@article{SpeckRaeuberKuekenshoeneretal.2013, author = {Speck, Janina and R{\"a}uber, Christina and K{\"u}kensh{\"o}ner, Tim and Niem{\"o}ller, Christoph and Mueller, Katelyn J. and Schleberger, Paula and Dondapati, Padmarupa and Hecky, Jochen and Arndt, Katja Maren and M{\"u}ller, Kristian M.}, title = {TAT hitchhiker selection expanded to folding helpers, multimeric interactions and combinations with protein fragment complementation}, series = {Protein engineering design \& selection}, volume = {26}, journal = {Protein engineering design \& selection}, number = {3}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {1741-0126}, doi = {10.1093/protein/gzs098}, pages = {225 -- 242}, year = {2013}, abstract = {The twin-arginine translocation (TAT) pathway of the bacterial cytoplasmic membrane mediates translocation only of proteins that accomplished a native-like conformation. We deploy this feature in modular selection systems for directed evolution, in which folding helpers as well as dimeric or oligomeric proteinprotein interactions enable TAT-dependent translocation of the resistance marker TEM -lactamase (L). Specifically, we demonstrate and analyze selection of (i) enhancers for folding by direct TAT translocation selection of a target protein interposed between the TorA signal sequence and L, (ii) dimeric or oligomeric proteinprotein interactions by hitchhiker translocation (HiT) selection of proteins fused to the TorA signal sequence and to the L, respectively and (iii) heterotrimeric proteinprotein interactions by combining HiT with protein fragment complementation selection of proteins fused to two split L fragments and TorA, respectively. The lactamase fragments were additionally engineered for improved activity and stability. Applicability was benchmarked with interaction partners of known affinity and multimerization whereby cellular fitness correlated well with biophysical protein properties. Ultimately, the HiT selection was employed to identify peptides, which specifically bind to leukemia- and melanoma-relevant target proteins (MITF and ETO) by coiled-coil or tetra-helix-bundle formation with high affinity. The various versions of TAT selection led to inhibiting peptides (iPEPs) of disease-promoting interactions and enabled so far difficult to achieve selections.}, language = {en} } @inproceedings{KuekenshoenerJeanChristophSpecketal.2011, author = {K{\"u}kensh{\"o}ner, Tim and Jean-Christoph, N. and Speck, J. and M{\"u}ller, Kristian M. and Arndt, Katja Maren}, title = {Targeting the microphthalmia associated transcription factor coiled coil domain with interfering peptides}, series = {The FEBS journal}, volume = {278}, booktitle = {The FEBS journal}, number = {6}, publisher = {Wiley-Blackwell}, address = {Malden}, issn = {1742-464X}, pages = {159 -- 159}, year = {2011}, language = {en} } @article{StaabWalossekNellessenetal.2010, author = {Staab, Paul R. and Walossek, J{\"o}rg and Nellessen, David and Gr{\"u}nberg, Raik and Arndt, Katja Maren and M{\"u}ller, Kristian M.}, title = {SynBioWave : a real-time communication platform for molecular and synthetic biology}, issn = {1367-4803}, doi = {10.1093/bioinformatics/btq518}, year = {2010}, abstract = {Synthetic Biology is advanced by many users and relies on the assembly of genetic elements to devices, systems and finally genomes. SynBioWave is a software suite that enables multiple distributed users to analyze and construct genetic parts in real-time collaboration. It builds on Google Wave and provides an extensible robot-robot-user communication framework, a menu driven user interface, biological data handling including DAS and an internal database communication. We demonstrate its use by implementing robots for gene-data retrieval, manipulation and display. The initial development of SynBioWave demonstrates the power of the underlying Google Wave protocol for Synthetic Biology and lays the foundation for continuous and user-friendly extensions. Specialized wave-robots with a manageable set of capabilities will divide and conquer the complex task of creating a genome in silico.}, language = {en} } @article{BrechunArndtWoolley2017, author = {Brechun, Katherine E. and Arndt, Katja Maren and Woolley, G. Andrew}, title = {Strategies for the photo-control of endogenous protein activity}, series = {Current opinion in structural biology : review of all advances ; evaluation of key references ; comprehensive listing of papers}, volume = {45}, journal = {Current opinion in structural biology : review of all advances ; evaluation of key references ; comprehensive listing of papers}, publisher = {Elsevier}, address = {London}, issn = {0959-440X}, doi = {10.1016/j.sbi.2016.11.014}, pages = {53 -- 58}, year = {2017}, language = {en} } @article{BrechunArndtWoolley2018, author = {Brechun, Katherine Emily and Arndt, Katja Maren and Woolley, G. Andrew}, title = {Selection of protein-protein interactions of desired affinities with a bandpass circuit}, series = {Journal of molecular biology : JMB}, volume = {431}, journal = {Journal of molecular biology : JMB}, number = {2}, publisher = {Elsevier}, address = {London}, issn = {0022-2836}, doi = {10.1016/j.jmb.2018.11.011}, pages = {391 -- 400}, year = {2018}, abstract = {We have developed a genetic circuit in Escherichia coli that can be used to select for protein-protein interactions of different strengths by changing antibiotic concentrations in the media. The genetic circuit links protein-protein interaction strength to beta-lactamase activity while simultaneously imposing tuneable positive and negative selection pressure for beta-lactamase activity. Cells only survive if they express interacting proteins with affinities that fall within set high- and low-pass thresholds; i.e. the circuit therefore acts as a bandpass filter for protein-protein interactions. We show that the circuit can be used to recover protein-protein interactions of desired affinity from a mixed population with a range of affinities. The circuit can also be used to select for inhibitors of protein-protein interactions of defined strength. (C) 2018 Elsevier Ltd. All rights reserved.}, language = {en} } @article{FeinerTeschnerTeschneretal.2019, author = {Feiner, Rebecca Christine and Teschner, Julian and Teschner, Kathrin E. and Radukic, Marco T. and Baumann, Tobias and Hagen, Sven and Hannappel, Yvonne and Biere, Niklas and Anselmetti, Dario and Arndt, Katja Maren and M{\"u}ller, Kristian Mark}, title = {rAAV Engineering for Capsid-Protein Enzyme Insertions and Mosaicism Reveals Resilience to Mutational, Structural and Thermal Perturbations}, series = {International journal of molecular sciences}, volume = {20}, journal = {International journal of molecular sciences}, number = {22}, publisher = {MDPI}, address = {Basel}, issn = {1422-0067}, doi = {10.3390/ijms20225702}, pages = {19}, year = {2019}, abstract = {Recombinant adeno-associated viruses (rAAV) provide outstanding options for customization and superior capabilities for gene therapy. To access their full potential, facile genetic manipulation is pivotal, including capsid loop modifications. Therefore, we assessed capsid tolerance to modifications of the structural VP proteins in terms of stability and plasticity. Flexible glycine-serine linkers of increasing sizes were, at the genetic level, introduced into the 587 loop region of the VP proteins of serotype 2, the best studied AAV representative. Analyses of biological function and thermal stability with respect to genome release of viral particles revealed structural plasticity. In addition, insertion of the 29 kDa enzyme beta-lactamase into the loop region was tested with a complete or a mosaic modification setting. For the mosaic approach, investigation of VP2 trans expression revealed that a Kozak sequence was required to prevent leaky scanning. Surprisingly, even the full capsid modification with beta-lactamase allowed for the assembly of capsids with a concomitant increase in size. Enzyme activity assays revealed lactamase functionality for both rAAV variants, which demonstrates the structural robustness of this platform technology.}, language = {en} } @book{Arndt2010, author = {Arndt, Katja Maren}, title = {Proteine zur Krebstherapie - Zielen, Steuern, Hemmen : Antrittsvorlesung 2010-12-08}, publisher = {Univ.-Bibl.}, address = {Potsdam}, year = {2010}, abstract = {Biotechnologie, Biologie, Protein Engineering, Therapeutische Peptide, Protein Design, Selektionssysteme / biotechnology, biology, protein enginieering, therapeutic peptides, protein design, selection systems}, language = {de} } @article{ZhangTimmArndtetal.2010, author = {Zhang, Fuzhong Z. and Timm, Katharina A. and Arndt, Katja Maren and Woolley, G. Andrew}, title = {Photocontrol of Coiled-Coil Proteins in Living Cells}, issn = {1433-7851}, doi = {10.1002/anie.201000909}, year = {2010}, abstract = {Light switching of the activity of a coiled-coil protein, the AP-1 transcription factor, in living cells was made possible by the introduction of a designed azobenzene-cross-linked dominant negative peptide, XAFosW (red and yellow in the picture). In the dark, XAFosW showed decreased helical content and decreased affinity for target Jun proteins (green); irradiation at 365 nm enhanced helicity and target affinity.}, language = {en} } @article{HagenBaumannWagneretal.2014, author = {Hagen, Sven and Baumann, Tobias and Wagner, Hanna J. and Morath, Volker and Kaufmann, Beate and Fischer, Adrian and Bergmann, Stefan and Schindler, Patrick and Arndt, Katja Maren and Mueller, Kristian M.}, title = {Modular adeno-associated virus (rAAV) vectors used for cellular virus-directed enzyme prodrug therapy}, series = {Scientific reports}, volume = {4}, journal = {Scientific reports}, publisher = {Nature Publ. Group}, address = {London}, issn = {2045-2322}, doi = {10.1038/srep03759}, pages = {11}, year = {2014}, abstract = {The pre-clinical and clinical development of viral vehicles for gene transfer increased in recent years, and a recombinant adeno-associated virus (rAAV) drug took center stage upon approval in the European Union. However, lack of standardization, inefficient purification methods and complicated retargeting limit general usability. We address these obstacles by fusing rAAV-2 capsids with two modular targeting molecules (DARPin or Affibody) specific for a cancer cell-surface marker (EGFR) while simultaneously including an affinity tag (His-tag) in a surface-exposed loop. Equipping these particles with genes coding for prodrug converting enzymes (thymidine kinase or cytosine deaminase) we demonstrate tumor marker specific transduction and prodrug-dependent apoptosis of cancer cells. Coding terminal and loop modifications in one gene enabled specific and scalable purification. Our genetic parts for viral production adhere to a standardized cloning strategy facilitating rapid prototyping of virus directed enzyme prodrug therapy (VDEPT).}, language = {en} } @article{HoffmannKruseArndt2016, author = {Hoffmann, Stefan A. and Kruse, Sabrina M. and Arndt, Katja Maren}, title = {Long-range transcriptional interference in E-coli used to construct a dual positive selection system for genetic switches}, series = {Nucleic acids research}, volume = {44}, journal = {Nucleic acids research}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {0305-1048}, doi = {10.1093/nar/gkw125}, pages = {12}, year = {2016}, abstract = {We have investigated transcriptional interference between convergent genes in E. coli and demonstrate substantial interference for inter-promoter distances of as far as 3 kb. Interference can be elicited by both strong \&\#963;70 dependent and T7 promoters. In the presented design, a strong promoter driving gene expression of a 'forward' gene interferes with the expression of a 'reverse' gene by a weak promoter. This arrangement allows inversely correlated gene expression without requiring further regulatory components. Thus, modulation of the activity of the strong promoter alters expression of both the forward and the reverse gene. We used this design to develop a dual selection system for conditional operator site binding, allowing positive selection both for binding and for non-binding to DNA. This study demonstrates the utility of this novel system using the Lac repressor as a model protein for conditional DNA binding, and spectinomycin and chloramphenicol resistance genes as positive selection markers in liquid culture. Randomized LacI libraries were created and subjected to subsequent dual selection, but mispairing IPTG and selection cues in respect to the wild-type LacI response, allowing the isolation of a LacI variant with a reversed IPTG response within three rounds of library generation and dual selection.}, language = {en} }