Examplepictures of DNA-Structures

M. Teresa Pisabarro - Structural Bioinformatics & Computational Biology

Computational approaches to functional genomics and rational engineering

Our group develops and applies computational strategies for functional genome annotation and rational engineering as strategies for target/drug discovery and biotechnology innovation.
By applying structure-based computational methods, molecular modeling and computer simulation techniques we try to decipher the relationships between protein structure and function in order to understand the molecular basis of protein recognition, which will allow us to unravel protein function and to rationally intervene with it. Our current research focuses on the discovery and functional characterization of novel proteins, the rational engineering of proteins with improved functional properties, and de novo design of molecular scaffolds for a variety of biotechnological and biomedical applications.

Note for accessing the SCOWLP and MSPocket tools:

  • SCOWLP (Teyra et al., BMC Bioinformatics 2011) has been moved to a new location.
  • ! Please note that the link www.scowlp.org is no longer functional.

  • MSPocket (Zhu and Pisabarro, Bioinformatics 2011) can be downloaded from here.
  •  

Research

Computational approaches to functional genomics and rational engineering for target/drug discovery and biotechnology innovation.

 

 Rational engineering and de novo design for biotechnological and/or medical applications 

De novo rational design of molecular scaffolds mimicking protein interactions for specific interference in cell signaling processes: 

We apply molecular modelling and computer simulation techniques for designing molecules with pharmacological/biotechnological interest. On one hand, we make use of scaffolds that are available in nature and rationally modify them in order to improve their properties in terms of stability, affinity and specificity. On the other hand, we de novo design scaffolds that mimic natural protein 3D templates involved in interactions of pharmacological relevance.

Rational engineering of biomaterials for tissue regeneration:

GAGs (glycosaminoglycans) are common constituents of cell surfaces and extracellular matrices, and their interactions with a wide variety of molecules such as growth factors and cytokines play a prominent role in basic biological phenomena like cell adhesion, migration, proliferation and differentiation. Thanks to these biocharacteristics, attachment of GAGs to biomaterials offers a great opportunity to modulate tissue response and create an appropriate environment for cellular signalling, both important issues in tissue engineering and regeneration. In close collaboration with experimentalists, we work on the characterization of the structural requirements for protein-GAG binding to understand the molecular basis of the affinity and specificity governing these interactions. We apply computational modelling and simulation techniques to understand the hetereogeneity of the GAG component and to study structural and physical characteristics of GAGs in the context of their interaction with their biological binding-partners. Our studies help in the design of building blocks for chemical and modular synthesis of GAGs-derivatives and matrix scaffolds in biomaterials to promote bio-specific cell behaviour.

This work is funded since 2009 by the German Research Council SFB-TRR 67 (TransRegio 67).

Rational engineering of enzymes with improved anti-HIV functional properties: 

We collaborate with experimental groups in the generation of new DNA recombinases with improved properties to excise HIV from infected human cells. The group of Prof. Buchholz (MPI CBG/TUD) uses in vitro evolution strategies to evolve DNA recombinases, which have been recently shown to be able to excise a sub-classe of HIV from human HIV infected cells (Sarkar et al, Science 2007; DOI: 10.1126/science.1141453). New recombinases are being engineered with improved properties, and we use computational approaches to rationalize the molecular recognition of these enzymes with the aim of establishing the bases for their structure-function relationships and to be able to rationally design evolved DNA recombinases with the desired properties of stability and specificity for different DNA sequences.

 Integrative bioinformatics for structure-based functional annotation of uncharacterized proteins and new target discovery

From cellular phenotypes to structure-based functional characterization of novel genes obtained from genome-wide RNAi screenings in human cells: 

We develop computational tools for integration and analysis of data for automatic protein functional annotation. We develop computational structure-based approaches to predict and/or confirm structural features of non-characterized proteins where classical sequence-based methods fail. We use computer modelling and simulation tools to build detailed 3D atomic models of the uncharacterized proteins and their complexes to derive hypotheses that, in close collaboration with the experimentalist, help to predict and understand their function and networks. 

Discovery and functional annotation of novel proteins using 3D descriptors

We combine fold recognition approaches and the development structure-based functional descriptors (3D descriptors) of protein folds for automatic genome-wide discovery of remote homologues members of different structural protein families (e.g. novel IL8-like chemokines). We are working on the identification and functional characterization of novel human proteins involved in inflammatory, immune and cancer processes that cannot be characterized by sequence -based methods due to their low or not existing sequence similarity to others. 

 Computational studies on molecular recognition 

Detailed characterization and classification of protein interfaces and implications for protein function and ligand design:

- Development of tools for structure-based functional annotation of proteins

- Comparative analysis and prediction of protein-protein and protein-ligand interactions.

We  develop  computational tools to extract, analyze and classify protein interaction information from the PDB in an automatic and comparative fashion. These methods help to obtain an accurate description of protein interfaces, which is needed in order to gain insight about protein function and to be able to properly characterize protein networks. We have built SCOWLP (Structural Characterization Of Water, Ligands and Proteins), a web-based relational database that allows detailed characterization (i.e. physicochemical properties) and visualization of all protein interfaces contained in the PDB, including proteins, peptidic ligands, DNA, saccharides and interface water molecules as descriptors of protein interfaces. SCOWLP is available here (SCOWLP)

SCOWLP: A web-based database developed in our group for detailed characterization, classification and visualization of protein interfaces. SCOWLP includes peptide-protein, DNA-protein and saccharide-protein interactions, and also all interfacial water-mediated interactions in PDB. (SCOWLP) 

 Analysis of the role of solvent in protein recognition: 

We carry out studies that highlight the importance of including solvent in protein interface definition and consequently in protein interaction studies. Water molecules can play an important role in interaction conservation in protein interfaces by allowing sequence variability. Our studies help to deepen our understanding of the physico?chemical nature underlying protein interactions and strengthen the idea of including solvent to qualitatively improve the accuracy of folding, docking and rational design algorithms. 

Publications

Ruiz-Gómez, G.; Hawkins, J. C.; Philipp, J.; Künze, G.; Wodtke, R.; Löser, R.; Fahmy, K.; Pisabarro, M. T. "Rational structure-based rescaffolding approach to de novo design of interleukin 10 (IL-10) receptor-1 mimetics".
Plos One,11(4):e0154046 (2016)

Meinke, G.; Bohm, A.; Hauber, J.; Pisabarro, M. T.; Buchholz, F. "Cre recombinase and other tyrosine recombinases".
Chemical Reviews, [Epub ahead of print] ASAP DOI: 10.1021/acs.chemrev.6b00077 (2016)

Karpinski, J.; Hauber, I.; Chemnitz, J.; Schäfer, C.; Paszkowski-Rogacz, M.; Chakraborty, D.; Beschorner, N.; Hofmann-Sieber, H.; Lange, U. C.; Grundhoff, A.; Hackmann, K.; Schrock, E.; Abi-Ghanem, J.; Pisabarro, M. T.; Surendranath, V.; Schambach, A.; Lindner, C.; van Lunzen, J.; Hauber, J.; Buchholz, F. "Directed evolution of a recombinase that excises the provirus of most HIV-1 primary isolates with high specificity".
Nature Biotechnology, 34(4):401-409 (2016)

Rother, S.; Samsonov, S. A.; Hofmann, T; Blaszkiewicz, J.; Köhling, S.; Moeller, S.; Schnabelrauch, M.; Rademann, J.; Kalkhof, S; von Bergen, M; Pisabarro, M. T.; Scharnweber, D; Hintze, V. "Structural and functional insights into the interaction of sulfated glycosamino-glycans with tissue inhibitor of metalloproteinase-3 - a possible regulatory role on extracellular matrix homeostasis".
Acta Biomaterialia, accepted (2016)

Karimova, M.; Splith, V.; Karpinski, J.; Pisabarro, M. T.; Buchholz, F. "Discovery of Nigri/nox and Panto/pox site-specific recombinase systems facilitates advanced genome engineering".
Scientific Reports, 6:30130 (2016)

Picke, A.-K.; Salbach-Hirsch, J.; Hintze, V.; Rother, S.; Rauner, M.; Kascholke, C.; Moeller, S.; Bernhardt, R.; Rammelt, S.; Pisabarro, M. T.; Ruiz-Gómez, G.; Schnabelrauch, M.; Schulz-Siegmund, M.; Hacker, M. C.; Scharnweber, D.; Hofbauer, C.; Hofbauer, L. C. "Sulfated hyaluronan improves bone regeneration of diabetic rats by prolonged binding of sclerostin and enhancing osteoblast function".
Biomaterials, 96:11-23 (2016)

Samsonov, S. A. and Pisabarro, M. T. "Computational analysis of interactions in structurally available protein-glycosaminoglycan complexes".
Glycobiology, accepted (2016)

Panitz, N.; Theisgen, S.; Samsonov, S. A.; Gehrcke, J. P.; Baumann, L.; Bellmann-Sickert, K.; Pisabarro, M. T.; Rademann, J.; Huster, D.; Beck-Sickinger, A. G. "The structural investigation of glycosaminoglycan binding to CXCL12 displays distinct interaction sites".
Glycobiology, accepted (2016)

Gehrcke, J. P. and Pisabarro, M. T. "Identification and characterization of a glycosaminoglycan binding site on Interleukin-10 via molecular simulation methods".
Journal of Molecular Graphics and Modelling, 62:97-104 (2015)

Abi-Ghanem, J.; Samsonov, S. A.; Pisabarro, M. T. "Insights into the preferential order of strand exchange in the Cre/loxP recombinase system: impact of the DNA spacer flanking sequence and flexibility".
Journal of Computer-Aided Molecular Design, 29(3):271-282 (2015)

Salbach-Hirsch, J.; Samsonov, S. A.; Hintze, V.; Hofbauer, C.; Picke, A.-K.; Rauner, M.; Gehrcke, J.-P.; Moeller, S.; Schnabelrauch, M.; Scharnweber, D.; Pisabarro, M. T.; Hofbauer, L. C. "Structural and functional insights into sclerostin-glycosaminoglycan interactions in bone".
Biomaterials, 67:335-345 (2015)

Anselmi, M. and Pisabarro, M. T."Exploring multiple binding modes using confined replica exchange molecular dynamics".
Journal of Chemical Theory and Computation, 11(8):3906-3918 (2015)

Scharnweber, D.; Hübner, J.; Rother, S.; Hempel, U.; Anderegg, U.; Samsonov, S. A.; Pisabarro, M. T.; Hofbauer, L.; Schnabelrauch, M.; Franz, S.; Simon, S.; Hintze, V. "Glycosaminoglycan derivatives - promising candidates for the design of functional materials".
Journal of Materials Science: Materials in Medicine, 26(9):232 (2015)

Hofmann, T.; Samsonov, S. A.; Pichert, A.; Lemmnitzer, K.; Schiller, J.; Huster, D.; Pisabarro, M. T.; von Bergen, M.; Kalkhof, S. "Structural analysis of the Interleukin-8/Glycosaminoglycan interactions by amide hydrogen/deuterium exchange mass spectrometry".
Methods, 89:45-53 (2015)

Andrault, P. M.; Samsonov, S. A.; Weber, G.; Coquet, L.; Nazmi, K.; Bolscher, J.; Lalmanach , A. C.; Jouenne, T.; Bromme, D.; Pisabarro, M. T.; Lalmanach, G.; Lecaille, F. "The antimicrobial peptide LL-37 is both a substrate of cathepsins S and K and a selective inhibitor of cathepsin L".
Biochemistry, 54(17):2785-2798 (2015)

Wodtke, R.; Ruiz-Gómez, G.; Kuchar, M.; Pisabarro, M. T.; Novotná, P.; Urbanová, M.; Steinbach, J.; Pietzsch, J.; Löser, R. "Cyclopeptides containing the DEKS motif as conformationally restricted collagen telopeptide analogues: synthesis and conformational analysis".
Organic & Biomolecular Chemistry, 13(6):1878-1896 (2015)

Samsonov, S. A.; Bichmann, L.; Pisabarro, M. T. "Coarse-grained model of glycosaminoglycans".
Journal of Chemical Information and Modeling, 55(1):114-124 (2015)

Hintze, V.; Samsonov, S. A.; Anselmi, M.; Möller, S.; Becher, J.; Schnabelrauch, M.; Scharnweber, D.; Pisabarro, M. T. "Sulfated glycosaminoglycans exploit the conformational plasticity of bone morphogenetic protein-2 (BMP-2) and alter the interaction profile with its receptor".
Biomacromolecules, 15(8):3083-3092 (2014)

Karpinski, J.; Chemnitz, J.; Hauber, I.; Abi-Ghanem, J.; Paszkowski-Rogacz, M.; Surendranath, V.; Chakrabort, D.; Hackmann, K.; Schröck, E.; Pisabarro, M.T.; Hauber, J.; Buchholz, F."Universal Tre (uTre) recombinase specifically targets the majority of HIV-1 isolates".
J Int AIDS Soc., 17(4, S3):19706 (2014)

Künze, G.; Gehrcke, J. P.; Pisabarro, M. T.; Huster, D. "NMR characterization of the binding properties and conformation of glycosaminoglycans interacting with interleukin-10".
Glycobiology, 24(11):1036-1049 (2014)

Samsonov, S. A.; Gehrcke, J. P.; Pisabarro, M. T. "Flexibility and explicit solvent in molecular dynamics-based docking of protein-glycosaminoglycan systems."
Journal of Chemical Information and Modelling
, 54(2):582-592 (2014)

Atkovska, K.; Samsonov, S. A.; Paszkowski-Rogacz, M.; Pisabarro, M. T. "Multipose binding in molecular docking".
International Journal of Molecular Sciences
, 15(2):2622-2645 (2014)

Samsonov, S. A.; Theisgen, S.; Riemer, T.; Huster, D.; Pisabarro, M. T. "Glycosaminoglycan monosaccharide blocks analysis by quantum mechanics, molecular dynamics and nuclear magnetic resonance". 
BioMed Research International
, 2014:808071 (2014)

Samsonov, S. A. and Pisabarro, M. T. "Importance of IdoA and IdoA(2S) ring conformations in computational studies of glycosaminoglycan-protein interactions".
Carbohydrate Research
, 381:133-137 (2013)

Abi-Ghanem, J.; Chusainow, J.; Karimova, M.; Spiegel, C.; Hofmann-Sieber, H.; Hauber, J.; Buchholz, F.; Pisabarro, M. T. "Engineering of a target site-specific recombinase by a combined evolution- and structure-guided approach".
Nucleic Acids Research
, 41(4):2394-2403 (2013)

Karimova, M.; Abi-Ghanem J.; Berger, N.; Surendranath, V.; Pisabarro, M. T.; Buchholz, F. " Vika/vox, a novel efficient and specific Cre/loxP-like site-specific recombination system".
Nucleic Acids Research, 41(2):e37 (2013)

Salbach-Hirsch, J.; Kraemer, J.; Rauner, M.; Samsonov, S. A.; Pisabarro, M. T.; Moeller, S.; Schnabelrauch, M.; Scharnweber, D.; Hofbauer, L. C.; Hintze, V. " The promotion of osteoclastogenesis by sulfated hyaluronan through interference with osteoprotegerin and receptor activator of NF-κB ligand/osteoprotegerin complex formation".
Biomaterials, 34(31):7653-7661 (2013)

van der Smissen, A.; Samsonov, S. A.; Hintze, V.; Scharnweber, D.; Moeller, S.; Schnabelrauch, M.; Pisabarro, M. T.; Anderegg, U. "Artificial extracellular matrix composed of collagen I and high-sulfated hyaluronan interferes with TGFβ1 signaling and prevents TGFβ1 induced myofibroblast differentiation".
Acta Biomaterialia
, 9(8):7775-7786 (2013)

Möbius, K.; Nordsieck, K.; Pichert, A.; Samsonov, S. A.; Thomas, L.; Schiller, J.; Kalkhof, S.; Pisabarro, M. T.; Beck-Sickinger, A. G.; Huster, D. "Investigation of lysine side chain interactions of Interleukin-8 with Heparin and other glycosaminoglycans studied by a methylation-NMR approach".
Glycobiology
, 23(11):1260-1269 (2013)

Sage, J.; Mallevre, F.; Barbarin-Costes, F.; Samsonov, S.; Gehrcke, J.-P.; Pisabarro, M. T.; Perrier, E.; Schnebert, S.; Roget, A.; Livache, T.; Nizard, C.; Lalmanach, G.; Lecaille, F. "Binding of chondroitin 4-sulfate to cathepsin S regulates its enzymatic activity".
Biochemistry
, 52(37):6487-6498 (2013)

Nordsieck, K.; Pichert, A.; Samsonov, S.A.; Thomas, L.; Berger, C.; Pisabarro, M. T.; Huster, D.; Beck-Sickinger, A.G. "Residue 75 of Interleukin-8 is crucial for its Interactions with Glycosaminoglycans".
ChemBioChem, 13(17):2558-2566 (2012)

Tomczak, A.; Sontheimer, J.; Drechsel, D.; Hausdorf, R.; Gentzel, M.; Shevchenko, A.; Eichler, S.; Fahmy, K.; Buchholz, F.; Pisabarro, M. T. "3D profile-based approach to proteome-wide discovery of novel human chemokines".
PLoS One, 7(5):e36151 (2012)

Hawkins, J. C.; Zhu, H.; Teyra, J. ; Pisabarro, M. T. "Reduced false positives in PDZ binding prediction using sequence and structural descriptors".
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 9(5):1492-1503 (2012)

Schlorke, D.; Thomas, L.; Samsonov, S. A.; Huster, D.; Arnhold, J.; Pichert, A. "The influence of glycosaminoglycans on IL-8-mediated functions of neutrophils".
Carbohydrate Research, 356:196-203 (2012)

Pichert, A.; Samsonov, S.A.; Theisgen, S.; Thomas, L.; Baumann, L.; Schiller, J.; Beck-Sickinger, A.G.; Huster, D.; Pisabarro, M.T." Characterization of the Interaction of Interleukin-8 with Hyaluronan, Chondroitin Sulfate, Dermatan Sulfate, and Their Sulfated Derivatives by Spectroscopy and Molecular Modelling".
Glycobiology, 22(1):134-145 (2012)

Teyra, J.; Samsonov, S.A.; Schreiber, S.; Pisabarro, M. T. "SCOWLP update: 3D classification of protein-protein, -peptide, -saccharide and -nucleic acid interactions, and structure-based binding inferences across folds".
BMC Bioinformatics, 12:398 (2011)

Samsonov, S.A.; Teyra, J.; Pisabarro, M. T. "Docking glycosaminoglycans to proteins: analysis of solvent inclusion".
Journal of Computer-Aided Molecular Design, 25(5):477-489 (2011)

Tomczak, A. and Pisabarro, M. T. "Identification of CCR2-binding features in Cytl1 by a CCL2-like chemokine model".
PROTEINS: Structure, Function and Bioinformatics, 79(4):1277-1292 (2011)

Teyra, J.; Hawkins, J.; Zhu, H.; Pisabarro, M. T. "Studies on the inference of protein binding regions across fold space based on structural similarities".
PROTEINS: Structure, Function and Bioinformatics, 79(2):499-508 (2011)

Zhu, H. and Pisabarro, M. T. "MSPocket: An Orientation Independent Algorithm for the Detection of Ligand Binding Pockets".
Bioinformatics, 27(3):351-358  (2011)

Slabicki, M.; Theis, M.; Krastev, D.; Samsonov, S.; Mundwiller, E.; Junqueira, M.; Paszkowski-Rogacz, M.; Teyra, J.; Heninger, A-K.; Poser, I.; Prieur, F.; Truchetto, J.; Confavreux, C.; Marelli, C.; Durr, A.; Camdessanche, J. P.; Brice, A.; Shevchenko, F.; Pisabarro, M. T.; Stevanin, G.; Buchholz, F. "A genome-scale DNA repair RNAi screen identifies SPG48 as a novel gene associated with hereditary spastic paraplegia".
PLoS Biology, 8(6):e1000408  (2010) 

Paszkowski-Rogacz, M.; Slabicki, M.; Pisabarro, M. T.; Buchholz, F. "PhenoFam - gene set enrichment analysis through protein structural information".
BMC Bioinformatics, 11:254  (2010) 

Palencia A.; Camara-Artigas A.; Pisabarro M.T.; Martinez J.C.; Luque I. "The role of interfacial water molecules in proline-rich ligand recognition by the SH3 domain of Abl".
J. Biol. Chem
., 285(4):2823-2833 (2010)

Samsonov, S.A.; Salwiczek, M.; Anders, G.; Koksch, B.; Pisabarro, M. T. "Fluorine in protein environments: A QM and MD study".
J. Phys. Chem. B.
, 113(51)16400-16408  (2009) 

Samsonov, S. A.; Teyra, J.; Anders, G.; Pisabarro, M. T. "Analysis of the impact of solvent on contacts prediction in proteins". 
BMC Struct. Biol.
, 9(1):22  (2009) 

Salwiczek, M.; Samsonov, S.; Vagt, T.; Nyakatura, E.; Fleige, E.; Numata, J.; Cölfen, H.; Pisabarro, M. T.; Koksch, B. "Position Dependent Effects of Fluorinated Amino Acids on Hydrophobic Core Formation of a Heterodimeric Coiled Coil".
Chem. Eur. J., 15(31):7628-7636  (2009) 

Ding, L.; Paszkowski-Rogacz, M.; Nitzsche, A.; Slabicki, M.; Heninger, A-K; Kittler, R. Junqueira, M.; Shevchenko, A.; Schulz, H.; Hubner, N.; Doss, M. X.; Sachinidis, A.; Hescheler, J.; Iacone, R.; Anastassiadis, K.; Stewart, F.; Pisabarro, M. T.; Caldarelli, A.; Poser, I.; Theis, M.; Buchholz, F. "A genome-scale RNAi screen for Oct4 modulators defines a role of the Paf1 complex for embryonic stem cell identity". 
Cell Stem Cell
, 4(5):403-515  (2009)

Theis, M.; Slabicki, M.; Junqueira, M.; Paszkowski-Rogacz, M.; Sontheimer, J.; Kittler, R.; Heninger, A.; Kruusmaa, K.; Poser, I.; Hyman, A.; Pisabarro, M. T.; Gstaiger, M.; Aebersold, R.; Shevchenko, A.; Buchholz, F. "Comparative Profiling Identifies C13orf3 as a Novel Component of the Ska Complex Required for Mammalian Cell Division".
EMBO J., 28(10):1453-1465 (2009)

Vagt, T.; Jäckel, C.; Samsonov, S.; Pisabarro, M. T.; Koksch, B. "Selection of a buried salt bridge by phage display".
Bioorg. Med. Chem. Lett.
, 19(14):3924-3927 (2009) 

Samsonov, S.; Teyra, J.; Pisabarro, M. T. "A molecular dynamics approach to study the importance of solvent in protein interactions". 
PROTEINS: Structure, Function and Bioinformatics
, 73(2):515-525 (2008)  

Baldauf, C.; Pisabarro, M. T. "Stable hairpins with beta-peptides - A route to tackle protein-protein interactions".  
J. Phys. Chem. B
,112(25):7581-7591(2008)

Teyra, J.; Paszkowski-Rogacz, M.; Anders, G.; Pisabarro, M. T. "SCOWLP classification: Structural comparison and analysis of protein binding regions".
BMC Bioinformatics, 9:9  (2008) 

Lättig, J.; Böhl, M.; Fischer, P.; Tischer, S.; Tietböhl, C.; Menschikowski, M.; Gutzeit, H. O.; Metz, P.; Pisabarro, M. T. "Mechanism of Inhibition of Human Secretory Phospholipase A2 by Flavonoids. Rationale for Lead Design".
Journal of Computer-Aided Molecular Design, 21(8):473-483 (2007)

Scheike, J.; Baldauf, C.; Spengler, J.; Albericio, F.; Pisabarro, M. T.; Koksch, B. "Amide-to-ester substitution in coiled coils: the effect of removing hydrogen bonds on protein structure". 
Angewandte Chemie
, 46(41):7766-7769 (2007) 

Teyra, J. and Pisabarro, M. T. "Characterization of Interfacial Solvent in Protein Complexes and Contribution of Wet Spots to the Interface Description".
PROTEINS: Structure, Function and Bioinformatics
, 67, 1087-1095 (2007) 

Pisabarro, M. T.; Leung, B; Kwong, M.; Corpuz, R.; Frantz, G. D.; Chiang, N.; Vandlen, R.; Diehl, L. J.; Skelton, N.; Eaton, D.; Schmidt, K. N. Novel Human Dendritic Cell- and Monocyte-attracting Chemokine-like Protein Identified by Fold Recognition Methods". Journal of Immunology, 176, 2069-2073 (2006) 

Teyra, J.; Doms, A.; Schroeder, M.; Pisabarro, M. T. "SCOWLP: a web-based database for detailed characterization and visualization of protein interfaces".
BMC Bioinformatics
, 7:104  (2006)

Kittler, R.; Putz, G.; Pelletier, L.; Poser, I.; Heninger, A. K.; Drechsel, D.; Fischer, S.; Konstantinova, I.; Habermann, B.; Grabner, H.; Yaspo, M. L.; Himmelbauer, H.; Korn, B.; Neugebauer, K; Pisabarro, M. T.; Buchholz, F. "An endoribonuclease- prepared siRNA screen in human cells identifies genes essential for cell division".
Nature, 432, 1036-1040 (2004) 

Cobos, E. S.; Pisabarro M.T., Vega, C., Lacroix E., Serrano L.; Ruiz-Sanz, J. Martinez J. C. "A miniprotein scaffold used to assemble the PPII binding epitope recognized by SH3 domains".
J. Mol. Biol., 342(1):355-365 (2004) 

Leung, B.; Kwong, M.; Pisabarro, M. T.; Schmidt K. N. "Dendritic cell / monocyte-attracting chemokine DMC is a novel chemokine that has a potential role in homeostasis". 
Clinical and Investigative Medicine
, 27(4), 2581 (2004) 

Skelton, N.J.; Koehler, M.F.; Zobel, K.; Wong, W.L.; Yeh, S.; Pisabarro, M.T.; Yin, J.P.; Lasky, L.A.; Sidhu, S.S. "Origins of PDZ domain ligand specificity. Structure determination and mutagenesis of Erbin PDZ". 
J. Biol. Chem., 278(9):7645-7654  (2003) 

Camenisch, G.*; Pisabarro, M.T.*; Sherman, D.; Kowalski, J.; Nagel, M.; Hass, P.; Gurney, A.; Bodary, S. C.; Liang, X.H.; Clark, K.R.; Beresini, M. H.; Ferrara, N.; Gerber, H.P. "ANGPTL3 stimulates endothelial cell adhesion and migration via integrin αVβ3 and induces blood vessel formation in vivo".      (* First co-authorship)
J. Biol. Chem.
, 277(19):17281-17290 (2002)

Vucic, D.; Deshayes, K.; Ackerly, H.; Pisabarro, M.T.; Kadkhodayan, S.; Fairbrother, W.J.; Dixit, V.M. "SMAC negatively regulates the anti-apoptotic activity of ML-IAP". 
J. Biol. Chem., 277(14):12275-12279 (2002)

Pisabarro, M. T.; Leung, B; Kwong, M.; Corpuz, R.; Vandlen, R.; Gurney, A.; Eaton, D. L.; Schmidt K. N. "Tissue localization and selectivity for immature dendritic cells and monocytes suggest a role for a novel dendritic cell/monocyte attracting chemokine in homeostasis". 
Journal of Interferon and Cytokine Research, 22(S1):11-36 (2002)

Wu Y.; Dowbenko D.; Pisabarro M. T.; Dillard-Telm L.; Koeppen H.; Lasky LA. "PTEN2, a Golgi-associated testis-specific homologue of the PTEN tumor suppressor lipid phosphatase". 
J. Biol. Chem., 276(24):21745-21753 (2001)

Skelton, N. J.; Chen, Y. M.; Dubree, N.; Quan, C.; Jackson, D.; Cochran, A.; Zobel, K.; Deshayes, K.; Baca, M.; Pisabarro, M.T.; Lowman, H. B. "Structure-function analysis of a phage display-derived peptide that binds to insulin-like growth factor binding protein 1". 
Biochemistry, 40(29):8487-8498 (2001)

Vucic, D.; Stennicke H.; Pisabarro, M.T.; Salvesen, G.; Dixit, V. M. "ML-IAP, a novel inhibitor of apoptosis that is preferentially expressed in human melanomas". 
Curr. Biol., 10(21):1359-1366 (2000)

Uren, A. G.; O'Rourke, K.; Aravind, L.; Pisabarro, M.T.; Seshagiri, S.; Koonin, E. V.; Dixit, V. M. "Identification of paracaspases and metacaspases: two ancient families of caspase-like proteins, one of which plays a key role in MALT lymphoma". 
Mol. Cell, 6:961-967 (2000)

Gille, H.; Kowalski, J.; Yu, L.; Chen, H.; Pisabarro, M.T.; Davis-Smyth, T.; Ferrara, N. "A repressor sequence in the juxtamembrane domain of Flt-1 (VEGFR-1) constitutively inhibits vascular endothelial growth factor-dependent phosphatidylinositol 3'-kinase activation and endothelial cell migration". 
EMBO J., 19(15):4064-4073 (2000)

Fuh, G.; Pisabarro, M. T.; Li, Y.; Quan, C.; Lasky, L. A.; Sidhu, S. S. "Analysis of PDZ domain-ligand interactions using carboxy-terminal phage display". 
J. Biol. Chem., 275(28):21486-21491 (2000)

Pisabarro, M. T. ; Serrano, L.; Wilmanns, M. "Crystal structure of the Abl-SH3 domain complexed with a designed high-affinity peptide ligand. Implications for SH3-ligand interactions". 
J. Mol. Biol., 281(3):513-521 (1998)

Martinez, J. C.; Pisabarro, M. T.; Serrano, L. "Obligatory steps in protein folding". 
Nature Struct. Biol., 5(8):721-729 (1998)

Wilcock, D., Pisabarro, M.T., Lopez-Hernandez, E., Serrano, L.; Coll, M. "Structure analysis of two CheY mutants: Importance of the hydrogen-bond contribution to protein stability". 
Acta Crystalographica D Biol. Crystallogr. 54(3):378-385 (1998)

Pisabarro, M. T. and Serrano, L. "Rational design of specific high-affinity peptide ligands for the Abl-SH3 domain". 
Biochemistry, 35(33):10634-10640 (1996)

Ortiz, A. R.; Pisabarro, M. T.; Gago, F.; Wade, R. C. "Prediction of drug binding affinities by comparative binding energy analysis". 
J. Med. Chem., 38:2681-2691 (1995)

Pisabarro, M. T.; Ortiz, A. R.; Gago, F.; Serrano, L."Molecular modeling of the interaction of polyproline-based peptides with the Abl-SH3 domain: rational modification of the interaction". 
Prot. Engineering, 7(12):1455-1462 (1994)

Pisabarro, M. T.; Ortiz, A. R.; Serrano, L.; Wade, R. C. "Homology modeling of the Abl-SH3 domain". 
Proteins: Structure, Function and Genetics, 2:203-215 (1994)

Pisabarro, M. T.; Ortiz, A. R.; Palomer, A.; Cabré, F.; García, M. L.; Wade, R. C.; Gago, F; Mauleón, D.; Carganico, G. "Rational modification of a human synovial fluid Phospholipase A2 inhibitor leading to enhanced activity". 
J. Med.Chem., 37:337-341 (1994)

Pisabarro, M. T.; Palomer, A.; Ortiz, A. R.; Wade, R. C.; Gago, F.; Mauleon, D.; Garganico, G. "Rational drug design: GRID- and LUDI-based structural modifications of a human synovial fluid Phospholipase A2 inhibitor leading to enhanced activity". 
J. Mol. Graphics, 12(1):72 (1994)

Ortiz, A. R.; Pisabarro, M. T.; Gago, F. "Molecular model of the interaction of bee venom Phospholipase A2 with Manoalide". 
J. Med. Chem., 36:1866-1879 (1993)

Ortiz, A. R.; Pisabarro, M. T.; Gallego, J.; Gago, F. "Implications of a consensus recognition site for phosphatidylcholine separate from the active site in cobra venom Phospholipase A2". 
Biochemistry, 31(11):2887-2896 (1992)

Funding

 

Klaus Tschira Stiftung

   

TRANSREGIO 67 

     

 

 

Group Leader short CV

M. Teresa Pisabarro

  • 1997: PhD, Structural and Computational Biology, EMBL Heidelberg, Germany
    (Boehringer Ingelheim Fonds Fellow)
  • 1997-1998: Postdoctoral, EMBL Heidelberg and UCSF, San Francisco, USA
  •  1998-2002: Group Leader, Protein Engineering, Genentech Inc., San Francisco, USA
  •  2002-2004: Visiting scientist, MPI CBG Dresden, Germany
  •  Since 2004: Group Leader, Structural Bioinformatics, BIOTEC TU Dresden, Germany

Contact information

Contact information about group members in the Staff Page.

Join our group

Interested in doing a Diploma / PhD / Postdoc in Structural Bioinformatics in Germany?
Send your c.v to sbjobs(at)biotec.tu-dresden.de 

Our group is member of the International PhD Programme Dresden

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