International Institute of Molecular and Cell Biology in Warsaw
IIMCB
02-109 Warsaw
Ks Trojdena 4
PL
http://www.iimcb.gov.pl

Dr hab. Janusz Bujnicki
Laboratory of Bioinformatics and Protein Engineering
02-109 Warsaw
Ks Trojdena 4
PL
Phone 0048-22-5970750
Fax 0048-22-5970715
e-mail: iamb@genesilico.pl
 
The International Institute of Molecular and Cell Biology in Warsaw (IIMCB) is a new (founded in 1999) and unique state-owned research institute in Poland. It is affiliated with UNESCO and the Polish Academy of Sciences. IIMCB has a status of a Centre of Excellence in Molecular BioMedicine (awarded by the European Commission). There are 7 independent research groups involved in research on cell biology, molecular biology, molecular neurology, structural biology, bioinformatics, and protein engineering. The number of researchers employed at the institute is currently approaching 100, including ~20 permanent scientists, ~20 post-docs and >50 graduate and undergraduate students (these numbers are growing as new laboratories are being organized). All the equipment necessary for research in cell biology, molecular biology (e.g. nucleic acid and protein purification and analysis), structural biology (crystallography) and computational biology (computer clusters, high-end workstations) is available in IIMCB. IIMCB is located in the heart of the Ochota campus, which groups the Life Sciences divisions of the Warsaw University, the Medical University and several institutes of the Academy of Sciences. Collaborations with these institutions provide the access to specialized heavy equipment not available in IIMCB (e.g. mass spectrometry, DNA sequencing, NMR).

Dr. hab. Bujnicki is a young, motivated and dynamic scientist employed as Professor and group leader in IIMCB. He has published ~100 articles in the fields of bioinformatics, molecular evolution, and intersection between computational and experimental biology. Since 2001, he has created a group of > 20 young scientists (average age ~26) working in the field of bioinformatics and molecular biology, including development and application of methods for protein structure prediction, molecular evolution and studies on sequence-function relationships. Dr. Bujnicki has been awarded as EMBO and Howard Hughes Medical Institute Young Investigator. Dr. Bujnicki and his group have been evaluated among the world’s best protein structure predictors in last two edition of the acclaimed biannual CASP experiment (http://predictioncenter.llnl.gov/). At the outset, the group comprised only undergraduate and 1st year graduate students and achieved the success in CASP5 only after one year of training in the Bujnicki laboratory. This demonstrates that the training of young and inexperienced students in bioinformatics is extremely successful in this laboratory. Dr. Bujnicki has also a part-time position at the Faculty of Biology of the Adam Mickiewicz University in Poznan, where he is involved in teaching and organizes courses in b ioinformatics.

Dr. Bujnicki’s group has experience with development of databases and computer software for analysis of genomes and protein structures, and in setting up and maintenance of publicly available prediction servers (e.g. http://genesilico.pl/meta/, http://asia.genesilico.pl/). The Bujnicki group is well funded thanks to support from EMBO and HHMI and several collaborative grants from the NIH (3 grants devoted to combination of bioinformatics with experimental analyses), 6th Framework Programme (genomics), and bilateral programmes of the Polish Ministry for Scientific Research and Information Technology.

In addition to software development and general interests in computational biology, inlcuding bioinformatics, genomics, and molecular evolution, Dr. Bujnicki has devoted a large part of his scientific career to the bioinformatics analyses of sequences and structures of various enzymes acting on nucleic acids, in particular restriction-modification systems and proteins involved in DNA recombination and repair. In 2003, the group has expanded to include an experimental section devoted to biochemical analyses of DNA enzymes and validation of predictions generated by the 'theoretical' section, and focused on bioinformatics-guided protein engineering. The results of the experimental work have been already published in several peer-reviewed articles. Because of this recent expansion of scope of the research activities, the whole group will greatly benefit from the intense transfer of know-how and specialised expertise from the other partners.

Summarizing, the Bujnicki group offers a unique expertise in combination of bioinformatics and molecular biology of proteins involved in DNA restriction, recombination and repair and an excellent environment for training of researchers interested in learning techniques of in silico biology and their application in connection with the “traditional” experimental analyses. The Warsaw group is already involved in collaborations with several partners in the consortium, including a long-standing cooperation with the Giessen group focused on nucleases, documented by 5 published co-authored papers and several submitted or in preparation

1. Pingoud V, Kubareva E, Stengel G, Friedhoff P, Bujnicki, JM, Urbanke C., Sudina A & Pingoud A (2002) Evolutionary relationship between different subgroups of restriction endonucleases. J. Biol. Chem. 277, 14306-14314
2. Pingoud V, Conzelmann C, Kinzebach S, Sudina A, Metelev V, Kubareva E, Bujnicki JM, Lurz R, Luder G, Xu SY & Pingoud A (2003) PspGI, a type II restriction endonuclease from the extreme thermophile Pyrococcus sp.: structural and functional studies to investigate an evolutionary relationship with several mesophilic restriction enzymes J. Mol. Biol. 329, 913 – 929
3. Scholz SR, Korn, C, Bujnicki JM, Gimadutdinow, O., Pingoud A, & Meiss, G. (2003) Experimental evidence for a ßßa-Me finger nuclease motiv to represent the active site of the caspase-activated DNase Biochemistry 42, 9288 – 9294
4. Schäfer P, Scholz SR, Gimadutdinow O, Cymerman IA, Bujnicki JM, Ruiz-Carillo A, Pingoud A, & Meiss, G. (2004) Structural and functional characterization of mitochondrial EndoG, a sugar non-specific nuclease which plays an important role during apoptosis J. Mol. Biol. 338, 217-228
5. Pingoud V, Sudina A, Geyer H, Bujnicki JM, Lurz R, Lüder G, Morgan R, Kubareva E, & Pingoud A (2005) Specificity changes in the evolution of type II restriction endonucleases: a biochemical and bioinformatic analysis of restriction enzymes that recognize unrelated sequences. J. Biol. Chem. 280, 4289-4298
6. Kosinski J, Steindorf I, Bujnicki JM, Giron-Monzon L & Friedhoff P (2005) Analysis of the quaternary structure of the MutL C-terminal domain. J Mol Biol. 351, 895-909

1. Armalyte E, Bujnicki JM, Giedriene J, Gasiunas G, Kosinski J & Lubys A (2005) Mva1269I: a monomeric type IIS restriction endonuclease from Micrococcus varians with two EcoRI- and FokI-like catalytic domains.
J Biol Chem. 280, 41584-94.
2. Cymerman IA, Obarska A, Skowronek KJ, Lubys A & Bujnicki JM (2006) Identification of a new subfamily of HNH nucleases and experimental characterization of a representative member, HphI restriction endonuclease.
Proteins 65, 867-76.

Recently collaborations were initiated with the Budapest group (focused on the characterization of stability centers in the methyltransferase superfamily) and with the Bristol group (structure prediction of the BspMI enzyme). Within the new network the existing collaborations will be intensified and new contacts will be established.

In the course of these collaborations we hope to improve our know-how in simulations of enzymatic reactions and most importantly in experimental analyses, especially cross-linking, mass spectrometry, and kinetic studies. In return, we will support our partners with our expertise in prediction and modeling of protein structures. The Warsaw group will also offer its facilities for training of early stage researchers in many other aspects of bioinformatics (genome analyses, phylogenetic studies, software development, database design, etc.).