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Functional dynamics of proteins

 

Staff scientists:

 

PhD Students/ Post-doctoral fellows

Bo Zhuang (PhD student)

Description of topic:


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. Many projects concern a variety of heme proteins, where ultrafast ligand photodissociation is used as an impulsive trigger of the system, corresponding to a step of protein functioning. In other 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. Our efforts to get detailed insight in the dynamics on a molecular level include combining experimental studies and molecular dynamics simulations.

Present projects include the dynamics of new classes of CO-sensor heme proteins, and configurational dynamics of the flexible active sites of the flavoenzyme ThyX. Both projects are performed in close collaboration with the pole Adaptive molecular mechanisms in microbial systems (U. Liebl, H. Myllykallio).

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 polytechnique.edu

 

 

                                                                        

Evidence for extremely rapid exchange between NO and H2O as heme ligands in the bacterial sensor protein YddV using transient absorption spectroscopy and MD simulations. See Lambry, et al. (2016)  J. Phys. Chem. Lett. 7, 69-74

 

 

                                                                                   

Dynamic characterization of the highly flexible active site of the flavoenzyme ThyX by time-resolved fluorescence spectroscopy using quenching of FAD fluorescence by electron transfer from Tyr91 as a probe. See Laptenok, et al. (2013)  Proc. Natl. Acad. Sci. USA 110, 8924-8929

 

 

 

 

 

Selected recent publications :


 

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

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

Lechauve, C., Bouzhir-Sima, L., Yamashita, T., Marden, M.C., Vos, M.H., Liebl, U & Kiger, L. (2009) Heme-Ligand Binding Properties and Intradimer Interactions in the Ful- Length Sensor Protein Dos from Escherichia coli and Its Isolated Heme Domain, J. Biol. Chem., 284, 36146-36159

Kapetanaki, S.M., Silkstone, G., Husu, I., Liebl, U., Wilson, M.T. & Vos, M.H. (2009) Interaction of carbon monoxide with the apoptosis-inducing cytochrome c-cardiolipin complex, Biochemistry 48, 1613-1619

Lukacs, A., Eker, A.P.M., Byrdin, M., Brettel, K. & Vos, M.H. (2008) Electron hopping through the 15 Å triple tryptophan molecular wire in DNA photolyase occurs within 30 ps, J. Am. Chem. Soc. 130, 14394-14395

Kapetanaki, S.M., Field, S.J., Hughes, R.J.L., Watmough, N.J., Liebl, U. & Vos, M.H. (2008) Ultrafast ligand binding dynamics in the active site of native bacterial nitric oxide reductase, Biochim. Biophys. Acta 1777, 919-924

Vos, M.H., Battistoni, A., Lechauve, C., Marden, M.C., Kiger, L., Desbois, A., Pilet, E., de Rosny, E. & Liebl, U. (2008) Ultrafast heme-residue bond formation in six-coordinate heme proteins: implications for functional ligand exchange, Biochemistry 47, 5718-5724

Yamashita, T., Bouzhir-Sima, L., Lambry, J.-C., Liebl, U. & Vos, M.H. (2008) Ligand dynamics and early signalling events in the heme domain of the sensor protein Dos from Escherichia coli, J. Biol. Chem. 283, 2344-2352

Vos, M.H. (2008) Ultrafast dynamics of ligands within heme proteins, Biochim. Biophys. Acta 1777, 15-31