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Items: 1 to 50 of 68

1.

Redox-coupled proton pumping drives carbon concentration in the photosynthetic complex I.

Schuller JM, Saura P, Thiemann J, Schuller SK, Gamiz-Hernandez AP, Kurisu G, Nowaczyk MM, Kaila VRI.

Nat Commun. 2020 Jan 24;11(1):494. doi: 10.1038/s41467-020-14347-4.

PMID:
31980611
2.

Ion Binding and Selectivity of the Na+/H+ Antiporter MjNhaP1 from Experiment and Simulation.

Warnau J, Wöhlert D, Okazaki KI, Yildiz Ö, Gamiz-Hernandez AP, Kaila VRI, Kühlbrandt W, Hummer G.

J Phys Chem B. 2020 Jan 16;124(2):336-344. doi: 10.1021/acs.jpcb.9b08552. Epub 2020 Jan 2.

3.

Benchmarking the Performance of Time-Dependent Density Functional Theory Methods on Biochromophores.

Shao Y, Mei Y, Sundholm D, Kaila VRI.

J Chem Theory Comput. 2020 Jan 14;16(1):587-600. doi: 10.1021/acs.jctc.9b00823. Epub 2019 Dec 26.

PMID:
31815476
4.

Corrigendum: Selective Inhibitors of FKBP51 Employ Conformational Selection of Dynamic Invisible States.

Jagtap PKA, Asami S, Sippel C, Kaila VRI, Hausch F, Sattler M.

Angew Chem Int Ed Engl. 2019 Sep 23;58(39):13619. doi: 10.1002/anie.201908888. Epub 2019 Aug 20. No abstract available.

PMID:
31549791
5.

Quantum Chemical and QM/MM Models in Biochemistry.

Saura P, Röpke M, Gamiz-Hernandez AP, Kaila VRI.

Methods Mol Biol. 2019;2022:75-104. doi: 10.1007/978-1-4939-9608-7_4.

PMID:
31396900
6.

Molecular mechanism of polyketide shortening in anthraquinone biosynthesis of Photorhabdus luminescens.

Zhou Q, Bräuer A, Adihou H, Schmalhofer M, Saura P, Grammbitter GLC, Kaila VRI, Groll M, Bode HB.

Chem Sci. 2019 May 14;10(25):6341-6349. doi: 10.1039/c9sc00749k. eCollection 2019 Jul 7.

7.

Autophosphorylation activates c-Src kinase through global structural rearrangements.

Boczek EE, Luo Q, Dehling M, Röpke M, Mader SL, Seidl A, Kaila VRI, Buchner J.

J Biol Chem. 2019 Aug 30;294(35):13186-13197. doi: 10.1074/jbc.RA119.008199. Epub 2019 Jul 22.

PMID:
31331936
8.

Selective Inhibitors of FKBP51 Employ Conformational Selection of Dynamic Invisible States.

Jagtap PKA, Asami S, Sippel C, Kaila VRI, Hausch F, Sattler M.

Angew Chem Int Ed Engl. 2019 Jul 8;58(28):9429-9433. doi: 10.1002/anie.201902994. Epub 2019 Jun 5. Erratum in: Angew Chem Int Ed Engl. 2019 Sep 23;58(39):13619.

PMID:
31100184
9.

Electric field modulated redox-driven protonation and hydration energetics in energy converting enzymes.

Saura P, Frey DM, Gamiz-Hernandez AP, Kaila VRI.

Chem Commun (Camb). 2019 May 23;55(43):6078-6081. doi: 10.1039/c9cc01135h.

10.

How cardiolipin modulates the dynamics of respiratory complex I.

Jussupow A, Di Luca A, Kaila VRI.

Sci Adv. 2019 Mar 20;5(3):eaav1850. doi: 10.1126/sciadv.aav1850. eCollection 2019 Mar.

11.

Absorption shifts of diastereotopically ligated chlorophyll dimers of photosystem I.

Suomivuori CM, Fliegl H, Starikov EB, Balaban TS, Kaila VRI, Sundholm D.

Phys Chem Chem Phys. 2019 Mar 27;21(13):6851-6858. doi: 10.1039/c9cp00616h.

PMID:
30874282
12.

Energetics and Dynamics of Proton-Coupled Electron Transfer in the NADH/FMN Site of Respiratory Complex I.

Saura P, Kaila VRI.

J Am Chem Soc. 2019 Apr 10;141(14):5710-5719. doi: 10.1021/jacs.8b11059. Epub 2019 Mar 27.

13.

Site-specific ubiquitylation and SUMOylation using genetic-code expansion and sortase.

Fottner M, Brunner AD, Bittl V, Horn-Ghetko D, Jussupow A, Kaila VRI, Bremm A, Lang K.

Nat Chem Biol. 2019 Mar;15(3):276-284. doi: 10.1038/s41589-019-0227-4. Epub 2019 Feb 15.

PMID:
30770915
14.

Molecular dynamics and structural models of the cyanobacterial NDH-1 complex.

Saura P, Kaila VRI.

Biochim Biophys Acta Bioenerg. 2019 Mar 1;1860(3):201-208. doi: 10.1016/j.bbabio.2018.11.010. Epub 2018 Nov 16.

15.

Dewetting transitions coupled to K-channel activation in cytochrome c oxidase.

Supekar S, Kaila VRI.

Chem Sci. 2018 Jul 9;9(32):6703-6710. doi: 10.1039/c8sc01587b. eCollection 2018 Aug 28.

16.

Redox-coupled quinone dynamics in the respiratory complex I.

Warnau J, Sharma V, Gamiz-Hernandez AP, Di Luca A, Haapanen O, Vattulainen I, Wikström M, Hummer G, Kaila VRI.

Proc Natl Acad Sci U S A. 2018 Sep 4;115(36):E8413-E8420. doi: 10.1073/pnas.1805468115. Epub 2018 Aug 17.

17.

How inter-subunit contacts in the membrane domain of complex I affect proton transfer energetics.

Di Luca A, Mühlbauer ME, Saura P, Kaila VRI.

Biochim Biophys Acta Bioenerg. 2018 Sep;1859(9):734-741. doi: 10.1016/j.bbabio.2018.06.001. Epub 2018 Jun 5.

18.

A switch point in the molecular chaperone Hsp90 responding to client interaction.

Rutz DA, Luo Q, Freiburger L, Madl T, Kaila VRI, Sattler M, Buchner J.

Nat Commun. 2018 Apr 16;9(1):1472. doi: 10.1038/s41467-018-03946-x.

19.

Long-range proton-coupled electron transfer in biological energy conversion: towards mechanistic understanding of respiratory complex I.

Kaila VRI.

J R Soc Interface. 2018 Apr;15(141). pii: 20170916. doi: 10.1098/rsif.2017.0916. Review.

20.

Catalytic mechanism and molecular engineering of quinolone biosynthesis in dioxygenase AsqJ.

Mader SL, Bräuer A, Groll M, Kaila VRI.

Nat Commun. 2018 Mar 21;9(1):1168. doi: 10.1038/s41467-018-03442-2.

21.

The low spin - high spin equilibrium in the S2-state of the water oxidizing enzyme.

Boussac A, Ugur I, Marion A, Sugiura M, Kaila VRI, Rutherford AW.

Biochim Biophys Acta Bioenerg. 2018 May;1859(5):342-356. doi: 10.1016/j.bbabio.2018.02.010. Epub 2018 Feb 28.

22.

Global collective motions in the mammalian and bacterial respiratory complex I.

Di Luca A, Kaila VRI.

Biochim Biophys Acta Bioenerg. 2018 May;1859(5):326-332. doi: 10.1016/j.bbabio.2018.02.001. Epub 2018 Feb 5.

23.

The protease GtgE from Salmonella exclusively targets inactive Rab GTPases.

Wachtel R, Bräuning B, Mader SL, Ecker F, Kaila VRI, Groll M, Itzen A.

Nat Commun. 2018 Jan 3;9(1):44. doi: 10.1038/s41467-017-02110-1.

24.

Correlating kinetic and structural data on ubiquinone binding and reduction by respiratory complex I.

Fedor JG, Jones AJY, Di Luca A, Kaila VRI, Hirst J.

Proc Natl Acad Sci U S A. 2017 Nov 28;114(48):12737-12742. doi: 10.1073/pnas.1714074114. Epub 2017 Nov 13.

25.

Terminal Electron-Proton Transfer Dynamics in the Quinone Reduction of Respiratory Complex I.

Gamiz-Hernandez AP, Jussupow A, Johansson MP, Kaila VRI.

J Am Chem Soc. 2017 Nov 15;139(45):16282-16288. doi: 10.1021/jacs.7b08486. Epub 2017 Nov 1.

26.

Conformational Selection of Dimethylarginine Recognition by the Survival Motor Neuron Tudor Domain.

Supekar S, Papageorgiou AC, Gemmecker G, Peltzer R, Johansson MP, Tripsianes K, Sattler M, Kaila VRI.

Angew Chem Int Ed Engl. 2018 Jan 8;57(2):486-490. doi: 10.1002/anie.201708233. Epub 2017 Dec 8.

PMID:
28980372
27.

Symmetry-related proton transfer pathways in respiratory complex I.

Di Luca A, Gamiz-Hernandez AP, Kaila VRI.

Proc Natl Acad Sci U S A. 2017 Aug 1;114(31):E6314-E6321. doi: 10.1073/pnas.1706278114. Epub 2017 Jul 17.

28.

Energetics and dynamics of a light-driven sodium-pumping rhodopsin.

Suomivuori CM, Gamiz-Hernandez AP, Sundholm D, Kaila VRI.

Proc Natl Acad Sci U S A. 2017 Jul 3;114(27):7043-7048. doi: 10.1073/pnas.1703625114. Epub 2017 Jun 13.

29.

To catalyze or not to catalyze: elucidation of the subtle differences between the hexameric capsules of pyrogallolarene and resorcinarene.

Zhang Q, Catti L, Kaila VRI, Tiefenbacher K.

Chem Sci. 2017 Feb 1;8(2):1653-1657. doi: 10.1039/c6sc04565k. Epub 2016 Nov 15.

30.

Hsp90 dependence of a kinase is determined by its conformational landscape.

Luo Q, Boczek EE, Wang Q, Buchner J, Kaila VR.

Sci Rep. 2017 Mar 14;7:43996. doi: 10.1038/srep43996.

31.

Oxidative Unfolding of the Rubredoxin Domain and the Natively Disordered N-terminal Region Regulate the Catalytic Activity of Mycobacterium tuberculosis Protein Kinase G.

Wittwer M, Luo Q, Kaila VR, Dames SA.

J Biol Chem. 2016 Dec 30;291(53):27062-27072. doi: 10.1074/jbc.M116.747089. Epub 2016 Nov 3.

32.

A Protonated Water Cluster as a Transient Proton-Loading Site in Cytochrome c Oxidase.

Supekar S, Gamiz-Hernandez AP, Kaila VR.

Angew Chem Int Ed Engl. 2016 Sep 19;55(39):11940-4. doi: 10.1002/anie.201603606. Epub 2016 Aug 19.

PMID:
27539738
33.

Exploring the Light-Capturing Properties of Photosynthetic Chlorophyll Clusters Using Large-Scale Correlated Calculations.

Suomivuori CM, Winter NO, Hättig C, Sundholm D, Kaila VR.

J Chem Theory Comput. 2016 Jun 14;12(6):2644-51. doi: 10.1021/acs.jctc.6b00237. Epub 2016 May 19.

PMID:
27153186
34.

Tuning the Protein-Induced Absorption Shifts of Retinal in Engineered Rhodopsin Mimics.

Suomivuori CM, Lang L, Sundholm D, Gamiz-Hernandez AP, Kaila VR.

Chemistry. 2016 Jun 6;22(24):8254-61. doi: 10.1002/chem.201505126. Epub 2016 Apr 27.

PMID:
27120137
35.

Redox-coupled substrate water reorganization in the active site of Photosystem II-The role of calcium in substrate water delivery.

Ugur I, Rutherford AW, Kaila VR.

Biochim Biophys Acta. 2016 Jun;1857(6):740-8. doi: 10.1016/j.bbabio.2016.01.015. Epub 2016 Jan 27.

36.

Conversion of light-energy into molecular strain in the photocycle of the photoactive yellow protein.

Gamiz-Hernandez AP, Kaila VR.

Phys Chem Chem Phys. 2016 Jan 28;18(4):2802-9. doi: 10.1039/c5cp05244k.

PMID:
26726853
37.

Redox-induced activation of the proton pump in the respiratory complex I.

Sharma V, Belevich G, Gamiz-Hernandez AP, Róg T, Vattulainen I, Verkhovskaya ML, Wikström M, Hummer G, Kaila VR.

Proc Natl Acad Sci U S A. 2015 Sep 15;112(37):11571-6. doi: 10.1073/pnas.1503761112. Epub 2015 Sep 1.

38.

Protein-Induced Color Shift of Carotenoids in β-Crustacyanin.

Gamiz-Hernandez AP, Angelova IN, Send R, Sundholm D, Kaila VR.

Angew Chem Int Ed Engl. 2015 Sep 21;54(39):11564-6. doi: 10.1002/anie.201501609. Epub 2015 Jul 21.

PMID:
26220698
39.

Conformational processing of oncogenic v-Src kinase by the molecular chaperone Hsp90.

Boczek EE, Reefschläger LG, Dehling M, Struller TJ, Häusler E, Seidl A, Kaila VR, Buchner J.

Proc Natl Acad Sci U S A. 2015 Jun 23;112(25):E3189-98. doi: 10.1073/pnas.1424342112. Epub 2015 Jun 8.

40.

Accessory NUMM (NDUFS6) subunit harbors a Zn-binding site and is essential for biogenesis of mitochondrial complex I.

Kmita K, Wirth C, Warnau J, Guerrero-Castillo S, Hunte C, Hummer G, Kaila VR, Zwicker K, Brandt U, Zickermann V.

Proc Natl Acad Sci U S A. 2015 May 5;112(18):5685-90. doi: 10.1073/pnas.1424353112. Epub 2015 Apr 20.

41.

New perspectives on proton pumping in cellular respiration.

Wikström M, Sharma V, Kaila VR, Hosler JP, Hummer G.

Chem Rev. 2015 Mar 11;115(5):2196-221. doi: 10.1021/cr500448t. Epub 2015 Feb 19. Review. No abstract available.

PMID:
25694135
42.

Coupled-cluster studies of extensive green fluorescent protein models using the reduced virtual space approach.

Send R, Suomivuori CM, Kaila VR, Sundholm D.

J Phys Chem B. 2015 Feb 19;119(7):2933-45. doi: 10.1021/jp5120898. Epub 2015 Feb 9.

PMID:
25613980
43.

Linear energy relationships in ground state proton transfer and excited state proton-coupled electron transfer.

Gamiz-Hernandez AP, Magomedov A, Hummer G, Kaila VR.

J Phys Chem B. 2015 Feb 12;119(6):2611-9. doi: 10.1021/jp508790n. Epub 2015 Jan 12.

PMID:
25485993
44.

Electrostatics, hydration, and proton transfer dynamics in the membrane domain of respiratory complex I.

Kaila VR, Wikström M, Hummer G.

Proc Natl Acad Sci U S A. 2014 May 13;111(19):6988-93. doi: 10.1073/pnas.1319156111. Epub 2014 Apr 28.

45.

Contradictions in X-ray structures of intermediates in the photocycle of photoactive yellow protein.

Kaila VR, Schotte F, Cho HS, Hummer G, Anfinrud PA.

Nat Chem. 2014 Apr;6(4):258-9. doi: 10.1038/nchem.1898. No abstract available.

46.

Spectral tuning of rhodopsin and visual cone pigments.

Zhou X, Sundholm D, Wesołowski TA, Kaila VR.

J Am Chem Soc. 2014 Feb 19;136(7):2723-6. doi: 10.1021/ja411864m. Epub 2014 Feb 7.

PMID:
24422511
47.

Electrostatic spectral tuning mechanism of the green fluorescent protein.

Kaila VR, Send R, Sundholm D.

Phys Chem Chem Phys. 2013 Apr 7;15(13):4491-5. doi: 10.1039/c3cp00058c.

PMID:
23420178
48.

Watching a signaling protein function in real time via 100-ps time-resolved Laue crystallography.

Schotte F, Cho HS, Kaila VR, Kamikubo H, Dashdorj N, Henry ER, Graber TJ, Henning R, Wulff M, Hummer G, Kataoka M, Anfinrud PA.

Proc Natl Acad Sci U S A. 2012 Nov 20;109(47):19256-61. doi: 10.1073/pnas.1210938109. Epub 2012 Nov 6.

49.

Ab initio, density functional theory, and semi-empirical calculations.

Johansson MP, Kaila VR, Sundholm D.

Methods Mol Biol. 2013;924:3-27. doi: 10.1007/978-1-62703-017-5_1.

PMID:
23034743
50.

The effect of protein environment on photoexcitation properties of retinal.

Kaila VR, Send R, Sundholm D.

J Phys Chem B. 2012 Feb 23;116(7):2249-58. doi: 10.1021/jp205918m. Epub 2012 Feb 14.

PMID:
22166007

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