Tanabe Lab

People

Telephone numbers: +49-345-55-XXXXX (see below for extensions)

 

Group leader extension e-mail
Mikio Tanabe, Ph.D.
1999-2002 BSc/MSc student under supervision of Prof. Masamitsu Futai at Osaka University
2003-2006 Ph.D. student under supervision of Dr. Bernadette Byrne & Dr. Katy Brown at Imperial Collge London
2006-2009 Postdoc with Prof. Tina Iverson at Vanderbilt University Medical Center
2009 Sep- ZIK HALOmem, Martin-Luther-Universität
-24923 .(JavaScript must be enabled to view this email address)
Postdoctoral Fellow
Frank Jaenecke -24875 .(JavaScript must be enabled to view this email address)
Caroline Haupt -24875 .(JavaScript must be enabled to view this email address)
Ph.D. student
Christof Kattner -24875 .(JavaScript must be enabled to view this email address)
Kumar Nagarathinam -24875 .(JavaScript must be enabled to view this email address)
HALOmem Coordinators
Ulla Niesbach-Klösgen -24866 .(JavaScript must be enabled to view this email address)
Rositta Mothes -24866 .(JavaScript must be enabled to view this email address)
Katja Möritz -24866 .(JavaScript must be enabled to view this email address)

 

 

Research

Many biologically important reactions are performed across membranes. The main aim of our study is to understand how cells sense extracellular events and transmit information across the membrane to elicit an intracellular response. To understand the function of membrane proteins on the membrane surface, both protein structure and its dynamics give indispensable information. Our group will use structural biology techniques to determine structure of membrane proteins. The research will proceed together with biophysical characterization and microscopic analysis to study functional behavior.

1. Structure and function of membrane proteins

Structural genomics projects suggest that 20-30% of all ORFs are predicted to encode membrane proteins, of which up to 50-70% are current drug targets. Possibilities for obtaining suitable preparations from native sources are limited; recombinant protein expression techniques are therefore necessary to overcome this situation. The expression system using insect or mammalian cells for structural work has also been available. For time and economical reasons, we will pursue the development and optimization of recombinant expression using yeast and E.coli and protein characterization techniques for structure determination by X-ray crystallography of both α-helical and β-barrel medically important membrane proteins.

2. Elucidation of ligand recognition mechanisms between membrane proteins

We are interested in the so-called “pathogen sensing mechanism”. Recognition of “non-self” proteins by the human immune system requires initial interactions between host immune cells and the invading microbe, leading to subsequent signaling across the membrane to activate downstream intracellular pathways. The mechanisms of recognition and signaling by the innate immune system has been expanded last decade but are still as yet poorly understood for pathogenic membrane protein recognition. The human immune system TLRs can recognize various types of ligand molecules, including specific outer membrane proteins (OMPs), themselves β-barrel membrane proteins. We aim to understand these recognition and signaling mechanisms through a combination of biochemical, biophysical and structural analyses.

3. Membrane protein reorganization and signaling mechanisms

Structures obtained using X-ray crystallography represent a snapshot of the molecular status. A detailed understanding of the reaction and signaling mechanism across the membrane requires knowledge of how ligand molecules trigger membrane protein reorganization for signaling. Our group will therefore investigate and develop sensitive real-time observation techniques to study the various stages of the membrane protein interaction. This will be performed at single molecule resolution using Fluorescence Correlation Spectroscopy / Laser Scanning Microscopy (FCS/LSM) as well as electron microscopy (EM) in collaboration with the Bacia group (HALOmem) which allows medium resolution interpretation of large scale structural rearrangements both in vivo and in vitro.

Publications

Kattner C, Pfenning S, Massari P & Tanabe M (2014) “One-step purification and porin transport activity of the major outer membrane proteins P2 from Haemophilus influenzae, FomA from Fusobacterium nucleatum and PorB from Neisseria meningitidis” in press

Kattner C, Toussi D, Zaucha J, Wezler L, Rüppel N, Zachariae U, Massari P & Tanabe M (2014) “Crystallographic analysis of Neisseria meningitidis PorB extracellular loops potentially implicated in TLR2 recognition” J. Struct. Biol. 185, 440-447.

Nakada-Nakura Y, Ogasawara S & Tanabe M (2013) “Crystallization of membrane proteins with antibody fragments” Frontiers of Protein Crystals CMC press. (Ed. by Sugiyama S.) 110-119.

Simeonov P, Werner S, Haupt C, Tanabe M*, Bacia K* (2013) “Membrane Protein Reconstitution into Liposomes Guided by Dual-Color Fluorescence Cross-Correlation Spectroscopy” Biophysical Chemistry, 184C, 37-43. *Co-correspondoing

Kattner C, Zaucha J, Jaenecke F, Zachariae U & Tanabe M (2013) “Identification of a cation transport pathway in Neisseria meningitidis PorB.” Proteins 81, 830-840.

Thaker TM, Tanabe M, Fowler ML, Preininger AM, Ingram-Smith C, Smith KS, and Iverson TM (2012) “Crystal Structures of Acetate Kinases from the Eukaryotic Pathogens Entamoeba histolytica and Cryptococcus neoformans” J. Struct. Biol.181, 185-189.

Tanabe, M, Nimigean, CM & Iverson, TM (2010) “Structural basis for solute transport, nucleotide regulation, and immunological recognition of Neisseria meningitidis PorB” Pro. Nat. Aca. Sci. USA. 107, 6811-6816.

Tanabe, M & Iverson, TM (2009) “Expression, purification and preliminary X-ray analysis of the Neisseria meningitidis outer membrane protein PorB” Acta Cryst. Section F65, 996-1000.

Tanabe, M. & Iverson, TM. (2009) “A practical guide to x-ray crystallography of β-barrel membrane proteins: expression, purification, detergent selection & crystallization” Current Topics in Membranes 63, 229-267.

Tanabe M, Szakonyi G, Brown KA, Henderson PFJ, Nield J & Byrne B (2009)
“The multidrug resistance efflux complex EmrAB from Escherichia coli forms a dimer in vitroBiochem. Biophys. Res. Commun. 380, 338-342.

Tanabe M, Mirza O, Bertrand T, Atkins HS, Titball RW, Iwata S, Byrne B & Brown KA (2007)
“Structures of OppA and PstS from Yersinia pestis indicate flexibility of substrate binding and variability of interactions with transmembrane domains.” Acta Cryst. Section D63, 1185-1193.

Tanabe M, Atkins HS, Harland DN, Elvin SJ, Stagg AJ, Mirza O, Titball RW, Byrne B & Brown KA (2006)
“The ABC transporter protein OppA provides protection against experimental Yersinia pestis infection” Infect. Immun. 74, 3687-3691.

Iko Y, Sambongi Y, Tanabe M, Iwamoto-Kihara A, Saito K, Ueda I, Wada Y & Futai M (2001)
“ATP synthase F(1) sector rotation. Defective torque generation in the beta subunit Ser-174 to Phe mutant and its suppression by second mutations” J. Biol. Chem. 276, 47508-47511.

Tanabe M, Nishio K, Iko Y, Sambongi Y, Iwamoto-Kihara A, Wada Y & Futai M (2001)
“Rotation of a complex of the gamma subunit and c ring of Escherichia coli ATP synthase. The rotor and stator are interchangeable.” J. Biol. Chem. 276, 15269-15274.

Sambongi Y, Iko Y, Tanabe M, Omote H, Iwamoto-Kihara A, Ueda I, Yanagida T, Wada Y & Futai M (1999)
“Mechanical rotation of the c subunit oligomer in ATP synthase (FoF1): direct observation”  Science 286, 1722-1724.

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Teaching

Participation in practical course “Allgemeine Biochemie”, B.Sc. Biochemistry (4th Semester), Institut für Biochemie und Biotechnologie

Participation in practical course “Molecular Biophysics”, B.Sc. Biochemistry (5th Semester), Institut für Biochemie und Biotechnologie

Participation in Master Module “Struckturbiologie und Bioinformatik”, M.Sc. Biochemistry, Institut für Biochemie und Biotechnologie