Publications | Protein Chemistry

Universiteit Leiden

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2012

Ubbink, M. , Dynamics in transient complexes of redox proteins, Biochem. Soc. Trans.

Keizers, P.H.J., Hiruma, Y., Ubbink, M. , Protein-Paramagnetic Protein Interactions, NMR of Biomolecules.Towards Mechanistic Systems Biology: Wiley-Blackwell, pp. 204-217.

Lindfors, H.E., Drijfhout, J.W., Ubbink, M. , The Src SH2 domain interacts dynamically with the focal adhesion kinase binding site as demonstrated by paramagnetic NMR spectroscopy, IUBMB Life.

Scanu, S., Förster, J., Finiguerra, M.G., Shabestari, M.H., Huber, M., Ubbink, M. , The complex of cytochrome f and plastocyaninfrom Nostoc sp. PCC 7119 is highly dynamic, ChemBioChem.

2011

de Groote, F.H., Jansen, J.G., Masuda, Y., Shah, D.M., Kamiya, K., de Wind, N., Siegal, G. , The Rev1 translesion synthesis polymerase has multiple distinct DNA binding modes, DNA Repair, vol. 10, no. 9, pp. 915-925.

Meschi, F., Wiertz, F., Klauss, L., Blok, A., Ludwig, B., Merli, A., Heering, H.A., Rossi, G.L., Ubbink, M. , Efficient Electron Transfer in a Protein Network Lacking Specific Interactions, Journal of the American Chemical Society, vol. 133, no. 42, pp. 16861-16867.

Farenc, C., Celie, P.H.N., Tensen, C.P., de Esch, I.J.P., Siegal, G. , Crystal structure of the EphA4 protein tyrosine kinase domain in the apo- and dasatinib-bound state, Febs Letters, vol. 585, no. 22, pp. 3593-3599.

Dasgupta, S., Hu, X.Y., Keizers, P.H.J., Liu, W.M., Luchinat, C., Nagulapalli, M., Overhand, M., Parigi, G., Sgheri, L., Ubbink, M. , Narrowing the conformational space sampled by two-domain proteins with paramagnetic probes in both domains, Journal of Biomolecular Nmr, vol. 51, no. 3, pp. 253-263.

Bashir, Q., Scanu, S., Ubbink, M. , Dynamics in electron transfer protein complexes, Febs Journal, vol. 278, no. 9, pp. 1391-1400.

Alagaratnam, S., Meeuwenoord, N.J., Navarro, J.A., Hervas, M., De la Rosa, M.A., Hoffmann, M., Einsle, O., Ubbink, M., Canters, G.W. , Probing the reactivity of different forms of azurin by flavin photoreduction, Febs Journal, vol. 278, no. 9, pp. 1506-1521.

De Wael, K., Bashir, Q., Van Vlierberghe, S., Dubruel, P., Heering, H.A., Adriaens, A. , Electrochemical determination of hydrogen peroxide with cytochrome c peroxidase and horse heart cytochrome c entrapped in a gelatin hydrogel, Bioelectrochemistry, vol. 83, pp. 15-18.

Fruh, V., Ijzerman, A.P., Siegal, G. , How to Catch a Membrane Protein in Action: A Review of Functional Membrane Protein Immobilization Strategies and Their Applications, Chemical Reviews, vol. 111, no. 2, pp. 640-656.

Lindfors, H.E., Venkata, B.S., Drijfhout, J.W., Ubbink, M. , Linker length dependent binding of a focal adhesion kinase derived peptide to the Src SH3-SH2 domains, Febs Letters, vol. 585, no. 4, pp. 601-605.

Keizers, P.M., Ubbink, M. , Paramagnetic tagging for protein structure and dynamics analysis, Progress in Nuclear Magnetic Resonance Spectroscopy, vol. 58, no. 1-2, pp. 88-96.

Volkov, A.N., Barrios, H., Mathonet, P., Evrard, C., Ubbink, M., Declercq, J.P., Soumillion, P., Fastrez, J. , Engineering an Allosteric Binding Site for Aminoglycosides into TEM1-beta-Lactamase, Chembiochem, vol. 12, no. 6, pp. 904-913.

Congreve, M., Rich, R.L., Myszka, D.G., Figaroa, F., Siegal, G., Marshall, F.H. , Fragment screening of stabilized 6-protein-coupled receptors using biophysical methods, Fragment-Based Drug Design: Tools, Practical Approaches, and Examples, vol. 493, pp. 115-136.

Singh, P.S., Goluch, E.D., Heering, H.A., Lemay, S.G. , Nanoelectrochemistry: Fundamentals and Applications to Biology., Applications of Electrochemistry and Nanotechnology in Biology and Medicine part II, vol. 53: Springer.

Keizers, P.H.J., Ubbink, M. , Paramagnetic tools in protein NMR, Protein NMR spectroscopy: Practical Techniques and applications: Wiley, Chichester, pp. 193-220.

2010

Xu, X.F., Scanu, S., Chung, J.S., Hirasawa, M., Knaff, D.B., Ubbink, M. , Structural and Functional Characterization of the Ga-Substituted Ferredoxin from Synechocystis sp PCC6803, a Mimic of the Native Protein, Biochemistry, vol. 49, no. 36, pp. 7790-7797.

Kobayashi, M., Retra, K., Figaroa, F., Hollander, J.G., Ab, E., Heetebrij, R.J., Irth, H., Siegal, G. , Target Immobilization as a Strategy for NMR-Based Fragment Screening: Comparison of TINS, STD, and SPR for Fragment Hit Identification, Journal of Biomolecular Screening, vol. 15, no. 8, pp. 978-989.

Meschi, F., Wiertz, F., Klauss, L., Cavalieri, C., Blok, A., Ludwig, B., Heering, H.A., Merli, A., Rossi, G.L., Ubbink, M. , Amicyanin Transfers Electrons from Methylamine Dehydrogenase to Cytochrome c-551i via a Ping-Pong Mechanism, not a Ternary Complex, Journal of the American Chemical Society, vol. 132, no. 41, pp. 14537-14545.

Overmeer, R.M., Gourdin, A.M., Giglia-Mari, A., Kool, H., Houtsmuller, A.B., Siegal, G., Fousteri, M. I, Mullenders, L.H.F., Vermeulen, W. , Replication Factor C Recruits DNA Polymerase delta to Sites of Nucleotide Excision Repair but Is Not Required for PCNA Recruitment, Molecular and Cellular Biology, vol. 30, no. 20, pp. 4828-4839.

Kobayashi, M., Eiso, A.B., Bonvin, A., Siegal, G. , Structure of the DNA-bound BRCA1 C-terminal Region from Human Replication Factor C p140 and Model of the Protein-DNA Complex, Journal of Biological Chemistry, vol. 285, no. 13, pp. 10087-10097.

Hass, M.A.S., Keizers, P.H.J., Blok, A., Hiruma, Y., Ubbink, M. , Validation of a Lanthanide Tag for the Analysis of Protein Dynamics by Paramagnetic NMR Spectroscopy, Journal of the American Chemical Society, vol. 132, no. 29, pp. 9952-9953.

Bashir, Q., Volkov, A.N., Ullmann, G.M., Ubbink, M. , Visualization of the Encounter Ensemble of the Transient Electron Transfer Complex of Cytochrome c and Cytochrome c Peroxidase, Journal of the American Chemical Society, vol. 132, no. 1, pp. 241-247.

Protein Chemistry