Publications

Recent publications

53. Rutz DA, Luo Q, Freiburger L, Madl T, Kaila VRI, Sattler M, Buchner J (2017) A switch point in the molecular chaperone Hsp90 responding to client interaction. (in review)

52. Schrepfer P, Ugur I, Klumpe S., Metterlein M, Kaila VRI*, Brück T (2017) Deciphering and harmonizing catalytic events in cembranoid biosynpthesis- a symphony of computational and synthetic biocatalysis. (in review)

51. Kaila VRI* (2017) Multi-scale Molecular Simulations on Respiratory Complex I. in Chemical Biology No. 5, “Mechanisms of Primary Energy Transduction in Biology”, Ed. Mårten Wikström, The Royal Society of Chemistry 2018, book chapter. (accepted for publication)

50. Wachtel R, Bräuning B, Mader SL, Ecker F, Kaila VRI, Groll M, Itzen A (2017) The protease GtgE from Salmonella exclusively targets inactive Rab-proteins (in review).

49. Mader SM, Bräuer A, Groll M, Kaila VRI* (2017) Mechanism and engineering of quinolone synthesis in the dioxygenase, AsqJ. (in review)

48. Gamiz-Hernandez AP, Jussupow A, Johansson MP, Kaila VRI* (2017) Terminal Electron-Proton Transfer Dynamics in the Quinone Reduction of Respiratory Complex I. J. Am. Chem. Soc. (accepted). [Full text]

47. Supekar S, Papageorgiou AC, Gemmecker G, Peltzer R, Johansson MP, Tripsianes K, Sattler M, Kaila VRI* (2017) Conformational Selection of Dimethylarginine Recognition by the Survival Motor Neuron Tudor Domain. Angew. Chemie. Intl. Ed. (accepted) [Full text]

46. Di Luca A, Gamiz-Hernandez AP, Kaila VRI* (2017) Symmetry related proton transfer pathways in respiratory Complex I. Proc. Natl. Acad. Sci. USA 114, E6314–E6321. [Full text]

45. Suomivuori CM, Gamiz-Hernandez AP, Sundholm D, Kaila VRI (2017). Energetics and dynamics of a light-driven sodium-pumping rhodopsin. Proc Natl Acad Sci U S A.  (in press) doi: 10.1073/pnas.1703625114. [Full text]

44. Zhang Q, Catti L, Kaila VRI, Tiefenbacher K (2016) To Catalyze or not to Catalyze: Elucidation of the Subtle Differences between the Hexameric Capsules of Pyrogallolarene and Resorcinarene. Chemical Science 8:1653-1657. [Full text]

43. Wittwer M, Luo Q, Kaila VRI, Dames S (2016) Oxidative Unfolding of the Rubredoxin Domain and the Natively Disordered N-terminal Region Regulate the Catalytic Activity of M. tuberculosis Protein Kinase G. J. Mol. Biol. 291:27062-27072. [Full text]

42. Suomivuori C-M, Winter N.O.C., Hättig C, Sundholm D, Kaila VRI (2016) Exploring the Light-Capturing Properties of Photosynthetic Chlorophyll Clusters Using Large-Scale Correlated Calculations. J. Chem. Theory Comput. 12:2644-2651. [Full text]

41. Luo Q, Boczek EE, Buchner J, Kaila VRI (2017) Conformational activation and Hsp90-dependence of c-Src and its oncogenic mutants. Sci. Rep. 7:43996. [Full text]

40. Suomivuori CM, Lang L, Sundholm D, Gamiz-Hernandez AP, Kaila VRI (2016) Tuning the protein-induced absorption shifts of retinal in engineered rhodopsin mimics. Chem – Eur. J. 22:8254-8861. [Full text]

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39. Supekar S, Gamiz-Hernandez AP, Kaila VRI (2016) A Protonated Water Cluster as a Transient Proton Loading Site in Cytochrome c Oxidase. Angew. Chemie Intl. Ed. 55:11940-11944.

38. Ugur I, Rutherford  AW, Kaila VRI (2016)  Redox-coupled substrate water reorganization in the active site of Photosystem II Biochim. Biophys. Acta – Bioenergetics 1857:740-748.  [Full text]

37. Sharma V, Belevich G, Gamiz-Hernandez AP, Róg T, Vattulainen I, Wikström M, Hummer G, Kaila VRI (2015) Redox-Induced Activation of the Proton Pump in the Respiratory Complex I Proc. Natl. Acad. Sci. USA 112:11571-11576. [Full text]

36. Gamiz-Hernandez AP, Kaila VRI (2016) Conversion of Light-Energy Into Molecular Strain in the Photocycle of the Photoactive Yellow Protein. Phys. Chem. Chem. Phys. 18:2802-2809. [Full text]

35. Gamiz-Hernandez AP, Neycheva IA, Send R, Sundholm D, Kaila VRI (2015) Protein-Induced Color Shift of Carotenoids in β-Crustacyanin Angew. Chemie Intl. Ed. 54:11564-11566.

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34. Kmita K, Wirth C, Warnau J, Guerrero-Castillo S, Hunte C, Hummer G, Kaila VRI, Zwicker K, Brandt U, Zickermann V. (2015) Accessory NUMM (NDUFS6) subunit harbors a Zn-binding site and is essential for biogenesis of mitochondrial complex I.  Proc. Natl. Acad. Sci. USA 112:5685-5690.

33. Boczek EE, Reefschläger LG, Dehling M, Struller T, Häusler E, Seidl A, Kaila VRI, Buchner J (2014) Conformational processing of oncogenic v-Src kinase by Hsp90. Proc. Natl. Acad. Sci. USA 112: E3189-3198.

32. Wikström M, Sharma V, Kaila VRI, Hosler J, Hummer G (2015) New perspectives on proton pumping in cellular respiration. Chem. Rev. 115, 2196-2221. [Full text]

31.Shao Y, Mei Y, Kaila VRI (2014) Performance of time-dependent density functional theory methods on biochromophores (submitted)

30.Gamiz-Hernandez AP, Magomedov A, Hummer G, Kaila VRI (2014) Linear energy relationships in ground state proton transfer and excited state proton-coupled electron transfer J. Phys. Chem. B (in press) [Full Text]

29. Kaila VRI , Schotte F, Hyun S-C, Hummer G, Anfinrud PA (2014) Reconciling contradictions in time-resolved x-ray structures of early intermediates in the photocycle of photoactive yellow protein Nature Chem 6:258-259. [Full Text]

28. Zhou X, Sundholm D, Wesolowski A,  Kaila VRI (2014) Spectral Tuning of Rhodopsin and Visual Cone Pigments. J. Am. Chem. Soc (Communication) 136:2723-2726. [Full Text]

27. Kaila VRI , Wikström M, Hummer G (2014) Electrostatics, Hydration, and Proton Transfer Dynamics in the Membrane Domain of Respiratory Complex I. Proc Natl Acad Sci USA 111, 6988-6993. [Full Text]

26. Send R, Suomivuori CM, Kaila VRI , Sundholm D (2015) Coupled-Cluster Studies of Extensive Green Fluorescent Protein Models using the Reduced Virtual Space Approach. J. Phys. Chem. B. [Full Text]

25. Kaila VRI, Send R, Sundholm D (2012) Electrostatic Spectral Tuning Mechanism of the Green Fluorescent Protein. Phys. Chem. Chem. Phys. 15, 4491-4495. [Full text]

24. Schotte F, Hyun S-C, Kaila VRI, Kamikubo H, Dashdorja N, Henry E, Graber T, Henning R, Wulff M, Hummer G, Kataoka M, Anfinruda PA (2012) Picosecond Photobiology: Watching a Signaling Protein Function in Real Time via Time-resolved Laue Crystallography. Proc Natl Acad Sci USA 109, 19256-19261. [Full Text]

23. Johansson MP, Kaila VRI, Sundholm D (2013) Ab initio, density functional theory, and semi-empirical calculations. Methods in Mol. Biol. 924, 3-27. [Full Text]

22. Kaila VRI, Send R, Sundholm D (2012) The effect of the protein environment on primary photoexcitation events of retinal. J Phys Chem B 116, 2249-2258. [Full Text]

21. Sharma V, Wikström M, Kaila VRI (2012) Dynamic water networks in cytochrome cbb3. Biochim Biophys Acta – Bioenergetics 1817, 726-734. [Full Text]

20. Kaila VRI, Hummer G (2011) Energetics of direct and water-mediated proton-coupled electron transfer. J Am Chem Soc 133: 19040-19043. [Full Text]

19. Kaila VRI, Hummer G (2011) Energetics and dynamics of proton transfer reactions along short water wires. Phys Chem Chem Phys 13: 13207-13215. [Full Text]

18. Send R, Kaila VRI, Sundholm D (2011) Benchmarking the Approximate Second-Order Coupled-Cluster Method on Biochromophores. J Chem Theory Comput 7: 2473-2484. [Full Text]

17. Send R, Kaila VRI, Sundholm D (2011) Reduction of the virtual space for coupled-cluster excitation energies of large molecules and embedded systems. J Chem Phys 134: 214114. [Full Text]

16. Sharma V, Wikström M, Kaila VRI (2011) Stabilization of the peroxy intermediate in the oxygen splitting reaction of cytchrome cbb3. Biochim. Biophys. Acta – Bioenergetics 1807: 813-818. [Full Text]

15. Kaila VRI, Oksanen E, Goldman A, Verkhovsky MI, Sundholm D, Wikström M (2011) A Combined Quantum Chemical and Crystallographic Study on the Oxidized Binuclear Center of Cytochrome c Oxidase. Biochim Biophys Acta – Bioenergetics 1807: 769-778. [Full Text]

14. Fliegl H, Lehtonen O, Sundholm D, Kaila VRI (2011) Hydrogen-bond strengths by magnetically induced currents. Phys Chem Chem Phys 13:434-437. [Full Text]

13. Kaila VRI, Sharma V, Wikström M (2011) The identity of the transient proton loading site of the proton-pumping mechanism of cytochrome c oxidase. Biochim Biophys Acta – Bioenergetics 1807:80-84. [Full Text]

12. Taubert S, Kaila VRI, Sundholm D (2011) Aromatic pathways in conjugated rings connected by single bonds. Int J Quantum Chem 111:848-857. [Full Text]

11. Kaila VRI, Verkhovsky MI, Wikström M (2010) Proton-coupled electron transfer in cytochrome oxidase. Chem Rev 110:7062-7081. [Full Text]

10. Kaila VRI, Johansson MP, Sundholm D, Wikström M (2010) Interheme electron tunneling in cytochrome c oxidase. Proc Natl Acad Sci USA 107: 21470-21475. [Full Text]

9. Sharma V, Wikström M, Kaila VRI (2010) Redox-coupled proton transfer in the active site of cytochrome cbb3. Biochim Biophys Acta – Bioeneregtics 1797:1512-1520. [Full Text]

8. Kaila VRI, Verkhovsky MI, Hummer G, Wikström M (2009) Mechanism and energetics by which glutamic acid 242 prevents leaks in cytochrome c oxidase. Biochim Biophys Acta 1787: 1205-1214. [Full Text]

7. Kaila VRI, Johansson MP, Sundholm D, Laakkonen L, Wikström M (2009) The chemistry of the CuB site in cytochrome c oxidase and the importance of its unique His-Tyr bond. Biochim Biophys Acta – Bioenergetics 1787: 221-233. [Full Text]

6. Sharma V, Kaila VRI, Annila A (2009) Protein folding as an evolutionary process. Physica A 388: 851-862.

5. Kaila VRI, Annila A (2008) Natural selection for least action. Proc Roy Soc A 464: 3055-3070.

4. Kaila VRI, Verkhovsky MI, Hummer G, Wikström M (2008) Prevention of leak in the proton pump of cytochrome c oxidase. Biophys Biochim Acta – Bioenergetics 1777: 890-892. [Full Text]

3. Kaila VRI, Verkhovsky MI, Hummer G, Wikström M (2008) Glutamic acid 242 is a valve in the proton pump of cytochrome c oxidase. Proc Natl Acad Sci USA 105:6255-6259. [Full Text]

2. Johansson MP, Kaila VRI, Laakkonen L (2008) Charge parameterization of the metal centers in cytochrome c oxidase. J. Comput. Chem. 29: 753-767. [Full Text]

1. Tuukkanen A, Kaila VRI, Laakkonen L, Hummer G, Wikström M (2008) Dynamics of the glutamic acid 242 side chain in cytochrome c oxidase. Biochim Biophys Acta – Bioenergetics 1767: 1102-1106 (shared first authorship). [Full Text]

Other scientific publications:

  • Johansson MP, Kaila VRI, Sundholm D, “Ab initio, density functional theory, and semi-empirical calculations in Biomolecular simulations: methods and protocol (book chapter).
  • “Theoretical studies on coupled electron and proton transfer in cytochrome c oxidase”, PhD thesis, 2009. [Full text]
  • “Beräkningskemiska studier av protontranslokeringsmekanismen i cytokrom c oxidas”, MSc thesis 2006.
  • “Fotosyntes och cellandning ur ett bioenergetiskt perspektiv”, Upper Secondary School thesis 2002.

 

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