User:Kersten S. Rabe

Contact Info

Kersten S. Rabe - Half of him

• Dr. rer. nat. Dipl. Biochem. Kersten S. Rabe
• California Institute of Technology
• Mailcode 210-41
• 1200 East California Boulevard
• Pasadena, CA 91125
• USA
• Email me through OpenWetWare

I work as a Post-Doc in the lab of Frances Arnold.

Education

• 2010-present Post-doc in the group of Frances Arnold as a DAAD stipendiary
• 2009-2010 Post-Doc with Prof. Niemeyer
• 2005-2009 phD work in the group of Prof. Niemeyer at University of Dortmund, Germany, on Protein-DNA-conjugates. Title of thesis: "Herstellung rekombinanter Proteine für die Synthese von DNA-Protein-Konjugaten". Mark: summa cum laude ("Ausgezeichnet")
• 2004 eight month research assistant at the group of Prof. Sprinzl, University of Bayreuth, Germany
• 2004 Diploma (Biochemistry), Group of Prof. Sprinzl, University of Bayreuth, Germany
• Research semester, Group of Dr. Ubbink, Protein Chemistry (former Metallo Protein Research), University of Leiden, Netherlands: "The Transient Complex of Cytochrome c and Cytochrome f - Investigated by Heteronuclear NMR"
• 1999-2004, Graduate studies in Biochemistry, University of Bayreuth
• 1999 Intermediate Diploma ("Vordiplom")
• 1997-1999, Undergraduate studies in Biochemistry, University of Bayreuth
• 1996/97 Thirteen month of civilian service
• 1996 finished Abitur (final secondary school examination) at the Graf-Anton-Günther-Schule, Oldenburg, Germany

Research interests

1. Synthetic biology
2. Nanobiotechnology
3. Chemical Biology

Artwork

Movie of CYP119A1, active site and surface

During my stay at Leiden University, where I did some NMR on transient protein complexes, I got into first contact with raytracing. At the moment I am using Swissprot Deepview and Chimera to work with .pdb files and Moray to set up whole scences. For rendering I usually use povray3.6 (esp. to generate .png files with transparent background). For the coverpicture shown below I used a combination of all programs.

I worked a lot with the thermostable P450 CYP119A1, therefore I prepared a little movie for my PhD defence (on the right). In this movie you can see the P450 enzyme CYP119A1 with the inhibitor phenylimidazol bound to the active site. First, the overall fold is shown with the α-helices displayed in blue, the β-sheets in green and turns in grey. Subsequently the van-der-waals surface of the protein is displayed. Then the camera zooms into the active center. You can nicely see that "underneath" the central iron in the heme cofactor there is a cystein as fifth ligand and that the inhibitor occupies the sixth coordinationsite. Afterwards the camera zooms out again and the primary amine groups on the surface of the protein are shown. The movie was prepared from the threedimensional structure 1F4T with the program Chimera and re-coded to the .ogg format using the SUPER Encoder.

Publications

First author

April 2009 I designed the coverpicture for ChemBioChem, where I could show my rendering skills again. [1]

1. Rabe KS, Erkelenz M, Kiko K, and Niemeyer CM. Peroxidase activity of bacterial cytochrome P450 enzymes: modulation by fatty acids and organic solvents. Biotechnol J. 2010 Aug;5(8):891-9. DOI:10.1002/biot.201000028 |
2. Rabe KS and Niemeyer CM. Hydrogels: Gene jelly. Nat Mater. 2009 May;8(5):370-2. DOI:10.1038/nmat2434 |
3. Rabe KS, Spengler M, Erkelenz M, Müller J, Gandubert VJ, Hayen H, and Niemeyer CM. Screening for cytochrome p450 reactivity by harnessing catalase as reporter enzyme. Chembiochem. 2009 Mar 2;10(4):751-7. DOI:10.1002/cbic.200800750 |

4. Rabe KS, Feldkamp U, and Niemeyer CM.

   Semisynthetic DNA-protein conjugates for fabrication of nucleic acid based nanostructures.

   AIP Conf. Proc. 2009; 1062(1) 19-32. doi: 10.1063/1.3012299 Permalink

5. Rabe KS, Gandubert VJ, Spengler M, Erkelenz M, and Niemeyer CM. Engineering and assaying of cytochrome P450 biocatalysts. Anal Bioanal Chem. 2008 Nov;392(6):1059-73. DOI:10.1007/s00216-008-2248-9 |
6. Rabe KS, Kiko K, and Niemeyer CM. Characterization of the peroxidase activity of CYP119, a thermostable P450 from Sulfolobus acidocaldarius. Chembiochem. 2008 Feb 15;9(3):420-5. DOI:10.1002/cbic.200700450 |

Co-author

7. Svahn MG, Rabe KS, Barger G, El-Andaloussi S, Simonson OE, Didier B, Olivier R, Dumy P, Brandén LJ, Niemeyer CM, and Smith CIE.

   High-Throughput Identification of Combinatorial Ligands for DNA Delivery in Cell Culture.

   AIP Conf. Proc. 2009; 1062(1) 73-88. doi: 10.1063/1.3012306 Permalink

8. Agafonov DE, Rabe KS, Grote M, Voertler CS, and Sprinzl M. C-terminal modifications of a protein by UAG-encoded incorporation of puromycin during in vitro protein synthesis in the absence of release factor 1. Chembiochem. 2006 Feb;7(2):330-6. DOI:10.1002/cbic.200500358 |
9. Agafonov DE, Rabe KS, Grote M, Huang Y, and Sprinzl M. The esterase from Alicyclobacillus acidocaldarius as a reporter enzyme and affinity tag for protein biosynthesis. FEBS Lett. 2005 Apr 11;579(10):2082-6. DOI:10.1016/j.febslet.2005.02.059 |
10. Crowley PB, Rabe KS, Worrall JA, Canters GW, and Ubbink M. The ternary complex of cytochrome f and cytochrome c: identification of a second binding site and competition for plastocyanin binding. Chembiochem. 2002 Jun 3;3(6):526-33. DOI:10.1002/1439-7633(20020603)3:6<526::AID-CBIC526>3.0.CO;2-N |

Patents

SPRINZL MATHIAS (DE); AGAFONOV DMITRY (DE); RABE KERSTEN (DE) ESTERASES FOR MONITORING PROTEIN BIOSYNTHESIS IN VITRO Publication number: WO2006082059

SPRINZL MATHIAS (DE); AGAFONOV DMITRY (DE); RABE KERSTEN (DE) CELL-FREE TRANSLATION SYSTEM FOR THE PRODUCTION OF (CHEMICALLY) MODIFIED PROTEINS Publication number: WO2006082058

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