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Proton transfer across and along biological membranes
Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
2020 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Proton-transfer reactions belong to the most prevalent reactions in the biosphere and make life on Earth possible, as they are central to energy conversion. In most known organisms, protons are translocated from one side of a membrane to the other, which generates an electrochemical gradient that drives ATP synthesis. Both the membranes and the proteins that are involved in these processes are vital components of energy-conversion machineries. This thesis presents and discusses proton transfer at surfaces of membranes and proteins, as well as proton translocation across membranes via enzymes.

In the first work, we developed a single-enzyme approach to study proton translocation by the proton pump cytochrome bo3 (cyt. bo3). The generated proton gradients were stable as long as substrate (electrons, oxygen) was available. Individual cyt. bo3 could generate proton gradients of ∼2 pH units, which correspond to the measured electrochemical gradient in Escherichia coli cells.

When acidic and basic amino acids are in close proximity to each other on a protein surface, their individual Coulomb cages can merge to form a proton antenna that enables fast proton transfer to specific groups. To investigate how the function of a proton pump is affected by structural changes in a proton antenna, close to a proton uptake pathway, we characterized the function and structure of genetic variants of cytochrome c oxidase (CytcO). When a Glu, located about 10 Å from the first residue of the D-pathway, was replaced by a non-protonatable residue (Ala) the proton pumping efficiency decreased by more than half compared to the wild-type enzyme. The proton-uptake kinetics was also altered in this variant.

Cardiolipin (CL) is found in membranes where ATP is generated. This phospholipid alters the membrane structure and binds a variety of proteins including all complexes that take part in oxidative phosphorylation. To investigate the role of CL in proton-transfer reactions on the surface of membranes we used fluorescence correlation spectroscopy to study inner mitochondrial membranes from Saccharomyces cerevisiae. The protonation rate at wild-type membranes was about 50% of that measured with membranes prepared from mitochondria lacking CL. The protonation rate on the surface of small unilamellar vesicles (SUVs) decreased by about a factor of three when DOPC-SUVs were supplemented with 20% CL. Furthermore, phosphate buffer titrations with SUVs showed that CL can act as a local proton buffer in a membrane.

The respiratory supercomplex factor 1 (Rcf1) has been suggested to facilitate direct electron transfer from the bc1 complex to CytcO by bridging the enzymes and binding cytochrome c (cyt. c) to a flexible domain of Rcf1. We investigated biding of cyt. c to Rcf1 reconstituted into different membrane environments. The apparent KD of the binding between cyt. c and DOPC-liposomes was almost five times lower when Rcf1 was present in the vesicles. Moreover, the apparent KD between cyt. c and liposome reconstituted CytcO was about nine times lower for CytcO isolated from a wild-type strain compared to a Rcf1-lacking strain.

Place, publisher, year, edition, pages
Stockholm: Department of Biochemistry and Biophysics, Stockholm University , 2020. , p. 93
Keywords [en]
biological membranes, cardiolipin, cytochrome bo3, cytochrome c oxidase, energy conversion, fluorescence correlation spectroscopy (FCS), localized coupling, mitochondria, proton transfer, Rcf1, respiration, single-enzyme measurement
National Category
Biochemistry and Molecular Biology
Research subject
Biochemistry
Identifiers
URN: urn:nbn:se:su:diva-177422ISBN: 978-91-7797-941-8 (print)ISBN: 978-91-7797-942-5 (electronic)OAI: oai:DiVA.org:su-177422DiVA, id: diva2:1382883
Public defence
2020-02-21, Magnélisalen, Kemiska övningslaboratoriet, Svante Arrhenius väg 16B, Stockholm, 10:00 (English)
Opponent
Supervisors
Note

At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 3: Manuscript. Paper 4: Manuscript.

Available from: 2020-01-29 Created: 2020-01-06 Last updated: 2020-01-23Bibliographically approved
List of papers
1. Single Proteoliposomes with E.coli Quinol Oxidase: Proton Pumping without Transmembrane Leaks
Open this publication in new window or tab >>Single Proteoliposomes with E.coli Quinol Oxidase: Proton Pumping without Transmembrane Leaks
2017 (English)In: Israel Journal of Chemistry, ISSN 0021-2148, Vol. 57, no 5, p. 437-445Article in journal (Refereed) Published
Abstract [en]

Respiratory oxidases are transmembrane enzymes that catalyze the reduction of dioxygen to water in the final step of aerobic respiration. This process is linked to proton pumping across the membrane. Here, we developed a method to study the catalytic turnover of the quinol oxidase, cytochromebo(3) from E.coli at single-molecule level. Liposomes with reconstituted cytochromebo(3) were loaded with a pH-sensitive dye and changes in the dye fluorescence, associated with proton transfer and pumping, were monitored as a function of time. The single-molecule approach allowed us to determine the orientation of cytochromebo(3) in the membrane; in approximate to 70% of the protein-containing liposomes protons were released to the outside. Upon addition of substrate we observed the buildup of a pH (in the presence of the K+ ionophore valinomycin), which was stable over at least approximate to 800s. No rapid changes in pH (proton leaks) were observed during steady state proton pumping, which indicates that the free energy stored in the electrochemical gradient in E.coli is not dissipated or regulated through stochastic transmembrane proton leaks, as suggested from an earlier study (Li etal. J. Am. Chem. Soc. (2015) 137, 16055-16063).

Keywords
proton translocation, single molecule, proton pump, electron transfer, membrane protein
National Category
Chemical Sciences
Research subject
Biochemistry
Identifiers
urn:nbn:se:su:diva-144709 (URN)10.1002/ijch.201600138 (DOI)000401329000010 ()
Available from: 2017-07-20 Created: 2017-07-20 Last updated: 2020-01-07Bibliographically approved
2. Structural changes at the surface of cytochrome c oxidase alter the proton-pumping stoichiometry
Open this publication in new window or tab >>Structural changes at the surface of cytochrome c oxidase alter the proton-pumping stoichiometry
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2020 (English)In: Biochimica et Biophysica Acta - Bioenergetics, ISSN 0005-2728, E-ISSN 1879-2650, Vol. 1861, no 2, article id 148116Article in journal (Refereed) Published
Abstract [en]

Data from earlier studies showed that minor structural changes at the surface of cytochrome c oxidase, in one of the proton-input pathways (the D pathway), result in dramatically decreased activity and a lower proton-pumping stoichiometry. To further investigate how changes around the D pathway orifice influence functionality of the enzyme, here we modified the nearby C-terminal loop of subunit I of the Rhodobacter sphaeroides cytochrome c oxidase. Removal of 16 residues from this flexible surface loop resulted in a decrease in the proton-pumping stoichiometry to <50% of that of the wild-type enzyme. Replacement of the protonatable residue Glu552, part of the same loop, by an Ala, resulted in a similar decrease in the proton-pumping stoichiometry without loss of the O2-reduction activity or changes in the proton-uptake kinetics. The data show that minor structural changes at the orifice of the D pathway, at a distance of ~40 Å from the proton gate of cytochrome c oxidase, may alter the proton-pumping stoichiometry of the enzyme.

Keywords
Mycobacterium smegmatis, Proton pumping, Respiratory chain, Electron transfer, Actinobacteria, Mitochondria
National Category
Biochemistry and Molecular Biology
Research subject
Biochemistry
Identifiers
urn:nbn:se:su:diva-177419 (URN)10.1016/j.bbabio.2019.148116 (DOI)000508749700004 ()
Available from: 2020-01-06 Created: 2020-01-06 Last updated: 2020-03-03Bibliographically approved
3. The role of cardiolipin in lateral proton transfer along inner mitochondrial membranes
Open this publication in new window or tab >>The role of cardiolipin in lateral proton transfer along inner mitochondrial membranes
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(English)Manuscript (preprint) (Other academic)
Keywords
cardiolipin, protonation kinetics, mitochondria, cytochrome c oxidase, fluorescence correlation spectroscopy
National Category
Biochemistry and Molecular Biology
Research subject
Biochemistry
Identifiers
urn:nbn:se:su:diva-177420 (URN)
Available from: 2020-01-06 Created: 2020-01-06 Last updated: 2020-01-23Bibliographically approved
4. A membrane-bound anchor for cytochrome c in S. cerevisiae
Open this publication in new window or tab >>A membrane-bound anchor for cytochrome c in S. cerevisiae
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(English)Manuscript (preprint) (Other academic)
National Category
Biochemistry and Molecular Biology
Research subject
Biochemistry
Identifiers
urn:nbn:se:su:diva-158698 (URN)
Available from: 2018-08-14 Created: 2018-08-14 Last updated: 2020-01-06Bibliographically approved

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