Senior Scientist

Dept. of Biochemistry,
University of Bayreuth, Germany.

Research Associate in the laboratory of Prof. Tilman Schirmer Biozentrum, University of Basel, Switzerland

Postdoctoral Fellow in the laboratory of Prof. Tilman Schirmer Biozentrum, University of Basel, Switzerland

Postdoctoral Fellow in the laboratory of Prof. Reza Ahmadian, Institute of Biochemistry and Molecular Biology II Heinrich-Heine-University Medical Center Düsseldorf, Germany

• http://www.rcsb.org/structure/4KAW
• http://www.rcsb.org/structure/4KB2
• http://www.rcsb.org/structure/4KB4
• http://www.rcsb.org/structure/4KC6
• http://www.rcsb.org/structure/4KDD
• http://www.rcsb.org/structure/5IDM
• http://www.rcsb.org/structure/5IDJ
• https://www.rcsb.org/structure/6GTM
• http://www.rcsb.org/pdb/results/results.do?tabtoshow=Unreleased&qrid=AA8A3A11
• http://www.rcsb.org/pdb/results/results.do?tabtoshow=Unreleased&qrid=FDE7AC16
• http://www.rcsb.org/pdb/results/results.do?tabtoshow=Unreleased&qrid=310860CB
• http://www.rcsb.org/structure/6QKJ
• http://www.rcsb.org/structure/6QKI

• Dubey, B. N., Agustoni, Elia, Böhm, Raphael, Kaczmarczyk, Andreas; Mangia, Francesca; von Arx, Christoph; Jenal, Urs; Hiller, Sebastian; Plaza-Menacho, Iván; Schirmer, Tilman (2020). Hybrid histidine kinase activation by cyclic di-GMP-mediated domain liberation. PNAS 117 (2), 1000-1008.
• Kaczmarczyk, A., Hempel, A.M., Arx, von, C., Böhm, R., Dubey, B. N., Nesper, J., Schirmer, T., Hiller, S., and Jenal, U. (2020). Precise transcription timing by a second-messenger drives a bacterial G1/S cell cycle transition. Nature Communication 11, 816.
• Stampfli, Anja R.; Goncharenko, Kristina V.; Meury, Marcel; Dubey, B. N.; Schirmer, Tilman; Seebeck, Florian P. (2019). An Alternative Active Site Architecture for O2 Activation in the Ergothioneine Biosynthetic EgtB from Chloracidobacterium thermophilum. Journal of American Chemical Society, 141 (13), 5275-5285.
• Dubey, B. N., C. Lori, S. Ozaki, G. Fucile, I. Plaza-Menacho, U. Jenal, T. Schirmer, (2016). Cyclic di-GMP mediates a histidine kinase/phosphatase switch by noncovalent domain cross-linking. Science Adv. 2, e1600823. Evaluated by F1000  https://f1000.com/prime/726763649?subscriptioncode=46cece48-85a0-4454-ae1b-a7cb24164dbb
• Lori, C., Ozaki, S., Steiner, S., Böhm, R., Abel, S., Dubey, B. N., Schirmer, T., Hiller, S., and Jenal, U. (2015). Cyclic di-GMP acts as a cell cycle oscillator to drive chromosome replication. Nature 523, 236–239.
• Selvaraj M, Govindan A, Seshadri A, Dubey, B, Varshney U and Vijayan M (2013). Molecular flexibility of Mycobacterium tuberculosis ribosome recycling factor and its functional consequences: An exploration involving mutants. J. Biosci. 38 845–855.
• Ehsan Amin, Dubey, B. N., Si-Cai Zhang, Lothar Gremer, Radovan Dvorsky, Jens M. Moll, Mohamed S. A. Taha, Lutz Schmitt, Georg Groth, Luitgard Nagel-Steger, Roland P. Piekorz and Mohammad R. Ahmadian (2013). Rho-kinase: Structure, regulation, (dys)function, and inhibition. Biol Chem. 394(11): 1399–1410.
• Jaiswal M, Dubey, B. N., Koessmeier KT, Gremer L, Ahmadian MR. (2011). Biochemical assay to characterize Rho GTPases. Methods in Molecular biology (827): 37-58.
• Seshadri A, Dubey B, Weber MH and Varshney U. (2009). Impact of rRNA methylations on ribosome recycling and fidelity of initiation in Escherichia coli. Mol Microbiol. 72(3):795-808 (Cover page)
• Ranjan A, Sinha AY, Dubey B, Saikia A, Buragohain AK and Ray SK (2008). Analysis of bacterial genomes for In-frame dinucleotide abundance, abundance of the encoded amino acids and synonymous codon choice reveals a common pattern. Current science, 94 no.2.
• Dubey B, Buragohain AK, and Ray SK (2008). Positive correlation of bacterial genome GC% with the number of different anticodons used by the genome to decode all the codons. Icfai Univ J Biotech, III

Manuscript in preparation

• Mitchell Brüderlin, Raphael Böhm, Firas Fadel, Urs Jenal, Sebastian Hiller, Tilman Schirmer* and Badri N. Dubey*. Crystal structure of receiver domain from cyclic-di-GMP controlled hybrid histidine kinase. *Correspondence: b.dubey@unibas.ch
• Dubey B. N., Viktoriya Shyp, Urs Jenal, and Tilman Schirmer. Crystal structure of c-di-GMP as bound to a mutated receptor at 1.4 Å resolution.
• Dubey B. N., Mohit, Jutta Nesper, Urs Jenal, and Tilman Schirmer. Crystal structure of HrcA: A novel fold for a c-di-GMP and ppGpp binding protein. (To be submitted in Structure)
• Dubey B. N., Ehsan Amin, Radovan Dvorsky, Lothar Gremer, Jens M. Moll, Martin Wolff, Yan Nie, Melissa Graewert, Britta Tschapek, Ingrid R. Vetter, Lutz Schmitt, Dmitri Svergun, Stefan Raunser, Georg Groth, Luitgard Nagel-Steger, and Mohammad R. Ahmadian. Structural and functional insights into the p160 Rho-associated coiled-coil-containing protein kinase.
• Dubey B. N., Ehsan Amin, Radovan Dvorsky and M. R. Ahmadian. Mechanism and role of the cooperative binding of the PKN homology region 1 to Rho GTPases.

• Molecular Biology: Cloning and site-directed mutagenesis.
• Biophysical techniques: Fluorescence Anisotropy, Fluorescence Spectrometry, Isothermal Titration Calorimetry (ITC), Microscale Thermophoresis (MST), Dye-based Thermal Shift Assay, Stopped-Flow, Analytical Ultra Centrifugation (AUC), Multi-Angle Light Scattering (MALS), Atomic Force Microscopy (AFM), and Circular Dichroism (CD).
• Protein biochemistry: Various techniques of protein purification, analytical gel filtration, pull-down assay and western blotting.
• Bioinformatics: Sequence analysis using HMMER, protein secondary structure prediction, protein homology modeling, Protein database uses, phylogenetic tree from sequence, Prediction of functional domain/signal peptide from protein sequences.
• X-ray Crystallography: Protein crystallization, screening and optimization, hanging drop, sitting drop, seeding, diffraction testing and data collection (in house and synchrotron source) and data processing. Macromolecular structure determination (Phasing, model building and refinement), model analysis and validation.
• Small angle X-ray scattering (SAXS): Data collection and data processing at DESY Hamburg.
• Cryo-EM: Negative staining, grids preparation for EM and Cryo-EM, handling microscopes, image processing and analysis.

2019	International Symposium on Structure Biology for Drug Discovery@SwissFEL Paul Scherrer Institute, Villigen, Switzerland
2018 and 2019	Attended Biozentrum symposium
2017	International Union of Crystallography 2017, Hyderabad, INDIA (Poster presentation)
2016	Oral presentation titled “Cyclic di-GMP mediates a histidine kinase/phosphatase switch by noncovalent domain cross-linking” in the Rhine-Knee Regional Meeting (Regio Meeting) on X-ray Crystallography of Biomacromolecules
2016	Poster presentation at 30th Meeting of the European Crystallographic Association ECM-30 Basel, Switzerland
2015	Basel Post-doc network retreat (Oral presentation)
2014, 2015 and 2016	Biozentrum symposium (Poster presentations from different projects)
2014	5th Murnau Conference on Structural Biology Focus Topic: Signal Transduction (Poster presentation)
2013	CCP4 study weekend meeting about molecular replacements, University of Nottingham, UK
2011	Biostruct master class “Macromolecular Interaction" September 12th-15th, 2011, Heinrich-Heine- University Düsseldorf, Germany (Oral and Poster presentation)
2011	Oral presentation titled “Insights into structure-function relationships in GTPase-effector interaction” in Etter Early Career Award symposium during American crystallographic association meeting, New Orleans, USA
2011	16th International AEK cancer congress, Heinrich-Heine- University Düsseldorf, Germany
2010	Biostruct master class approaches to determine protein structures, Heinrich-Heine-University Düsseldorf, Germany
2009	Regulation and function of small GTPase, Aussois, France

• Scientific writing 2016: Papers, Proposals, and Presentations, Biozentrum, University of Basel
• Python course 2014: Biozentrum, University of Basel
• Cross-cultural communication – How to act successfully in an international environment 2010: Heinrich-Heine-University Düsseldorf, Germany
• Optimizing writing srategies for publishing in English 2010: Heinrich-Heine-University Düsseldorf, Germany
• Introduction into patent issues 2010: Heinrich-Heine-University Düsseldorf, Germany
• Presenting Science – comprehensive, competent and convincing 2009: Heinrich-Heine-University Düsseldorf, Germany
• Self-Management 2009: Heinrich-Heine-University Düsseldorf, Germany
• Shaping up teaching – designing academic lessons according to learner’s needs 2009: Heinrich-Heine-University Düsseldorf, Germany
• Introduction to good scientific practice 2009: Heinrich-Heine-University Düsseldorf, Germany

- Associate member of International Union of Crystallography (IUCr), Since 2018

- Member of American Crystallographic Association (ACA), 2011- 2014