User:Kersten S. Rabe

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NEW WEBPAGE! STILL SOMEWHAT UNDER CONSTRUCTION:
 +
https://sites.google.com/site/kerstenstefanrabe/home
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==Contact Info==
==Contact Info==
 +
 +
NEW WEBPAGE! STILL SOMEWHAT UNDER CONSTRUCTION:
 +
https://sites.google.com/site/kerstenstefanrabe/home
 +
[[Image:KerstenSRabe.jpg|thumb|right|Kersten S. Rabe - Half of him]]
[[Image:KerstenSRabe.jpg|thumb|right|Kersten S. Rabe - Half of him]]
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*Dipl. Biochem. Kersten S. Rabe
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*Dr. rer. nat. Dipl. Biochem. Kersten S. Rabe
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*TU Dortmund
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*California Institute of Technology
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*Otto-Hahn Strasse 6
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*Mailcode 210-41
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*BCMT
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*1200 East California Boulevard
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*44227 Dortmund, Germany
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*Pasadena, CA 91125
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*USA
*[[Special:Emailuser/Kersten S. Rabe|Email me through OpenWetWare]]
*[[Special:Emailuser/Kersten S. Rabe|Email me through OpenWetWare]]
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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")
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NEW WEBPAGE! STILL SOMEWHAT UNDER CONSTRUCTION:
 +
https://sites.google.com/site/kerstenstefanrabe/home
 +
 
 +
I work as a Post-Doc in the lab of Frances Arnold.
==Education==
==Education==
<!--Include info about your educational background-->
<!--Include info about your educational background-->
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* From June 2010 on I will join the group of [http://www.che.caltech.edu/groups/fha/ Frances Arnold] as a DAAD stipendiary
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* 2010-present Post-doc in the group of [http://www.che.caltech.edu/groups/fha/ Frances Arnold] as a DAAD stipendiary
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* 2009-present Post-Doc with Prof. Niemeyer
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* 2009-2010 Post-Doc with Prof. Niemeyer
* 2005-2009 phD work in the [http://www.chemie.uni-dortmund.de/groups/niemeyer/index.html group of Prof. Niemeyer] at University of [http://www.uni-dortmund.de/uni/Uni/index.html Dortmund], Germany, on Protein-DNA-conjugates. Title of thesis: ''"Herstellung rekombinanter Proteine für die Synthese von DNA-Protein-Konjugaten"''. Mark: summa cum laude ("Ausgezeichnet")
* 2005-2009 phD work in the [http://www.chemie.uni-dortmund.de/groups/niemeyer/index.html group of Prof. Niemeyer] at University of [http://www.uni-dortmund.de/uni/Uni/index.html 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, [http://www.uni-bayreuth.de/ University of Bayreuth], Germany
* 2004 eight month research assistant at the group of Prof. Sprinzl, [http://www.uni-bayreuth.de/ University of Bayreuth], Germany
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# Nanobiotechnology
# Nanobiotechnology
# Chemical Biology
# Chemical Biology
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==Artwork==
 
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[[Image:CYP119A1_fat.png|thumb|right|120px|[[Media:CYP119A1.ogg|Movie of CYP119A1, active site and surface]]]]
 
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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 whole 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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<br><br>
 
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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).
 
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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.
 
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Afterwards the camera zooms out again and the primary amine groups on the surface of the protein are shown.
 
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The movie was prepared from the threedimensional structure 1F4T with the program [http://www.cgl.ucsf.edu/chimera/ Chimera] and re-coded to the .ogg format using the [http://www.erightsoft.com/SUPER.html SUPER Encoder].
 
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<br>
 
==Publications==
==Publications==
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If the external linking system seems broken, you will have to go to pubmed yourself. -> Click this: [http://www.ncbi.nlm.nih.gov/pubmed?term=Rabe%20KS]
'''First author'''
'''First author'''
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[[Image:091230CoverCBC.png|thumb|right|April 2009 I designed the coverpicture for ChemBioChem, where I could show my rendering skills again. [http://www3.interscience.wiley.com/journal/122213416/issue]]]
[[Image:091230CoverCBC.png|thumb|right|April 2009 I designed the coverpicture for ChemBioChem, where I could show my rendering skills again. [http://www3.interscience.wiley.com/journal/122213416/issue]]]
<biblio>
<biblio>
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#Paper1 pmid=19387449
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#Paper1 pmid=20632328
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#Paper2 pmid=19241405
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#Paper2 pmid=19387449
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#Paper3 Rabe KS, Feldkamp U, and Niemeyer CM.
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#Paper3 pmid=19241405
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#Paper4 Rabe KS, Feldkamp U, and Niemeyer CM.
''Semisynthetic DNA-protein conjugates for fabrication of nucleic acid based nanostructures.''  
''Semisynthetic DNA-protein conjugates for fabrication of nucleic acid based nanostructures.''  
AIP Conf. Proc. 2009; 1062(1) 19-32. doi: 10.1063/1.3012299 [http://link.aip.org/link/?APCPCS/1062/19/1 Permalink]
AIP Conf. Proc. 2009; 1062(1) 19-32. doi: 10.1063/1.3012299 [http://link.aip.org/link/?APCPCS/1062/19/1 Permalink]
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#Paper4 pmid=18622752
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#Paper5 pmid=18622752
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#Paper5 pmid=18157853
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#Paper6 pmid=18157853
</biblio>
</biblio>
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<biblio>
<biblio>
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#Paper6 Svahn MG, Rabe KS, Barger G, El-Andaloussi S, Simonson OE, Didier B, Olivier R, Dumy P, Brandén LJ, Niemeyer CM, and Smith CIE.
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#Paper7 pmid=21031395
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#Paper8 pmid=20721950
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#Paper9 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.''  
''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 [http://link.aip.org/link/?APCPCS/1062/73/1 Permalink]
AIP Conf. Proc. 2009; 1062(1) 73-88. doi: 10.1063/1.3012306 [http://link.aip.org/link/?APCPCS/1062/73/1 Permalink]
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#Paper7 pmid=16444758
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#Paper10 pmid=16444758
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#Paper8 pmid=15811322
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#Paper11 pmid=15811322
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#Paper9 pmid=12325008
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#Paper12 pmid=12325008
</biblio>
</biblio>
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CELL-FREE TRANSLATION SYSTEM FOR THE PRODUCTION OF (CHEMICALLY) MODIFIED PROTEINS
CELL-FREE TRANSLATION SYSTEM FOR THE PRODUCTION OF (CHEMICALLY) MODIFIED PROTEINS
Publication number: [http://www.wipo.int/pctdb/en/wo.jsp?IA=WO2006082058&DISPLAY=DESC WO2006082058]
Publication number: [http://www.wipo.int/pctdb/en/wo.jsp?IA=WO2006082058&DISPLAY=DESC WO2006082058]
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 +
==Artwork==
 +
[[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 whole 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.
 +
<br><br>
 +
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.
 +
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 to the .ogg format using the [http://www.erightsoft.com/SUPER.html SUPER Encoder].
 +
<br>
==Useful links==
==Useful links==
*[[OpenWetWare:Welcome|Introductory tutorial]]
*[[OpenWetWare:Welcome|Introductory tutorial]]
*[[Help|OpenWetWare help pages]]
*[[Help|OpenWetWare help pages]]

Current revision

NEW WEBPAGE! STILL SOMEWHAT UNDER CONSTRUCTION: https://sites.google.com/site/kerstenstefanrabe/home

Contents

Contact Info

NEW WEBPAGE! STILL SOMEWHAT UNDER CONSTRUCTION: https://sites.google.com/site/kerstenstefanrabe/home

Kersten S. Rabe - Half of him
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

NEW WEBPAGE! STILL SOMEWHAT UNDER CONSTRUCTION: https://sites.google.com/site/kerstenstefanrabe/home

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

Publications

If the external linking system seems broken, you will have to go to pubmed yourself. -> Click this: [2]

First author

April 2009 I designed the coverpicture for ChemBioChem, where I could show my rendering skills again. [1]
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. . pmid:20632328. PubMed HubMed [Paper1]
  2. Rabe KS and Niemeyer CM. . pmid:19387449. PubMed HubMed [Paper2]
  3. Rabe KS, Spengler M, Erkelenz M, Müller J, Gandubert VJ, Hayen H, and Niemeyer CM. . pmid:19241405. PubMed HubMed [Paper3]
  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 [Paper4]
  5. Rabe KS, Gandubert VJ, Spengler M, Erkelenz M, and Niemeyer CM. . pmid:18622752. PubMed HubMed [Paper5]
  6. Rabe KS, Kiko K, and Niemeyer CM. . pmid:18157853. PubMed HubMed [Paper6]
All Medline abstracts: PubMed HubMed

Co-author

  1. Saccà B, Meyer R, Erkelenz M, Kiko K, Arndt A, Schroeder H, Rabe KS, and Niemeyer CM. . pmid:21031395. PubMed HubMed [Paper7]
  2. Rajendran V, König A, Rabe KS, and Niemeyer CM. . pmid:20721950. PubMed HubMed [Paper8]
  3. 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 [Paper9]
  4. Agafonov DE, Rabe KS, Grote M, Voertler CS, and Sprinzl M. . pmid:16444758. PubMed HubMed [Paper10]
  5. Agafonov DE, Rabe KS, Grote M, Huang Y, and Sprinzl M. . pmid:15811322. PubMed HubMed [Paper11]
  6. Crowley PB, Rabe KS, Worrall JA, Canters GW, and Ubbink M. . pmid:12325008. PubMed HubMed [Paper12]
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

Artwork

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.

Useful links

Personal tools