User:Kersten S. Rabe

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==Artwork==
==Artwork==
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[[Image:CYP119A1_fat.png|thumb|right|120px|[[Media:CYP119A1.ogg|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 [http://spdbv.vital-it.ch/ Swissprot Deepview] and [http://www.cgl.ucsf.edu/chimera/ Chimera] to work with .pdb files and [http://www.stmuc.com/moray/ Moray] to set up whloe scences. For rendering I usually use [http://www.povray.org/ povray3.6] (esp. to generate .png files with transparent background). For the coverpicture shown below I used a combination of all programs.
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 [http://spdbv.vital-it.ch/ Swissprot Deepview] and [http://www.cgl.ucsf.edu/chimera/ Chimera] to work with .pdb files and [http://www.stmuc.com/moray/ Moray] to set up whloe scences. For rendering I usually use [http://www.povray.org/ povray3.6] (esp. to generate .png files with transparent background). For the coverpicture shown below I used a combination of all programs.
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I worked a lot with the thermostable P450 CYP119A1, therefore I prepared a little [[Media:CYP119A1.ogg|movie]] for my PhD defence (on the right). [[Image:CYP119A1_fat.png|thumb|right|120px|[[Media:CYP119A1.ogg|Movie of CYP119A1, active site and surface]]]]
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I worked a lot with the thermostable P450 CYP119A1, therefore I prepared a little [[Media:CYP119A1.ogg|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.
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.
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 [http://www.cgl.ucsf.edu/chimera/ Chimera] and re-coded using the [http://www.erightsoft.com/SUPER.html SUPER Encoder].
The movie was prepared from the threedimensional structure 1F4T with the program [http://www.cgl.ucsf.edu/chimera/ Chimera] and re-coded using the [http://www.erightsoft.com/SUPER.html SUPER Encoder].
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Revision as of 08:53, 30 December 2009

Contents

Contact Info

Kersten S. Rabe - Half of him
Kersten S. Rabe - Half of him

I work as a Post-Doc in the Niemeyer lab at Dortmund University. In Dec. 2009 I finished my time as Doktorand with "summa cum laude" ("Ausgezeichnet")

Education

  • 2009-present 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
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 whloe 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 using the SUPER Encoder.

Publications

First author

April 2009 I could design the coverpicture for ChemBioChem, where I could show my rendering skills again. [1]
April 2009 I could design the coverpicture for ChemBioChem, where I could show my rendering skills again. [1]
  1. Rabe KS and Niemeyer CM. . pmid:19387449. PubMed HubMed [Paper1]
  2. Rabe KS, Spengler M, Erkelenz M, Müller J, Gandubert VJ, Hayen H, and Niemeyer CM. . pmid:19241405. PubMed HubMed [Paper2]
  3. 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 [Paper3]
  4. Rabe KS, Gandubert VJ, Spengler M, Erkelenz M, and Niemeyer CM. . pmid:18622752. PubMed HubMed [Paper4]
  5. Rabe KS, Kiko K, and Niemeyer CM. . pmid:18157853. PubMed HubMed [Paper5]
All Medline abstracts: PubMed HubMed

Co-author

  1. 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 [Paper6]
  2. Agafonov DE, Rabe KS, Grote M, Voertler CS, and Sprinzl M. . pmid:16444758. PubMed HubMed [Paper7]
  3. Agafonov DE, Rabe KS, Grote M, Huang Y, and Sprinzl M. . pmid:15811322. PubMed HubMed [Paper8]
  4. Crowley PB, Rabe KS, Worrall JA, Canters GW, and Ubbink M. . pmid:12325008. PubMed HubMed [Paper9]
All Medline abstracts: PubMed HubMed

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

Useful links

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