Marcellus Ubbink
Scientific Director / Professor of Protein chemistry
- Name
- Prof.dr. M. Ubbink
- Telephone
- +31 71 527 4628
- m.ubbink@chem.leidenuniv.nl
- ORCID iD
- 0000-0002-2615-6914
Marcellus Ubbink studies the relation between evolution, structure, dynamics and function of enzymes, with a particular interest in beta-lactamases. He uses a range of biophysical techniques for this purpose.
More information about Marcellus Ubbink
PhD Candidates
News
-
Grants for fundamental research in Leiden -
Antwerp Honorary Doctorate for Marc Koper: Significant recognition for sustainable energy research -
Ten lecturers obtain Senior Teaching Qualification -
‘It’s important that people are happy in their work’ -
Marcellus Ubbink new Scientific Director of the LIC institute -
Leiden researchers join forces against tuberculosis -
Magic Angle Spinning NMR structure determination in magnetic environments on the cover of SSNMR -
Paradigm-shifting theory highlights the importance of substrate flexibility in enzymatic reactions -
Minute molecular movements might lead to more efficient biofuel cells -
17.9 million euro for national NMR Roadmap consortium -
Marcellus Ubbink receives grant for research into evolution of enzymes -
How our single-celled relatives package their DNA -
A cobalt cage for proteins -
Marcellus Ubbink in Leidsch Dagblad: "Nanodisk biedt kans op beter griepvaccin" -
Changing enzymes for clean energy and disease prevention -
Research shows protein movement is important
-
Substantial investment in Leiden centre for NMR spectroscopy
Teaching
Former PhD candidates
-
Ilona van Alen -
Aleksandra Chikunova
-
Fatema Rashid
-
Rubin Dasgupta
-
Soumya Chatterjee
-
Antonella Di Savino
-
Lian Qing
-
Heyi Zhang
-
Qing Miao
-
Wouter Elings
-
Rafaella Tassoni
-
Mathilde Lescanne
-
Fredj Ben Bdira
-
Ramon van der Valk
-
Jesika Schilder
-
Dan Chen
-
Dipen Shah
-
Yoshitaka Hiruma
-
Wei-Min Liu
-
Sandra Scanu
-
Simon Skinner
-
Jia-Ying Guan
-
Carine Farenc
-
Bharat Somireddy Venkata
-
Michelina Finiguerra
-
Qamar Bashir
Curriculum Vitae
Personal information
Nationality: Dutch
Year of birth: 1965
Education
1994 PhD, Leiden Institute of Chemistry, Leiden University, The Netherlands, 19 May 1994 (cum laude)
Thesis title: ‘Cytochrome c-550 and the MADH redox chain from Thiobacillus versutus’
Advisor: Prof. Dr. G.W. Canters
1989 MSc in Biology, Faculty of Biology, Utrecht University, The Netherlands (cum laude)
Current and previous research positions
2022 – now Scientific Director of the Leiden Institute of Chemistry
2019 – 2022 Director of Studies of the Leiden/Delft Bachelor Life Science and Technology
2010 – now Full professor in Protein Chemistry, Leiden, Institute of Chemistry, Leiden University
2004 – 2010 Associate Professor, Leiden Institute of Chemistry, Leiden University, The Netherlands
1997 – 2003 Assistant Professor, Leiden Institute of Chemistry, Leiden University,
1994 – 1997 Postdoctoral Research Associate at Dept. Biochemistry, Cambridge University (UK)
1994 Postdoctoral project (six months) at the laboratories of Dr. A. Pastore (EMBL, Heidelberg, Germany) and Dr. J. van der Oost (VU University, Amsterdam, The Netherlands)
Grants, awards, recognitions since 2012
2020 ENW-Klein grant (k€ 341)
2018 TTW Open technology grant (k€ 800)
2017 NWO-CW ECHO grant (k€ 260)
2016 NWO-CW ECHO grant (k€ 260)
2014 NWO-CW KIEM project (k€ 19)
2013 NWO-CW ECHO grant (k€ 260)
2013 NWO NMARRS Graduate School programme with H.J.M. de Groot (k€ 200)
2012 NWO Groot for Paramagnetic NMR Facility (k€ 2,163)
2012 EU Marie Curie ITN “paramagnetic NMR (pNMR)”, (co-applicant k€ 244)
2012 ESF funding International Conference on Molecular Aspects of Protein-Protein Interactions (k€ 30)
2012 Co-applicant of the grant for an ultra-high field NMR facility for the Netherlands (uNMR-NL) from the National Roadmap Program for Large Research Infrastructures (k€ 18,500)
Contribution to teaching and supervision
Current: Undergraduate course Biochemistry 1 for 1st years students Life Science and Technology. Graduate course Enzyme Dynamics. Bachelor course Anthropocene in the minor Sustainable Chemistry and Biotechnology (with Dr. Hetterscheid).
Supervision as promotor: 28 PhD students (2010-2023), as co-promotor: 10 PhD students (1998-2010).
Other responsibilities since 2010
- Editorial Board member for Emerging Topics in Life Sciences (since 2016)
- Secretary of the Netherlands Society for Biochemistry and Molecular Biology (NVBMB, 2008-2012)
- Board member of the Netherlands Magnetic Resonance Research School (since 2015)
- Member, Secretary and Chair of the board of the NWO Proteins Study Group (2013-2015)
- Chair of the organising committee for the Lorentz Workshop ‘Proteins and Beyond’, Leiden (2014)
- Member of the scientific committee of the 2nd and 3rd International Conference on Molecular Aspects of Protein-Protein Interactions (2007, 2010)
- Chair of the 4th IC on Molecular Aspects of Protein-Protein Interactions, Poland (2012)
- Chair of the ESF-EMAR workshop “Paramagnetic tagging in NMR”, Spain (2010)
- Member of the organising committee of the FEBS workshops Trends in Transient Interactions between Biological Macromolecules (2005, 2007, 2010)
- Representative of the Faculty in the Program Board of the Medical Delta Organisation (2012-2016)
- Organiser of the Annual Institute’s Research Symposium (with Prof. Koper, since 2011)
- Member (2010-2013) and chair (2014-2016) C.J. Kok committee to select best Science thesis within the Faculty
- Member of the Faculty Council (2011-2019)
Publication record including five recent representative publications
Ca. 160 papers with >5000 citations, H-index 43 (Google Scholar)
Full publication record: ResearcherID, or Leiden University
Scientific Director / Professor of Protein chemistry
- Science
- Leiden Institute of Chemistry
- Sun J., Boyle A.L., Brünle S. & Ubbink M. (2024), A low-barrier proton shared between two aspartates acts as a conformational switch that changes the substrate specificity of the β-lactamase BlaC, International Journal of Biological Macromolecules 278: 134665.
- Knetsch T.G.J. & Ubbink M. (2024), Lipid composition affects the thermal stability of cytochrome P450 3A4 in nanodiscs, Biochimica et Biophysica Acta (BBA) - Biomembranes 1866(7): 184372.
- Saberi M., Chikunova A., Ben Bdira F., Cramer‐Blok A., Timmer M., Voskamp P. & Ubbink M. (2024), Bimodal substrate binding in the active site of the glycosidase BcX, FEBS Journal 291(19): 4222-4239.
- Chikunova A., Manley M.P., Heijjer C.N., Drenth C.S., Cramer‐Blok A.J., Ahmad M. Ud Din, Perrakis A. & Ubbink M. (2024), Conserved proline residues prevent dimerization and aggregation in the β‐lactamase BlaC, Protein Science 33(4): e4972.
- Miao Q., Dekkers M.W.A., Sai Sankar Gupta K.B., Overhand M., Dasgupta R. & Ubbink M. (2023), Rigidified and Hydrophilic DOTA-like Lanthanoid Ligands: Design, Synthesis, and Dynamic Properties, Inorganic Chemistry 62(9): 3776–3787.
- Sun J., Chikunova A., Boyle A.L., Voskamp P., Timmer M. & Ubbink M. (2023), Enhanced activity against a third-generation cephalosporin by destabilization of the active site of a class A beta-lactamase, International Journal of Biological Macromolecules 250: 126160.
- Alen I. van, Aguirre García M.A., Maaskant J.J, Kuijl C.P., Bitter W., Meijer A.H. & Ubbink M. (2023), Mycobacterium tuberculosis β-lactamase variant reduces sensitivity to ampicillin/avibactam in a zebrafish-Mycobacterium marinum model of tuberculosis, Scientific Reports 13: 15406.
- Alen I. van, Chikunova A., Zanten D.B. van, Block A.A. de, Timmer M., Brünle S. & Ubbink M. (2023), Asp179 in the class A β‐lactamase from Mycobacterium tuberculosis is a conserved yet not essential residue due to epistasis, FEBS Journal 290: 4933-4949.
- Knetsch T.G.J. & Ubbink M. (2023), The effect of lipid composition on the thermal stability of nanodiscs, Biochimica et Biophysica Acta (BBA) - Biomembranes 1866(1): 184239.
- Miao Q., Nitsche C., Orton H., Overhand M., Otting G. & Ubbink M. (2022), Paramagnetic chemical probes for studying biological macromolecules, Chemical Reviews 122(10): 9571-9642.
- Chikunova A. & Ubbink M. (2022), The roles of highly conserved, non‐catalytic residues in class A β‐lactamases, Protein Science 31(6): e4328.
- Dasgupta R., Sai Sankar Gupta K.B., Groot H.J.M. de & Ubbink M. (2021), Towards resolving the complex paramagnetic (NMR) spectrum of small laccase: assignments of resonances to residue specific nuclei, Magnetic Resonance 2(1): 15-23.
- Marneth K., Elst H. van den, Cramer-Blok A.J., Codee J.D.C., Overkleeft H.S., Aerts J.M.F.G., Ubbink M. & Ben Bdira F. (2021), Tuning the transglycosylation reaction of a GH11 xylanase by a delicate enhancement of its thumb flexibility, ChemBioChem 22(10): 1743-1749.
- Dasgupta R., Sai Sankar Gupta K.B., Groot H.J.M. de & Ubbink M. (2021), The resting oxidized state of small laccase analyzed with paramagnetic NMR spectroscopy, ChemPlusChem 22(8): 733-740.
- Dasgupta R., Sai Sankar Gupta K.B., Elam D., Ubbink M. & Groot H.J.M. de (2021), Dipolar dephasing for structure determination in a strongly paramagnetic environment, Solid State Nuclear Magnetic Resonance 113: 101728.
- Chatterjee S.D. Zhou J. Dasgupta R. Cramer-Blok A.J. Timmer M. Stelt M. van der Ubbink M. (2021), Protein dynamics influence the enzymatic activity of phospholipase a/acyltransferases 3 and 4, Biochemistry 60(15): 1178-1190.
- Di Savino A., Foerster J.M., Ullmann G.M. & Ubbink M. (2021), Enhancing the population of the encounter complex affects protein complex formation efficiency, FEBS Journal 289(2): 535-548.
- Skinner S.P., Follmer A.H., Ubbink M., Poulos T.L., Houwing-Duistermaat J.J. & Paci E. (2021), Partial opening of cytochrome P450cam (CYP101A1) is driven by allostery and putidaredoxin binding, Biochemistry 60(39): 2932-2942.
- Elings W., Chikunova A., Zanten D.B. van, Drenth R., Ahmad M.U.D., Blok A.J., Timmer M., Perrakis A. & Ubbink M. (2021), Two β-lactamase variants with reduced clavulanic acid inhibition display different millisecond dynamics, Antimicrobial Agents and Chemotherapy 65(8): e02628-20.
- Alen I. van, Chikunova A., Safeer A.A., Ahmad M.U.D., Perrakis A. & Ubbink M. (2021), The G132S mutation enhances the resistance of mycobacterium tuberculosis β-lactamase against sulbactam, Biochemistry 60(28): 2236-2245.
- Chikunova A., Manley M.P., Ahmad M.U.D., Bilman T., Perrakis A. & Ubbink M. (2021), Conserved residues Glu37 and Trp229 play an essential role in protein folding of β‐lactamase, FEBS Journal 288(19): 5708-5722.
- Di Savino A., Foerster J.M., Ullmann G.M. & Ubbink M. (2021), The charge distribution on a protein surface determines whether productive or futile encounter complexes are formed, Biochemistry 60(10): 747-755.
- Ben Bdira F., Erkelens A.M., Qin L., Volkov A.N., Lippa A.M., Bowring N., Boyle A.L., Ubbink M., Dove S.L. & Dame R.T. (2021), Novel anti-repression mechanism of H-NS proteins by a phage protein, Nucleic Acids Research 49(18): 10770-10784.
- Qin L., Ben Bdira F., Sterckx Y.G.J., Volkov A.N., Vreede J., Giachin G., Schaik P., Ubbink M. & Dame R.T. (2020), Structural basis for osmotic regulation of the DNA binding properties of H-NS proteins, Nucleic Acids Research 48(4): 2156-2172.
- Dasgupta R., Sai Sankar Gupta K.B., Nami F., Groot H.J.M. de, Canters G.W., Groenen E.J.J. & Ubbink M. (2020), Chemical exchange at the tri-nuclear copper centre of small laccase from Streptomyces coelicolor, Biophysical Journal 119(1): 9-14.
- Ubbink M., Ben Bdira F, Waudby C.A., Volkov A.N., Schröder S.P., Ab E., Codée J.D.C., Overkleeft H.S., Aerts J.M.F.G. & Ingen H. van (2020), Dynamics of ligand binding to a rigid glycosidase, Angewandte Chemie (International Edition) 59(46): 20508-20514.
- ElingsW., Gaur A., Blok A.J., Timmer M., Ingen H. van & Ubbink M. (2020), β-Lactamase of mycobacterium tuberculosis shows dynamics in the active site that increase upon inhibitor binding, Antimicrobial Agents and Chemotherapy 64(3): e02025-19.
- Son M. van, Schilder J.T., Di Savino A., Blok A.J., Ubbink M. & Huber M.I. (2020), The transient complex of cytochrome c and cytochrome c peroxidase: insights into the encounter complex from multifrequency EPR and NMR spectroscopy, ChemPhysChem 21(10): 1060-1069.
- Miao Q., Zurlo E., Bruin D. de, Wondergem A.J., Timmer M., Blok A.J., Heinrich D.M., Overhand M., Huber M.I. & Ubbink M. (2020), A two‐armed probe for in‐cell DEER measurements on proteins, Chemistry: a European Journal 26(71): 17128-17133.
- Miao Q., Liu W.-M., Kock T., Blok A.J., Timmer M., Overhand M. & Ubbink M. (2019), A double-armed, hydrophilic transition metal complex as paramagnetic NMR probe, Angewandte Chemie (International Edition) 58(37): 13093-13100.
- Tassoni R., Blok A.J., Pannu N.S. & Ubbink M. (2019), New Conformations of Acylation Adducts of Inhibitors of beta-Lactamase from Mycobacterium tuberculosis, Biochemistry 58(7): 997-1009.
- Ben Bdira F., Artola Perez de Azana M.E., Overkleeft H.S., Ubbink M. & Aerts J.M.F.G. (2018), Distinguishing the differences in beta-glycosylceramidase folds, dynamics, and actions informs therapeutic uses, Journal of Lipids 59(12): 2262-2276.
- Lescanne M., Ahuja P., Blok A., Timmer M., Akerud T. & Ubbink M. (2018), Methyl group reorientation under ligand binding probed by pseudocontact shift, Journal of Biomolecular NMR 71: 275-285.
- Chatterjee S.D., Ubbink M. & Ingen H. van (2018), Removal of slow-pulsing artifacts in in-phase N-15 relaxation dispersion experiments using broadband H-1 decoupling, Journal of Biomolecular NMR 71(2): 69-77.
- Di Savino A. & Ubbink M. (2018), Protein-protein interactions. In: Luchinat C., Parigi G. & Ravera E. (Eds.), Paramagnetism in Experimental Biomolecular NMR. New Developments in NMR no. 16: Royal Society of Chemistry. 134-162.
- Andralojc W., Hiruma Y., Liu W.M., Ravera E., Nojiri M., Parigi G., Luchinat C. & Ubbink M. (2017), Identification of productive and futile encounters in an electron transfer protein complex, Proceedings of the National Academy of Sciences 114(10): E1840-E1847.
- Ben Bdira F., Kallemeijn W.W., Oussoren S.V., Scheij S., Bleijlevens B., Florea B.I., Roomen C.P.A.A. van, Ottenhoff R., Kooten M.J.F.M. van, Walvoort M.T.C., Witte M.D., Boot R.G., Ubbink M., Overkleeft H.S. & Aerts J.M.F.G. (2017), Stabilization of Glucocerebrosidase by Active Site Occupancy, ACS Chemical Biology 12(7): 1830-1841.
- Tassoni R., Aart L.T. van der, Ubbink M., Wezel G.P. van & Pannu N.S. (2017), Structural and functional characterization of the alanine racemase from Streptomyces coelicolor A3(2), Biochemical and Biophysical Research Communications 483(1): 122-128.
- Elings W., Tassoni R., Schoot S.A. van der, Luu W., Kynast J.P., Dai L., Blok A.J., Timmer M., Florea B.I., Pannu N.S. & Ubbink M. (2017), Phosphate Promotes the Recovery of Mycobacterium tuberculosis beta-Lactamase from Clavulanic Acid Inhibition, Biochemistry 56(47): 6257-6267.
- Lescanne M., Skinner S.P., Blok A., Timmer M., Cerofolini L., Fragai M., Luchinat C. & Ubbink M. (2017), Methyl group assignment using pseudocontact shifts with PARAssign, Journal of Biomolecular NMR 69(4): 183-195.
- Venkata B.S., Keizers P.H.J., Drijfhout J.W. & Ubbink M. (2016), A Focal Adhesion Kinase-Derived Peptide Binds the Src SH3 Domain in Two Orientations, As Demonstrated Using Paramagnetic Nuclear Magnetic Resonance, Biochemistry 55(1): 29-37.
- Schilder J., Liu W.M., Kumar P., Overhand M., Huber M.I. & Ubbink M. (2016), Protein docking using an ensemble of spin labels optimized by intra-molecular paramagnetic relaxation enhancement, Physical Chemistry Chemical Physics 18(8): 5729-5742.
- Ben Bdira F., Jiang J., Kallemeijn W.W., Haan A. de, Florea B.I., Bleijlevens B., Boot R.G., Overkleeft H.S., Aerts J.M.F.G. & Ubbink M. (2016), Hydrophobic interactions contribute to conformational stabilization of endoglycoceramidase II by mechanism-based probes, Biochemistry 55(34): 4823-4835.
- Schilder J. & Ubbink M. (2016), Weak self-association of cytochrome c peroxidase molecules observed by paramagnetic NMR, Journal of Biomolecular NMR 65(1): 29-40.
- Schilder J., Liu W.M., Kumar P., Overhand M., Huber M.I. & Ubbink M. (2016), Protein docking using an ensemble of spin labels optimized by intra-molecular paramagnetic relaxation enhancement, Physical Chemistry Chemical Physics 18(8): 5729-5742.
- Camacho-Zarco A.R., Munari F., Wegstroth M., Liu W.M., Ubbink M., Becker S. & Zweckstetter M. (2015), Multiple Paramagnetic Effects through a Tagged Reporter Protein, Angewandte Chemie (International Edition) 54(1): 336-339.
- Skinner S.P., Liu W.M., Hiruma Y., Timmer M., Blok A., Hass M.A.S. & Ubbink M. (2015), Delicate conformational balance of the redox enzyme cytochrome P450cam, Proceedings of the National Academy of Sciences 112(29): 9022-9027.
- Hiruma Y., Sacristan C., Pachis S.T., Adamopoulos A., Kuijt T., Ubbink M., Castelmur E. von der, Perrakis A. & Kops G.J.P.L. (2015), Competition between MPS1 and microtubules at kinetochores regulates spindle checkpoint signaling, Science 348(6240): 1264-1267.
- Hass M.A.S., Liu W.-M., Agafonov R.V., Otten R., Phung L.A., Schilder J.T., Kern D. & Ubbink M. (2015), A minor conformation of a lanthanide tag on adenylate kinase characterized by paramagnetic relaxation dispersion NMR spectroscopy, Journal of Biomolecular NMR 61(2): 123-136.
- Howe C.J., Rich P.R. & Ubbink M. (2015), Derek Bendall (1930-2014), Photosynthesis Research 124(3): 249-252.
- Hiruma Y., Gupta A., Kloosterman A., Olijve C., Ölmez B., Hass S.A.M. & Ubbink M. (2014), Hot spot Residues in the Cytochrome P450cam-Putidaredoxin Binding Interface, ChemBioChem 15(1): 80-86.
- Schilder J., Loehr F., Schwalbe H. & Ubbink M. (2014), The cytochrome c peroxidase and cytochrome c encounter complex: The other side of the story, FEBS Letters 588(10): 1873-1878.
- Bashir Q., Meulenbroek E.M., Pannu N.S. & Ubbink M. (2014), Engineering specificity in a dynamic protein complex with a single conserved mutation, FEBS Journal 281(21): 4892-4905.
- Liu W.M., Skinner S.P., Timmer M., Blok A., Hass M.A.S., Filippov D.V., Overhand M. & Ubbink M. (2014), A Two-Armed Lanthanoid-Chelating Paramagnetic NMR Probe Linked to Proteins via Thioether Linkages, Chemistry: a European Journal 20(21): 6256-6258.
- Liu W.M., Overhand M. & Ubbink M. (2014), The application of paramagnetic lanthanoid ions in NMR spectroscopy on proteins, Coordination Chemistry Reviews 273: 2-12.
- Guan Jia-Ying, Foerster Johannes M., Drijfhout Jan W., Timmer Monika, Blok Anneloes, Ullmann G. Matthias & Ubbink Marcellus (2014), An Ensemble of Rapidly Interconverting Orientations in Electrostatic Protein-Peptide Complexes Characterized by NMR Spectroscopy, ChemBioChem 15(4): 556-566.
- Díaz-Moreno I., Hulsker R., Skubak P., Foerster J.M., Cavazzini D., Finiguerra M.G., Díaz-Quintana A., Moreno-Beltrán B., Rossi G.-L., Ullmann G.M., Pannu N.S., De la Rosa M.A. & Ubbink M. (2014), The dynamic complex of cytochrome c6 and cytochrome f studied with paramagnetic NMR spectroscopy, Biochimica et Biophysica Acta (BBA) - Bioenergetics 1837(8): 1305-1315.
- Hass M.A.S. & Ubbink M. (2014), Structure determination of protein-protein complexes with long-range anisotropic paramagnetic NMR restraints, Current Opinion in Structural Biology 24: 45-53.
- Hervas M., Bashir Q., Leferink N.G.H., Ferreira P., Moreno-Beltran B., Westphal A.H., Diaz-Moreno I., Medina M., Rosa M.A. de la, Ubbink M., Navarro J.A. & Berkel W.J.H. van (2013), Communication between L-galactono-1,4-lactone dehydrogenase and cytochrome c, FEBS Journal 280(8): 1830-1840.
- Schilder J. & Ubbink M. (2013), Formation of transient protein complexes, Current Opinion in Structural Biology 23(6): 911-918.
- Skinner S.P., Moshev M., Hass M.A.S. & Ubbink M. (2013), PARAssign-paramagnetic NMR assignments of protein nuclei on the basis of pseudocontact shifts, Journal of Biomolecular NMR 55(4): 379-389.
- Scanu S., Foerster J.M., Ullmann G.M. & Ubbink M. (2013), Role of Hydrophobic Interactions in the Encounter Complex Formation of the Plastocyanin and Cytochrome f Complex Revealed by Paramagnetic NMR Spectroscopy, Journal of the American Chemical Society 135(20): 7681-7692.
- Guan J.Y., Keizers P.H.J., Liu W.M., Loehr F., Skinner S.P., Heeneman E.A., Schwalbe H., Ubbink M. & Siegal G. (2013), Small-molecule binding sites on proteins established by paramagnetic NMR spectroscopy, Journal of the American Chemical Society 135(15): 5859-5868.
- Hiruma Y., Hass M.A.S., Kikui Y., Liu W.M., Olmez B., Skinner S.P., Blok A., Kloosterman A., Koteishi H., Loehr F., Schwalbe H., Nojiri M. & Ubbink M. (2013), The Structure of the Cytochrome P450cam-Putidaredoxin Complex Determined by Paramagnetic NMR Spectroscopy and Crystallography, Journal of Molecular Biology/JMB Online 425(22): 4353-4365.
- Scanu S., Foerster J.M., Timmer M., Ullmann G.M. & Ubbink M. (2013), Loss of electrostatic interactions causes increase of dynamics within the plastocyanin-cytochrome f complex, Biochemistry 52: 6615-6626.
- Schilder J.T., Hass M.A.S., Keizers P.H.J. & Ubbink M. (2012), Paramagnetic NMR Spectroscopy and Lowly Populated States. In: Clore M. & Potts J. (Eds.), Recent Developments in Biomolecular NMR. RSC Biomolecular Sciences: The Royal Society of Chemistry. 130-150.
- Keizers P.H.J., Hiruma Y. & Ubbink M. (2012), Protein-Paramagnetic Protein Interactions. In: Bertini I., McGreevy K.S. & Parigi G. (Eds.), NMR of Biomolecules.Towards Mechanistic Systems Biology: Wiley-Blackwell. 204-217.
- Ubbink M. (2012), Dynamics in transient complexes of redox proteins, Biochemical Society Transactions 40: 415-418.
- Lindfors H.E., Drijfhout J.W. & Ubbink M. (2012), The Src SH2 domain interacts dynamically with the focal adhesion kinase binding site as demonstrated by paramagnetic nmr spectroscopy, IUBMB Life 64(6): 538-544.
- Liu W.M., Keizers P.H.J., Hass M.A.S., Blok A.J., Timmer M., Sarris A.J.C., Overhand M. & Ubbink M. (2012), A pH-Sensitive, Colorful, Lanthanide-Chelating Paramagnetic NMR Probe, Journal of the American Chemical Society 134(41): 17306-17313.
- Scanu S., Förster J., Finiguerra M.G., Hashemi Shabestari M., Huber M.I. & Ubbink M. (2012), The Complex of Cytochrome f and Plastocyanin from Nostoc sp. PCC 7119 is Highly Dynamic, ChemBioChem 13: 1312-1318.
- Meschi F., Wiertz F., Klauss L., Blok A., Ludwig B., Merli A., Heering H.A., Rossi G.L. & Ubbink M. (2011), Efficient Electron Transfer in a Protein Network Lacking Specific Interactions, Journal of the American Chemical Society 133(42): 16861-16867.
- Keizers P.M. & Ubbink M. (2011), Paramagnetic tagging for protein structure and dynamics analysis, Progress in Nuclear Magnetic Resonance Spectroscopy 58(1-2): 88-96.
- Bashir Q., Scanu S. & Ubbink M. (2011), Dynamics in electron transfer protein complexes, FEBS Journal 278(9): 1391-1400.
- Lindfors H.E., Venkata B.S., Drijfhout J.W. & Ubbink M. (2011), Linker length dependent binding of a focal adhesion kinase derived peptide to the Src SH3-SH2 domains, FEBS Letters 585(4): 601-605.
- Dasgupta S., Hu X.Y., Keizers P.H.J., Liu W.M., Luchinat C., Nagulapalli M., Overhand M., Parigi G., Sgheri L. & Ubbink M. (2011), Narrowing the conformational space sampled by two-domain proteins with paramagnetic probes in both domains, Journal of Biomolecular NMR 51(3): 253-263.
- Volkov A.N., Barrios H., Mathonet P., Evrard C., Ubbink M., Declercq J.P., Soumillion P. & Fastrez J. (2011), Engineering an Allosteric Binding Site for Aminoglycosides into TEM1-beta-Lactamase, ChemBioChem 12(6): 904-913.
- Alagarathnam S., Meeuwenoord N.J., Navarro J.A., Hervás M., Rosa M.A. de la, Hoffmann M., Einsle O., Ubbink M. & Canters G.W. (2011), Probing the reactivity of different forms of azurin by flavin photoreduction, FEBS Journal 278(9): 1506-1521.
- Keizers P.H.J. & Ubbink M. (2011), Paramagnetic tools in protein NMR. In: Roberts G.C.K. & Lian Y.A. (Eds.), Protein NMR Spectroscop: Practical Techniques and Applications. Chichester: John Wiley & Sons. 193-220.
- Volkov A.N., Ubbink M. & Nuland N. van (2010), Mapping the encounter state of a transient protein complex by PRE NMR spectroscopy, Journal of Biomolecular NMR 48(4): 225-236.
- Bashir Q., Volkov A.N., Ullmann G.M. & Ubbink M. (2010), Visualisation of the encounter state of the transient electron transfer complex of cytochrome c and cytochrome c peroxidase, Journal of the American Chemical Society 132(1): 241-247.
- Hass M.A.S., Keizers P.H.J., Blok A., Hiruma Y. & Ubbink M. (2010), Validation of a Lanthanide Tag for the Analysis of Protein Dynamics by Paramagnetic NMR Spectroscopy, Journal of the American Chemical Society 132(29): 9952-9953.
- Meschi F., Wiertz F., Klauss L., Cavalieri C., Blok A., Ludwig B., Heering H.A., Merli A., Rossi G.L. & Ubbink M. (2010), 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 132(41): 14537-14545.
- Volkov A.N., Bashir Q., Worrall J.A.R., Ullmann G.M. & Ubbink M. (2010), Shifting the Equilibrium between the Encounter State and the Specific Form of a Protein Complex by Interfacial Point Mutations, Journal of the American Chemical Society 132(33): 11487-11495.
- Keizers P.H.J., Mersinli B., Reinle W., Donauer J., Hiruma Y., Hannemann F., Overhand M., Bernhardt R. & Ubbink M. (2010), A Solution Model of the Complex Formed by Adrenodoxin and Adrenodoxin Reductase Determined by Paramagnetic NMR Spectroscopy, Biochemistry 49(32): 6846-6855.
- Xu X.F., Scanu S., Chung J.S., Hirasawa M., Knaff D.B. & Ubbink M. (2010), Structural and Functional Characterization of the Ga-Substituted Ferredoxin from Synechocystis sp PCC6803, a Mimic of the Native Protein, Biochemistry 49(36): 7790-7797.
- Impagliazzo A., Tepper A.W., Verrips TC, Ubbink M. & Maarel S.M. van der (2010), Structural basis for a PABPN1 aggregation-preventing antibody fragment in OPMD, FEBS Letters 584(8): 1558-1564.
- Milikisyants S., Scarpelli F., Finiguerra M.G., Ubbink M., Groenen E.J.J. & Huber M.I. (2010), Novel approaches for distance determination by EPR: large anisotropy, fast relaxing paramagnetic centres, such as Fe(III), as markers, Biophysical Journal 98(3): 399a.
- Keizers P.H., Saragliadis A., Hiruma Y., Overhand M. & Ubbink M. (2008), Design, Synthesis, and Evaluation of a Lanthanide Chelating Protein Probe: CLaNP-5 Yields Predictable Paramagnetic Effects Independent of Environment, Journal of the American Chemical Society 130: 14802-14812.
- Finiguerra M.G., Prûdencio M., Ubbink M. & Huber M.I. (2008), Accurate long-range distance measurements in a doubly spin-labeled protein by a four-pulse, double electron-electron resonance method, Magnetic Resonance in Chemistry 46: 1096-1101.
- Jongh T.E. de, Hoffman M., Einsle O., Cavazzini D., Rossi G., Ubbink M. & Canters G.W. (2007), Inter- and intramolecular electron transfer in modified azurin dimers, European Journal of Inorganic Chemistry 2007(18): 2627-2634.
- Vlasie M.D., Comuzzi C., Nieuwendijk A.M.C.H. van den, Prudencio M., Overhand M. & Ubbink M. (2007), Long-range-distance NMR effects in a protein labeled with a lanthanide-DOTA chelate, Chemistry: a European Journal 13(6): 1715-1723.
- Hulsker R., Mery A., Thomassen E.A.J., Ranieri A., Sola M., Verbeet M.P., Kohzuma T. & Ubbink M. (2007), Protonation of a Histidine Copper Ligand in Fern Plastocyanin, Journal of the American Chemical Society 129: 4423-4429.
- Xu X., Kim S.K., Schürmann P., Hirasawa M., Tripathy J.N., Smith J., Knaff D.B. & Ubbink M. (2006), Ferredoxin/ferredoxin-thioredoxin reductase complex: Complete NMR mapping of the interaction site on ferredoxin by gallium substitution, 580: 6714-6720.
- Volkov A.N., Worrall J.A.R., Holtzmann E. & Ubbink M. (2006), Solution structure and dynamics of the complex between cytochrome c and cytochrome c peroxidase determined by paramagnetic NMR, Proceedings of the National Academy of Sciences 103: 18945-18950.
- Worrall J.A.R., Machczynski M.C., Keijser B.J.F., Rocco G. di, Ceola S., Ubbink M., Vijgenboom E. & Canters G.W. (2006), Spectroscopic characterization of a high-potential lipo-cupredoxin found in Streptomyces coelicolor, Journal of the American Chemical Society 128(45): 14579-14589.
- Jongh T.E. de, Roon A. van, Prudêncio M., Ubbink M. & Canters G.W. (2006), Click-chemistry with an active site variant of azurin, European Journal of Inorganic Chemistry 2006(9): 3861-3868.
- Hirota S., Fujimoto Y., Choi J., Baden N., Katagiri N., Akiyama R., Hulsker R., Ubbink M., Okajima T., Takabe T., Funasaki N., Watanabe Y. & Terazima M. (2006), Conformational changes during apoplastocyanin folding observed by photocleavable modification and transient grating, Journal American Chemical Society 128: 7551-7558.
- Finiguerra M.G., Blok H., Ubbink M. & Huber M.I. (2006), High-field (275 GHz) Spin-Label EPR for High-Resolution Polarity Determination in Proteins, Journal of Magnetic Resonance 180: 197-202.
- Vlasie M.D., Comuzzi C., Nieuwendijk A.M.C.H. van den, Prudêncio M., Overhand M. & Ubbink M. (2006), Long-range distance NMR effects in a protein labeled with a lanthanide-DOTA chelate, Chemistry: a European Journal : .
- Worrall J.A.R., Roon A.M.M. van, Ubbink M. & Canters G.W. (2005), The effect of replacing the axial methionine ligand with a lysine residue in cytochrome c-550 from Paracoccus versutus assessed by X-ray crystallography and unfolding: X-ray and unfolding studies of cyt c-550, FEBS Journal 272(10): 2441-2455.
- Worrall J.A.R., Diederix R.E.M., Prudencio M., Lowe C.E., Ciofi-Baffoni S., Ubbink M. & Canters G.W. (2005), The effects of ligand exchange and mobility on the peroxidase activity of a bacterial cytochrome c upon unfolding, ChemBioChem 6(4): 747-758.
- Duquesne A.E., Ruijter M. de, Brouwer J., Drijfhout J.W., Nabuurs S.B., Spronk C.A.E.M., Vuister G.W., Ubbink M. & Canters G.W. (2005), Solution structure of the second PDZ domain of the neuronal adaptor X11alpha and its interaction with the C-terminal peptide of the human copper chaperone for superoxide dismutase, Journal of Biomolecular NMR 32: 209-218.
- Navarro J.A., Lowe C.E., Amons R., Kohzuma T., Canters G.W., De la Rosa M.A., Ubbink M. & Hervas M. (2004), Functional characterization of the evolutionarily divergent fern plastocyanin, European Journal of Biochemistry 271(16): 3449-3456.
- Diederix R.E.M., Busson S., Ubbink M. & Canters G.W. (2004), Increase of the peroxidase activity of cytochrome c-550 by the interaction with detergents, Journal of Molecular Catalysis B: Enzymatic 27(2-3): 75-82.
- Diederix R.E.M., Fittipaldi M., Worrall J.A.R., Huber M.I., Ubbink M. & Canters G.W. (2003), Kinetic stability of the peroxidase activitity of unfoled cytochrome c: heme degradation and catalyst inactivation by hydrogen peroxide, Inorganic Chemistry 42(22): 7249-7257.
- Finiguerra M.G., Amsterdam I.M.C. van, Alagaratnam S., Ubbink M. & Huber M.I. (2003), Anisotropic spin label mobilities in azurin from 95 GHz electron paramagnetic resonance spectroscopy, Chemical Physics Letters 382: 528-533.
- Amsterdam I.M.C. van, Ubbink M., Canters G.W. & Huber M.I. (2003), Measurememt of a Cu-Cu distance of 26 a by a pulsed EPR method, Angewandte Chemie - International Edition in English 42(1): 62-64.
- Worrall J.A.R., Reinle W., Bernhardt R. & Ubbink M. (2003), Transient protein interactions studied by NMR spectroscopy: The case of cytochrome C and adrenodoxin, Biochemistry 42: 7068-7076.
- Prudencio M., Impagliazzo A., Ubbink M., Rohovec J. & Peters J. (2003), CLaNP - An artificial paramagnetic centre to study proteins by NMR, 96: 213.
- Crowley P.B. & Ubbink M. (2003), Close encounters of the transient kind: Protein interactions in the photosynthetic redox chain investigated by NMR spectroscopy, Accounts of Chemical Research 36: 723-730.
- Crowley P.B., Diaz-Quintana A., Molina-Heredia F.P., Nieto P., Sutter M., Haehnel W., Rosa M.A. de la & Ubbink M. (2003), The interactions of cyanobacterial cytochrome c(6) and cytochrome f, characterized by NMR, Journal of Biological Chemistry 277(50): 48685-48689.
- Crowley P.B., Vintonenko N., Bullerjahn G.S. & Ubbink M. (2003), Plastocyanin-cytochrome f interactions: The influence of hydrophobic patch mutations studied by NMR spectroscopy, Biochemistry 41: 15698-15705.
- Ubbink M., Worrall J.A.R., Canters G.W., Groenen E.J.J. & Huber M.I. (2002), Paramagnetic resonance of biogical metal centers, Annual Review of Biophysics 31: 393-422.
- Louro R.O., Waal E.C. de, Ubbink M. & Turner D.L. (2002), Replacement of the methionine axial ligand in cytochrome c(550) by a lysine: effects on the haem electronic structure, FEBS Letters 510(3): 185-188.
- Amsterdam M.C. van, Ubbink M. & Canters G.W. (2002), Anti-cooperativity in the two electron oxidation of the S118C disulfide dimer of azurin, Inorganica Chimica Acta 331(1): 296-302.
- Amsterdam I.M.C. van, Ubbink M., Bosch M. van den, Rotsaert F., Sander-Loehr J. & Canters G.W. (2002), A new type 2 copper cysteinate azurin: Involvement of an engineered exposed cysteine in copper binding trough internal rearrangement , The Journal of Biological Chemistry 277(46): 44121-44130.
- Diederix R.E.M., Ubbink M. & Canters G.W. (2002), Peroxidase Activity as a Tool for Studying the Folding of c-Type Cytochromes, Biochemistry 41(43): 13067-13077.
- Diederix R.E.M., Ubbink M. & Canters G.W. (2002), Effect of the protein matrix of cytochrome c in supressing the inherent peroxidase activity of its heme group, ChemBioChem 3(1): 110-112.
- Crowley P.B., Rabe K.S., Worrall J.A.R., Canters G.W. & Ubbink M. (2002), The ternary complex of Cytochrome f and Cytochrome c: Identification of a Second Binding Site and Competition for Plastocyanin Binding, ChemBioChem 3(6): 526-533.
- Diederix R.E.M., Ubbink M. & Canters G.W. (2001), The peroxidase activity of cytochrome c-550 from Paracoccus versutus, European Journal of Biochemistry 268(15): 4207-4216.
- Crowley P.B., Otting G., Schlarb B.G., Canters G.W. & Ubbink M. (2001), Hydrophobic interactions in a cyanobacterial plastocyanin-cytochrome f complex, Journal of the American Chemical Society 123(143): 10444-10453.
- Ubbink M. (2001), Cytochrome f / Plastocyanin Complex, Handbook of metalloproteins : 182-192.
- Amsterdam I.M.C. van, Ubbink M., Einsle O., Messerschmidt A., Merli A., Cavazzini D., Rossi G.L. & Canters G.W. (2001), Dramatic modulation of electron transfer in protein complexes by crosslinking, Nature Structural Biology 9(1): 48-52.
- Prudencio M., Rohovec J., Peters J., Velders A.H., Haasnoot J.G., Verbeet M. & Ubbink M. (2001), Development of a paramagnetic probe for the study of protein-protein complexes, 86: 384-384.
- Worrall J., Kolczak U., Canters G.W. & Ubbink M. (2001), Interaction of yeast iso-1-cytochrome c with cytochrome c peroxidase investigated by [15N, 1H] heteronuclear NMR spectroscopy, Biochemistry 40(24): 7069–7076.
- Amsterdam M.C. van, Ubbink M., Jeuken L.J.C., Verbeet M.P., Canters G.W. & Messerschmidt A. (2001), Effects of dimerization on protein electron transfer, Chemistry: a European Journal 7(11): 2398-2406.
- Crowley P.B., Ubbink M. & Otting G. (2000), Phi angle restraints in protein backbones from dipole-dipole cross-correlation between 1HN-15N and 1HN-1Ha Vectors, Journal of the American Chemical Society 122(12): 2968-2969.
- Ejdeback M., Bergkvist A., Karlsson B.G. & Ubbink M. (2000), Side-chain interactions in the plastocyanin-cytochrome f complex, Biochemistry 39: 5022-5027.
- Jeuken L.J.C., Ubbink M., Bitter J.H., Vliet P.H. van, Meijer-Klaucke W. & Canters G.W. (2000), The structural role of the copper coordinating and surface-exposed histidine in the blue copper protein azurin, Journal of Molecular Biology/JMB Online 299(3): 739-757.
- Kalverda A.P., Gilardi G., Wymenga S.S., Crawford A., Jeuken L.J.C., Ubbink M. & Canters G.W. (1999), Backbone dynamics of azurin in solution: the slow conformational change associated with deprotonation of Histidine 35, Biochemistry 38(39): 12690-12697.
- Schlarb B.G., Wagner M.J., Vijgenboom E., Ubbink M., Bendall D.S. & Howe C.J. (1999), Expression of plastocyanin and cytochrome f of the cyanobacterium Phormidium laminosum in escherichia coli and Paracoccus denitrificans and the role of leader peptides, Gene 234(2): 275-283.
- Bendall D.S., Wagner M.J., Schlarb B.G., Soellick T.R., Ubbink M. & Howe C.J. (1999), Electron transfer between cytochrome f and plastocyanin in Phormidium laminosum, The Phototrophic Prokaryotes : 315-328.
- Ubbink M., Ejdeback M., Karlsson B.G. & Bendall D.S. (1998), The structure of the complex of plastocyanin and cytochrome f, determined by paramagnetic NMR and restrained rigid-body molecular dynamics, Structure Fold Design 6(3): 323-335.
- Meskers S.C.J., Ubbink M., Canters G.W. & Dekkers H.P.J.M. (1998), pH Dependence of the enantioselective excited-state quencing of L,D-lanthanide(III) tris (pyridine-2,6-dicarboxylate) chelates by ferricytochrome c from horse heart and ferricytochrome c-550 from Paracoccus versutus, Journal of Biological Inorganic Chemistry 5: 463-469.
- Ubbink M. & Bendall D.S. (1997), Complex of plastocyanin and cytochrome c characterized by NMR chemical shift analysis, Biochemistry 36(21): 6326-6335.
- Ubbink M., Lian L.Y., Modi S., Evans P.A. & Bendall D.S. (1996), Analysis of the H-1-NMR chemical shifts of Cu(I)-, Cu(II)- and Cd-substituted pea plastocyanin - Metal-dependent differences in the hydrogen-bond network around the copper site, European Journal of Biochemistry 242(1): 132-147.
- Meskers S.C.J., Ubbink M., Canters G.W. & Dekkers H.P.J.M. (1996), Chiral recognition between dissymmetric Tb- and Eu(pyridine-2,6-dicarboxylate)(3)(3-) complexes and Fe(III) proteins in aqueous solution. Luminescence quenching by cytochrome c from horse heart and cytochrome c-550 from Thiobacillus versutus and its Lys14- Glu and Lys99- Glu mutants, Journal of Physical Chemistry 100(45): 17957-17969.
- Ubbink M., Pfuhl M., Oost J. van der, Berg A. & Canters G.W. (1996), NMR assignments and relaxation studies of Thiobacillus versutus ferrocytochrome c-550 indicate the presence of a highly mobile 13-residues long C-terminal tail, Protein Science 5(12): 2494-2505.
- Ubbink M., Warmerdam G.C.M., Campos A.P., Teixeira M. & Canters G.W. (1994), The role of lysine-99 of Thiobacillus versutus cytochrome c-550 in the alkaline transition, FEBS Letters 351(1): 100-104.
- Ubbink M., Campos A.P., Teixeira M., Hunt N.I., Hill H.A.O. & Canters G.W. (1994), Characterization of mutant met100lys of cytochrome c-550 from thibacillus-versutus with Lysine-histidine heme ligation, Biochemistry 33(33): 10051-10059.
- Ubbink M., Hunt N.I., Hill H.A.O. & Canters G.W. (1994), Kinetics of the reduction of wilt-type and mutant cytochrome c-550 by methylamin dehydrogenase and amicyanin from thiobacillus-versutus, European Journal of Biochemistry 222(2): 561-571.
- Visse R., Ruijter M. de, Ubbink M., Brandsma J.A. & Putte P. van de (1993), The 1st zinc-binding domain of UvrA is not essential for UvrABC-mediated DNA excision repair , Mutation Research : DNA Repair 294(3): 263-274.
- Ubbink M. & Canters G.W. (1993), Mutagenesis of the conserved lysine 14 of cytochrome c-550 from Thiobacillus versutus affects the protein structure and the electron self-exchange rate, Biochemistry 32(50): 13893-13901.
- Ubbink M., Beeumen J. van & Canters G.W. (1992), Cytochrome c550 from Thiobacillus versutus: cloning, expression in Escherichia coli, and purification of the heterologous holoprotein , Journal of Bacteriology 174(11): 3707-3714.
- Ubbink M., Keef M.A.G. van, Kleinjan D.J., Hoitink C.W.G., Huitema F., Beintema J.J., Duine J.A. & Canters G.W. (1991), Cloning, sequencing and expression studies of the genes encoding amicyanin and the beta-subunit of methylamine dehydrogenase from thiobacillus-versutus , European Journal of Biochemistry 202(3): 1003-1012.