Ville R I Kaila

Summary

Affiliation: National Institutes of Health
Country: USA

Publications

  1. ncbi Electrostatic spectral tuning mechanism of the green fluorescent protein
    Ville R I Kaila
    Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Building 5, Bethesda, Maryland 20892 0520, USA
    Phys Chem Chem Phys 15:4491-5. 2013
  2. ncbi The effect of protein environment on photoexcitation properties of retinal
    Ville R I Kaila
    Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
    J Phys Chem B 116:2249-58. 2012
  3. ncbi Energetics of direct and water-mediated proton-coupled electron transfer
    Ville R I Kaila
    Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Building 5, Bethesda, Maryland 20892 0520, USA
    J Am Chem Soc 133:19040-3. 2011
  4. ncbi Energetics and dynamics of proton transfer reactions along short water wires
    Ville R I Kaila
    Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 5 Memorial Drive, Bethesda, Maryland 20892 0520, USA
    Phys Chem Chem Phys 13:13207-15. 2011
  5. ncbi A combined quantum chemical and crystallographic study on the oxidized binuclear center of cytochrome c oxidase
    Ville R I Kaila
    Institute of Biotechnology, University of Helsinki, FI 00014 Helsinki, Finland
    Biochim Biophys Acta 1807:769-78. 2011
  6. ncbi Interheme electron tunneling in cytochrome c oxidase
    Ville R I Kaila
    Helsinki Bioenergetics Group, Structural Biology and Biophysics Programme, Institute of Biotechnology, University of Helsinki, PO Box 65, FI 00014 Helsinki, Finland
    Proc Natl Acad Sci U S A 107:21470-5. 2010
  7. ncbi The chemistry of the CuB site in cytochrome c oxidase and the importance of its unique His-Tyr bond
    Ville R I Kaila
    Helsinki Bioenergetics Group, Programme of Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
    Biochim Biophys Acta 1787:221-33. 2009
  8. ncbi Glutamic acid 242 is a valve in the proton pump of cytochrome c oxidase
    Ville R I Kaila
    Helsinki Bioenergetics Group, Structural Biology and Biophysics Program, Institute of Biotechnology, University of Helsinki, Viikinkaari 1, P O Box 65, 00014, Helsinki, Finland
    Proc Natl Acad Sci U S A 105:6255-9. 2008
  9. ncbi Dynamic water networks in cytochrome cbb3 oxidase
    Vivek Sharma
    Helsinki Bioenergetics Group, Programme for Structural Biology and Biophysics, Institute of Biotechnology, PB 65 Viikinkaari 1, University of Helsinki, 00014, Finland
    Biochim Biophys Acta 1817:726-34. 2012
  10. ncbi Prevention of leak in the proton pump of cytochrome c oxidase
    Ville R I Kaila
    Helsinki Bioenergetics Group, Structural Biology and Biophysics Programme, Institute of Biotechnology, University of Helsinki, PB 65 Viikinkaari 1, 00014 University of Helsinki, Helsinki, Finland
    Biochim Biophys Acta 1777:890-2. 2008

Collaborators

Detail Information

Publications19

  1. ncbi Electrostatic spectral tuning mechanism of the green fluorescent protein
    Ville R I Kaila
    Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Building 5, Bethesda, Maryland 20892 0520, USA
    Phys Chem Chem Phys 15:4491-5. 2013
    ..We find that the protein environment redshifts the absorption spectra by ∼0.56 eV and ∼0.22 eV for the two states, which can be attributed to ∼80% electrostatic effects and ∼20% steric effects...
  2. ncbi The effect of protein environment on photoexcitation properties of retinal
    Ville R I Kaila
    Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
    J Phys Chem B 116:2249-58. 2012
    ..The energy of the relaxed excited state was found to be 30 kcal/mol (1.3 eV) above the minimum ground state energy, and might be related to the transition state of the thermal activation process...
  3. ncbi Energetics of direct and water-mediated proton-coupled electron transfer
    Ville R I Kaila
    Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Building 5, Bethesda, Maryland 20892 0520, USA
    J Am Chem Soc 133:19040-3. 2011
    ..Our calculations suggest that the π-stacking of the tyrosine dimer in RNR results in strong electronic coupling and adiabatic PCET. Water participation in the PCET can be identified perturbatively in a Brønsted analysis...
  4. ncbi Energetics and dynamics of proton transfer reactions along short water wires
    Ville R I Kaila
    Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 5 Memorial Drive, Bethesda, Maryland 20892 0520, USA
    Phys Chem Chem Phys 13:13207-15. 2011
    ..We find that the barrier of the pT reaction depends linearly on the proton affinity of the donor but is nearly independent of the proton affinity of the acceptor, corresponding to Brønsted slopes of one and zero, respectively...
  5. ncbi A combined quantum chemical and crystallographic study on the oxidized binuclear center of cytochrome c oxidase
    Ville R I Kaila
    Institute of Biotechnology, University of Helsinki, FI 00014 Helsinki, Finland
    Biochim Biophys Acta 1807:769-78. 2011
    ..We show that the presence of O(2) is consistent with the X-ray data. We also discuss how other structures, such as a mixture of the aqueous species (H(2)O+OH(-) and H(2)O) and chloride fit the experimental data...
  6. ncbi Interheme electron tunneling in cytochrome c oxidase
    Ville R I Kaila
    Helsinki Bioenergetics Group, Structural Biology and Biophysics Programme, Institute of Biotechnology, University of Helsinki, PO Box 65, FI 00014 Helsinki, Finland
    Proc Natl Acad Sci U S A 107:21470-5. 2010
    ..We argue that this modification may be necessary at short donor/acceptor distances comparable to the donor/acceptor radii...
  7. ncbi The chemistry of the CuB site in cytochrome c oxidase and the importance of its unique His-Tyr bond
    Ville R I Kaila
    Helsinki Bioenergetics Group, Programme of Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
    Biochim Biophys Acta 1787:221-33. 2009
    ..The combined results provide an explanation for why the heme-copper oxidases need two pathways of proton uptake, and why the K-pathway is active only in the second half of the reaction cycle...
  8. ncbi Glutamic acid 242 is a valve in the proton pump of cytochrome c oxidase
    Ville R I Kaila
    Helsinki Bioenergetics Group, Structural Biology and Biophysics Program, Institute of Biotechnology, University of Helsinki, Viikinkaari 1, P O Box 65, 00014, Helsinki, Finland
    Proc Natl Acad Sci U S A 105:6255-9. 2008
    ..Suppression of proton leakage is particularly important in mitochondria under physiological conditions, where production of ATP takes place in the presence of a high electrochemical proton gradient...
  9. ncbi Dynamic water networks in cytochrome cbb3 oxidase
    Vivek Sharma
    Helsinki Bioenergetics Group, Programme for Structural Biology and Biophysics, Institute of Biotechnology, PB 65 Viikinkaari 1, University of Helsinki, 00014, Finland
    Biochim Biophys Acta 1817:726-34. 2012
    ..Protonation of Glu323 provides a mechanism to tune the redox potential of heme b(3) with possible implications for proton pumping...
  10. ncbi Prevention of leak in the proton pump of cytochrome c oxidase
    Ville R I Kaila
    Helsinki Bioenergetics Group, Structural Biology and Biophysics Programme, Institute of Biotechnology, University of Helsinki, PB 65 Viikinkaari 1, 00014 University of Helsinki, Helsinki, Finland
    Biochim Biophys Acta 1777:890-2. 2008
    ....
  11. ncbi Mechanism and energetics by which glutamic acid 242 prevents leaks in cytochrome c oxidase
    Ville R I Kaila
    Helsinki Bioenergetics Group, Structural Biology and Biophysics Program, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
    Biochim Biophys Acta 1787:1205-14. 2009
    ..Our model provides a suggestion for why reduction of the former state is coupled to proton translocation while reduction of the latter is not...
  12. ncbi Dynamics of the glutamic acid 242 side chain in cytochrome c oxidase
    Anne Tuukkanen
    Helsinki Bioenergetics Group, Structural Biology and Biophysics Programme, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
    Biochim Biophys Acta 1767:1102-6. 2007
    ....
  13. ncbi Stabilization of the peroxy intermediate in the oxygen splitting reaction of cytochrome cbb(3)
    Vivek Sharma
    University of Helsinki, Helsinki, Finland
    Biochim Biophys Acta 1807:813-8. 2011
    ..The major molecular basis for this stabilization is a glutamate residue, polarizing the proximal histidine ligand of heme b(3) in the active site...
  14. ncbi The identity of the transient proton loading site of the proton-pumping mechanism of cytochrome c oxidase
    Ville R I Kaila
    Helsinki Bioenergetics Group, Programme of Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, P O Box 65, FI 00014 Helsinki, Finland
    Biochim Biophys Acta 1807:80-4. 2011
    ..These findings suggest that the propionate region of heme a₃ fulfills the criteria of the pump site in the proton translocation mechanism of CcO...
  15. ncbi Charge parameterization of the metal centers in cytochrome c oxidase
    Mikael P Johansson
    Department of Chemistry, University of Helsinki, P O Box 55, FI 00014 Helsinki, Finland
    J Comput Chem 29:753-67. 2008
    ..Several relevant charge and ligand states are considered. Charges for two different force fields, CHARMM and AMBER, are presented...
  16. ncbi Redox-coupled proton transfer in the active site of cytochrome cbb3
    Vivek Sharma
    Helsinki Bioenergetics Group, Structural Biology and Biophysics Programme, Institute of Biotechnology, PB 65 Viikinkaari 1, University of Helsinki, FIN 00014, Helsinki, Finland
    Biochim Biophys Acta 1797:1512-20. 2010
    ....
  17. ncbi Ab initio, density functional theory, and semi-empirical calculations
    Mikael P Johansson
    Department of Chemistry, University of Helsinki, Helsinki, Finland
    Methods Mol Biol 924:3-27. 2013
    ..We start by presenting ab initio methods, followed by a treatment of density functional theory (DFT) and some recent advances in semi-empirical methods. Treatment of excited states as well as basis sets are also presented...
  18. ncbi Hydrogen-bond strengths by magnetically induced currents
    Heike Fliegl
    Department of Chemistry, University of Helsinki, P O Box 55 A I Virtanens Plats 1, FI 00014 Helsinki, Finland
    Phys Chem Chem Phys 13:434-7. 2011
    ..The method is calibrated using H-bonding dimers, and applied on Watson-Crick DNA base pairs and proton wires in carbonic anhydrase...
  19. ncbi Watching a signaling protein function in real time via 100-ps time-resolved Laue crystallography
    Friedrich Schotte
    Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
    Proc Natl Acad Sci U S A 109:19256-61. 2012
    ....