@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{AzumaKuekenshoenerMaetal.2014, author = {Azuma, Yusuke and Kuekenshoener, Tim and Ma, Guangyong and Yasunaga, Jun-ichiro and Imanishi, Miki and Tanaka, Gen and Nakase, Ikuhiko and Maruno, Takahiro and Kobayashi, Yuji and Arndt, Katja Maren and Matsuoka, Masao and Futaki, Shiroh}, title = {Controlling leucine-zipper partner recognition in cells through modification of a-g interactions}, series = {Chemical communications}, volume = {50}, journal = {Chemical communications}, number = {48}, publisher = {Royal Society of Chemistry}, address = {Cambridge}, issn = {1359-7345}, doi = {10.1039/c4cc00555d}, pages = {6364 -- 6367}, year = {2014}, abstract = {By focusing on the a-g interactions, successful design and selection were accomplished to obtain a leucine-zipper segment that discriminates the appropriate partner over another that provides very similar patterns of electrostatic interactions.}, language = {en} } @misc{AzumaKuekenshoenerMaetal.2014, author = {Azuma, Yusuke and K{\"u}kensh{\"o}ner, Tim and Ma, Guangyong and Yasunaga, Jun-ichiro and Imanishi, Miki and Tanaka, Gen and Nakase, Ikuhiko and Maruno, Takahiro and Kobayashi, Yuji and Arndt, Katja Maren and Matsuoka, Masao and Futaki, Shiroh}, title = {Controlling leucine-zipper partner recognition in cells through modification of a-g interactions}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-98758}, pages = {4}, year = {2014}, abstract = {By focusing on the a-g interactions, successful design and selection were accomplished to obtain a leucine-zipper segment that discriminates the appropriate partner over another that provides very similar patterns of electrostatic interactions.}, language = {en} } @misc{BaumannArndtMueller2013, author = {Baumann, Tobias and Arndt, Katja Maren and M{\"u}ller, Kristian M.}, title = {Directional cloning of DNA fragments using deoxyinosine-containing oligonucleotides and endonuclease V}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {983}, issn = {1866-8372}, doi = {10.25932/publishup-43108}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-431085}, pages = {13}, year = {2013}, abstract = {Background: DNA fragments carrying internal recognition sites for the restriction endonucleases intended for cloning into a target plasmid pose a challenge for conventional cloning. Results: A method for directional insertion of DNA fragments into plasmid vectors has been developed. The target sequence is amplified from a template DNA sample by PCR using two oligonucleotides each containing a single deoxyinosine base at the third position from the 5' end. Treatment of such PCR products with endonuclease V generates 3' protruding ends suitable for ligation with vector fragments created by conventional restriction endonuclease reactions. Conclusions: The developed approach generates terminal cohesive ends without the use of Type II restriction endonucleases, and is thus independent from the DNA sequence. Due to PCR amplification, minimal amounts of template DNA are required. Using the robust Taq enzyme or a proofreading Pfu DNA polymerase mutant, the method is applicable to a broad range of insert sequences. Appropriate primer design enables direct incorporation of terminal DNA sequence modifications such as tag addition, insertions, deletions and mutations into the cloning strategy. Further, the restriction sites of the target plasmid can be either retained or removed.}, language = {en} } @article{BaumannArndtMueller2013, author = {Baumann, Tobias and Arndt, Katja Maren and M{\"u}ller, Kristian M.}, title = {Directional cloning of DNA fragments using deoxyinosine-containing oligonucleotides and endonuclease V}, series = {BMC biotechnology}, volume = {13}, journal = {BMC biotechnology}, number = {10}, publisher = {BioMed Central}, address = {London}, issn = {1472-6750}, doi = {10.1186/1472-6750-13-81}, pages = {11}, year = {2013}, abstract = {Background: DNA fragments carrying internal recognition sites for the restriction endonucleases intended for cloning into a target plasmid pose a challenge for conventional cloning. Results: A method for directional insertion of DNA fragments into plasmid vectors has been developed. The target sequence is amplified from a template DNA sample by PCR using two oligonucleotides each containing a single deoxyinosine base at the third position from the 5' end. Treatment of such PCR products with endonuclease V generates 3' protruding ends suitable for ligation with vector fragments created by conventional restriction endonuclease reactions. Conclusions: The developed approach generates terminal cohesive ends without the use of Type II restriction endonucleases, and is thus independent from the DNA sequence. Due to PCR amplification, minimal amounts of template DNA are required. Using the robust Taq enzyme or a proofreading Pfu DNA polymerase mutant, the method is applicable to a broad range of insert sequences. Appropriate primer design enables direct incorporation of terminal DNA sequence modifications such as tag addition, insertions, deletions and mutations into the cloning strategy. Further, the restriction sites of the target plasmid can be either retained or removed.}, 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} } @misc{BrechunWoolleyArndt2017, author = {Brechun, Katherine E. and Woolley, Andrew and Arndt, Katja Maren}, title = {A Bacterial Bandpass Assay for Protein-Protein Interactions}, series = {Protein science : a publication of the Protein Society}, volume = {26}, journal = {Protein science : a publication of the Protein Society}, publisher = {Wiley}, address = {Hoboken}, issn = {0961-8368}, pages = {198 -- 198}, year = {2017}, language = {en} } @article{BrechunZhenJaikaranetal.2019, author = {Brechun, Katherine E. and Zhen, Danlin and Jaikaran, Anna and Borisenko, Vitali and Kumauchi, Masato and Hoff, Wouter D. and Arndt, Katja Maren and Woolley, Andrew G}, title = {Detection of Incorporation of p-Coumaric Acid into Photoactive Yellow Protein Variants in Vivo}, series = {Biochemistry}, volume = {58}, journal = {Biochemistry}, number = {23}, publisher = {American Chemical Society}, address = {Washington}, issn = {0006-2960}, doi = {10.1021/acs.biochem.9b00279}, pages = {2682 -- 2694}, year = {2019}, abstract = {We report the design and characterization of photoactive yellow protein (PYP)-blue fluorescent protein (mTagBFP) fusion constructs that permit the direct assay of reconstitution and function of the PYP domain. These constructs allow for in vivo testing of co-expression systems for enzymatic production of the p-coumaric acid-based PYP chromophore, via the action of tyrosine ammonia lyase and p-coumaroyl-CoA ligase (pCL or 4CL). We find that different 4CL enzymes can function to reconstitute PYP, including 4CL from Arabidopsis thaliana that can produce similar to 100\% holo-PYP protein under optimal conditions. mTagBFP fusion constructs additionally enable rapid analysis of effects of mutations on PYP photocycles. We use this mTagBFP fusion strategy to demonstrate in vivo reconstitution of several PYP-based optogenetic tools in Escherichia coli via a biosynthesized chromophore, an important step for the use of these optogenetic tools in vivo in diverse hosts.}, 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} }