Functional dynamics of biomolecules

Functional dynamics of biomolecules

Protein functioning relies on their capacity to efficiently adopt distinct configurations. Our research concerns the internal dynamics associated with these specific changes, in particular in proteins involved in catalysis and in signal transduction. The fastest and most specific changes take place on the timescale of the internal protein vibrations. Therefore we employ and develop femtosecond spectroscopic techniques to probe these motions in real time. Our efforts to get detailed insight in the dynamics on a molecular level include combining experimental studies and molecular dynamics simulations. In many of our present projects we study, or exploit, photoinduced charge transfers in flavoproteins. Here we both study functional charge transfer chains composed of flavin and aromatic residues, like those in cryptochromes and photolyases, and use the exquisite sensitivity of electron transfer kinetics on the configuration of donor-acceptor pairs as a probe of configurational dynamics. Recently we have also discovered two completely novel photochemical reactions in flavoproteins: ultrafast photo-oxidation of semi-reduced flavins and ultrafast photodissociation of charge transfer interactions between flavins and inhibitors. We aim at exploting these reactions to develop new flavoprotein-based photoswitches and photocatalysts. Other projects concern a variety of heme proteins, where ultrafast ligand photodissociation is used as an impulsive trigger of the system, and photoproducts of Fe-S proteins.
Present research topics include photocatalysis in the flavoenzyme Fatty Acid Photodecarboxylase  (FAP) and the mechanism and possible applications of photodissociation of the charge transfer complex between the flavoprotein MSOX and its MTA inhibitor. The latter project is financed by a collaborative ANR grant (ANR PHOTOCT, 2024-2027) that we coordinate, and involves collaborations with IBS Grenoble (Martin WEIK) and ITODYS, Université Paris-Cité (Antonio MONARI).

Much work is developed along with other themes in our lab, in particular  "Adaptive molecular mechanisms in microbial systems" and "Coherent spectroscopy and coherent control in biological systems", and in addition with a number of external collaborations.

Contact : marten.vos at



Photocycle of Fatty Acid Photodecarboxylase (FAP). See Sorigué, D. et al, (2021) Science 372, eabd5687


Photoswitching in the MSOX-MTA complex. See  Zhuang, B. & Vos, M.H. (2022) J. Am. Chem. Soc. 144, 11569-11573

Publications récentes selectionnées:

Raics, K., Pirisi, K., Zhuang, B., Fekete, Z., Kis-Bicskei, N., Pecsi, I., Pozsonyi Ujfalusi, K., Telek, E., Li, Y., Tolentino Collado, J., Tonge, P.J., Meech, S.R., Vos,M.H., Bodis, E. & Lukacs, A. (2023) Accelerated electron transfer and increased enzymatic activity in genetically modified photoactivable adenylate cyclase OaPAC, J. Biol. Chem. 299, 105056

Zhuang, B., Aleksandrov, A. Seo, D. & Vos, M.H. (2023) Excited-State Properties of Fully Reduced Flavins in Ferredoxin-NADP+ Oxidoreductase, J. Phys. Chem. Lett. 14, 1086-1102

Diuba, A.V., Vygodina, T.V., Azarkina, N.V., Arutyunyan, A.M., Soulimane, T., Vos, M.H. & Konstantinov, A.A. (2023) Individual heme a and heme a3 contributions to the Soret absorption spectrum of the reduced bovine cytochrome c oxidase, Biochim. Biophys. Acta 1864, 148937

Vos, M.H., Salman, M. & Liebl,U. (2022) Early processes in heme-based CO-sensing proteinsFront. Mol. Biosci. 9, 1046412

Zhuang, B., Vos, M.H.  & Aleksandrov, A. (2022) Photochemical and Molecular Dynamics Studies of Halide Binding in Flavoenzyme Glucose Oxidase, ChemBioChem 23, e202200227 

Zhuang, B. & Vos, M.H. (2022) Photoswitching Behavior of Flavin–Inhibitor Complex in a Nonphotocatalytic Flavoenzyme, J. Am. Chem. Soc. 144, 11569-11573

Kapetanaki, S.M., Fekete, S., Dorlet, P., Vos, M.H., Liebl, U. & Lukacs, A. (2022) Molecular insights of the role of heme in the transcriptional regulatory system AppA/PpsR, Biophys. J. 121, 2135-2151

Zhuang, B., Liebl, U. & Vos, M.H. (2022) Flavoprotein photochemistry: fundamental processes and photocatalytic perspectives, J. Phys. Chem. B 126, 3199-3207

Zhuang, B., Ramodiharilafy, R., Liebl, U., Aleksandrov, A. & Vos, M.H. (2022) Ultrafast Photooxidation of Protein-bound Anionic Flavin Radical, Proc. Natl. Acad. Sci. USA 119, e2118924119

Zhuang, B., Nag, L., Sournia, P., Croitoru, A., Ramodiharilafy, R, Lambry, J.-C., Myllykallio, H., Aleksandrov, A., Liebl, U. & Vos, M.H. (2021) Photochemical processes in flavo-enzymes as a probe for active site dynamics: TrmFO of Thermus thermophilus, Photochem. Photobiol. Sci., 20, 663-670

Sorigué, D., Hadjidemetriou, K., Blangy, S., Gotthard, G., Bonvalet, A., Coquelle, N., Samire, P., Aleksandrov, A., Antonucci, L., Benachir, A., Boutet, S., Byrdin, M., Cammarata, M., Carbajo, S., Cuiné, S., Doak, R.B., Foucar, L., Gorel, A., Grünbein, M., Hartmann, E., Hienerwadel, R., Hilpert, M., Kloos, M., Lane, T. J., Légeret,  B., Legrand, P., Li-Beisson, Y., Moulin, S., Nurizzo, D., Peltier, G., Schirò, G., Shoeman, R.L., Sliwa, M., Solinas, X., Zhuang, B., Barends, T.R.M., Colletier, J.-P., Joffre, M., Royant, A., Berthomieu, C., Weik, M., Domratcheva, T., Brettel, K., Vos, M.H., Schlichting, I., Arnoux, P., Müller, P. & Beisson, F. (2021) Mechanism and dynamics of fatty acid photodecarboxylase, Science 372, eabd5687

Pirisi, K., Nag, L., Fekete, Z., Iuliano, J.N., Tollentino Collado, J., Clark, I.P., Pécsi, I., Sournia, P., Liebl, U., Greetham, G.M., Tonge, P.J., Meech, S.R., Vos, M.H. & Lukacs, A. (2021) Identification of the vibrational marker of tyrosine cation radical using ultrafast transient infrared spectroscopy of flavoprotein systems, Photochem. Photobiol. Sci. 20, 369-378

Zhuang, B., Seo, D., Aleksandrov, A. & Vos, M.H. (2021) Characterization of Light-Induced Short-Lived Interacting Radicals in the Active Site of Flavoprotein Ferredoxin-NADP+ Oxidoreductase, J. Am. Chem. Soc. 143, 2457-2768

Vos, M.H., Salman, M., Ramodiharilafy, O. & Liebl, U. (2021) Fluorescent iron-sulfur centers: Photochemistry of the PetA Rieske protein from Aquifex aeolicus , Biochim. Biophys. Acta, 1862, 148385

Karadi, K., Kapetanaki, S.M., Raics, K., Pecsi, I., Kapronczai, R., Fekete, Z., Iuliano, J., Tolentino, J., Gil, A., Orban, J., Nyitrai, M., Greetham, G.M., Vos, M.H., Tonge, P.J., Meech, S.R. & Lukacs, A. (2020) Functional dynamics of a single tryptophan residue in a BLUF protein revealed by fluorescence spectroscopy, Sci. Rep. 10, 2061

Salman, M., Villamil Franco, C., Ramodiharilafy, O., Liebl, U. & Vos, M.H. (2019) Interaction of the full-length heme-based CO sensor protein RcoM-2 with ligands, Biochemistry 58, 4028-4034

Nag, L., Lukacs, A & Vos, M.H. (2019) Short-lived radical intermediates in the photochemistry of glucose oxidase, ChemPhysChem 20, 1793-1798

Kapetanaki, S.M., Burton, M.J., Basran, J., Uragami, C., Moody, P.C.E., Mitcheson, J.S., Schmid, R., Davies, N.W., Dorlet, P., Vos, M.H., Storey, N.M. & Raven, E.L. (2018) A mechanistic basis for understanding the interplay of heme and CO in ion channel regulation, Nature Comm. 9, 907 (correction Nature Comm. 9, 3354)

Nag, L., Sournia, P., Myllykallio, H., Liebl, U. & Vos, M.H. (2017) Identification of the TyrOH●+ radical cation in the flavoenzyme TrmFO, J. Am. Chem. Soc. 139, 11500-11505 (correction J. Am. Chem. Soc. 139, 15554)

Vos, M.H., Reeder, B.J., Daldal, F. & Liebl, U. (2017) Ultrafast photochemistry of the bc1 complex; Phys. Chem. Chem. Phys. 19, 6807-6813   (correction Phys. Chem. Chem. Phys. 19, 9320)

Brettel, K, Byrdin, M. & Vos, M.H. (2016) Ultrafast light-induced processes in DNA-photolyase and its substrate-bound complex in Ultrafast Dynamics at the Nanoscale: Biomolecules and Supramolecular Assemblies (Burghardt, I. &Haacke, S., Eds.) Pan Stanford, Singapore, pp. 65-90

Ferrante, C., Pontecorvo, E., Cerullo, G., Vos, M.H. & Scopigno, T. (2016) Direct observation of sub-picosecond vibrational dynamics in photoexcited myoglobin, Nature Chem. 8, 1137-1143

Bouzhir-Sima, L., Motterlini, R., Gross, J., Vos, M.H. &  Liebl, U. (2016) Unusual Dynamics of Ligand Binding to the Heme Domain of the Bacterial CO Sensor Protein RcoM-2, J. Phys. Chem. B 120, 10686-10694

Lambry, J.-C., Stranava, M., Lobato, L., Martinkova, M., Shimizu, T., Liebl, U. & Vos, M.H. (2016) Ultrafast spectroscopy evidence for picosecond ligand exchange at the binding site of a heme protein: heme-based sensor YddV, J. Phys. Chem. Lett. 7, 69-74

Fojtikova, V., Stranava, M., Vos, M.H., Liebl, U., Hranicek, J., Kitanishi, K., Shimizu, T. & Martinkova, M. (2015) Kinetic Analysis of a Globin-coupled Histidine Kinase, AfGcHK: Effects of the Heme Iron Complex, Response Regulator and Metal Cations on Autophosphorylation Activity, Biochemistry 54, 5017-5029

Vos, M.H. & Liebl, U. (2015) Time resolved infrared spectroscopic studies of ligand dynamics in the active site from cytochrome c oxidase, Biochim. Biophys. Acta 1847, 79-85

Lobato, L., Bouzhir-Sima, L., Yamashita, T., Wilson, M.T., Vos, M.H. & Liebl, U. (2014) Dynamics of the heme-binding bacterial gas sensing dissimilative nitrate respiration regulator (DNR) and activation barriers for ligand binding and escape, J. Biol. Chem. 289, 26514-26524

Becker, H.F., Djaout, K., Lamarre, I., Ulmer, J.E., Schaming, D., Balland, V., Liebl, U., Myllykallio, H. & Vos, M.H. (2014) Substrate interaction dynamics and oxygen control in the active site of thymidylate synthase ThyX, Biochem. J. 459, 37-45

Laptenok, S.P., Nuernberger, P., Lukacs, A. & Vos, M.H. (2014) Subpicosecond Kerr-gate spectrofluorometry in Methods in Molecular Biology, Fluorescence Spectroscopy and Microscopy: Methods and Protocols , vol. 1076 (Engelborghs, Y. & Visser, A.J.W.G., Eds.), Humana Press, New York, pp. 321-336

Liebl ,U., Lambry, J.-C. & Vos, M.H. (2013) Primary processes in heme-based sensor proteins, Biochim. Biophys. Acta 1834, 1684-1692

Laptenok, S.P., Bouzhir-Sima, L., Lambry, J.-C., Myllykallio, H., Liebl, U., & Vos, M.H. (2013) Ultrafast real time visualization of the active site flexibility of the flavoenzyme thymidylate synthase ThyX, Proc. Natl. Acad. Sci. USA 110, 8924-8929

Silkstone, G., Kapetanaki, S.M., Husu, I., Vos, M.H. & Wilson, M.T. (2012) Nitric oxide binding to the cardiolipin complex of ferric cytochrome c, Biochemistry 51, 6760-6766

Jasaitis, A., Ouellet, H., Lambry, J.-C., Martin, J.-L., Friedman, J.M., Guertin, M. & Vos, M.H. (2012) Ultrafast Heme-Ligand Recombination in Truncated Hemoglobin HbO from Mycobacterium tuberculosis: a Ligand Cage, Chem. Phys. 396, 10-16

Vos, M.H., Bouzhir-Sima, L., Lambry, J.-C., Luo, H., Eaton-Rye, J.J., Ioanoviciu, A., Ortiz de Montellano, P.R. & Liebl, U. (2012) Ultrafast ligand dynamics in the heme-based GAF sensor domains of the histidine kinases DevS and DosT from Mycobacterium tuberculosis, Biochemistry 51, 159-166

Nuernberger, P., Lee, K.F., Bonvalet, A, Bouzhir-Sima, L., Lambry, J.-C., Liebl, U., Joffre ,M. & Vos, M.H. (2011) Strong ligand-protein interactions revealed by ultrafast infrared spectroscopy of CO in the heme pocket of the oxygen sensor FixL, J. Am. Chem. Soc. 133, 17110 –17113

Kruglik, S.G., Lambry, J.-C., Martin, J.-L. Vos, M.H. & Négrerie, M. (2011) Sub-picosecond Raman spectrometer for time-resolved studies of structural dynamics in heme proteins, J. Raman Spectrosc. 42, 265-275

Groma, G.I., Colonna, A, Martin, J.-L. & Vos, M.H. (2011) Vibrational motions associated with primary processes in bacteriorhodopsin studied by coherent infrared emission spectroscopy, Biophys. J. 100, 1578-1586

Kruglik, S.G., Yoo, B.-K., Franzen, S., Vos, M.H., Martin, J.-L. & Négrerie, M. (2010) Picosecond primary structural transition of the heme retarded after nitric oxide binding to heme proteins, Proc. Natl. Acad. Sci. USA, 107, 13678-13683

Nuernberger, P., Lee, K.F., Bonvalet, A, Vos, M.H. & Joffre, M. (2010) Multiply excited vibration of carbon monoxide in the primary docking site of hemoglobin following photolysis from the heme, J. Phys. Chem. Lett. 1, 2077-2081

Rappaport, F., Zhang, J., Vos, M.H., Gennis, R.B., & Borisov, V.B. (2010) Heme-heme and heme-ligand interactions in the di-heme oxygen-reducing site of cytochrome bd from Escherichia coli revealed by nanosecond absorption spectroscopy, Biochim. Biophys. Acta 1797, 1657-1664

Silkstone, G., Kapetanaki, S.M., Husu, I., Vos, M.H. & Wilson, M.T. (2010) Nitric Oxide binds to the proximal heme coordination site of the ferrocytochrome c / cardiolipin complex: formation mechanism and dynamics, J. Biol. Chem. 285, 19785-19792

Byrdin, M., Lukacs, A., Eker, A.P.M., Thiagarajan, V., Brettel, K. & Vos, M.H. (2010) Quantum yield measurements of short-lived photoactivation intermediates in DNA photolyase: towards a detailed understanding of the triple tryptophan electron transfer chain, J. Phys. Chem. A, 114, 3207-3214