10 A niversary of IIMCB

Publications in 2008
• Orlowski J, Mebrhatu MT, Michiels CW, Bujnicki JM,
Aertsen A. Mutational analysis and a structural model of
methyl-directed restriction enzyme Mrr. Biochem Biophys
Res Commun 377, 2008; 862–866
• Gyrd-Hansen M, Darding M, Miasari M, Santoro MM,
Zender L, Xue W, Tenev T, da Fonseca PCA, Zvelebil M,
Bujnicki JM, Lowe S, Silke J, Meier P. IAPs contain an
evolutionarily conserved ubiquitin-binding domain
that regulates NF-kappaB as well as cell survival and
oncogenesis. Nature Cell Biol, 2008; 10:1309-17
• Purta E, O’Connor M, Bujnicki JM, Douthwaite S. YccW
is the m5C methyltransferase specific for 23S rRNA
nucleotide 1962. J Mol Biol, 2008; 383:641-651
• 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 modelling. J Mol Biol, 2008;
376:438-452
• Sunita S, Tkaczuk KL, Purta E, Kasprzak J, Douthwaite
S, Bujnicki JM, Sivaraman J. Crystal structure of the
Escherichia coli 23S rRNA:m5C methyltransferase
RlmI (YccW) reveals evolutionary links between RNA
modification enzymes. J Mol Biol, 2008; 383:652-666
• Pawlowski M, Gajda MJ, Matlak R, Bujnicki JM.
MetaMQAP: a meta-server for the quality assessment of
protein models. BMC Bioinformatics, 2008; 9:403
• Purta E, Kaminska KH, Kasprzak J, Bujnicki JM,
Douthwaite S. YbeA is the m3Psi methyltransferase RlmH
that targets nucleotide 1915 in 23S rRNA. RNA, 2008;
14:2234-44
• Kosinski J, Plotz G, Guarne A, Bujnicki JM, Friedhoff P. The
PMS2 subunit of human MutLalpha contains a metal ion
binding domain of the iron-dependent repressor protein
family. J Mol Biol, 2008; 382:610-627
• White J, Li Z, Sardana R, Bujnicki JM, Marcotte EM,
Johnson AW. Bud23 methylates G1575 of 18S rRNA and is
required for efficient nuclear export of pre-40S subunits.
Mol Cell Biol, 2008; 28:3151-61
• Orlowski J, Bujnicki JM. Structural and evolutionary
classification of Type II restriction enzymes based on
theoretical and experimental analyses. Nucleic Acids Res,
2008; 36:3552-69
• Roovers M, Kaminska KH, Tkaczuk KL, Gigot D,
Droogmans L, Bujnicki JM. The YqfN protein of Bacillus
subtilis is the tRNA:m1A22 methyltransferase (TrmK).
Nucleic Acids Res, 2008; 36:3252-62
• Khiang CT, Bujnicki JM, Chye TT, Huynh F, Patel BK,
Sivaraman J. Mechanism of action and binding mode
revealed by the structure of sucrose phosphate synthase
from Halothermothrix orenii. Plant Cell, 2008; 20:1059-72
• Sen TZ, Kloster M, Jernigan RL, Kolinski A, Bujnicki JM,
Kloczkowski A. Predicting the complex structure and
functional motions of the outer membrane transporter
and signal transducer FecA. Biophys J, 2008; 94:2482-91
• Cymerman IA, Chung I, Beckmann BM, Bujnicki JM, Meiss
G. EXOG, a novel paralog of Endonuclease G in higher
eukaryotes. Nucleic Acids Res, 2008; 36:1369-79
• Carpenter MA, Bujnicki JM, Bhagwat AS. Is AID a
monomer in solution? DNA Repair, 2008; 7:349-350. Letter
to the Editor.
• Feder M, Purta E, Koscinski L, Cubrilo S, Vlahovicek
G, Bujnicki JM. Virtual screening and experimental
verification to identify potential inhibitors of the ErmC
methyltransferase responsible for bacterial resistance
against macrolide antibiotics. ChemMedChem, 2008;
3:316-322
• Mittra B, Zamudio JR, Bujnicki JM, Stepinski J,
Darzynkiewicz E, Campbell DA, Sturm NR. The TbMTr1
spliced leader RNA cap 1 2’-O-ribose methyltransferase
from Trypanosoma brucei acts with substrate specificity.
J Biol Chem, 2008; 283:3161-72
• Kaminska KH, Bujnicki JM. Bacteriophage Mu Mom
protein responsible for DNA modification is a new
member of the acyltransferase superfamily. Cell Cycle,
2008; 7:120-121
• Roovers M, Oudjama Y, Kaminska KH, Purta E, Caillet J,
Droogmans L, Bujnicki JM. Sequence-structure-function
analysis of the bifunctional enzyme MnmC that catalyses
the two last steps in the biosynthesis of hypermodified
nucleoside mnm5s2U in tRNA. Proteins, 2008; 71:2076-85
• Kaminska KH, Baraniak U, Boniecki M, Nowaczyk K,
Czerwoniec A, Bujnicki JM, Structural bioinformatics
analysis of enzymes involved in the biosynthesis pathway
of the hypermodified nucleoside ms2io6A37 in tRNA.
Proteins, 2008; 70:1-18
• Vasu K, Saravanan M, Bujnicki JM, Nagaraja V. Structural
integrity of the betabetaalpha-metal finger motif is
required for DNA binding and stable protein-DNA
complex formation in R.KpnI. Biochim Biophys Acta,
2008;1784:269-275
• Vlahovicek-Maravic G, Cubrilo S, Tkaczuk KL, Bujnicki JM.
Modeling and experimental analyses reveal a two-domain
structure and amino acids important for the activity
of aminoglycoside resistance methyltransferase Sgm.
Biochim Biophys Acta, 2008; 1784:582-590
• Smit S, Rother K, Heringa J, Knight R. From knotted
to nested RNA structures: a variety of computational
methods for pseudoknot removal. RNA, 2008; 14:410-416
• Kaminska KH, Kawai M, Boniecki M, Kobayashi I,
Bujnicki JM. Type II restriction endonuclease R.Hpy188I
belongs to the GIY-YIG nuclease superfamily, but exhibits
an unusual active site. BMC Struct Biol, 2008; 8:48
• Bauer RA, Rother K, Bujnicki JM, Preissner R. Suffix
techniques as a rapid method for RNA substructure
search. Genome Inf, 2008; 20:183-198.
Laboratory of Bioinformatics and Protein Engineering 29