Lab Members | Research | Publications

Membrane Protein Structural Biology,
The Ubarretxena Laboratory

Our laboratory investigates the role of eukaryotic membrane proteins in cellular processes and in disease. Membrane proteins constitute over 30% of all proteins encoded in a cell genome and are the target of more than half of the therapeutic drugs currently used in medicine. We use high-resolution electron cryomicroscopy, X-ray crystallography and solution NMR to determine the structure of membrane proteins and we then integrate the structural information with mechanistic and functional studies. The long-term aim is to learn how to modulate membrane protein function to open new avenues for therapeutic strategies.

Iban Ubarretxena, Ph.D.

Assistant Professor, Structural and Chemical Biology

Training and Education

• Postdoctoral Training, MRC Laboratory of Molecular Biology, Cambridge, UK
• Postdoctoral Training, Yale University, New Haven, USA
• Ph.D. Utrecht University, The Netherlands

Laboratory Members

• Jose Chavez Assistant Researcher/Student
• Imane Djemil Research, Technician
• Sampada Kalan, Trainee
• Fabiana Renzi, Postdoctoral Fellow
• Kumiko Sagawara ,Volunteer
• Celia Torres, Assistant Researcher/Student

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Research Projects

Molecular mechanism of b-amyloid peptide production. gamma-Secretase is a human membrane protein complex responsible for the activation of pools of membrane-bound latent transcriptional activators through a process termed regulated intramembrane proteolysis (RIP). The cleaved domains are then released to the cytosol as active transcriptional activators. Examples of transcriptional activators processed by gamma-Secretase include the developmental signaling molecule Notch and the human epidermal growth factor receptor-like protein ErbB-4. gamma-Secretase also plays a prominent role in the pathogenesis of Alzheimer’s disease, through the processing of the amyloid precursor protein (APP) and the generation of beta-amyloid peptides (Ab). An understanding of the molecular mechanism of Ab production could enable the development of new therapeutics against Alzheimer’s disease.

Structure and function of Rhomboid intramembrane proteases. Rhomboids are serine intramembrane proteases found in organisms ranging from bacteria to humans and shown to play a role intercellular signaling. In Drosophila melanogaster, Rhomboid cleaves the membrane bound epidermal growth factor receptor (EGFR) ligands - Spitz, Keren and Gurken, leading to their extracellular release and activation of the single EGF receptor pathway in a neighboring cell. We are using Rhomboids from eukaryotic and prokaryotic origin to gain insight shed light into the general mechanism of proteolysis within biological membranes.

 Structure determination of membrane proteins by electron crystallography. The overall goal of this project is to foster membrane protein structure determination by electron crystallography, which involves the application of cryo-electron microscopy (cryo-EM) on two-dimensional (2D) crystals. Electron crystallography has developed into a powerful tool to elucidate the 3D structure of membrane proteins at medium and high-resolution. This methodology has yielded the medium-resolution structure (5-8 Å) of approximately 20 unique membrane proteins and atomic structures in the case of bacteriorhodopsin, light harvesting complex, aquaporin and glutathione transferase. 2D crystals are formed by achieving high density of a single protein species constrained to a 2D lipid bilayer that resembles the native biological membrane and thus offer a unique advantage for structure determination of delicate membrane protein complexes from eukaryotic sources. By implementing technologies for automated screening of 2D crystallization trials, we aim to make electron crystallography a viable alternative for membrane protein structure determination.

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 Publications

1. Brok, R.G.P.M., Belandia, I.U, Dekker, N., Tommassen, J., & Verheij, H.M. 1996 E. coli outer membrane phospholipase A: role of two serines in enzymatic activity. Biochemistry 35, 7787-7793.
2. Grant, K.A., Belandia, I.U., Dekker, N., Richardson, P.T., & Park, S.F. 1997 Molecular characterization of pldA, the structural gene for a phospholipase A from Campilobacter coli, and its contribution to cell-associated hemolysis. Infect and Immun 65, 1172-1180.
3. Ubarretxena-Belandia, I., Boots, J-W.P., Verheij, H.M., & Dekker, N. 1998 Role of the cofactor calcium in the activation of the outer membrane phospholipase A. Biochemistry 37, 16011-16018.
4. Ubarretxena-Belandia, I., Hozeman, L., van der Brink-van der Laan, E., Pap, E.H.M., Egmond, M.R., Verheij, H.M., & Dekker, N. 1999 Outer membrane phospholipase A is dimeric in phospholipid bilayers: a cross-linking and fluorescence resonance energy transfer study. Biochemistry 38, 7398-7405.
5. Simons, J.-W.F.A., van Kampen, M. D., Ubarretxena-Belandia, I., Cox, R. C., Alves dos Santos, C. M., Egmond, M. R., & Verheij, H. M. 1999 Identification of a calcium binding site in Staphylococcus hyicus lipase. Generation of calcium-independent variants. Biochemistry 38, 2-10.
6. Ubarretxena-Belandia, I., Cox, R. C., Dijkman, R., Egmond, M.R., Verheij, H. M., & Dekker, N. 1999 Half-of-the-sites reactivity of outer membrane phospholipase A against an active site-directed  inhibitor. Eur J Biochem 260, 794-800.
7. Snijder, H.J., Ubarretxena-Belandia, I., Blaauw, M., Kalk, K.H., Verheij, H.M., Egmond M.R., Dekker, N., & Dijkstra, B.W. 1999 Structural evidence for dimerization-regulated activation of an integral membrane phospholipase. Nature 401, 717-721.
8. ^*Senes, A., ^*Ubarretxena-Belandia, I., & Engelman, D.M. 2001 The Calpha-H…O bond: a determinant of stability and specificity in transmembrane helix interactions. PNAS 98, 9056-9061. ^*co-first authors.
9. Ubarretxena-Belandia, I., & Engelman, D.M. 2001 Helical membrane proteins: diversity of functions in the context of simple architecture. Curr Opin Struct Biol 11, 370-376.
10. Constantinescu, S.N., Keren, T., Russ, W.P., Ubarretxena-Belandia, I., Engelman, D.M., Lodish, H.F., & Henis, Y.L. 2003 The Epo Receptor Transmembrane Domain Mediates Complex Formation with Viral Anemic and Polycythemic gp55 Proteins. JBC. 278, 43755-43763.
11. Tate C.G., Ubarretxena-Belandia, I., & Baldwin, J.M. 2003 Conformational changes in the multidrug transporter EmrE associated with substrate binding. JMB 332, 229-242.
12. Ubarretxena-Belandia, I., Baldwin, J.M., Schuldiner, S., & Tate C.G. 2003 Three-dimensional structure of the bacterial multidrug transporter EmrE shows it is an asymmetric homo-dimer. EMBO J. 22, 6175-6178.
13. ^*Mitra, K., ^*Ubarretxena-Belandia, I., Taguchi, T., Warren, G. & Engelman, D.M. 2004 Proteins rather than cholesterol set the bilayer thickness of exocytic pathway membranes.  PNAS, 101, 4083-4088.  ^*co-first authors.
14. Ubarretxena-Belandia, I., & Tate C.G. 2004 New insights into the structure and oligomeric state of the bacterial multidrug transporter EmrE: an unusual asymmetric homo-dimer. FEBS Letters 564, 234-238.
15. Butler, P.J.G., Ubarretxena-Belandia, I., Warne, T., & Tate C.G. 2004 The Escherichia coli multidrug transporter EmrE is a dimer in the detergent-solubilised state. JMB, 340, 797-808.
16. Ilag, L.L., Ubarretxena-Belandia, I., Tate C.G., & Robinson C.V. 2004 Drug binding revealed by tandem mass spectrometry of a protein-micelle complex. JACS, 126, 14362-14363. Featured as Editor’s Choice in Science (2004): 306, 943-44 and in Chemical & Engineering News (2004): 82.
17. Del Rio, A., Dutta, K., Chavez, J., ^*Ubarretxena-Belandia, I., ^*Ghose, R. 2007 Solution structure and dynamics of the N-terminal cytosolic domain of Rhomboid intramembrane protease from Pseudomonas aeruginosa: Insights into a functional role in intramembrane proteolysis. JMB, 365, 109-122. ^*co-corresponding authors
18. Vink M, Derr K, Love J, Stokes DL, & Ubarretxena-Belandia I. 2007 A high-throughput strategy to screen 2D crystallization trials of membrane proteins.
J Struct Biol. ,160, 295-304.

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