10 A niversary of IIMCB

cross-linking, mass spectrometry, circular dichroism,
limited proteolysis, etc.
3. Protein engineering to obtain enzymes with new,
useful features, in particular, altered substrate specificity
(e.g. restriction enzymes that recognize and cut new
sequences). Other protein engineering projects include
attempts to design and obtain proteins with altered
tertiary and quaternary structures.
The research in all three sections is tightly integrated,
as demonstrated by publications of articles comprising
the combination of theoretical and experimental
analyses, e.g. prediction and characterization of new RNA
methyltransferases. In particular, protein engineering
involves iterative protein structure model building, modelbased
experiment planning, series of experimental analyses,
and experiment-based improvement of the models and the
tools used for model building.
Recent highlights:
Protein Structure Prediction
The GeneSilico human predictors’ group and several
servers developed in our laboratory achieved high positions
in rankings of the 8 th Community-Wide Experiment on the
Critical Assessment of Techniques for Protein Structure
Prediction (CASP8), organized by the Protein Structure
Prediction Center. Servers for protein structure prediction
and model quality assessment achieved respectable
positions in their respective categories. The most successful
was the GeneSilico metaserver for protein disorder
prediction, which ranked as number 1 in its category.
These successful servers are freely available to all academic
researchers via the GeneSilico toolkit.
New rRNA modification enzymes predicted and
confirmed experimentally
Researchers from our laboratory predicted (with
bioinformatics) and then experimentally confirmed that
two so far uncharacterized open reading frames encode
methyltransferases acting on 23S rRNA. YbeA is the m3Psi
methyltransferase RlmH that targets nucleotide 1915,
while YccW is the m5C methyltransferase RlmI specific for
nucleotide 1962. Computational docking analysis revealed
the potential way how RlmH may interact with the ribosome
(as visualized on the figure p. 26). The experimental analysis
was done in collaboration with a group in Odense headed by
Fig. A novel putative RNA-binding domain discovered to be frequently
associated with the Rossmann-fold methyltransferase domains in
various RNA-modifying enzymes (Sunita et al., J Mol Biol 2008 Nov
14;383(3):652-66.).
A) rRNA:m5U methyltransferase RlmD in complex with the substrate RNA
(PDB id: 2bh2),
B) tRNA:yW-86 synthesizing enzyme Trm12/Tyw2 (PDB id: 2frn),
C) rRNA:m5C methyltransferase RlmI (discovered and characterized with
coworkers from Dennmark and Singapore) modeled as a complex with a
fragment of the substrate RNA; PDB id: 3c0k)
D) hypothetical RNA modification enzyme (PDB id: 2igt) The catalytic
Rossmann-fold methyltransferase domain is shown in blue.
The newly discovered domain nick-named „EEHEE” (abbreviation for
the description of its secondary structure: extended-extended-helixextended-extended”)
is shown in red. A beta-hairpin linker is shown in
green. Other protein parts are in grey. RNA is shown in magenta, smallmolecule
ligands are shown in black (author: Janusz M. Bujnicki).
Prof. Stephen Douthwaite (University of Southern Denmark).
Moreover, researchers from our laboratory analyzed the
crystal structure of YccW/RlmI solved by a collaborating
group (prof. Jayaraman Sivaraman, University of Singapore)
and found that it provides a missing link in the evolutionary
history of several different families of methyltransferases
that modify cytosine in DNA or RNA as well as uridine in
RNA. They have also identified a new putative RNA-binding
domain dubbed „EEHEE”. This domain is common to RlmI
and several other RNA-modification enzymes, including
methyltransferases involved in m5U formation and in Wye
base biosynthesis.
Laboratory of Bioinformatics and Protein Engineering 31