography and the purity of the CytcO was confirmed using optical absorption spectroscopy and SDS-PAGE. The lipid composition of the native nanodiscs was the same as that of the mitochondrial inner membranes. The native nanodiscs remained in solution after removal of the excess SMA. The CytcO displayed a steady-state activity similar to that in the mitochondrial membranes. The kinetics of CO-ligand binding to heme a3 in the catalytic site of CytcO was similar to that in mitochondria. All kinetic components seen during reaction of the reduced CytcO-native nanodiscs with O2 were observed. References 1. J.M. Dörr, S. Scheidelaar, M.C. Koorengevel, J.J. Dominguez, M. Schäfer, C.A. van Walree, J.A. Killian, The styrene–maleic acid copolymer: a versatile tool in membrane research, European Biophysics Journal, 45 (2016) 3-21. doi:10.1016/j.bbabio.2016.04.317
03.31 Human mitochondrial cytochrome b variants studied in yeast: not all are silent polymorphisms Zehua Songa, Anaïs Lalevea, Cindy Vallièresa, John E. McGeehanb, Rhiannon E. Lloydc, Brigitte Meuniera a Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris‐Sud, Université Paris‐Saclay, Gif‐sur‐Yvette, France b Molecular Biophysics Laboratories, University of Portsmouth, Portsmouth, UK c Brain Tumour Research Centre, University of Portsmouth, Portsmouth, UK E-mail address: [email protected] (B. Meunier) Variations in the mitochondrial cytochrome b gene, encoding the core subunit of the bc1 complex are frequently found within the healthy population, but also occur within a spectrum of mitochondrial and common disease cohorts. Despite significant efforts, most