Laboratory of Bioinformatics and Protein Engineering

El Capo: Software development: Sr.Research Assistant: Ph.D. students: Research Assistants: Applied Bioinformatics: Ph.D. students: Research Assistants: Undergraduate students: Molecular Biology: Research Coordinator: Ph.D. students: Research Assistants: Undergraduate students: Office management: Computer administration: Alumni, former members, former students, visitors etc.:

Janusz M. Bujnicki (PhD, DHabil bioinformatics) Michal Gajda (MSc computer science) Michal A. Kurowski (MD medicine) Joanna M. Sasin (MSc computer science, MSc biology) Michal Boniecki (MSc chemistry) Ryszard Matlak (MSc computer science) Michal Pietal (MSc mathematics) Andrzej Kaminski (MSc biotechnology, BSc computer science) Maciej Fijalkowski Marcin Feder (MSc biotechology) Karolina L. Tkaczuk (MSc biotechnology) Grzegorz Papaj (MSc biotechnology) Jan Kosinski (MSc biotechnology) Marcin Pawlowski (MSc microbiology) Irina Tuszynska (MSc chemistry) Agnieszka Obarska (BSc) Stanislaw Dunin-Horkawicz (BSc) Anna Muszewska (BSc) Jerzy Orlowski (BSc) Krzysztof J. Skowronek (PhD microbiology) Iwona A. Cymerman (MSc biotechnology) Agnieszka Chmiel (MSc biotechnology) Sebastian Pawlak (MSc molecular biology) Elzbieta Purta (MSc biochemistry) Malgorzata Durawa (MSc molecular biology) Katarzyna Filip Michal Wrzesinski (MSc) Jan Kogut Elizaveta Koudan (FEBS short-term fellow 2003) Sylwia Owczarek (student-volunteer 2003) Aleksandra Solyga (student-volunteer 2003) Janusz Debski (MSc bioinformatics 2003, now IBB, Warsaw) Mariusz Zawadzki (student-volunteer 2003) Tomasz Jurkowski (MSc molecular biology/bioinformatics 2004, now International University Bremen) Paulina Sonta (student-volunteer 2004) Anna Augustyn (student-volunteer 2004) Marta Kaczor (research assistant 2004) Grzegorz Wrona (student-volunteer 2004) Anna Karnkowska (student-volunteer 2004) Dominik Sidorek (student-volunteer 2004) Agnieszka Kwiatek (postdoc 2004) Michal Rajkowski (computer administrator 2005) Eva Chovancova (short-term fellow 2005) Anastasia Bakulina (short term fellow 2005) Rut Klinger (student-volunteer 2005) Maciej Stopa (computer administrator 2005) Luis Giron (short-term fellow 2005) Agata Kamaszewska (student-volunteer 2005) Krzysztof Jurkowski (student-volunteer 2005) Szymon Micyk (student-volunteer 2005) Paulina Sroczynska-Obuchowicz (research assistant, 2004-2005)

Projects:

• Development of methods for protein structure determination based on low-resolution experimental data is our current focus. We collaborate on several complementary projects with various structural biologists - theoreticians and experimentalists: Dr. Matthias Bochtler (IIMCB, Warsaw, Poland), Andrzej Kolinski (Univeristy of Warsaw, Poland), Prof. Alan Friedman (Purdue Univeristy, W.Lafayette, IN, USA), Dr. Chris Bailey-Kellogg (Darmouth College, USA).
  
• Modeling and experimental validation of structure predictions for restriction enzymes and related nucleases. A combination of fold recognition and homology modeling techniques is used to predict the overall fold and identify catalytic and DNA-binding residues of various REases. Site-directed mutagenesis, cross-linking, and biophysical methods for low-resolution structural characterization are employed to validate the models. Some of the experiments are analyzed in house, others in collaboration or by collaborators: Prof. Alfred Pingoud (Justus-Liebig Universitaet, Giessen), Prof. Valakunja Nagaraja and Prof. D.N.Rao (Indian Institute of Science, Bangalore), Dr. Alexander Solonin (Russian Academy of Sciences, Puschino, Russia), Prof. Jacek Otlewski (Univeristy of Wroclaw, Poland)
  
• Discovery of novel human DNA repair enzymes using bioinformatics is a collaborative project initiated by Prof. Ashok S. Bhagwat (Wayne State University, Detroit, MI, USA), which aims at identification and characterization of novel human DNA repair enzymes in silico, in vitro and in vivo.
  
• Engineering of DNA methyltransferases This project is focused on bioinformatics-guided engineering of structures and functional properties of DNA MTases (different permutations, substrate specificities and mechanisms of the enzymatic reaction). This project is carried out in collaboration with Dr. Monika Radlinska (Institute of Microbiology, University of Warsaw, Poland) and Dr. Saulius Klimasauskas (Institute of Biotechnology, Vilnius, Lithuania).
  
• RNA methyltransferases - the evolution of structure-function relationships in RNA MTases is studied by combination of theoretical and experimental approaches. Novel RNA modification enzymes are predicted using bioinformatics tools and characterized experimentally. Key collaborators: Dr. Bruno Lapeyre (CNRS, Montpellier, France), Dr. Henri Grosjean (CNRS, Gif-sur-Yvette, France), Dr. Louis Droogmans (University of Bruxelles, Belgium), Dr. James Anderson (Marquette University, Milwaukee, WI, USA), Dr. Kent Redman (Indiana University School of Medicine, Fort Wayne, IN, USA), Prof. David Campbell (UCLA, CA, USA)
  
• Classification and evolution of S-adenosylmethionine-dependent methyltransferases is a collaborative project with Drs. Eugene Koonin and L. Aravind (NCBI, NIH, Bethesda, USA) aiming at detailed classification of the MTase superfamily in the evolutionary and functional context.
  
• Mechanism of transgene integration and expression in crop plant plastids is a collaborative project headed by Prof. John Gray (University of Cambridge, UK). The aim of the project is to characterize the mechanisms of several key stages of plastid transformation and foreign gene expression in different plastid types in tobacco, tomato and potato. The focus of our group is to use bioinformatics to identify genes and proteins involved in transgene integration and marker gene excision via homologous recombination, regulation of gene expression, and protein degradation in different plastid types.
  

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