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Book ; Online ; Thesis: Electrostatic determined conformations

Wölke, Anna Lena

exploring binding specificity of selectins and proton gating in cytochrome c oxidase

2014

Title variant	Elektrostatisch bedingte Konformationen
Author's details	vorgelegt von Anna Lena Wölke
Language	English
Size	Online-Ressource, Ill., graph. Darst.
Document type	Book ; Online ; Thesis
Thesis / German Habilitation thesis	Freie Univ., Diss.--Berlin, 2014
Database	Former special subject collection: coastal and deep sea fishing

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Book ; Online ; Thesis: Electrostatic-Determined Conformations – Exploring Binding Specificity of Selectins and Proton Gating in Cytochrome c Oxidase

Wölke, Anna Lena [Verfasser]

2014

Author's details	Anna Lena Wölke
Keywords	Biowissenschaften, Biologie ; Life Science, Biology
Subject code	sg570
Language	English
Publisher	Freie Universität Berlin
Publishing place	Berlin
Document type	Book ; Online ; Thesis
Database	Digital theses on the web

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Article ; Online: Retraction Notice to: Protonation State-Dependent Communication in Cytochrome c Oxidase.

Helabad, Mahdi Bagherpoor / Ghane, Tahereh / Reidelbach, Marco / Woelke, Anna Lena / Knapp, Ernst Walter / Imhof, Petra

Biophysical journal

2017 Volume 113, Issue 1, Page(s) 223

Language	English
Publishing date	2017--11
Publishing country	United States
Document type	Journal Article ; Retraction of Publication
ZDB-ID	218078-9
ISSN	1542-0086 ; 0006-3495
ISSN (online)	1542-0086
ISSN	0006-3495
DOI	10.1016/j.bpj.2017.06.036
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Article: Lysine 362 in cytochrome c oxidase regulates opening of the K-channel via changes in pKA and conformation.

Woelke, Anna Lena / Galstyan, Gegham / Knapp, Ernst-Walter

Biochimica et biophysica acta

2014 Volume 1837, Issue 12, Page(s) 1998–2003

Abstract: The metabolism of aerobic life uses the conversion of molecular oxygen to water as an energy source. This reaction is catalyzed by cytochrome e oxidase (CeO) consuming four electrons and four protons, which move along specific routes. While all four ... ...

Abstract	The metabolism of aerobic life uses the conversion of molecular oxygen to water as an energy source. This reaction is catalyzed by cytochrome e oxidase (CeO) consuming four electrons and four protons, which move along specific routes. While all four electrons are transferred via the same cofactors to the binuclear reaction center (BNC), the protons take two different routes in the A-type CeO, i.e., two of the four chemical protons consumed in the reaction arrive via the D-channel in the oxidative first half starting after oxygen binding. The other two chemical protons enter via the K-channel in the reductive second half of the reaction cycle. To date, the mechanism behind these separate proton transport pathways has not been understood. In this study, we propose a model that can explain the reaction-step specific opening and closing of the K-channel by conformational and pKA changes of its central lysine 362. Molecular dynamics simulations reveal an upward movement of Lys362 towards the BNC, which had already been supposed by several experimental studies. Redox state-dependent pKA calculations provide evidence that Lys362 may protonate transiently, thereby opening the K-channel only in the reductive second half of the reaction cycle. From our results, we develop a model that assigns a key role to Lys362 in the proton gating between the two proton input channels of the A-type CeO.
MeSH term(s)	Bacterial Proteins/chemistry ; Bacterial Proteins/metabolism ; Biocatalysis ; Crystallography, X-Ray ; Electron Transport Complex IV/chemistry ; Electron Transport Complex IV/metabolism ; Electrons ; Hydrogen-Ion Concentration ; Kinetics ; Lysine/chemistry ; Lysine/metabolism ; Molecular Dynamics Simulation ; Oxidation-Reduction ; Protein Conformation ; Protein Subunits/chemistry ; Protein Subunits/metabolism ; Protons ; Rhodobacter sphaeroides/enzymology ; Rhodobacter sphaeroides/metabolism ; Time Factors
Chemical Substances	Bacterial Proteins ; Protein Subunits ; Protons ; Electron Transport Complex IV (EC 1.9.3.1) ; Lysine (K3Z4F929H6)
Language	English
Publishing date	2014-12
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	60-7
ISSN	1879-2596 ; 1879-260X ; 1872-8006 ; 1879-2642 ; 1879-2618 ; 1879-2650 ; 0006-3002 ; 0005-2728 ; 0005-2736 ; 0304-4165 ; 0167-4838 ; 1388-1981 ; 0167-4889 ; 0167-4781 ; 0304-419X ; 1570-9639 ; 0925-4439 ; 1874-9399
ISSN (online)	1879-2596 ; 1879-260X ; 1872-8006 ; 1879-2642 ; 1879-2618 ; 1879-2650
ISSN	0006-3002 ; 0005-2728 ; 0005-2736 ; 0304-4165 ; 0167-4838 ; 1388-1981 ; 0167-4889 ; 0167-4781 ; 0304-419X ; 1570-9639 ; 0925-4439 ; 1874-9399
DOI	10.1016/j.bbabio.2014.08.003
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Article: Lysine 362 in cytochrome c oxidase regulates opening of the K-channel via changes in pKA and conformation

Woelke, Anna Lena / Gegham Galstyan / Ernst-Walter Knapp

Biochimica et biophysica acta. 2014 Dec., v. 1837, no. 12

2014

Abstract: The metabolism of aerobic life uses the conversion of molecular oxygen to water as an energy source. This reaction is catalyzed by cytochrome c oxidase (CcO) consuming four electrons and four protons, which move along specific routes. While all four ... ...

Abstract	The metabolism of aerobic life uses the conversion of molecular oxygen to water as an energy source. This reaction is catalyzed by cytochrome c oxidase (CcO) consuming four electrons and four protons, which move along specific routes. While all four electrons are transferred via the same cofactors to the binuclear reaction center (BNC), the protons take two different routes in the A-type CcO, i.e., two of the four chemical protons consumed in the reaction arrive via the D-channel in the oxidative first half starting after oxygen binding. The other two chemical protons enter via the K-channel in the reductive second half of the reaction cycle. To date, the mechanism behind these separate proton transport pathways has not been understood.In this study, we propose a model that can explain the reaction-step specific opening and closing of the K-channel by conformational and pKA changes of its central lysine 362. Molecular dynamics simulations reveal an upward movement of Lys362 towards the BNC, which had already been supposed by several experimental studies. Redox state-dependent pKA calculations provide evidence that Lys362 may protonate transiently, thereby opening the K-channel only in the reductive second half of the reaction cycle. From our results, we develop a model that assigns a key role to Lys362 in the proton gating between the two proton input channels of the A-type CcO.
Keywords	cytochrome-c oxidase ; electrons ; energy ; lysine ; metabolism ; models ; molecular dynamics ; oxygen ; potassium channels ; protons
Language	English
Dates of publication	2014-12
Size	p. 1998-2003.
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	282711-6
ISSN	0005-2728 ; 0304-4173
ISSN	0005-2728 ; 0304-4173
DOI	10.1016/j.bbabio.2014.08.003
Database	NAL-Catalogue (AGRICOLA)

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Article: Redox induced protonation of heme propionates in cytochrome c oxidase: Insights from surface enhanced resonance Raman spectroscopy and QM/MM calculations.

Sezer, Murat / Woelke, Anna-Lena / Knapp, Ernst Walter / Schlesinger, Ramona / Mroginski, Maria Andrea / Weidinger, Inez M

Biochimica et biophysica acta. Bioenergetics

2016 Volume 1858, Issue 2, Page(s) 103–108

Abstract: Understanding the coupling between heme reduction and proton translocation in cytochrome c oxidase (CcO) is still an open problem. The propionic acids of heme ... ...

Abstract	Understanding the coupling between heme reduction and proton translocation in cytochrome c oxidase (CcO) is still an open problem. The propionic acids of heme a
MeSH term(s)	Electron Transport Complex IV/metabolism ; Heme/metabolism ; Oxidation-Reduction ; Propionates/metabolism ; Proton Pumps/metabolism ; Protons ; Spectrum Analysis, Raman/methods
Chemical Substances	Propionates ; Proton Pumps ; Protons ; Heme (42VZT0U6YR) ; Electron Transport Complex IV (EC 1.9.3.1)
Language	English
Publishing date	2016-10-31
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	60-7
ISSN	1879-2596 ; 1879-260X ; 1872-8006 ; 1879-2642 ; 1879-2618 ; 1879-2650 ; 0005-2728 ; 0006-3002 ; 0005-2736 ; 0304-4165 ; 0167-4838 ; 1388-1981 ; 0167-4889 ; 0167-4781 ; 0304-419X ; 1570-9639 ; 0925-4439 ; 1874-9399
ISSN (online)	1879-2596 ; 1879-260X ; 1872-8006 ; 1879-2642 ; 1879-2618 ; 1879-2650
ISSN	0005-2728 ; 0006-3002 ; 0005-2736 ; 0304-4165 ; 0167-4838 ; 1388-1981 ; 0167-4889 ; 0167-4781 ; 0304-419X ; 1570-9639 ; 0925-4439 ; 1874-9399
DOI	10.1016/j.bbabio.2016.10.009
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Article ; Online: RETRACTED: Protonation State-Dependent Communication in Cytochrome c Oxidase.

Helabad, Mahdi Bagherpoor / Ghane, Tahereh / Reidelbach, Marco / Woelke, Anna Lena / Knapp, Ernst Walter / Imhof, Petra

publication RETRACTED

Biophysical journal

2016 Volume 111, Issue 3, Page(s) 492–503

Abstract: Proton transfer in cytochrome c oxidase from the cellular inside to the binuclear redox center (BNC) can occur through two distinct pathways, the D- and K-channels. For the protein to function as both redox enzyme and proton pump, proton transfer out of ... ...

Abstract	Proton transfer in cytochrome c oxidase from the cellular inside to the binuclear redox center (BNC) can occur through two distinct pathways, the D- and K-channels. For the protein to function as both redox enzyme and proton pump, proton transfer out of either of the channels toward the BNC or into the protein toward a proton loading site, and ultimately through the membrane, must be highly regulated. The O→E intermediate of cytochrome c oxidase is the first redox state in its catalytic cycle, where proton transfer through the K-channel, from K362 to Y288 at the BNC, is important. Molecular dynamics simulations of this intermediate with 16 different combinations of protonation states of key residues in the D- and K-channel show the mutual impact of the two proton-conducting channels to be protonation state-dependent. Strength as well as means of communication, correlations in positions, or connections along the hydrogen-bonded network, change with the protonation state of the K-channel residue K362. The conformational and hydrogen-bond dynamics of the D-channel residue N139 regulated by an interplay of protonation in the D-channel and K362. N139 thus assumes a gating function by which proton passage through the D-channel toward E286 is likely facilitated for states with protonated K362 and unprotonated E286, which would in principle allow proton transfer to the BNC, but no proton pumping until a proton has reached E286.
MeSH term(s)	Electron Transport Complex IV/chemistry ; Electron Transport Complex IV/metabolism ; Hydrogen Bonding ; Molecular Dynamics Simulation ; Protein Conformation ; Protons
Chemical Substances	Protons ; Electron Transport Complex IV (EC 1.9.3.1)
Language	English
Publishing date	2016--09
Publishing country	United States
Document type	Journal Article ; Retracted Publication
ZDB-ID	218078-9
ISSN	1542-0086 ; 0006-3495
ISSN (online)	1542-0086
ISSN	0006-3495
DOI	10.1016/j.bpj.2016.06.038
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Article ; Online: Protonation-State-Dependent Communication in Cytochrome c Oxidase.

Bagherpoor Helabad, Mahdi / Ghane, Tahereh / Reidelbach, Marco / Woelke, Anna Lena / Knapp, Ernst Walter / Imhof, Petra

Biophysical journal

2015 Volume 113, Issue 4, Page(s) 817–828

Abstract: Proton transfer in cytochrome c oxidase from the cellular inside to the binuclear redox center (BNC) can occur through two distinct pathways, the D- and K-channels. For the protein to function as both a redox enzyme and a proton pump, proton transfer ... ...

Abstract	Proton transfer in cytochrome c oxidase from the cellular inside to the binuclear redox center (BNC) can occur through two distinct pathways, the D- and K-channels. For the protein to function as both a redox enzyme and a proton pump, proton transfer into the protein toward the BNC or toward a proton loading site (and ultimately through the membrane) must be highly regulated. The P
MeSH term(s)	Electron Transport Complex IV/chemistry ; Electron Transport Complex IV/metabolism ; Hydrogen Bonding ; Molecular Dynamics Simulation ; Oxidation-Reduction ; Protein Conformation ; Protons
Chemical Substances	Protons ; Electron Transport Complex IV (EC 1.9.3.1)
Language	English
Publishing date	2015-06-02
Publishing country	United States
Document type	Journal Article
ZDB-ID	218078-9
ISSN	1542-0086 ; 0006-3495
ISSN (online)	1542-0086
ISSN	0006-3495
DOI	10.1016/j.bpj.2017.07.005
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Article ; Online: Influence of Heterogeneity on the Ultrafast Photoisomerization Dynamics of Pfr in Cph1 Phytochrome.

Stensitzki, Till / Yang, Yang / Wölke, Anna Lena / Knapp, Ernst-Walter / Hughes, Jon / Mroginski, Maria Andrea / Heyne, Karsten

Photochemistry and photobiology

2017 Volume 93, Issue 3, Page(s) 703–712

Abstract: Photoisomerization of a protein-bound chromophore is the basis of light sensing and signaling in many photoreceptors. Phytochrome photoreceptors can be photoconverted reversibly between the Pr and Pfr states through photoisomerization of the methine ... ...

Abstract	Photoisomerization of a protein-bound chromophore is the basis of light sensing and signaling in many photoreceptors. Phytochrome photoreceptors can be photoconverted reversibly between the Pr and Pfr states through photoisomerization of the methine bridge between rings C and D. Ground-state heterogeneity of the chromophore has been reported for both Pr and Pfr. Here, we report ultrafast visible (Vis) pump-probe and femtosecond polarization-resolved Vis pump-infrared (IR) probe studies of the Pfr photoreaction in native and
MeSH term(s)	Isomerism ; Models, Molecular ; Phytochrome/chemistry ; Spectrophotometry, Infrared
Chemical Substances	Phytochrome (11121-56-5)
Language	English
Publishing date	2017-05-12
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	123540-0
ISSN	1751-1097 ; 0031-8655
ISSN (online)	1751-1097
ISSN	0031-8655
DOI	10.1111/php.12743
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Article ; Online: VaccImm: simulating peptide vaccination in cancer therapy.

von Eichborn, Joachim / Woelke, Anna Lena / Castiglione, Filippo / Preissner, Robert

BMC bioinformatics

2013 Volume 14, Page(s) 127

Abstract: Background: Despite progress in conventional cancer therapies, cancer is still one of the leading causes of death in industrial nations. Therefore, an urgent need of progress in fighting cancer remains. A promising alternative to conventional methods is ...

Abstract	Background: Despite progress in conventional cancer therapies, cancer is still one of the leading causes of death in industrial nations. Therefore, an urgent need of progress in fighting cancer remains. A promising alternative to conventional methods is immune therapy. This relies on the fact that low-immunogenic tumours can be eradicated if an immune response against them is induced. Peptide vaccination is carried out by injecting tumour peptides into a patient to trigger a specific immune response against the tumour in its entirety. However, peptide vaccination is a highly complicated treatment and currently many factors like the optimal number of epitopes are not known precisely. Therefore, it is necessary to evaluate how certain parameters influence the therapy. Results: We present the VaccImm Server that allows users to simulate peptide vaccination in cancer therapy. It uses an agent-based model that simulates peptide vaccination by explicitly modelling the involved cells (immune system and cancer) as well as molecules (antibodies, antigens and semiochemicals). As a new feature, our model uses real amino acid sequences to represent molecular binding sites of relevant immune cells. The model is used to generate detailed statistics of the population sizes and states of the single cell types over time. This makes the VaccImm web server well suited to examine the parameter space of peptide vaccination in silico. VaccImm is publicly available without registration on the web at http://bioinformatics.charite.de/vaccimm; all major browsers are supported. Conclusions: The VaccImm Server provides a convenient way to analyze properties of peptide vaccination in cancer therapy. Using the server, we could gain interesting insights into peptide vaccination that reveal the complex and patient-specific nature of peptide vaccination.
MeSH term(s)	Amino Acid Sequence ; Cancer Vaccines/immunology ; Cancer Vaccines/therapeutic use ; Computer Simulation ; Epitopes/chemistry ; Epitopes/immunology ; Genotype ; Humans ; Major Histocompatibility Complex ; Neoplasms/immunology ; Neoplasms/therapy ; Peptides/chemistry ; Peptides/immunology ; Software ; Tumor Burden ; Vaccines, Subunit/immunology ; Vaccines, Subunit/therapeutic use
Chemical Substances	Cancer Vaccines ; Epitopes ; Peptides ; Vaccines, Subunit
Language	English
Publishing date	2013-04-15
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2041484-5
ISSN	1471-2105 ; 1471-2105
ISSN (online)	1471-2105
ISSN	1471-2105
DOI	10.1186/1471-2105-14-127
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