Publications

Recent publications

84.Mühlbauer ME, Saura P, Nuber F, Di Luca A, Friedrich T, Kaila VRI* (2020) Water-gated proton transfer dynamics in respiratory complex I. J Am Chem Soc (in press). [Full Text]

83. Bräuer A, Zhou Q, Grammbitter GLC, Schmalhofer M, Kaila VRI, Bode HB, Groll M (2020) Structural Snapshots of the Minimal PKS System Responsible for Octaketide Biosynthesis. Nature Chemistry [Full Text]

82. Schuller JM, Saura P, Thiemann J, Schuller S, Gamiz-Hernandez AP, Kurisu G, Nowaczyk MM, Kaila VRI* (2020) Redox-Coupled Proton Pumping Drives Carbon Concentration in the Photosynthetic Complex I, Nature Comms 11, 494: 1-7; [Full Text]

81. Mader SL, Lopez A, Lawatscheck J, Luo Q, Rutz DA, Gamiz-Hernandez AP, Sattler M, Buchner J, Kaila VRI* (2020) Conformational dynamics modulate the catalytic activity of the molecular chaperone Hsp90. Nature Comms 11: 11410; 1-12 [Full text]

80. Rehn A, Lawatscheck J, Mader SL, Luo Q, Blank B, Richter K, Kaila VRI, Buchner, J. (2020) A methylated lysine is a switch point for conformational communication in the chaperone Hsp90. Nature Comms 11: 1219; 1-14. [Full Text]

79. Kaila VRI* (2019) Molekularn Mechanismen der biologischen Energieumwandlung. Nachr Chem 67. [Full Text]

78. Wanzke C, Jussupow A, Kohler F, Dietz H, Kaila VRI, Boekhoven J (2020) Dynamic vesicles formed by dissipative self-assembly, ChemSystemsChem 2, e1900044.  |[Full Text]

77. Johansson MP, Niederegger L; Rauhalahti M; Hess CR; Kaila VRI (2019) Dispersion-Driven Water Oxidation in Molecular Ruthenium Catalysts. (in review)

76. Shao Y, Mei Y, Sundholm D, Kaila VRI* (2020) Performance of time-dependent density functional theory methods on biochromophores. J Chem Theor Comput 16(1):587-600. [Full Text]

75. Lauenstein R; Mader S; Derondeau H; Block M; Römer A; Jandl C; Riedle E; Kaila VRI, Hauer J; Thyrhaug E; Hess CR (2020). The central role of the metal ion in photocatalysis: Zn- vs. Ni-Mabiq. (in review)

74. Warnau J, Wöhlert D, Okazaki K, Yildiz O, Gámiz-Hernández AP, Kaila VRI*, Kühlbrandt W, Hummer G (2020) Ion Binding and Selectivity of the Na+/H+ Antiporter MjNhaP1. J. Phys Chem B 124(2):336-344. [Full Text]

73. Saura P, Kaila VRI* (2019) Energetics and Dynamics of NADH-Driven Proton-Coupled Electron Transfer in Respiratory Complex I. J Am Chem Soc 141:5710-5719. [Full text]

72. Jussupow A, Di Luca A, Kaila VRI* (2019) How cardiolipin modulates the activity of complex I. Science Adv 5, eaav1850. doi: 10.1126/sciadv.aav1850 [Full text]

71. Suomivuori CM, Fliegl H, Starikov EB, Balaban TS, Kaila VRI, and Sundholm D (2019) Absorption Shifts of Diastereotopically Ligated Chlorophyll Dimers of Photosystem I. Phys Chem Chem Phys 21, 6851-6858. [Full text]

70. Kaila VRI* (2019) Redox- and light-driven hydration dynamics (2019) in Oxygen Production and Reduction in Artificial and Natural Systems, Eds. J. Barber, A. Ruban, P. Nixon. https://doi.org/10.1142/9789813276925_0003 [Full Text]

69. Jagtap PKA, Asami S, Sippel C, Kaila VRI, Hausch F, Sattler M (2019). Selective inhibitors of FKBP51 employ conformational selection of dynamic invisible states. Angew Chemie 58:9429-9433. [Full text]

68. Saura P, Frey D, Gamiz-Hernandez AP, Kaila VRI* (2019) Electric Field Modulated Redox-Driven Protonation and Hydration Energetics in Energy Converting Enzymes. Chem Comm 55(43):6078-6081. [Full text]

67. Zhou Q, Bräuer A, Adihou H, Schmalhofer M, Saura P, Kaila VRI, Groll M, Bode H (2019) Molecular mechanism of polyketide shortening in anthraquinone biosynthesis of Photorhabdus luminescens. Chem Science 10:6341-6349. [Full text]

66. Boczek E, Luo Q, Dehling M, Röpke M, Mader S, Seidl A, Kaila VRI*, Buchner J (2019) Autophosphorylation activates c-Src kinase through global structural rearrangements. J Biol Chem 294:13186-13197. [Full text]

65. Fottner M, Brunner A-D, Bittl V Horn-Ghetko D, Jussupow A, Kaila VRI, Bremm A, Lang K (2019) Site-specific ubiquitylation and SUMOylation using genetic code expansion and sortase-mediated transpeptidation. Nature Chem Biol 5:276-284. [Full text]

64. Saura P, Kaila VRI* (2019) Structure and dynamics of the cyanobacterial NDH-1 complex. Biochim Biophys Acta – Bioenergetics 1860:201-208. [Full text]

63. Warnau J, Sharma V, Gamiz-Hernandez AP, Di Luca A, Haapanen O, Vattulainen I, Wikström M, Hummer G, Kaila VRI* (2018) Redox-coupled quinone dynamics in the respiratory complex I. Proc Natl Acad Sci USA 115(36):E8413-E8420. [Full text]

62. Mader SL, Bräuer A, Groll M, Kaila VRI* (2018) Catalytic mechanism and molecular engineering of quinolone biosynthesis in dioxygenase AsqJ. Nature Comm 9, 1168:1-8. [Full text]

61. Supekar S, Kaila VRI* (2018) Dewetting transitions coupled to K-channel activation in cytochrome c oxidase. Chem Science 9, 6703-6710. [Full text]

60. Di Luca A, Mühlbauer M, Saura P, Kaila VRI* (2018) How inter-subunit contacts in the membrane domain of complex I affect proton transfer energetics. Biochim Biophys Acta – Bioenergetics S0005-2728, 30147-30146. [Full text]

59. Kaila VRI* (2018) Long-Range Proton-Coupled Electron Transfer in Biological Energy Conversion: Towards Mechanistic Understanding of Respiratory Complex I. J R Soc Interfaces 15: 20170916 [Full text]

58. Saura P, Röpke M, Gamiz-Hernandez AP, Kaila VRI* (2019) Quantum Chemical and QM/MM Models in Biochemistry. Biomolecular Simulations, Methods in Mol Biol 2022:75-104. [Full text]

57. Lindsay S, Mader SL, Kaila VRI*, Hess CR (2018) C‐H Oxidation by a Diiron Complex with Facially Opposing Active Sites. ChemistrySelect 3(5). doi:10.1002/slct.201800192 [Full text]

56. Boussac A, Ugur I, Marion A, Sugiura M, Kaila VRI, Rutherford AW (2017) The low spin – high spin equilibrium in the S2-state of the water oxidizing enzyme. Biochim Biophys Acta – Bioenergetics 1859:342-356. [Full text]

55. Di Luca, A Kaila VRI* (2018) Global Collective Motions in the Mammalian and Bacterial Respiratory Complex I. Biochim Biophys Acta – Bioenergetics 1859:326-332. [Full text]

54. Fedor J, Di Luca A, Kaila VRI, Hirst J (2017) Correlating kinetic and structural data on ubiquinone binding and reduction by respiratory complex I. Proc Natl Acad Sci USA 114: 12737-12742. [Full text]

53. Rutz DA, Luo Q, Freiburger L, Madl T, Kaila VRI, Sattler M, Buchner J (2018) A switch point in the molecular chaperone Hsp90 responding to client interaction. Nature Comm 9, 1472. [Full text]

52. Kaila VRI* (2018) 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.  [Full text],  Free ArXive: [Full Text]

51. Schrepfer P, Ugur I, Klumpe S., Metterlein M, Loll B, Kaila VRI*, Brück T (2020)  Exploring the catalytic cascade of cembranoid biosynthesis by combination of genetic engineering and molecular simulations. Comput Struct Biotech J  (in press). doi.org/10.1016/j.csbj.2020.06.030  [Full Text]

50. Wachtel R, Bräuning B, Mader SL, Ecker F, Kaila VRI, Groll M, Itzen A (2018) The protease GtgE from Salmonella exclusively targets inactive Rab-proteins. Nature Comm 9(1):44.  [Full text]

49. 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 139:16282-16288. [Full text]

48. 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  114(27):7043-7048. doi: 10.1073/pnas.1703625114. [Full text]

47. Supekar S, Papageorgiou AC, Gemmecker G, Peltzer R, Johansson MP, Tripsianes K, Sattler M, Kaila VRI* (2018) Conformational Selection of Dimethylarginine Recognition by the Survival Motor Neuron Tudor Domain. Angew Chemie Intl Ed 57:486-490. [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. 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]

44. 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]

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. 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]

41. 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]

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]

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. [Full text]

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, 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. [Full Text]

35. 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.

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. [Full Text]

33. 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]

32. 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 119: 2933-2945. [Full Text]

31. 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 119: 2611-2619. [Full Text]

30. 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]

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 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]

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

27. 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]

26. 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]

25. 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]

24. 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]

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

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

21. 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]

20. 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]

19. 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]

18. 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]

17. 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]

16. 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]

15. 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]

14. 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]

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

12. 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]

11. Sharma V, Wikström M, Kaila VRI* (2010) Redox-coupled proton transfer in the active site of cytochrome cbb3. Biochim Biophys Acta – Bioenergetics1797:1512-1520. [Full Text]

10. 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 – Bioenergetics 1787: 1205-1214. [Full Text]

9. 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]

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

7. Kaila VRI, Annila A (2008) Natural selection for least action. Proc Roy Soc A 464: 3055-3070. [Full Text]

6. 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]

5. 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]

4. 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]

3. 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]

2. Kaila VRI (2009), “Theoretical Studies on Coupled Electron and Proton Transfer in Cytochrome Oxidase”. ISBN 978-952-10- 5263-7, ISSN 1795-7079, Yliopistopaino, Helsinki University Printing House. [Full Text]

1. Kaila VRI (2006) “Beräkningskemiska studier av proton-translokeringsmekanismen i cytokrom c oxidas”, MSc thesis.