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Agnieszka Obarska-Kosinska's home page

Postdoctoral Researcher

Research
CV
Publications
Contact

Research

The main area of interest:

  • Peptide design
  • Structural modeling of protein and protein complexes
  • Analysis of protein sequence and structure

CV

Educations

  • 2010 - PhD in biochemistry; thesis: "Structural modeling of the multi-domain Type I, III, and IIC restriction-modification systems in combination with experimental data"
  • 2006 - 2010: PhD studies at the Institute of Biochemistry and Biophysics PAS, Pawinskiego 5a, 02-106 Warsaw
  • 2008 - M.Sc. degree in biophysics; thesis: "Estimation of the effective length of chemical cross-linkers using computer simulations" defended at the Faculty of Physics, Collegium of Individual Inter-faculty Studies in Mathematics and Computer Sciences, University of Warsaw
  • 2006 - M.Sc. degree in molecular biology; thesis "Comparing analysis of type I restriction-modification systems and structural model for the multisubunit type IC R-M DNA methyltransferase M.EcoR124I in complex with DNA" defended at the Faculty of Biology, Collegium of Individual Inter-faculty Studies in Mathematics and Computer Sciences, University of Warsaw
  • 2004 - B.Sc. degree in molecular biology; thesis "Homology modelling of the HsdR subunit of type I restriction enzyme EcoR124I" defended at the Faculty of Biology, Collegium of Individual Inter-faculty Studies in Mathematics and Computer Sciences, University of Warsaw
  • 2001-2008: studies at the Collegium of Individual Inter-faculty Studies in Mathematics and Computer Sciences, University of Warsaw

Professional experience

  • 03.2010 - present: Postdoctoral researcher in Biocomputing Group at the Department of Biochemical Sciences, "Sapienza" University, Rome, Italy
  • 10.2008 - Participation in the EMBO course on Docking Predictions of Protein-Protein Interactions, Barcelona
  • 2006 - 2010: PhD student, Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland (supervisor: prof. Dr. hab. Janusz M. Bujnicki)
  • 12.2006 -Visiting student at the Chemistry Department, University of Edinburgh, (supervisor: Dr. David T.F. Dryden)
  • 05-08.2006 - Participation in 7th edition of the Critical Assessment of Techniques for Protein Structure Prediction (CASP7) as a member of Genesilico group
  • 12.2005 - Visiting Student, National Centre for Biomolecular Research, Masaryk University, Faculty of Science, Brno, Czech Republic (Dr. J. Damborsky group)
  • 09/10.2005 - Visiting Student at the Computational Biochemistry and Biophysics lab, Research Group on Biomedical Informatics (GRIB) - IMIM/UPF, Barcelona, Spain (Dr. J. Villà i Freixa group) – HPC-Europa Fellowship
  • 08.2004 - Visiting Student, National Centre for Biomolecular Research, Masaryk University, Faculty of Science, Brno, Czech Republic (Dr. J. Damborsky group)
  • 07.2004 - Participation in the EMBO Practical Course on Biomolecular Simulation, Paris
  • 07-09.2004 - Participation in 6th edition of Critical Assessment of Techniques for Protein Structure Prediction (CASP6) as a member of one of the winner groups - Genesilico group
  • 2003-2006 - Student Volunteer, Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland (supervisor: prof. Dr. hab. Janusz M. Bujnicki)

Publications

  1. Kennaway CK, Taylor JE, Song CF, Potrzebowski W, Nicholson W, White JH, Swiderska A, Obarska-Kosinska A, Callow P, Cooper LP, Roberts GA, Artero JB, Bujnicki JM, Trinick J, Kneale GG, Dryden DTF "Structure and operation of the DNA-translocating Type I DNA restriction enzymes" Genes Dev 2012 Jan 1;26(1):92-104.
  2. Kennaway CK J, Obarska-Kosinska A, White JK, Tuszynska I, Cooper LP, Bujnicki JM, Trinick J, Dryden DTF. "The structure of M.EcoKI Type I DNA methyltransferase with a DNA mimic antirestriction protein" Nucleic Acids Res 2009 Feb;37(3):762-70
  3. Nakonieczna J, Kaczorowski T, Obarska-Kosinska A, Bujnicki JM. "Functional analysis of the MmeI restriction-modification enzyme from a methanol utilizer Methylophilus methylotrophus: A subtype IIC enzyme related to Type I enzymes" Appl Environ Microbiol 2009 Jan;75(1):212-23
  4. Obarska-Kosinska A, Taylor JE, Callow P, Orlowski J, Bujnicki JM, Kneale GG "HsdR subunit of the Type I restriction-modification enzyme EcoR124I: biophysical characterisation and structural modeling" J Mol Biol 2008 Feb 15;376(2):438-52
  5. Cymerman IA, Obarska A, Skowronek KJ, Lubys A, Bujnicki JM. "Identification of a new subfamily of HNH nucleases and experimental characterization of a representative member, HphI restriction endonuclease" Proteins 2006 Dec 1;65(4):867-76
  6. Obarska A, Blundell A, Feder M, Patel J, Vejsadova S, Sisakova E, Weiserova M, Bujnicki JM, Firman K. "Structural model for the multisubunit Type IC restriction-modification DNA methyltransferase M.EcoR124I in complex with DNA" Nucleic Acids Res 2006 Apr 13;34(7):1992-2005
  7. Tkaczuk KL, Obarska A, Bujnicki JM. "Molecular phylogenetics and comparative modeling of HEN1, a methyltransferase involved in plant microRNA biogenesis" BMC Evol Biol 2006 Jan 24;6(1):6
  8. Kosinski J, Gajda MJ, Cymerman IA, Kurowski MA, Pawlowski M, Boniecki M, Obarska A, Papaj G, Sroczynska-Obuchowicz P, Tkaczuk KL, Sniezynska P, Sasin JM, Augustyn A, Bujnicki JM, Feder M "FRankenstein becomes a cyborg: the automatic recombination and realignment of Fold-Recognition models in CASP6" Proteins 2005;61 Suppl 7:106-13

Contact

Biocomputing group
Department of Biochemical Sciences
"Sapienza" University
P.le A. Moro, 5
00185 Rome - Italy
email: aobarska@gmail.com
email: Agnieszka.Obarska@uniroma1.it

Last Updated ( Wednesday, 22 February 2012 14:50 )