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1

Protein folding as an evolutionary process

Vivek Sharma, Ville R.I. Kaila, Arto Annila

Journal:

Physica A: Statistical Mechanics and its Applications

Année:

2009

Langue:

english

Fichier:

PDF, 1.40 MB

english, 2009

2

Electrostatic spectral tuning mechanism of the green fluorescent protein

Kaila, Ville R. I., Send, Robert, Sundholm, Dage

Journal:

Physical Chemistry Chemical Physics

Année:

2013

Langue:

english

Fichier:

PDF, 671 KB

english, 2013

3

Human Adipose Tissue Extract Induces Angiogenesis and Adipogenesis In Vitro

Sarkanen, Jertta-Riina, Kaila, Ville, Mannerström, Bettina, Räty, Sari, Kuokkanen, Hannu, Miettinen, Susanna, Ylikomi, Timo

Journal:

Tissue Engineering Part A

Année:

2012

Langue:

english

Fichier:

PDF, 703 KB

english, 2012

4

Natural Selection for Least Action

Ville R. I. Kaila and Arto Annila

Journal:

Proceedings Mathematical Physical & Engineering Sciences

Année:

2008

Langue:

english

Fichier:

PDF, 1.68 MB

english, 2008

5

New Perspectives on Proton Pumping in Cellular Respiration

Wikström, Mårten, Sharma, Vivek, Kaila, Ville R. I., Hosler, Jonathan P., Hummer, Gerhard

Journal:

Chemical Reviews

Année:

2015

Langue:

english

Fichier:

PDF, 1.33 MB

english, 2015

6

The protease GtgE from Salmonella exclusively targets inactive Rab GTPases

Wachtel, Rudolf, Bräuning, Bastian, Mader, Sophie L., Ecker, Felix, Kaila, Ville R. I., Groll, Michael, Itzen, Aymelt

Journal:

Nature Communications

Année:

2018

Langue:

english

Fichier:

PDF, 3.50 MB

english, 2018

7

C-H Oxidation by a Diiron Complex with Facially Opposing Active Sites

Lindsay, Stacey, Mader, Sophie L., Kaila, Ville R. I., Hess, Corinna R.

Journal:

ChemistrySelect

Année:

2018

Langue:

english

Fichier:

PDF, 1.45 MB

english, 2018

8

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

Fottner, Maximilian, Brunner, Andreas-David, Bittl, Verena, Horn-Ghetko, Daniel, Jussupow, Alexander, Kaila, Ville R. I., Bremm, Anja, Lang, Kathrin

Journal:

Nature Chemical Biology

Année:

2019

Langue:

english

Fichier:

PDF, 1.84 MB

english, 2019

9

Absorption shifts of diastereotopically ligated chlorophyll dimers of photosystem I

Suomivuori, Carl-Mikael, Fliegl, Heike, Starikov, Evgeni B., Balaban, T. Silviu, Kaila, Ville R. I., Sundholm, Dage

Journal:

Physical Chemistry Chemical Physics

Année:

2019

Langue:

english

Fichier:

PDF, 4.64 MB

english, 2019

10

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

Schuller, Jan M., Saura, Patricia, Thiemann, Jacqueline, Schuller, Sandra K., Gamiz-Hernandez, Ana P., Kurisu, Genji, Nowaczyk, Marc M., Kaila, Ville R. I.

Journal:

Nature Communications

Année:

2020

Langue:

english

Fichier:

PDF, 1.88 MB

english, 2020

11

Charge parameterization of the metal centers in cytochrome c oxidase

Mikael P. Johansson, Ville R. I. Kaila, Liisa Laakkonen

Journal:

Journal of Computational Chemistry

Année:

2008

Langue:

english

Fichier:

PDF, 302 KB

english, 2008

12

Aromatic pathways in conjugated rings connected by single bonds

Stefan Taubert, Ville R. I. Kaila, Dage Sundholm

Journal:

International Journal of Quantum Chemistry

Année:

2011

Langue:

english

Fichier:

PDF, 241 KB

english, 2011

13

The chemistry of the CuB site in cytochrome c oxidase and the importance of its unique His–Tyr bond

Ville R.I. Kaila, Mikael P. Johansson, Dage Sundholm, Liisa Laakkonen, Mårten Wikström

Journal:

Biochimica et Biophysica Acta (BBA) - Bioenergetics

Année:

2009

Langue:

english

Fichier:

PDF, 1.88 MB

english, 2009

14

Mechanism and energetics by which glutamic acid 242 prevents leaks in cytochrome c oxidase

Ville R.I. Kaila, Michael I. Verkhovsky, Gerhard Hummer, Mårten Wikström

Journal:

Biochimica et Biophysica Acta (BBA) - Bioenergetics

Année:

2009

Langue:

english

Fichier:

PDF, 1.15 MB

english, 2009

15

Redox-coupled proton transfer in the active site of cytochrome cbb3

Vivek Sharma, Mårten Wikström, Ville R.I. Kaila

Journal:

Biochimica et Biophysica Acta (BBA) - Bioenergetics

Année:

2010

Langue:

english

Fichier:

PDF, 1.24 MB

english, 2010

16

A combined quantum chemical and crystallographic study on the oxidized binuclear center of cytochrome c oxidase

Ville R.I. Kaila, Esko Oksanen, Adrian Goldman, Dmitry A. Bloch, Michael I. Verkhovsky, Dage Sundholm, Mårten Wikström

Journal:

Biochimica et Biophysica Acta (BBA) - Bioenergetics

Année:

2011

Langue:

english

Fichier:

PDF, 1.60 MB

english, 2011

17

The identity of the transient proton loading site of the proton-pumping mechanism of cytochrome c oxidase

Ville R.I. Kaila, Vivek Sharma, Mårten Wikström

Journal:

Biochimica et Biophysica Acta (BBA) - Bioenergetics

Année:

2011

Langue:

english

Fichier:

PDF, 980 KB

english, 2011

18

Stabilization of the peroxy intermediate in the oxygen splitting reaction of cytochrome cbb3

Vivek Sharma, Mårten Wikström, Ville R.I. Kaila

Journal:

Biochimica et Biophysica Acta (BBA) - Bioenergetics

Année:

2011

Langue:

english

Fichier:

PDF, 559 KB

english, 2011

19

Dynamic water networks in cytochrome cbb3 oxidase

Vivek Sharma, Mårten Wikström, Ville R.I. Kaila

Journal:

Biochimica et Biophysica Acta (BBA) - Bioenergetics

Année:

2012

Langue:

english

Fichier:

PDF, 1.48 MB

english, 2012

20

Dynamics of the glutamic acid 242 side chain in cytochrome c oxidase

Anne Tuukkanen, Ville R.I. Kaila, Liisa Laakkonen, Gerhard Hummer, Mårten Wikström

Journal:

Biochimica et Biophysica Acta (BBA) - Bioenergetics

Année:

2007

Langue:

english

Fichier:

PDF, 600 KB

english, 2007

21

Prevention of leak in the proton pump of cytochrome c oxidase

Ville R.I. Kaila, Michael Verkhovsky, Gerhard Hummer, Mårten Wikström

Journal:

Biochimica et Biophysica Acta (BBA) - Bioenergetics

Année:

2008

Langue:

english

Fichier:

PDF, 252 KB

english, 2008

22

S13.27 Fidelity of water-gated mechanism in cytochrome c oxidase

Ville R.I. Kaila, Gerhard Hummer, Mårten Wikström

Journal:

Biochimica et Biophysica Acta (BBA) - Bioenergetics

Année:

2008

Langue:

english

Fichier:

PDF, 72 KB

english, 2008

23

Proton-Coupled Electron Transfer in Cytochrome Oxidase

Kaila, Ville R. I., Verkhovsky, Michael I., Wikström, Mårten

Journal:

Chemical Reviews

Année:

2010

Langue:

english

Fichier:

PDF, 3.03 MB

english, 2010

24

Water Mediated Membrane Transport: From Channels to Proton Pumps

Hummer, Gerhard, Kaila, Ville R.I., Zhu, Fangqiang, Okazaki, Kei-ichi, Wikström, Mårten

Journal:

Biophysical Journal

Année:

2013

Langue:

english

Fichier:

PDF, 37 KB

english, 2013

25

Water Gated Transitions in Proton Pumping of Respiratory Complex I

Kaila, Ville R.I., Wikström, Marten, Hummer, Gerhard

Journal:

Biophysical Journal

Année:

2014

Langue:

english

Fichier:

PDF, 96 KB

english, 2014

26

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

Kaila, Ville R. I., Schotte, Friedrich, Cho, Hyun Sun, Hummer, Gerhard, Anfinrud, Philip A.

Journal:

Nature Chemistry

Année:

2014

Langue:

english

Fichier:

PDF, 908 KB

english, 2014

27

Proton transfer pathways in the Respiratory Complex I

Kaila, Ville, Wikström, Mårten, Hummer, Gerhard

Journal:

Biochimica et Biophysica Acta (BBA) - Bioenergetics

Année:

2014

Langue:

english

Fichier:

PDF, 62 KB

english, 2014

28

Energetics of Direct and Water-Mediated Proton-Coupled Electron Transfer

Kaila, Ville R. I., Hummer, Gerhard

Journal:

Journal of the American Chemical Society

Année:

2011

Langue:

english

Fichier:

PDF, 1.74 MB

english, 2011

29

The Effect of Protein Environment on Photoexcitation Properties of Retinal

Kaila, Ville R. I., Send, Robert, Sundholm, Dage

Journal:

Journal of Physical Chemistry B

Année:

2012

Langue:

english

Fichier:

PDF, 2.90 MB

english, 2012

30

Spectral Tuning of Rhodopsin and Visual Cone Pigments

Zhou, Xiuwen, Sundholm, Dage, Wesołowski, Tomasz A., Kaila, Ville R. I.

Journal:

Journal of the American Chemical Society

Année:

2014

Langue:

english

Fichier:

PDF, 989 KB

english, 2014

31

Benchmarking the Approximate Second-Order Coupled-Cluster Method on Biochromophores

Send, Robert, Kaila, Ville R. I., Sundholm, Dage

Journal:

Journal of Chemical Theory and Computation

Année:

2011

Langue:

english

Fichier:

PDF, 2.88 MB

english, 2011

32

Energetics and dynamics of proton transfer reactions along short water wires

Kaila, Ville R. I., Hummer, Gerhard

Journal:

Physical Chemistry Chemical Physics

Année:

2011

Langue:

english

Fichier:

PDF, 2.27 MB

english, 2011

33

[IEEE 2009 IEEE International Conference on Pervasive Computing and Communications (PerCom) - Galveston, TX, USA (2009.03.9-2009.03.13)] 2009 IEEE International Conference on Pervasive Computing and Communications - Development of a location-aware speech control and audio feedback system

Kaila, Lasse, Hyvnen, Jouni, Ritala, Markus, Makinen, Ville, Vanhala, Jukka

Année:

2009

Langue:

english

Fichier:

PDF, 2.40 MB

english, 2009

34

Linear Energy Relationships in Ground State Proton Transfer and Excited State Proton-Coupled Electron Transfer

Gamiz-Hernandez, Ana P., Magomedov, Artiom, Hummer, Gerhard, Kaila, Ville R. I.

Journal:

Journal of Physical Chemistry B

Année:

2015

Langue:

english

Fichier:

PDF, 3.89 MB

english, 2015

35

Coupled-Cluster Studies of Extensive Green Fluorescent Protein Models Using the Reduced Virtual Space Approach

Send, Robert, Suomivuori, Carl-Mikael, Kaila, Ville R. I., Sundholm, Dage

Journal:

Journal of Physical Chemistry B

Année:

2015

Langue:

english

Fichier:

PDF, 2.35 MB

english, 2015

36

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

Kmita, Katarzyna, Wirth, Christophe, Warnau, Judith, Guerrero-Castillo, Sergio, Hunte, Carola, Hummer, Gerhard, Kaila, Ville R. I., Zwicker, Klaus, Brandt, Ulrich, Zickermann, Volker

Journal:

Proceedings of the National Academy of Sciences

Année:

2015

Langue:

english

Fichier:

PDF, 996 KB

english, 2015

37

[IEEE 2015 International Conference on Learning and Teaching in Computing and Engineering (LaTiCE) - Taipei, Taiwan (2015.4.9-2015.4.12)] 2015 International Conference on Learning and Teaching in Computing and Engineering - Interactive Learning Content for Introductory Computer Science Course Using the ViLLE Exercise Framework

Karavirta, Ville, Haavisto, Riku, Kaila, Erkki, Laakso, Mikko-Jussi, Rajala, Teemu, Salakoski, Tapio

Année:

2015

Langue:

english

Fichier:

PDF, 670 KB

english, 2015

38

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

Boczek, Edgar E., Reefschläger, Lasse G., Dehling, Marco, Struller, Tobias J., Häusler, Elisabeth, Seidl, Andreas, Kaila, Ville R. I., Buchner, Johannes

Journal:

Proceedings of the National Academy of Sciences

Année:

2015

Langue:

english

Fichier:

PDF, 1.35 MB

english, 2015

39

Protein-Induced Color Shift of Carotenoids in β-Crustacyanin

Gamiz-Hernandez, Ana P., Angelova, Iva Neycheva, Send, Robert, Sundholm, Dage, Kaila, Ville R. I.

Journal:

Angewandte Chemie International Edition

Année:

2015

Fichier:

PDF, 1.89 MB

2015

40

Protein-Induced Color Shift of Carotenoids in β-Crustacyanin

Gamiz-Hernandez, Ana P., Angelova, Iva Neycheva, Send, Robert, Sundholm, Dage, Kaila, Ville R. I.

Journal:

Angewandte Chemie International Edition

Année:

2015

Langue:

english

Fichier:

PDF, 1.89 MB

english, 2015

41

Interheme electron tunneling in cytochrome c oxidase

Ville R. I. Kaila, Mikael P. Johansson, Dage Sundholm, Mårten Wikström and Harry B. Gray

Journal:

Proceedings of the National Academy of Sciences

Année:

2010

Langue:

english

Fichier:

PDF, 1.49 MB

english, 2010

42

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

Gamiz-Hernandez, Ana P., Kaila, Ville R. I.

Journal:

Physical Chemistry Chemical Physics

Année:

2016

Langue:

english

Fichier:

PDF, 3.48 MB

english, 2016

43

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

Suomivuori, Carl-Mikael, Winter, Nina O. C., Hättig, Christof, Sundholm, Dage, Kaila, Ville R. I.

Journal:

Journal of Chemical Theory and Computation

Année:

2016

Langue:

english

Fichier:

PDF, 6.31 MB

english, 2016

44

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

Ugur, Ilke, Rutherford, A. William, Kaila, Ville R.I.

Journal:

Biochimica et Biophysica Acta (BBA) - Bioenergetics

Année:

2016

Langue:

english

Fichier:

PDF, 1.01 MB

english, 2016

45

Protein-induzierte Farbverschiebung von Carotenoiden in β-Crustacyanin

Gamiz-Hernandez, Ana P., Angelova, Iva Neycheva, Send, Robert, Sundholm, Dage, Kaila, Ville R. I.

Journal:

Angewandte Chemie

Année:

2015

Langue:

german

Fichier:

PDF, 1.92 MB

german, 2015

46

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

Suomivuori, Carl-Mikael, Lang, Lucas, Sundholm, Dage, Gamiz-Hernandez, Ana P., Kaila, Ville R. I.

Journal:

Chemistry - A European Journal

Année:

2016

Langue:

english

Fichier:

PDF, 4.13 MB

english, 2016

47

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

Supekar, Shreyas, Gamiz-Hernandez, Ana P., Kaila, Ville R. I.

Journal:

Angewandte Chemie International Edition

Année:

2016

Langue:

english

Fichier:

PDF, 1.85 MB

english, 2016

48

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

Supekar, Shreyas, Gamiz-Hernandez, Ana P., Kaila, Ville R. I.

Journal:

Angewandte Chemie

Année:

2016

Langue:

english

Fichier:

PDF, 1.78 MB

english, 2016

49

Computational investigation of the redox-coupled proton pumping in respiratory complex I

Sharma, Vivek, Warnau, Judith, Gamiz-Hernandez, Ana P., Haapanen, Outi, di Luca, Andrea, Vattulainen, Ilpo, Wikström, Mårten, Hummer, Gerhard, Kaila, Ville R.I.

Journal:

Biochimica et Biophysica Acta (BBA) - Bioenergetics

Année:

2016

Langue:

english

Fichier:

PDF, 49 KB

english, 2016

50

Towards a mechanistic model for redox-driven proton pumping in respiratory complex I

Kaila, Ville R.I., di Luca, Andrea, Gamiz-Hernandez, Ana P., Jussupow, Alexander, Johansson, Mikael P., Sharma, Vivek, Wikström, Mårten, Hummer, Gerhard

Journal:

Biochimica et Biophysica Acta (BBA) - Bioenergetics

Année:

2016

Langue:

english

Fichier:

PDF, 51 KB

english, 2016