Understanding proton transfer in phytochrome and cytochrome c oxidase

Principal Investigator: Prof. Dr. Maria Andrea Mroginski (TU)

Proton translocation can be driven by light excitation as in phytochromes or by redox reactions as in cytochrome c oxidase. These processes significantly alter protein electrostatics and, in turn, induce changes of local electric fields at relevant functional sites. Thus, the goal of this project is to find a general concept linking protonation dynamics, transient changes of local electric fields and conformational dynamics that are responsible for triggering protein function. For this purpose, we will implement QM/MM based approaches for estimating the strength of local electric fields on the basis of the vibrational Stark effect and combine these approaches with constant-pH molecular dynamics simulations to identify proton transfer pathways within the protein matrix.

Publications

2021 - 2024

Blain-Hartung, M., Sass, G.J. von., Plaickner, J., Hoang, O.T., Katz, S., Mroginski, M.A.¸ Esser, N., Budisa, N., Forest, K.T., Hildebrandt, P. (2023). On the Role of a Conserved Tryptophan in the Chromophore Pocket of Cyanobacteriochrome. J Mol Biol. doi: 10.1016/j.jmb.2023.168227.

Dragelj, J., Mroginski, M.A., and Knapp, E.W. (2021). Beating Heart of Cytochrome c Oxidase: The Shared Proton of Heme a3 Propionates. J Phys Chem B, 125: 9668-9677. doi: 10.1021/acs.jpcb.1c03619.

Hontani, Y., Baloban, M., Escobar, F.V., Jansen, S. A., Shcherbakova, D.M., Weißenborn, J., Kloz, M., Mroginski, M.A., Verkhusha, V.V., and Kennis, J.T.M. (2021). Real-time observation of tetrapyrrole binding to an engineered bacterial phytochrome. Commun Chem, 4: 1-11. doi: 10.1038/s42004-020-00437-3.

Kraskov, A., von Sass, J., Nguyen, A.D., Hoang, T.O., Buhrke, D., Katz, S., Michael, N., Kozuch, J., Zebger, I., Siebert, F., Scheerer, P., Mroginski, M.A., Budisa, N., and Hildebrandt P. (2021). Local Electric Field Changes during the Photoconversion of the Bathy Phytochrome Agp2. Biochemistry, 60, 40: 2967-2977. doi: 10.1021/acs.biochem.1c00426.

Kruse, F., Nguyen, A.D., Dragelj, J., Heberle, J., Hildebrandt, P., Mroginski, M.A., and Weidinger, I.M. (2021). A Resonance Raman Marker Band Characterizes the Slow and Fast Form of Cytochrome c Oxidase. J Am Chem Soc, 143: 2769-2776. doi: 10.1021/jacs.0c10767.

Lopez, M.F., Dahl, M., Escobar, F.V., Bonomi, H.R., Kraskov, A., Michael, N., Mroginski, M.A., Scheerer, P. and Hildebrandt, P. (2022). Photoinduced reaction mechanisms in prototypical and bathy phytochromes. Phys Chem Chem Phys, 24, 19: 11967-11978. doi: 10.1039/d2cp00020b.

Mroginski, M.A., Adam, S., Amoyal, G.S., Barnoy, A., Bondar, A.-N., Borin, V.A., Church, J.R., Domratcheva, T., Ensing, B., Fanelli, F., Ferré, N., Filiba, O., Pedraza-González, L., González, R., González-Espinoza, C.E., Kar, R.K., Kemmler, L., Kim, S.S., Kongsted, J., Krylov, A.I., Lahav, Y., Lazaratos, M., NasserEddin, Q., Navizet, I., Nemukhin, A., Olivucci, M., Olsen, J.M.H., Pérez de Alba Ortíz, A., Pieri, E., Rao, A.G., Rhee, Y.M., Ricardi, N., Sen, S., Solov'yov, I.A., De Vico, L., Wesolowski, T.A., Wiebeler, C., Yang, X., and Schapiro, I. (2021). Frontiers in Multiscale Modeling of Photoreceptor Proteins. Photochem Photobiol, 97: 243-269. doi: 10.1111/php.13372.

Theiß, M., Grupe, M., Lamparter, T., Mroginski, M.A., and Diller, R. (2021). Ultrafast proton release reaction and primary photochemistry of phycocyanobilin in solution observed with fs-time-resolved mid-IR and UV/Vis spectroscopy. Photochem Photobiol Sci, 20, 6: 715-732. doi: 10.1007/s43630-021-00045-7.

Yang, Y., Stensitzki, T., Sauthof, L., Schmidt, A., Piwowarski, P., Velazquez Escobar, F., Michael, N., Nguyen, A.D., Szczepek, M., Brünig, F. N., Netz, R. R., Mroginski, M. A., Adam, S., Bartl, F., Schapiro, I., Hildebrandt, P., Scheerer, P., and Heyne, K. (2022). Ultrafast proton-coupled isomerization in the phototransformation of phytochrome. Nat Chem. doi: 10.1038/s41557-022-00944-x.

2017 - 2020

Battocchio, G., González, R., Rao, A., Schapiro, I and Mroginski, M.A. (2020). Dynamic Properties of the Photosensory Domain of Deinococcus Radiodurans Bacteriophytochrome. J. Phys. Chem. B 124, 1740-1750. doi: 10.1021/acs.jpcb.0c00612

Gonzalez, R. and Mroginski M.A. (2019). Fully Quantum Chemical Treatment of Chromophore-Protein Interactions in Phytochromes. J. Phys. Chem. B 123, 9819-9830. doi: 10.1021/acs.jpcb.9b08938

Helabad, M.B., Ghane, T., Reidelbach, M., Woelke, A.L., Knapp, E.W., and Imhof, P. (2017). Protonation state-dependent communication in cytochrome c oxidase. Biophysical Journal 113, 817-828. doi: 10.1016/j.bpj.2017.07.005

Kielb, P., Utesch, T., Kozuch, J., Jeoung, J.-H., Dobbek, H., Mroginski, M.A., Hildebrandt, P., and Weidinger, I. (2017). Switchable Redox Chemistry of the Hexameric Tyrosine-Coordinated Heme Protein. Journal of Physical Chemistry B 121, 3955-3964. doi: 10.1021/acs.jpcb.7b01286

Kraskow, A., Nguyen, A. D., Goerling, J., Buhrke, D., Velazquez, F.†, Fernandez, M., Michael, N., Sauthof, L., Schmidt, A., Piwowarski, P., Yang,Y., Stensitzki,T., Adam, S., Bartl, F., Schapiro, I., Heyne, K., Siebert, F., Scheerer,P., Mroginski, M.A, and Hildebrandt, P. (2020). Intramolecular Proton Transfer Controls Protein Structural Changes in Phytochrome. Biochemistry 59, 1023-1037. doi: 10.1021/acs.biochem.0c00053

Kruse, F., Nguyen, A.D., Dragelj, J., Schlesinger, R., Heberle, J., Mroginski, M.A. and Weidinger I. (2020). Characterisation of the cyanate inhibited state of Cytochrome c Oxidase. Sci. Rep. 10, 3863. doi: 10.1038/s41598-020-60801-0

Lopez, M. F., Nguyen, A. D., Escobar, F. V., Gonzalez, R., Michael, N., Nogacz, Z., Piwowarski, P., Bartl, F., Siebert, F., Heise, I., Scheerer, P., Gaertner, W., Mroginski, M. A., and Hildebrandt, P. (2019) Role of the Propionic Side Chains for the Photoconversion of Bacterial Phytochromes. Biochemistry 58, 3504–3519; doi: 10.1021/acs.biochem.9b00526

Rossini, E., Bochevarov, A. D., and Knapp, E.W. (2018). Empirical Conversion of pKa Values between Different Solvents and Interpretation of the Parameters: Application to Water, Acetonitrile, Dimethyl Sulfoxide, and Methanol. ACS Omega 3, 1653-1662.; doi: 10.1021/acsomega.7b01895

Schmidt, A., Sauthof, L., Szczepek, M., Lopez, M., Velázquez, F., Qureshi, B. M., Michael, N., Buhrke, D., Stevens, T., Kwiatkowski, D., von Stetten, D., Mroginski, M.A., Krauß, N., Lamparter, T. , Hildebrandt, P., and Scheerer, P. (2018). Structural snapshot of a bacterial phytochrome in its functional intermediate state. Nature Commun 9, 4912; doi: 10.1038/s41467-018-07392-7

Sezer, M., Woelke, A.-L., Knapp, E.W., Schlesinger, R., Mroginski, M.A., Weidinger, I.M. (2017). Redox induced protonation of heme propionates in cytochrome c oxidase: Insights from surface enhanced resonance Raman spectroscopy and QM/MM calculations. Biochimica et Biophysica Acta (BBA) - Bioenergetics 1858, 103-108; doi: 10.1016/j.bbabio.2016.10.009

Song, C., Mroginski, M.A., Lang, C., Kopycki, J., Gartner, W., Matysik, J., and Hughes, J. (2018). 3D Structures of Plant Phytochrome A as Pr and Pfr From Solid-State NMR: Implications for Molecular Function. Front Plant Sci 9, 498; doi: 10.3389/fpls.2018.00498

Stensitzki, T., Yang, Y., Wölke, A.L., Knapp, E.-W., Hughes, J., Mroginski, M.A., and Heyne, K. (2017). Influence of Heterogeneity on the Ultrafast Photoisomerization Dynamics of Pfr in Cph1 Phytochrome. Photochemistry and Photobiology 93, 703-712; doi: 10.1111/php.12743

Takiden, A., Velazquez-Escobar, F., Dragelj, J., Woelke, A.L., Knapp E.-W., Piwowarski, P., Bartl, F., Hildebrandt, P., and Mroginski, M.A. (2017). Structural and Vibrational Characterization of the Chromophore Binding Site of Bacterial Phytochrome Agp1. Photochemistry and Photobiology 93, 713-723; doi: 10.1111/php.12737

Velazquez Escobar, F., Kneip, C., Michael, N., Hildebrandt, T., Tavraz, N., Gärtner, W., Hughes, J., Friedrich, T., Scheerer, P., Mroginski, M.A., and Hildebrandt, P. (2020). The Lumi-R Intermediates of Prototypical Phytochromes. Journal of Physical Chemistry B 124, 4044-4055. doi: 10.1021/acs.jpcb.0c01059.

Velázquez 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

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. Sci. 11, 3804-3811; doi: 10.1039/C9SC06463J

2013 - 2016

Chernev, P., Zaharieva, I., Rossini, E., Galstyan, A., Dau, H., and Knapp, E.-W. (2016). Merging structural information from X-ray crystallography, quantum chemistry and EXAFS spectra: The oxygen-evolving complex in PSII. Journal of Physical Chemistry B 120, 10899-10922.

Galstyan, G., and Knapp, E.-W. (2015). Computing pK_A values of hexa-aqua transition metal complexes. Journal of Computational Chemistry 36, 69-78.

Meyer, T., and Knapp, E.-W. (2014). Database of protein complexes with multivalent binding ability: Bival-bind. Proteins 82, 744-751.

Meyer, T., and Knapp, E.W. (2015). pK(a) Values in Proteins Determined by Electrostatics Applied to Molecular Dynamics Trajectories. J. Chem. Theory Comput. 11, 2827-2840.

Robertazzi, A., Galstyan, A., and Knapp, E.W. (2014). PSII manganese cluster: Protonation of W2, 05, 04 and His337 in the Si state explored by combined quantum chemical and electrostatic energy computations. Biochim. Biophys. Acta 1837, 1316-1321.

Robertazzi, A., Galstyan, A., and Knapp, E.W. (2014). Reprint of PSII Manganese Cluster: Protonation of W2, O5, O4 and His337 in the S1 state explored by combined quantum chemical and electrostatic energy computations. Biochim. Biophys. Acta 1837, 1389-1394.

Rossini, E., and Knapp, E.-W. (2016). Proton Solvation in Protic and Aprotic Solvents. Journal of Computational Chemsitry 37, 1082-1091.

Rossini, E., and Knapp, E.-W. (2016). Erratum: Proton Solvation in Protic and Aprotic Solvents [J. Comput. Chem. 2015, 37, 1082–1091]. Journal of Computational Chemsitry 37, 2163-2164.

Rossini, E., Netz, R.R., and Knapp, E.W. (2016). Computing pK_a values in different solvents by electrostatic transformation. Journal of Chemical Theory and Computation 12, 3360-3369.

Sakalli, I., and Knapp, E.-W. (2015). pKA in proteins solving the Poisson–Boltzmann equation with finite elements. Journal of Computational Chemistry 36, 2147-2157.

Sakalli, I., Schoberl, J., and Knapp, E.W. (2014). mFES: A Robust Molecular Finite Element Solver for Electrostatic Energy Computations. Journal of Chemical Theory and Computation 10, 5095-5112.

Schlaich, A., Knapp, E.W., and Netz, R.R. (2016). Water Dielectric Effects in Planar Confinement. Physical Review Letters 117, 048001. [Link to news section.]

Woelke, A.L., Galstyan, G., Galstyan, A., Meyer, T., Heberle, J., and Knapp, E.-W. (2013). Exploring the Possible Role of Glu286 in CcO by Electrostatic Energy Computations Combined with Molecular Dynamics. Journal of Physical Chemistry B 117, 12432-12441.

Woelke, A.L., Galstyan, G., and Knapp, E.-W. (2014). Lysine 362 in cytochrome c oxidase regulates opening of the K-channel via changes in pK(A) and conformation. Biochimica et Biophysica Acta (BBA) - Bioenergetics 1837, 1998-2003.

Woelke, A.L., Kuehne, C., Meyer, T., Galstyan, G., Dernedde, J., and Knapp, E.-W. (2013). Understanding Selectin Counter-Receptor Binding from Electrostatic Energy Computations and Experimental Binding Studies. Journal of Physical Chemistry B 117, 16443-16454.

Woelke, A.L., Wagner, A., Galstyan, G., Meyer, T., and Knapp, E.-W. (2014). Proton Transfer in the K-Channel Analog of B-Type Cytochrome c Oxidase from Thermus thermophilus. Biophysical Journal 107, 2177-2184.