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Publications of the Bujnicki laboratory
2010 and in press
206. Kosinski J, Hinrichsen I, Bujnicki JM, Friedhoff P,
Plotz G
2009
2008 (editor) Bujnicki JM Book: "Prediction of Protein Structures, Functions and Interactions". Wiley & Sons (2008), December 2008. 302 Pages, Hardcover. ISBN-10: 0-470-51767-0, ISBN-13: 978-0-470-51767-3 Including 4 co-authored chapters: 177. Kaminska KH, Milanowska K, Bujnicki JM 169. Purta E, O'Connor M, Bujnicki JM, Douthwaite S YccW is the m5C methyltransferase specific for 23S rRNA nucleotide 1962 J Mol Biol 2008 Nov 14;383(3):641-51. [Epub 2008 Aug 29] [pdf] 168. 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 Nov 14;383(3):652-66. [Epub 2008 Aug 29] [pdf] 167. Bauer RA, Rother K, Bujnicki JM,
Preissner R
150. 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 Feb;1784(2):269-75. [pdf] 149. 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 Jan 1;70(1):1-18; [Epub 2007 Oct 1] [pdf] 2007
143. Jakubauskas A, Giedriene J, Bujnicki JM, Janulaitis A Identification of a single HNH active site in Type IIS restriction endonuclease Eco31I J Mol Biol 2007 Jun 29;370(1):157-69. [Epub 2007 May 4] [pdf] 142. Sunita S, Purta E, Durawa M, Tkaczuk KL, Swaathi J, Bujnicki JM, Sivaraman J Functional specialization of domains tandemly duplicated within 16S rRNA methyltransferase RsmC Nucleic Acids Res 2007 Jul 1;35(13):4264-4274. [Epub 2007 Jun 18] [pdf] 141. Koscinski L, Feder M, Bujnicki JM, Identification of a missing sequence and functionally important residues of 16S rRNA:m1A1408 methyltransferase KamB that causes bacterial resistance to aminoglycoside antibiotics Cell Cycle 2007 May;6(10):1268-71. [Epub 2007 May 2] [pdf] 140. Koudan EV, Brevnov MG, Subach OM, Rechkoblit OA, Bujnicki JM, Gromova ES Probing of contacts between EcoRII DNA methyltransferase and DNA using substrate analogs and molecular modeling Mol Biol (Mosc.) 2007 41(5):806–19. [pdf] 139. Pietal M, Tuszynska I, Bujnicki JM PROTMAP2D: visualization, comparison, and analysis of 2D maps of protein structure Bioinformatics 2007 Jun 1;23(11):1429-30. [Epub 2007 Mar 30] [pdf] 138. Tkaczuk KL, Dunin-Horkawicz S, Purta E, Bujnicki JM Structural and evolutionary bioinformatics of the SPOUT superfamily of methyltransferases BMC Bioinformatics 2007, Mar 5;8:73. doi:10.1186/1471-2105-8-73 [pdf] 137. Kosinski J, Kubareva EA, Bujnicki JM A model of restriction endonuclease MvaI in complex with DNA: a template for interpretation of experimental data and a guide for specificity engineering Proteins 2007 Jul 1;68(1):324-36. [Epub 2007 Apr 3] [pdf] 136. Miyazono K, Watanabe M, Kosinski J, Ishikawa K, Kamo M, Sawasaki T, Nagata K, Bujnicki JM, Endo Y, Tanokura M, Kobayashi I Novel protein fold discovered in the PabI family of restriction enzymes Nucleic Acids Res 2007;35(6):1908-18. [Epub 2007 Mar 1] [pdf] 135. Orlowski, J, Boniecki M, Bujnicki JM I-Ssp6803I: the first homing endonuclease from the PD-(D/E)XK superfamily exhibits an unusual mode of DNA recognition Bioinformatics Mar 1;23(5):527-30. [Epub 2007 Jan 22] [pdf] 134. Pena V, Liu S, Bujnicki JM, Luhrmann R, Wahl MC Structure of a multipartite protein-protein interaction domain in splicing factor Prp8 and its link to retinitis pigmentosa Mol Cell 2007, Feb 23, 25, 615-624. [pdf] 133. Skowronek KJ, Bujnicki JM Restriction and homing endonucleases. Chapter 21 in "Industrial Enzymes. Structure, Function and Applications"; Editors: Polaina J, MacCabe AP. Springer-Verlag 2007 ISBN: 978-1-4020-5376-4 [pdf] 132. Schafer P, Cymerman IA, Bujnicki JM, Meiss G Human lysosomal DNase IIalpha contains two requisite PLD-signature (HxK) motifs: Evidence for a pseudodimeric structure of the active enzyme species Protein Sci 2007 Jan;16(1):82-91. [pdf] 131. Chovancova E, Kosinski J, Bujnicki JM, Damborsky J Phylogenetic analysis of haloalkane dehalogenases Proteins 2007 May 1;67(2):305-16. [pdf] 130. Sasin JM, Godzik A, Bujnicki JM SURF'S UP! - protein classification by surface comparisons J Biosci 2007 Jan;32(1):97-100. [pdf] 2006 129. Wyszynska A, Pawlowski M, Bujnicki JM, Pawelec D, Van Putten JP, Brzuszkiewicz E, Jagusztyn-Krynicka EK Genetic characterisation of the cjaAB operon of Campylobacter coli Pol J Microbiol 2006;55(2):85-94. [no pdf available] 128. Gros L, Renodon-Corniere A, de Saint Vincent BR, Feder M, Bujnicki JM, Jacquemin-Sablon A Characterization of PRMT7alpha and beta isozymes from Chinese hamster cells sensitive and resistant to topoisomerase II inhibitors Biochim Biophys Acta 2006 Nov;1760(11):1646-56. Epub 2006 Sep 14. [pdf] 127. Purta E, van Vliet F, Tkaczuk KL, Dunin-Horkawicz S, Mori H, Droogmans L, Bujnicki JM The yfhQ gene of Escherichia coli encodes a tRNA:Cm32/Um32 methyltransferase BMC Mol Biol 2006 Jul 18;7:23 [pdf] 126. Carpenter M, Divvela P, Pingoud V, Bujnicki JM, Bhagwat AS. Sequence-dependent enhancement of hydrolytic deamination of cytosines in DNA by the restriction enzyme PspGI Nucleic Acids Res 2006 Aug 7;34(13):3770-8. [pdf] 125. 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. [Epub Oct 6] [pdf] 124. Han R, Lukomska E, Caswell CC, Keene DR, Pawlowski M, Bujnicki JM, Lukomski S Binding of the low density lipoprotein by streptococcal collagen-like protein Scl1 of Streptococcus pyogenes Mol Microbiol 2006 Jul;61(2):351-67. [pdf] 123. Dunin-Horkawicz S, Feder M, Bujnicki JM Phylogenomic analysis of the GIY-YIG nuclease superfamily BMC Genomics 2006 Apr 28;7(1):98 [pdf] 122. Zamudio JR, Mittra B, Zeiner GM, Feder M, Bujnicki JM, Sturm NR, Campbell DA Complete cap 4 formation is not required for viability in Trypanosoma brucei Eukaryotic Cell 2006 Jun;5(6):905-15. [pdf] 121. Gabant G, Auxilien S, Tuszynska I, Locard M, Gajda MJ, Chaussinand G, Fernandez B, Dedieu1 A, Grosjean H, Golinelli-Pimpaneau B, Bujnicki JM, Armengaud J. THUMP from archaeal tRNA:m22G10 methyltransferase, a genuine autonomously folding domain. Nucleic Acids Res 2006 May 10;34(9):2483-94. [pdf] 120. 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. [pdf] 119. Zegers I, Gigot D, van Vliet F, Tricot C, Aymerich S, Bujnicki JM, Kosinski J, Droogmans L. Crystal structure of Bacillus subtilis TrmB, the tRNA (m7G46) methyltransferase. Nucleic Acids Res 2006 Apr 5;34(6):1925-34. [pdf] 118. Sikora E, Bielak-Zmijewska A, Magalska A, Piwocka K, Mosieniak G, Kalinowska M, Widlak P, Cymerman IA, Bujnicki JM. Curcumin induces caspase-3 dependent apoptotic pathway but inhibits DFF40/CAD endonuclease in human Jurkat cells. Mol Cancer Ther 2006 Apr;5(4):927-34. [pdf] 117. 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 [pdf] 116. Bheemanaik S, Bujnicki JM, Nagaraja V, Rao DN. Functional analysis of amino acid residues in the dimerisation interface of KpnI DNA methyltransferase. Biol Chem 2006 May;387(5):515-23. [pdf] 115. Samaranayake M, Bujnicki JM, Carpenter M, Bhagwat AS. Evaluation of molecular models for the affinity maturation of antibodies: roles of cytosine deamination by AID and DNA repair. Chem Rev 2006 Feb;106(2):700-19. [pdf] 114. Chiang PK, Bujnicki JM, Su XZ, Lanar DE. Malaria: therapy, genes and vaccines. Current Mol Med 2006 May; 6(3):309-26 [pdf] 113. Skowronek KJ, Kosinski J, Bujnicki JM. A theoretical model of restriction endonuclease HpaI in complex with DNA, predicted by fold-recognition and validated by site-directed mutagenesis. Proteins 2006 Jun 1;63(4):1059-68. [pdf] 112. Mikula M, Karczmarski J, Dzwonek A, Rubel T, Hennig E, Dadlez M, Bujnicki JM, Bomsztyk K, Ostrowski J Casein kinases phosphorylate multiple residues spanning the entire hnRNP K length. Biochim Biophys Acta 2006 Feb;1764(2):299-306. [pdf] 111. Klimek-Tomczak K, Mikula M, Dzwonek A, Paziewska A, Karczmarski J, Hennig E, Bujnicki JM, Bragoszewski P, Denisenko O, Bomsztyk K, Ostrowski J. Editing of hnRNP K protein mRNA in colorectal adenocarcinoma and surrounding mucosa. Br J Cancer 2006 Feb 27;94(4):586-92. [pdf] 110. Metz J, Wachter A, Schmidt B, Bujnicki JM, Schwappach B. The yeast Arr4p ATPase binds the chloride transporter Gef1p when copper is available in the cytosol. J Biol Chem 2006 Jan 6;281(1):410-7. Epub 2005 Oct 31. [pdf] 109. Dunin-Horkawicz S, Czerwoniec A, Gajda MJ, Feder M, Grosjean H, Bujnicki JM MODOMICS: a database of RNA modification pathways. Nucleic Acids Res 2006 Jan 1;34(Database issue):D145-9 [pdf] 108. Bujnicki JM Protein structure prediction by recombination of fragments ChemBioChem 2006 Jan 9;7(1):19-27. [pdf] 107. Godlewska R, Dzwonek A, Mikula M, Ostrowski J, Pawlowski M, Bujnicki JM, Jagusztyn-Krynicka EK, Helicobacter pylori protein oxidation influences the colonization process. Inter J Med Microbiol 2006 Aug;296(4-5):321-4. [pdf] 2005 106. Smiech B, Kazmierkiewicz R, Bujnicki JM, Lammek B Theoretical predictions of the impact of the trisubstituted pyrophosphate internucleotide bond on B DNA fragments J Mol Struct THEOCHEM 2005 756: 63–71 [pdf] 105. Armalyte E, Bujnicki JM, Giedriene J, Gasiunas G, Kosinski J, Lubys A. Mva1269I: a monomeric type IIS restriction endonuclease from Micrococcus varians with two EcoRI- and FokI-like catalytic domains. J Biol Chem 2005 Dec 16;280(50):41584-94. Epub 2005 Oct 11. [pdf] 104. Cymerman IA, Meiss G, Bujnicki JM DNase II is a member of the phospholipase D superfamily. Bioinformatics 2005 Nov 1;21(21):3959-62 [pdf] 103. Kosinski J, Feder M, Bujnicki JM The PD-(D/E)XK superfamily revisited: identification of new members among proteins involved in DNA metabolism and functional predictions for domains of (hitherto) unknown function BMC Bioinformatics 2005 Jul 12;6(1):172 [pdf] 102. Ishikawa K, Watanabe M, Kuroita T, Uchiyama I, Bujnicki JM, Kawakami B, Tanokura M, Kobayashi I Discovery of a novel restriction endonuclease by genome comparison and application of a wheat-germ-based cell-free translation assay: PabI (5'GTA/C) from the hyperthermophilic archaeon Pyrococcus abyssi Nucleic Acids Res 2005 Jul 21;33(13):e112 [pdf] 101. Kosinski J, Steindorf I, Bujnicki JM, Giron-Monzon L, Friedhoff P Analysis of the quaternary structure of the MutL C-terminal domain J Mol Biol 2005 Aug 26;351(4):895-909. [pdf] 100. Radlinska M, Piekarowicz A, Galimand M, Bujnicki JM Cloning and preliminary characterization of a GATC-specific beta2-class DNA:m6A methyltransferase encoded by a transposon Tn1549 from Enterococcus spp. Pol J Microbiol 2005 54(3), 249-252 [pdf] 99. Tkaczuk KL, Bujnicki JM, Bialkowska A, Bielecki S, Turkiewicz M, Cieslinski H, Kur J Molecular modelling of a psychrophilic beta-galactosidase Biocatal Biotransform 2005 23(3/4), 201-209 [pdf] 98. 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. [pdf] 97. Kolinski A, Bujnicki JM Generalized protein structure prediction based on combination of fold-recognition with de novo folding and evaluation of models Proteins 2005;61 Suppl 7:84-90. [pdf] 96. Pingoud V, Geyer H, Geyer R, Kubareva E, Bujnicki JM, Pingoud AM Identification of base-specific contacts in protein-DNA complexes by photocrosslinking and mass spectrometry: a case study using the restriction endonuclease SsoII Mol BioSyst 2005 1(2):135-141. DOI: 10.1039/b503091a [pdf] 95. Purushothaman SK, Grosjean H, Bujnicki JM, Lapeyre B Trm11p and Trm112p are both required for the formation of 2-methylguanosine at position 10 in yeast tRNA Mol Cell Biol 2005 Jun;25(11):4359-70 [pdf] 94. Chmiel AA, Radlinska M, Pawlak SD, Krowarsch D, Bujnicki JM, Skowronek KJ A theoretical model of restriction endonuclease NlaIV in complex with DNA, predicted by fold-recognition and validated by site-directed mutagenesis and circular dichroism spectroscopy Protein Eng Des Sel 2005 Apr;18(4):181-189 [pdf] 93. Pawlak SD, Radlinska M, Chmiel AA, Bujnicki JM, Skowronek KJ Inference of relationships in the "twilight zone" of homology using a combination of bioinformatics and site-directed mutagenesis: a case study of restriction endonucleases Bsp6I and PvuII Nucleic Acids Res 2005 Jan 31;33(2):661-71. [pdf] 92. Feder M, Bujnicki JM Identification of a new family of putative PD-(D/E)XK nucleases with unusual phylogenomic distribution and a new type of the active site BMC Genomics 2005 Feb 18;6(1):21 [pdf] 91. Chmiel AA, Bujnicki JM, Skowronek KJ A homology model of restriction endonuclease SfiI in complex with DNA BMC Struct Biol 2005 Jan 24;5(1):2. [pdf] 90. Purta E, van Vliet F, Tricot C, De Bie LG, Feder M, Skowronek KJ, Droogmans L, Bujnicki JM Sequence-structure-function relationships of a tRNA (m7G46) methyltransferase studied by homology modeling and site-directed mutagenesis Proteins 2005 May 15;59(3):482-8. [pdf] 89. Raczko A, Bujnicki JM, Pawlowski M, Godlewska R, Lewandowska M, Jagusztyn-Krynicka EK Characterisation of new DsbB-like thiol-oxidoreductases of Campylobacter jejuni and Helicobacter pylori and classification of the DsbB family based on phylogenomic, structural, and functional criteria Microbiology 2005 Jan;151(Pt 1):219-31. [pdf] 88. Radlinska M, Kondrzycka-Dada A, Piekarowicz A, Bujnicki JM Identification of amino acids important for the target recognition by the DNA:m5C methyltransferase M.NgoPII by alanine-scanning mutagenesis of residues at the protein-DNA interface. Proteins 2005 Feb 1;58(2):263-70. [pdf] 87. Pingoud V, Sudina A, Geyer H, Bujnicki JM, Lurz R, Luder G, Morgan R, Kubareva E, Pingoud A 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 2005 Feb 11;280(6):4289-98. Epub 2004 Nov 24. [pdf] 2004 86. Saravanan M, Bujnicki JM, Cymerman IA, Rao DN, Nagaraja V Type II restriction endonuclease R.KpnI is a member of the HNH nuclease superfamily Nucleic Acids Res 2004 Nov 23;32(20):6129-6135 [pdf] 85. Ye X, O'Neil PK, Foster AN, Gajda MJ, Kosinski J, Kurowski MA, Bujnicki JM, Friedman AM, Bailey-Kellogg C Probabilistic cross-link analysis and experiment planning for high-throughput elucidation of protein structure Protein Sci 2004 Dec;13(12):3298-313 [pdf] 84. Paziewska A, Wyrwicz LS, Bujnicki JM, Bomsztyk K, Ostrowski J Cooperative binding of the hnRNP K three KH domains to mRNA targets FEBS Lett 2004 Nov 5;577(1-2):134-40. [pdf] 83. Koudan EV, Bujnicki JM, Gromova ES Homology modeling of the CG-specific DNA methyltransferase SssI and its complexes with DNA and AdoHcy. J Biomol Struct & Dyn 2004 Dec;22(3):339-46. [pdf] 82. Armengaud J, Urbonavicius J, Fernandez B, Chaussinand G, Bujnicki JM, Grosjean H N2-methylation of guanosine at position 10 in tRNA is catalyzed by a THUMP domain containing, AdoMet-dependent methyltransferase, conserved in Archaea and Eukaryota J Biol Chem 2004 Aug 27;279(35):37142-52 [pdf] 81. Bujnicki JM, Oudjama Y, Roovers M, Owczarek S, Caillet J, Droogmans L Identification of a bifunctional enzyme MnmC involved in the biosynthesis of a hypermodified uridine in the wobble position of tRNA RNA 2004 Aug;10(8):1236-42. [pdf] 80. Sasin JM, Bujnicki JM COLORADO3D, a web server for the visual analysis of protein structures Nucleic Acids Res 2004 Jul 1;32(Web Server issue):W586-9. [pdf] 79. Bujnicki JM, Feder M, Ayres CL, Redman KL Sequence-structure-function studies of tRNA:m5C methyltransferase Trm4p and its relationship to DNA:m5C and RNA:m5U methyltransferases Nucleic Acids Res 2004 Apr 30;32(8):2453-63. [pdf] 78. Schafer P, Scholz SR, Gimadutdinow O, Cymerman IA, Bujnicki JM, Ruiz-Carrillo A, Pingoud A, Meiss G. Structural and functional characterization of mitochondrial EndoG, a sugar non-specific nuclease which plays an important role during apoptosis. J Mol Biol 2004 Apr 23;338(2):217-28. [pdf] 77. Roovers M, Wouters J, Bujnicki JM, Tricot C, Stalon V, Grosjean H, Droogmans L. A primordial RNA modification enzyme: the case of tRNA:m1A methyltransferase Nucleic Acids Res 2004 Jan 22; 32(2):465-476 [pdf] 76. Nes WD, Jayasimha P, Zhou W, Kanagasabai R, Jin C, Jaradat TT, Shaw RW, Bujnicki JM Sterol methyltransferase: functional analysis of highly conserved residues by site-directed mutagenesis. Biochemistry 2004 Jan 20;43(2):569-76. [pdf] 75. Potluri S, Khan AA, Kuzminykh A, Bujnicki JM, Friedman AM, Bailey-Kellogg C Geometric analysis of cross-linkability for protein fold discrimination Pac Symp Biocomput 2004 447-58 [pdf] 74. Bujnicki JM Molecular phylogenetics of restriction endonucleases. In "Restriction Endonucleases: Structure, Function, and Evolution", Vol. 14 in Nucleic Acids and Molecular Biology series; Editor: Pingoud AM. Springer-Verlag 2004 [pdf] Book: "Practical Bioinformatics". Vol. 15 in Nucleic Acids and Molecular Biology series; Editor: Bujnicki JM, Springer-Verlag 2004; ISBN: 3-540-20613-2 including 3 chapters: 73. Cymerman IA, Feder M, Pawlowski M, Kurowski MA, Bujnicki JM Computational methods for protein structure prediction and fold-recognition. In Nucleic Acids and Molecular Biology series, "Practical Bioinformatics". Editor: Bujnicki JM. Springer-Verlag 2004 [pdf] 72. Bujnicki JM, Fischer D 'Meta' approaches to protein structure prediction. In Nucleic Acids and Molecular Biology series, "Practical Bioinformatics". Editor: Bujnicki JM. Springer-Verlag 2004 [pdf] 71. Bujnicki JM, Droogmans L, Grosjean H, Purushothaman SK, Lapeyre B Bioinformatics-guided identification and experimental characterization of novel RNA methyltransferases. In Nucleic Acids and Molecular Biology series, "Practical Bioinformatics". Editor: Bujnicki JM. Springer-Verlag 2004 [pdf] 70. Maravic G, Bujnicki JM, Flogel M. Mutational analysis of basic residues in the N-terminus of the rRNA:m6A methyltransferase ErmC' Folia Microbiol 2004;49(1):3-7. [pdf] 69. Rychlewski L, Bujnicki JM, Fischer D Protein fold-recognition and experimental structure determination. In "The New Avenues in Bioinformatics", Vol 8 in the COLE series, "Origins: genesis, evolution and diversity of life". Editor: Seckbach J, Rubin E. Springer-Verlag 2004, ISBN 1-4020-2639-0 [pdf] 2003 68. Kurowski MA, Bhagwat AS, Papaj G, Bujnicki JM Phylogenomic identification of five new human homologs of the DNA repair enzyme AlkB. BMC Genomics 2003 4:48 [pdf] 67. Bujnicki JM Crystallographic and bioinformatics studies on restriction endonucleases: inference of evolutionary relationships in the "midnight zone" of homology. Current Protein and Peptide Science 2003 Oct;4(5):327-37. [pdf] 66. Scholz SR, Korn C, Bujnicki JM, Gimadutdinow O, Pingoud A, Meiss G. Experimental evidence for a beta beta alpha-Me-finger nuclease motif to represent the active site of the caspase-activated DNase. Biochemistry 2003 Aug 12;42(31):9288-94. [pdf] 65. Maravic G, Bujnicki JM, Feder M, Pongor S, Flogel M. Alanine-scanning mutagenesis of the predicted rRNA-binding domain of ErmC' redefines the substrate-binding site and suggests a model of protein-RNA interactions Nucleic Acids Res 2003 Aug 15;31(16):4941-9. [pdf] 64. Maravic G, Feder M, Pongor S, Flogel M, Bujnicki JM. Mutational analysis defines the roles of conserved amino acid residues in the predicted catalytic pocket of the rRNA:m6A methyltransferase ErmC' J Mol Biol 2003 Sep 5;332(1):99-109. [pdf] 63. Gordon R, Ginalski K, Rudnicki WR, Rychlewski L, Pankaskie M, Hershfield MS, Bujnicki JM, Chiang PK. Anti-HIV-1 activity of 3-deaza-adenosine analogs: inhibition of S-adenosylhomocysteine hydrolase and nucleotide congeners Eur J Biochem 2003 Sep;270(17):3507-3517. [pdf] 62. Mouaikel J, Bujnicki JM, Tazi J, Bordonne R. Sequence-structure-function relationships of Tgs1, the yeast snRNA/snoRNA hypermethylase Nucleic Acids Res 2003 Aug 15;31(16):4899-909 [pdf] 61. Kosinski J, Cymerman IA, Feder M, Kurowski MA, Sasin JM, Bujnicki JM A 'Frankenstein's monster' approach to comparative modeling: merging the finest fragments of fold-recognition models and iterative model refinement aided by 3D structure evaluation. Proteins 2003 53 Suppl 6:369-79. (CASP5 special issue) [pdf] 60. Kurowski MA, Bujnicki JM GeneSilico protein structure prediction meta-server Nucleic Acids Res 2003 Jul 1;31(13):3305-7. [pdf] 59. Ginalski K, Pas J, Wyrwicz LS, von Grotthuss M, Bujnicki JM, Rychlewski L ORFeus: detection of distant homology using sequence profiles and predicted secondary structure Nucleic Acids Res 2003 Jul 1;31(13):3804-7. [pdf] 58. Kurowski MA, Sasin JM, Feder M, Debski J, Bujnicki JM Characterization of the cofactor-binding site in the SPOUT-fold methyltransferases by computational docking of S-adenosylmethionine to three crystal structures. BMC Bioinformatics 2003 Mar 14;4(1):9. [pdf] 57. Sasin JM, Kurowski MA, Bujnicki JM STRUCLA: a WWW meta-server for protein structure comparison and evolutionary classification Bioinformatics 2003 Jul;19 Suppl 1:I252-I254 [pdf] 56. Pingoud V, Conzelmann C, Kinzebach S, Sudina A, Metelev V, Kubareva E, Bujnicki JM, Lurz R, Luder G, Xu S-Y, Pingoud AM 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 2003 Jun 20;329(5):913-29. [pdf] 55. Bujnicki JM, Albert MA, Nelson DJ, Thurlow DL Fold recognition, homology modeling, docking simulations, kinetics analysis and mutagenesis of ATP/CTP:tRNA nucleotidyltransferase from Methanococcus jannaschii. Proteins 2003 Aug 15;52(3):349-59. [pdf] 54. Bujnicki JM, Prigge TS, Caridha D, Chiang PK Structure, evolution, and inhibitor interaction of S-Adenosyl-L-homocysteine hydrolase from Plasmodium falciparum Proteins 2003 Sep 1;52(4):624-32. [pdf] 53. Tchernaenko V, Radlinska M, Drabik C, Bujnicki JM, Halvorson HR, Lutter LC Topological measurement of an A-tract bend angle: I. Comparison of the bent and straight states J Mol Biol 2003 Feb 21;326(3):737-49. [pdf] 52. Droogmans L, Roovers M, Bujnicki JM, Tricot C, Hartsch T, Stalon V, Grosjean H Cloning and characterization of tRNA (m1A58) methyltransferase (TrmI) from Thermus thermophilus HB27, a protein required for cell growth at extreme temperatures. Nucleic Acids Res 2003 Apr 15;31(8):2148-56 [pdf] 51. De Bie LGS, Roovers M, Oudjama Y, Wattiez R, Tricot C, Stalon V, Droogmans L, Bujnicki JM The yggH gene of Escherichia coli encodes a tRNA (m7G46) methyltransferase. J Bacteriol 2003 May;185(10):3238-43. [pdf] 50. Feder M, Pas J, Wyrwicz SL, Bujnicki JM Molecular phylogenetics of the RrmJ/fibrillarin superfamily of ribose 2'-O-methyltransferases. Gene 2003 Jan 2;302(1-2):129-38. [pdf] 2002 49. Bujnicki JM, Feder M, Rychlewski L, Fischer D, Errors in the D. radiodurans large ribosomal subunit structure detected by fold recognition and structure evaluation tools FEBS Lett 2002 Aug 14;525(1-3):174. [pdf] 48. Godlewska R, Bujnicki JM, Ostrowski J, Jagusztyn-Krynicka EK The hppA gene of Helicobacter pylori encodes the class C acid phosphatase precursor. FEBS Lett 2002 Aug 14;525(1-3):39. [pdf] 47. Bujnicki JM, Feder M, Radlinska M, Blumenthal RM. Structure prediction and phylogenetic analysis of a functionally diverse family of proteins homologous to the MT-A70 subunit of the human mRNA:m6A methyltransferase J Mol Evol 2002 Oct;55(4):431-44. [pdf] 46. Bujnicki JM, Rychlewski L In silico identification, structure prediction, and phylogenetic analysis of the 2'-O-ribose (cap 1) methyltransferase domain in the large structural protein of ssRNA negative-strand viruses. Protein Eng 2002 Feb;15(2):101-8. [pdf] 45. Pintard L, Lecointe F, Bujnicki JM, Bonnerot C, Grosjean H, Lapeyre B Trm7p catalyses the formation of two 2'-O-methylriboses in yeast tRNA anticodon loop EMBO J 2002 Apr 2;21(7):1811-20. [pdf] 44. Pingoud V, Kubareva E, Stengel G, Friedhoff P, Bujnicki JM, Urbanke C, Sudina A, Pingoud A Evolutionary relationship between different subgroups of restriction endonucleases J Biol Chem 2002 Apr 19;277(16):14306-14. [pdf] 43. Xu Y, Keene DR, Bujnicki JM, Hook M, Lukomski S Streptococcal Scl1 and Scl2 proteins form collagen-like triple helices J Biol Chem 2002 Jul 26;277(30):27312-8 [pdf] 42. Bujnicki JM, Blumenthal RM, Rychlewski L. Sequence analysis and structure prediction of 23S rRNA:m1G methyltransferases reveals a conserved core augmented with a putative Zn-binding domain in the N-terminus and family-specific elaborations in the C-terminus. J Mol Microbiol Biotechnol 2002 Jan;4(1):93-9. [pdf] 41. Pintard L, Bujnicki JM, Lapeyre B, Bonnerot C MRM2 encodes a novel mitochondrial 21S rRNA methyltransferase EMBO J. 2002 Mar 1;21(5):1139-1147. [pdf] 40. Bujnicki JM, Rychlewski L RNA:(guanine-N2) methyltransferases RsmC/RsmD and their homologs revisited - bioinformatic analysis and prediction of the active site based on the uncharacterized Mj0882 protein structure. BMC Bioinformatics 2002 Apr 3;3(1):10. [pdf] 39. Bujnicki JM, Rychlewski L Fold-recognition analysis predicts that the Tag protein family shares a common domain with the helix-hairpin-helix DNA glycosylases DNA Repair 2002 34:1-5 [pdf] 38. Bujnicki JM, Rychlewski L, Fischer D, Fold-recognition detects an error in Protein Data Bank Bioinformatics 2002 18(10):1391-1395. [pdf] 37. Bujnicki JM, Sequence permutations in the molecular evolution of DNA methyltransferases BMC Evol Biol 2002 Mar 12;2(1):3 [pdf] 36. Bujnicki JM, Leach RA, Debski J, Rychlewski L Bioinformatic analysis of the tRNA:(guanine 26, N2,N2)-dimethyltransferase (Trm1) family. J Mol Microbiol Biotechnol 2002 4(4):405-15. [pdf] 35. Zhang P, Nicholson DE, Bujnicki JM, Su X, Brendle JJ, Ferdig M, Kyle DE, Milhous WK, Chiang PK Angiogenesis inhibitors specific for methionine aminopeptidase 2 as drugs for malaria and leishmaniasis. J Biomed Sci. 2002 9(1):34-40 [pdf] 34. Lutter LC, Tchernaenko V, Radlinska M, Drabik CE, Bujnicki JM, Halvorson HR Measurement of DNA bend angles using DNA topology. In "New Approaches to Structural Mechanics, Shells and Biological Structures" (Drew HR & Pellegrino S, eds), pp. 475-484, Kluwer, Dordrecht. 2002 [pdf - not available] 2001 33. Bujnicki JM, Radlinska M, Rychlewski L Polyphyletic evolution of type II restriction enzymes revisited: two independent sources of second-hand folds revealed. Trends Biochem Sci 2001 26(1):9-11 [pdf] 32. Bujnicki JM In silico analysis of the tRNA:m1A58 methyltransferase family: homology-based fold prediction and identification of new members from Eubacteria and Archaea FEBS Lett 2001 507(2): 123-127) [pdf] 31. Bujnicki JM, Rychlewski L Identification of a PD-(D/E)XK-like domain with a novel configuration of the endonuclease active site in the methyl-directed restriction enzyme Mrr and its homologs from all three domains of life. Gene 2001 267(2):183-91 [pdf] 30. Bujnicki JM, Elofsson A, Fischer D, Rychlewski L LiveBench-2: Large-scale automated evaluation of protein structure prediction servers Proteins 2001; Suppl 5:184-91. [pdf] 29. Bujnicki JM, Elofsson A , Fischer D, Rychlewski L Structure Prediction Meta Server. Bioinformatics 2001 17(8):750-751. [pdf] 28. Bujnicki JM Understanding the evolution of restriction-modification systems: clues from sequence and structure comparisons. Acta Biochim Pol 2001 48(4), 935-967 [pdf] 27. Bujnicki JM, Radlinska M, Zaleski P, Piekarowicz A Cloning of the Haemophilus influenzae Dam methyltransferase and analysis of its relationship to the Dam methyltransferase encoded by the HP1 phage. Acta Biochim Pol 2001 48(4), 969-983 [pdf] 26. Bujnicki JM A model of structure and action of Sau3AI restriction endonuclease that comprises two MutH-like endonuclease domains within a single polypeptide Acta Microbiol Pol 2001 50, 219-229 [pdf] 25. Bujnicki JM, Rychlewski L Unusual evolutionary history of the tRNA splicing endonuclease EndA: Relationship to the LAGLIDADG and PD-(D/E)XK deoxyribonucleases Protein Sci 2001 10: 656-660 [pdf] 24. Bujnicki JM, Rotkiewicz P, Kolinski A, Rychlewski L Three-dimensional modeling of the I-TevI homing endonuclease catalytic domain, a GIY-YIG superfamily member, using NMR restraints and Monte Carlo dynamics Protein Eng 2001 14(10):717-721. [pdf] 23. Lundstrom J, Rychlewski L, Bujnicki JM, Elofsson A Pcons: a neural network based consensus predictor that improves fold recognition. Protein Sci 2001 10(11):2354-62. [pdf] 22. Bujnicki JM, Elofsson A, Fischer D, Rychlewski L LiveBench-1: continuous benchmarking of protein structure prediction servers. Protein Sci 2001 10: 352-361 [pdf] 21. Radlinska M, Bujnicki JM Cloning of enterohemorrhagic Escherichia coli phage VT-2 Dam methyltransferase. Acta Microbiol Pol 2001 50(2), 157-163 [pdf] 20. Bujnicki JM, Rychlewski L Sequence analysis and structure prediction of aminoglycoside-resistance 16S rRNA:m7G methyltransferases. Acta Microbiol Pol 2001 50(1), 7-17 [pdf] 19. Bujnicki JM, Rychlewski L The Herpesvirus alkaline exonuclease belongs to the restriction endonuclease PD-(D/E)XK superfamily: insight from molecular modeling and phylogenetic analysis. Virus Genes 2001 22(2):219-230 [pdf] 18. Radlinska M, Bujnicki JM Site-directed mutagenesis defines the catalytic aspartate in the active site of the atypical DNA:m4C methyltransferase M.NgoMXV Acta Microbiol Pol 2001 50(2), 93-101 [pdf] 17. Bujnicki JM, Rychlewski L Grouping together highly diverged PD-(D/E)XK nucleases and identification of novel superfamily members using structure-guided alignment of sequence profiles. J Mol Microbiol Biotechnol 2001 3(1):69-72 [pdf] 16. Bujnicki JM, Rychlewski L Reassignment of specificities of two cap methyltransferase domains in the reovirus lambda2 protein Genome Biology 2001 2(9):38 [pdf] 15. Bujnicki JM, Radlinska M. Cloning and characterization of M.LmoA118I, a novel DNA:m4C methyltransferase from the Listeria monocytogenes phage A118, a close homolog of M.NgoMXV. Acta Microbiol Pol 2001 50(2), 151-166 [pdf] 14. Bujnicki JM, Feder M, Radlinska M, Rychlewski L mRNA:guanine-N7 cap methyltransferases: identification of novel members of the family, evolutionary analysis, homology modeling, and analysis of sequence-structure-function relationships. BMC Bioinformatics 2001 2:2 [pdf] 2000 13. Bujnicki JM Phylogenomic analysis of 16S rRNA:(guanine-N2) methyltransferases suggests new family members and reveals highly conserved motifs and domain structure similar to other nucleic acid amino-methyltransferases FASEB J 2000 14(14):2365-2368 [pdf] 12. Bujnicki JM Phylogeny of the restriction endonuclease-like superfamily inferred from comparison of protein structures. J Mol Evol 2000 50(1):39-44 [pdf] 11. Bujnicki JM, Radlinska M, Rychlewski L Atomic model of the 5-methylcytosine-specific restriction enzyme McrA reveals an atypical zinc-finger and structural similarity to beta-beta-alpha-Me endonucleases Mol Microbiol 2000 37(5):1280-1281 [pdf] 10. Bujnicki JM Sequence, structural, and evolutionary analysis of prokaryotic ribosomal protein L11 methyltransferases Acta Microbiol Pol 2000 49(1):19-29 [pdf] 9. Bujnicki JM, Rychlewski L Prediction of a common fold for all four subunits of the yeast tRNA splicing endonuclease - implications for the evolution of the EndA/Sen family. FEBS Lett 2000 486(3):328-329 [pdf] 8. Bujnicki JM, Rychlewski L Prediction of a novel RNA 2'-O-ribose methyltransferase subfamily encoded by the Escherichia coli YgdE open reading frame and its orthologs Acta Microbiol Pol 2000 49(3-4):253-261 [pdf] 7. Bujnicki JM Homology modelling of the DNA m5C methyltransferase M.BssHII. Is permutation of functional subdomains common to all subfamilies of DNA methyltransferases? Int J Biol Macromol 2000 27(3):195-204 [pdf] 1999
Papers in Polish (4 invited review articles and book chapters). 4. Bujnicki JM, Ginalski K, Kolinski A, Kosinski J [Odgadywanie struktur zycia] Scientific American, Polish edition [Swiat Nauki], 2006, 2, 174 [pdf] 3. Turkiewicz M, Bialkowska A, Tkaczuk KL, Kaluzewska M, Makowski K, Cieslinski H, Wanarska M, Kur J, Bujnicki JM [Antarktyczna beta-galaktozydaza - wlasciwosci i wykorzystanie w hydrolizie laktozy] chapter 18 in [Enzymatyczna modyfikacja skladnikow zywnosci], 2005. Editors, Kolakowski E, Bendarski W, Bielecki S. [pdf - not available] 2. Bujnicki JM [Przewidywanie struktury bialek: Boltzmann i Darwin] Kosmos, 2005, 54, 155-162 [pdf] 1. Cymerman IA, Sasin JM, Bujnicki JM [Przewidywanie struktury bialek: od modelowania opartego na szablonach do rekombinacji fragmentow metoda Frankensteina]. In [Na pograniczu Chemii i Biologii], vol X, 2004. Editors, Koroniak H, Barciszewski J [pdf]
Publications of other group members (with affiliation of IIMCB or UAM - shown in colors) The mitotic kinesin-14 Ncd drives directional microtubule-microtubule sliding. Fink G, Hajdo L, Skowronek KJ, Reuther C, Kasprzak AA, Diez S. Nat Cell Biol. 2009 Jun;11(6):717-23. Epub 2009 May 10. [pdf] Trm13p, the tRNA:Xm4 modification enzyme from Saccharomyces cerevisiae is a member of the Rossmann-fold MTase superfamily: prediction of structure and active site. Tkaczuk KL J Mol Model. 2009 Aug 22. [Epub ahead of print] [pdf] Voronoia: analyzing packing in protein structures. Rother K, Hildebrand PW, Goede A, Gruening B, Preissner R. Nucleic Acids Res. 2009 Jan;37(Database issue):D393-5. Epub 2008 Oct 23. [pdf] Tip-alpha (hp0596 gene product) is a highly immunogenic Helicobacter pylori protein involved in colonization of mouse gastric mucosa. Godlewska R, Pawlowski M, Dzwonek A, Mikula M, Ostrowski J, Drela N, Jagusztyn-Krynicka EK. Curr Microbiol. 2008 Mar;56(3):279-86. Epub 2008 Jan 3. [pdf] From knotted to nested RNA structures: a variety of computational methods for pseudoknot removal. Smit S, Rother K, Heringa J, Knight R. RNA. 2008 Mar;14(3):410-6. Epub 2008 Jan 29. [pdf] The sequence and model structure analysis of three Polish peanut stunt virus strains. Obrepalska-Steplowska A, Nowaczyk K, Budziszewska M, Czerwoniec A, Pospieszny H. Virus Genes. 2008 Feb;36(1):221-9. Epub 2007 Nov 30. [pdf] eMovie: a storyboard-based tool for making molecular movies. Hodis E, Schreiber G, Rother K, Sussman JL. Trends Biochem Sci. 2007 May;32(5):199-204. Epub 2007 Apr 19. [pdf]
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