Protonation and conformational changes at the surface of proteins

Principal Investigator: Prof. Dr. Ulrike Alexiev (FU)

Advanced fluorescence spectroscopic methods in combination with molecular biology are applied to understand the interplay between activation of the embedded cofactor and protonation, conformational and hydration dynamics at the protein surface of cytochrome c oxidase (CcO) and the photoreceptor phytochrome. We will address the enigmatic proton release pathways in CcO using probes attached to surface residues and internal groups such as R473. Vibrational Stark Effect probes at single cysteine mutants for electric field changes and proton release and uptake studies at the protein surface will facilitate the understanding of signal transfer in phytochromes.

Publications

2021 - 2024

Balke, J., Diaz Gutierrez, P., Rafaluk-Mohr, T., Proksch, J., Koksch, B. and Alexiev, U. (2023). Osmolytes Modulate Photoactivation of Phytochrome: Probing Protein Hydration. Molecules, 28, 16: doi: 10.3390/molecules28166121.

Dong, P., Stellmacher, J., Bouchet, L.M., Nieke, M., Kumar, A., Osorio-Blanco, E.R., Nagel, G., Lohan, S.B., Teutloff, C., Patzelt, A., Schäfer-Korting, M., Calderón, M., Meinke, M.C., and Alexiev, U. (2021). A Dual Fluorescence-Spin Label Probe for Visualization and Quantification of Target Molecules in Tissue by Multiplexed FLIM – EPR Spectroscopy. Angew. Chem. Int. Ed., 60, 14938. doi: 10.1002/ange.202012852.

Nagano, S., Sadeghi, M., Balke, J., Fleck, M., Heckmann, N., Psakis, G. and Alexiev, U. (2022). Improved fluorescent phytochromes for in situ imaging. Sci Rep, 12, 1: 5587. doi: 10.1038/s41598-022-09169-x.

Sadeghi, M., Balke, J., Rafaluk-Mohr, T. and Alexiev, U. (2022). Long-Distance Protonation-Conformation Coupling in Phytochrome Species. Molecules, 27, 23: 8395. doi: 10.3390/molecules27238395.

Silapetere, A., Hwang, S., Hontani, Y., Fernandez Lahore, R.G., Balke, J., Escobar, F.V., Tros, M., Konold, P.E., Matis, R., Croce, R., Walla, P.J., Hildebrandt, P., Alexiev, U., Kennis, J.T.M., Sun, H., Utesch, T. and Hegemann, P. (2022). QuasAr Odyssey: the origin of fluorescence and its voltage sensitivity in microbial rhodopsins. Nat Commun, 13, 1: 5501. doi: 10.1038/s41467-022-33084-4.

Wolf, A., Volz-Rakebrand, P., Balke, J. and Alexiev, U. (2023). Diffusion Analysis of NAnoscopic Ensembles: A Tracking-Free Diffusivity Analysis for NAnoscopic Ensembles in Biological Samples and Nanotechnology. Small, 19, 16: 2206722. doi: 10.1002/smll.202206722.

2017 - 2020

Balke, J., Volz, P., Neumann, F., Brodwolf, R., Wolf, A., Pischon, H., Radbruch, M., Mundhenk, L., Gruber, A. D., Ma, N., and Alexiev, U. (2018). Visualizing Oxidative Cellular Stress Induced by Nanoparticles in the Subcytotoxic Range using Fluorescence Lifetime Imaging. Small 14 (23), doi: 10.1002/smll.201800310.

Ober, K., Volz-Rakebrand, P., Stellmacher, J., Brodwolf, R., Licha, K., Haag, R., and Alexiev, U. (2019). Expanding the scope of reporting nanoparticles: sensing of lipid phase transitions and nanoviscosities in lipid membranes. Langmuir 35, 11422-11434; doi: 10.1021/acs.langmuir.9b01372

Sadeghi, M., Balke, J., Schneider, C., Nagano, S., Stellmacher, J., Lochnit, G., Lang, C, Weise, C., Hughes, J., and Alexiev, U. (2020). Transient de-protonation of the chromophore affects protein dynamics proximal and distal to the linear tetrapyrrole chromophore in phytochrome Cph1. Biochemistry 59, 1051-1062; doi: 10.1021/acs.biochem.9b00967

Velazquez Escobar, F., Lang, C., Takiden, A., Schneider, C., Balke, J., Hughes, J., Alexiev, U., Hildebrandt, P., and Mroginski, M.A. (2017). Protonation-Dependent Structural Heterogeneity in the Chromophore Binding Site of Cyanobacterial Phytochrome Cph1. Journal of Physical Chemistry B 121, 47-57; doi: 10.1021/acs.jpcb.6b09600

Volz, P., Schilrreff, P., Brodwolf, R., Wolff, C., Stellmacher, J., Balke, J., Morilla, M.J., Zoschke, C., Schäfer‐Korting, M., Alexiev, U. (2017). Pitfalls in using fluorescence tagging of nanomaterials: tectodendrimers in skin tissue as investigated by Cluster‐FLIM. Ann. N.Y. Acad. Sci. 1405, 202-214; doi: 10.1111/nyas.13473

Volz, P., Brodwolf, R., Zoschke, C., Haag, R., Schäfer-Korting, M., and Alexiev, U. (2018). White-Light Supercontinuum Laser-Based Multiple Wavelength Excitation for TCSPC-FLIM of Cutaneous Nanocarrier Uptake. Z. Phys. Chem. 232, 671-688; doi: 10.1515/zpch-2017-1050

Wolf, A., Dragelj, J., Wonneberg, J., Stellmacher, J., Balke, J., Woelke, A.L., Hodoscek, M., Knapp, E.W., and Alexiev, U. (2020). The redox-coupled proton-channel opening in cytochrome c oxidase. Chem. Science 11, 3804-3811; doi: 10.1039/C9SC06463J

Wolf, A., Wonneberg, J., Balke, J., and Alexiev, U. (2019). Electronation-dependent structural change at the proton exit side of cytochrome c oxidase as revealed by site-directed fluorescence labeling. FEBS Journal; doi: 10.1111/febs.15084.

2013 - 2016

Alexiev, U., and Farrens, D.L. (2014). Fluorescence spectroscopy of rhodopsins: Insights and approaches. Biochimica et Biophysica Acta (BBA) - Bioenergetics 1837, 694-709.

Kirchberg, K., Michel, H., and Alexiev, U. (2013). Exploring the entrance of proton pathways in cytochrome c oxidase from Paracoccus denitrificans: Surface charge, buffer capacity and redox-dependent polarity changes at the internal surface. Biochimica et Biophysica Acta (BBA) - Bioenergetics 1827, 276-284.

Richter, C., Schneider, C., Quick, M.T., Volz, P., Mahrwald, R., Hughes, J., Dick, B., Alexiev, U., and Ernsting, N.P. (2015). Dual-fluorescence pH probe for bio-labelling. Physical Chemistry Chemical Physics 17, 30590-30597.

Volz, P., Boreham, A., Wolf, A., Kim, T.-Y., Balke, J., Frombach, J., Hadam, S., Afraz, Z., Rancan, F., Blume-Peytavi, U., Vogt, A., and Alexiev, U. (2015). Application of Single Molecule Fluorescence Microscopy to Characterize the Penetration of a Large Amphiphilic Molecule in the Stratum Corneum of Human Skin. International Journal of Molecular Sciences 16, 6960-6977.

Volz, P., Krause, N., Balke, J., Schneider, C., Walter, M., Schneider, F., Schlesinger, R., and Alexiev, U. (2016). Light and pH-induced changes in structure and accessibility of transmembrane helix B and its immediate environment in Channelrhodopsin-2. Journal of Biological Chemistry 291, 17382-17393.

Wolf, A., Schneider, C., Kim, T.Y., Kirchberg, K., Volz, P., and Alexiev, U. (2016). A simulation-guided fluorescence correlation spectroscopy tool to investigate to protonation dynamics of cytrochrome c oxidase. Physical Chemistry Chemical Physics 18, 12877-12885.