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Laboratory of Bioinformatics and Protein Engineering: Bujnicki Laboratory

Janusz LL

Janusz Bujnicki, PhD, Professor 

Correspondence address:
Laboratory of Bioinformatics and Protein Engineering
International Institute of Molecular and Cell Biology
4 Ks. Trojdena Street, 02-109 Warsaw, Poland
Email: This email address is being protected from spambots. You need JavaScript enabled to view it.
www http://iimcb.genesilico.pl
tel: +48 (22) 597 0750; fax: +48 (22) 597 0715

Scientific degrees
- 25.09.2009 - Professor of Biological Sciences, title awarded by the President of the Republic of Poland
- 11.01.2005 - D.habil. in biochemistry, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
- 04.06.2001 - Ph.D. in bioinformatics, University of Warsaw, Faculty of Biology, Warsaw, Poland
- 16.06.1998 - M.Sc. in microbiology, University of Warsaw, Faculty of Biology, Warsaw, Poland 

Professional experience – present
- 06/2002 - : professor, head of the Laboratory of Bioinformatics and Protein Engineering, IIMCB, Warsaw, Poland (100% appointment)
- 10/2006 - : visiting professor, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland (currently 25% appointment)

Professional experience – past
- 06/2010-05/2011: deputy director, International Institute of Molecular and Cell Biology in Warsaw (1 year rolling position)
- 01-02/2008: visiting professor, University of Tokyo, Japan (sabbatical)
- 10/2004-09/2006: assistant professor (adjunct), Bioinformatics Laboratory, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
- 03/2002-05/2002: Acting head of the Laboratory of Bioinformatics at the IIMCB
- 02/2001-02/2002: Group Leader, Laboratory of Bioinformatics, IIMCB, Warsaw, Poland (with Dr. L Rychlewski)
- 06-09/2001: Visiting Scientist, National Center for Biotechnology Information, NLM, NIH, Bethesda, USA (with Dr. EV Koonin)
- 12/1999-02/2001: Research Scientist, Bioinformatics Unit, IIMCB, Warsaw, Poland (with Dr. L Rychlewski)
- 10/1998-07/2000: Senior Research Assistant, Henry Ford Health System, Detroit, MI, USA (with Dr. L.C. Lutter)

Professional affiliations – present
- High Level Group of scientific advisors within the Scientific Advice Mechanism (HLG-SAM) for the European Commission (member, 11.2015-)
- Science Policy Committee, Polish Ministry of Science and Higher Education (member 2014-2016-2018, chairman 04-10.2015, 06-12.2016)
- Council of the National Science Congress, Polish Ministry of Science and Higher Education (member, 09.2016-10.2017)
- Polish Society for Bioinformatics, PTBI (founding member, vice-president 2007-2010, president 2011-2013)
- Society of Bioinformatics in Northern Europe, SocBiN (board member, 2004-)
- RNA Society (member, 2007-), International Society for Computational Biology, ISCB (member, 2001-, Senior Member 2015-)
- Committee of Molecular Cell Biology, Polish Academy of Sciences (2016-2019)
- Committee of Biochemistry and Biophysics, Polish Academy of Sciences (ex officio AMU-PAN member, 2016-2019)

Professional affiliations – past
- Scientific Committee of the Innovative Medicines Initiative (member, 2013-2016)
- EC Advisory Group on European Research Infrastructures including e-Infrastructures, member (2013-2015)
- Science Promotion Council, Polish Academy of Sciences, RUN-PAN (2013-2016)
- Young Academy, Polish Academy of Sciences, AMU-PAN (2011-2016)
- Science Europe, Life, Environmental and Geo Sciences (LEGS) Scientific Committee, member (2013-2015)
- Committee of Evolutionary and Theoretical Biology, Polish Academy of Sciences (2008-2011, 2011-2015)
- Committee of Biochemistry and Biophysics, Polish Academy of Sciences (2011-2015)

Editorial activities
- Executive Editor, Nucleic Acids Research (2013-)
- Series editor, Nucleic Acids and Molecular Biology (Springer Verlag, 2009-2013)
- Deputy Section Editor, BMC Bioinformatics (2010-2014), Editorial Advisor (2014-)
- Editorial board member of: Nucleic Acids Research (2005-2012), Advances in Bioinformatics (2008-2011), Journal of Applied Genetics (2004-), the Database Journal (2008-2015), Journal of Nucleic Acids (2008-2013), Biology Direct (2013-)

International awards
2018 Elected as a member of Academia Europaea
- 2018 Elected as an EMBO member
- 2010 ERC Starting Grant (2011-2015) – first ERC Starting Grant in biological sciences awarded for a proposal from Poland
- 2006 Young Researcher Award in Structural and Evolutionary Biology of the Visegrad Group Academies of Sciences
- 2003-2005 EMBO & HHMI Young Investigator Programme Award

National awards
- 2017 Award of the Ministry of Science for Organizational Achievements
- 2016 Elected as a corresponding member to Polish Academy of Sciences – (youngest /41/ member of the Academy in 2016)
- 2016 Crystal Brussels Sprout – special award of the National Contact Point of the EU
- 2015 Parnas Award of the Polish Biochemical Society – 1 awardee per year (for the best publication in biochemistry)
- 2014 Award of the Polish National Research Center (NCN) – 1 awardee per year in Life Sciences (for researchers under 40)
- 2014 MISTRZ Award from the Foundation for Polish Science – 8 awardees per 4 years in Life and Geo Sciences
- 2014 Award of the Prime Minister for Outstanding Research Achievements – 6 awardees in all disciplines of science in 2014
- 2014 Selected as one of “25 leaders for the next 25 years” by “Teraz Polska” magazine of the Polish Promotional Emblem Foundation
- 2014 Award of the Knight’s Cross of the Order of Polonia Restituta
- 2013 Won the national plebiscite “Poles with Verve” in in the Science category
- 2013 Award of the Polish Genetics Society (coauthor in the best Polish genetics-related publication in 2012)
- 2012 Award of the Ministry of Science for Outstanding Research Achievements
- 2011, 2013, 2014 Adam Mickiewicz University Rector Special Award for Top Performance in Publishing High Impact Research Articles
- 2009 Award of the Ministry of Science for Research Achievements (Individual work)
- 2009 Fellowship for Outstanding Young Scientists (Ministry of Science, Republic of Poland)
- 2008 Adam Mickiewicz University Rector Award for Research Achievement (Individual work)
- 2007 Adam Mickiewicz University Rector Award for Research Achievement (Team work)
- 2006 Award of the Prime Minister of the Republic of Poland for the D.Habil thesis
- 2003, 2004 Fellowship for Young Scientists from the Foundation for Polish Science
- 2002 Award of the Polish Genetics Society (first author of the best Polish genetics-related publication in 2001)
- 2001 Award of Sigma-Aldritch and the Polish Biochemical Society (sole author of the best Polish publication on nucleic acid biochemistry in 2000)

Bibliography & citations
Total number of articles in English is 316 (296 peer-reviewed original and review articles in international journals, 20 book chapters and commentaries/white papers), and 2 edited books. Additionally 4 review articles or book chapters in Polish. Two international patents, one Polish patent.
The most up to date list is available at http://iimcb.genesilico.pl/publications.htm
Citations according to Scopus, as of 2017.12.07: [Bujnicki-J]: 311 articles, Sum of the times cited (excl. self-citations): 7457, h-index (excl. self-citations): 44

Supervision of junior scientists and teaching/mentoring (2002.06.01-2017.12.07)
Supervised 29 defended BSc/Eng theses, 50 defended M.Sc. theses and 31 defended Ph.D. theses, 24 postdoc

Current Research
Our group is involved in theoretical and experimental research on sequence structure-function relationships in proteins, nucleic acids, and macromolecular complexes. Theoretical research involves the development of computer software for the analysis of biological macromolecules. We are currently focusing on developing software for the structural prediction and modeling of RNA and RNA protein complexes. To date, we have developed and made publicly available one of the first methods for the automated comparative (template-based) modeling of three-dimensional (3D) RNA structures (ModeRNA; http://iimcb.genesilico.pl/moderna/) and a method for de novo (template-free) RNA structure modeling (SimRNA; http://genesilico.pl/software/stand-alone/simrna, also available as a web server at http://genesilico.pl/SimRNAweb). We have also developed a method for predicting metal ion binding sites in RNA structures (MetalionRNA; http://metalionrna.genesilico.pl), a method for modeling RNA-ligand complexes (LigandRNA; http://ligandrna.genesilico.pl), and a method for predicting the structure of RNA-protein complexes (http://genesilico.pl/NPDock). Other methods for RNA bioinformatics include a server for the continuous benchmarking of automated methods for RNA secondary structure prediction (CompaRNA; http://iimcb.genesilico.pl/comparna/), and a method for classification of contacts in RNA 3D structures (ClaRNA; http://iimcb.genesilico.pl/clarna/). We have also developed various databases, including a database of RNA modification pathways and enzymes (MODOMICS; http://modomics.genesilico.pl) and a database of RNA 3D motifs and their interactions (RNA Bricks; http://iimcb.genesilico.pl/rnabricks/)

Our suite of programs for prediction and analysis of protein structures and macromolecular complexes includes the GeneSilico MetaServer (https://www.genesilico.pl/meta2/), methods for modeling large macromolecular complexes with the use of restraints derived from experimental data (PyRy3D; http://genesilico.pl/pyry3d/, and MikoFit3D; http://iimcb.genesilico.pl/minkofit3d/), and a method for discriminating models according to their agreement with experimental data (FILTREST3D; http://filtrest3d.genesilico.pl/). We also developed methods for predicting order/disorder in protein structures (http://iimcb.genesilico.pl/metadisorder/) and protein localization in Gram-negative bacterial cells (MetaLocGramN; http://genesilico.pl/MetaLocGramN/). 

Our experimental research focuses on elucidating sequence structure-function relationships in proteins and nucleic acids using biophysics, biochemistry, molecular biology, and cell biology. We integrate theoretical and experimental research quite tightly. We often experimentally test functional and structural predictions for proteins and RNAs and their complexes using computational methods. For structural studies, we combine X-ray crystallography and low-resolution structural probing methods, such as mutagenesis, chemical modification, crosslinking, mass spectrometry, and circular dichroism. We also use experimental methods for protein engineering to obtain enzymes with new, useful features, particularly alterations in substrate specificity (e.g., nucleases that exhibit new substrate specificities).

Recent highlights
Towards small molecule inhibitors of methyltransferases involved in RNA cap synthesis
Previously, we identified genes encoding the enzymes responsible for cap1 and cap2 methylations in human cells (CMTr1 and CMTr2 methyltransferases). We determined a crystal structure of CMTr1 in complex with its substrate RNA, and we generated a computational model of CMTr2-RNA complex structure. This finding provided mechanistic insight into the process by which the human methyltransferases recognize and chemically modify the cap structure in RNA molecules. It has also led us to identify key differences between human and viral enzymes responsible for the same cap methylations. We found that human and viral methyltransferases share extensive similarity in the active sites, but differ completely in the way they recognize the m7G moiety. The results of this research explained why human cap methyltransferases are relatively insensitive to the presence of a methyl group at m7G, which makes them different from the viral enzymes. The structures we obtained suggested how the cap analogs could be modified to make them block the viral enzymes but not the human ones, which may help in the development of new antiviral drugs. On the other hand, small molecules that block human cap methyltransferases could be used as research tools to study the function and dysfunction of cap methylation in human cells, especially the effect of the lack of methylation on the fate of human mRNAs. In the ongoing MISTRZ project funded by the Foundation for Polish Science, based on the structural information for human and viral cap methyltransferases and on our discovery that these enzymes do it differently, we set to develop small molecule inhibitors that selectively block either human or viral cap methyltransferases.

Thus far, we applied various computational methods to perform virtual screening analysis of large databases of commercially available drug-like small molecules. Computational docking performed for each of the methyltransferases enabled identification of the potentially most selective ones. From the results of the initial virtual screen, we selected 208 compounds as CMTr1 methyltransferase inhibitors, 76 compounds as VP39 (vaccinia virus methyltransferase) inhibitors and 105 compounds as NS5 (Dengue virus methyltransferase) inhibitors. Top-scoring ligands were subjected to experimental analyses.

Compounds chosen for experimental analysis were obtained and analyzed for their influence on the cap methyltransferase activity. To confirm whether the chosen compounds block human methyltransferase through direct interaction with the binding pocket of the catalytic domain, we tested their analysis directly with the isolated CMTr1 catalytic domain. We have tested the influence of the 208 compounds and selected 10 that significantly decreased the level of the methyltransferase catalytic domain. Then, the activity of these 10 compounds was tested on the full-length CMTr1 protein and IC50 was determined. The next step in the project was to validate the selectivity of the chosen compounds. All the compounds (in 100µM concentration) that showed the highest blocking potential against the human CMTr1 enzyme were tested on the viral protein, and vice versa. For the human methyltransferase inhibitors, one totally blocks the activity of VP39, four decrease protein activity by 50% and two by 30%, while three have almost no influence on the viral methyltransferase activity. We have also performed attempts to co-crystallize CMTr1 with two of the chosen compounds, using commercial crystallization screens and optimizing the conditions already published.

The second line of analyses carried out in the project has focused on finding the viral methyltransferase inhibitors. We have chosen 76 compounds among those predicted to be the most effective VP39 inhibitors.. We have tested the activity of these compounds on the VP39 protein. As a result, 8 inhibitors with the highest impact on VP39 activity at 100 µM concentration were identified. We found that 7 out of these 8 viral methyltransferase inhibitors significantly blocked the activity of human protein methyltransferase. The remaining one decreased the activity of CMTr1 by 30%. This single viral methyltransferase inhibitor has been used as a starting point to carry out as computational search for structurally related ligands which are our current targets for testing, with the goal to obtain compounds that block the VP39 methyltransferase and have little effects on human enzymes. This approach is also currently used to test the predicted inhibitors of the Dengue virus methyltransferases.

 

 

 
 

Lab Leader:
Janusz M. Bujnicki, PhD, DSc, Professor 

Office Manager:
Katarzyna Grzelak, MSc  

Bioinformatics/Theory
Research Coordinator:
Filip Stefaniak, PhD

Postdoctoral Researchers:
Michał Boniecki, PhD
Nithin Chandran, PhD
Pritha Ghosh, PhD
Sunandan Mukherjee, PhD
Tomasz Wirecki, PhD

PhD students:
Pietro Boccaletto, MSc
Magdalena Orłowska, MSc
Masoud A. Farsani, MSc  
Sachin Gaddakh, PhD
Iswarya Pandara Nayaka PJ, PhD

Undergraduate student:
Dharm Skandh Jain, B.Eng.

Biochemistry/Experiment
Research Coordinator:
Elżbieta Purta, PhD

Postdoctoral Researchers:
Lucyna Budźko, PhD

PhD student:
Diana Toczydłowska-Socha, MSc
Błażej Bagiński, MSc

Research Technicians:
Ewa Skowronek, PhD
Agata Bernat, MSc
Małgorzata Kurkowska, MSc
Katarzyna Merdas, MSc
Magdalena Sroka, MSc

2018

Pluta R, Espinosa M.

Antisense and yet sensitive: Copy number control of rolling circle-replicating plasmids by small RNAs.

Foik IP, Tuszynska I, Feder M, Purta E, Stefaniak F, Bujnicki JM.

Novel inhibitors of the rRNA ErmC' methyltransferase to block resistance to macrolides, lincosamides, streptogramine B antibiotics.

Kumari P, Aeschimann F, Gaidatzis D, Keusch JJ, Ghosh P, Neagu A, Pachulska-Wieczorek K, Bujnicki JM, Gut H, Großhans H, Ciosk R.

Evolutionary plasticity of the NHL domain underlies distinct solutions to RNA recognition.

Nithin C, Ghosh P, Bujnicki JM.

Bioinformatics Tools and Benchmarks for Computational Docking and 3D Structure Prediction of RNA-Protein Complexes.

Fernandes H, Czapinska H, Grudziaz K, Bujnicki JM, Nowacka M.

Crystal structure of human Acinus RNA recognition motif domain.

Sweeney BA et al. (Bujnicki JM, Boccaletto P)

RNAcentral: a hub of information for non-coding RNA sequences.

Toczydlowska-Socha D, Zielinska MM, Kurkowska M, Astha, Almeida CF, Stefaniak F, Purta E, Bujnicki JM.

Human RNA cap1 methyltransferase CMTr1 cooperates with RNA helicase DHX15 to modify RNAs with highly structured 5' termini.

Jantsch MF et al. (Bujnicki J, Purta E)

Positioning Europe for the EPITRANSCRIPTOMICS challenge.

Voigt C, Dobrychlop M, Kruse E, Czerwoniec A, Kasprzak JM, Bytner P, Campo CD, Leeder WM, Bujnicki JM, Göringer HU.

The OB-fold proteins of the Trypanosoma brucei editosome execute RNA-chaperone activity.

Boccaletto P, Magnus M, Almeida C, Zyla A, Astha A, Pluta R, Baginski B, Jankowska E, Dunin-Horkawicz S, Wirecki TK, Boniecki MJ, Stefaniak F, Bujnicki JM.

RNArchitecture: a database and a classification system of RNA families, with a focus on structural information.

Boccaletto P, Machnicka MA, Purta E, Piatkowski P, Baginski B, Wirecki TK, de Crécy-Lagard V, Ross R, Limbach PA, Kotter A, Helm M, Bujnicki JM.

MODOMICS: a database of RNA modification pathways. 2017 update.

2017

Patel T, Chojnowski G, Astha, Koul A, McKenna S, Bujnicki JM

Structural studies of RNA-protein complexes: A hybrid approach involving hydrodynamics, scattering and computational methods

Miao Z, Adamiak RW, Antczak M, Batey RT, Becka A, Biesiada M, Boniecki MJ, Bujnicki JM, Chen S, Cheng CY, Chou F, Ferré-D'Amaré AR, Das R, Dawson WK, Ding F, Dokholyan NV, Dunin-Horkawicz S, Geniesse C, Kappel K, Kladwang W, Krokhotin A, Lach GE, Major F, Mann TH, Magnus M, Pachulska-Wieczorek K, Patel DJ, Piccirilli JA, Popenda M, Purzycka KJ, Ren A, Rice GM, Santalucia J Jr, Sarzynska J, Szachniuk M, Tandon A, Trausch JJ, Tian S, Wang J, Weeks KM, Williams B II, Xiao Y, Xu X, Zhang D, Zok T, Westhof E

RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme

Karlowicz A, Wegrzyn K, Gross M, Kaczynska D, Ropelewska M, Siemiątkowska M, Bujnicki JM, Konieczny I

Defining the crucial domain and amino acid residues in bacterial Lon protease for DNA binding and processing of DNA-interacting substrates

Budzko L, Jackowiak P, Kamel K, Sarzynska J, Bujnicki JM, Figlerowicz M

Mutations in human AID differentially affect its ability to deaminate cytidine and 5-methylcytidine in ssDNA substrates in vitro

Piątkowski P, Jabłońska J, Żyła A, Niedziałek, Matelska D, Jankowska E, Waleń T, Dawson WK, Bujnicki JM.

SupeRNAlign: a new tool for flexible superposition of homologous RNA structures and inference of accurate structure-based sequence alignments.

Chawla M, Chermak E, Zhang Q, Bujnicki JM, Oliva R, Cavallo L.

Occurrence and stability of lone pair-π stacking interactions between ribose and nucleobases in functional RNAs.

Dzananovic E, Astha, Chojnowski G, Deo S, Booy EP, Padilla-Meier P, McEleney K, Bujnicki JM, Patel TR, McKenna SA.

Impact of the structural integrity of the three-way junction of adenovirus VAI RNA on PKR inhibition.

2016

Magnus MM, Boniecki MJ, Dawson WK, Bujnicki JM

SimRNAweb: a web server for RNA 3D structure modeling with optional restraints

Yahara K, Furuta Y, Morimoto S, Kikutake C, Komukai S, Matelska D, Dunin-Horkawicz S, Bujnicki JM, Uchiyama I, Kobayashi I

Genome-wide survey of codons under diversifying selection in a highly recombining bacterial species, Helicobacter pylori

Matelska D, Kurkowska M, Purta E, Bujnicki JM, Dunin-Horkawicz S

Loss of conserved non-coding RNAs in genomes of bacterial endosymbionts

Ukleja M, Cuellar J, Siwaszek A, Kasprzak JM, Czarnocki-Cieciura M, Bujnicki JM, Dziembowski A, Valpuesta J

The architecture of the Schizosaccharomyces pombe CCR4-NOT complex

Boniecki MJ, Lach G, Dawson WK, Tomala K, Lukasz P, Soltysinski T, Rother KM, Bujnicki JM

SimRNA: a coarse-grained method for RNA folding simulations and 3D structure prediction

Dawson WK, Bujnicki JM

Computational modeling of RNA 3D structures and interactions

Van Laer B, Roovers M, Wauters L, Kasprzak JM, Dyzma M, Deyaert E, Singh R, Feller A, Bujnicki JM, Droogmans L, Versées W

Structural and functional insights into tRNA binding and adenosine N1-methylation by an archaeal Trm10 homologue

Glow D, Kurkowska M, Czarnecka J, Szczepaniak K, Pianka D, Kappert V, Bujnicki JM, Skowronek KJ

Identification of protein structural elements responsible for the diversity of sequence preferences among Mini-III RNases.

Iskierko Z, Sharma PS, Prochowicz D, Fronc K, D'Souza F, Toczydłowska D, Stefaniak F, Noworyta K

Molecularly Imprinted Polymer (MIP) Film with Improved Surface Area Developed by Using Metal-Organic Framework (MOF) for Sensitive Lipocalin (NGAL) Determination.

Pawlowski M, Kozlowski L, Kloczkowski A

MQAPsingle: A quasi single-model approach for estimation of the quality of individual protein structure models

Urulangodi M, Dhanaraju R, Gupta K, Roy RP, Bujnicki JM, Rao DN

Asymmetric DNA methylation by dimeric EcoP15I DNA methyltransferase

Machnicka MA, Dunin-Horkawicz S, de Crécy-Lagard V, Bujnicki JM

tRNAmodpred: A computational method for predicting posttranscriptional modifications in tRNAs

Dawson WK, Maciejczyk M, Jankowska EJ, Bujnicki JM

Coarse-grained modeling of RNA 3D structure

Głów D, Nowacka M, Skowronek KJ, Bujnicki JM.

Sequence-specific endoribonucleases.

2015

Roszczenko P, Grzeszczuk M, Kobierecka P, Wywial E, Urbanowicz P, Wincek P, Nowak E, Jagusztyn-Krynicka EK

Helicobacter pylori HP0377, a member of the Dsb family, is an untypical multifunctional CcmG that cooperates with dimeric thioldisulfide oxidase HP0231

Bocian-Ostrzycka KM, Łasica AM, Dunin-Horkawicz S, Grzeszczuk MJ, Drabik K, Dobosz AM, Godlewska R, Nowak E, Collet J-F, Jagusztyn-Krynicka EK

Functional and evolutionary analyses of Helicobacter pylori HP0231 (DsbK) protein with strong oxidative and chaperone activity characterized by a highly diverged dimerization domain

Blatter M, Dunin-Horkawicz S, Grishina I, Maris C, Thore S, Maier T, Bindereif A, Bujnicki JM, Allain FHT

The signature of the five-stranded vRRM fold defined by functional, structural and computational analysis of the hnRNP L protein

Boekema C, Owens F, Love A, Li Z, Sakkaris P, Dawson WK

A magnetic origin of cuprate superconductivity? A MaxEnt-mu SR view

Chawla M, Oliva R, Bujnicki JM, Cavallo L

An atlas of RNA base pairs involving modified nucleobases with optimal geometries and accurate energies

Chojnowski G, Walen T, Piatkowski P, Potrzebowski W, Bujnicki JM

Brickworx builds recurrent RNA and DNA structural motifs into medium and low-resolution electron density maps

Czerwoniec A, Kasprzak JM, Bytner P, Dobrychlop M, Bujnicki JM

Structure and intrinsic disorder of the proteins of the Trypanosoma brucei editosome

Deo S, Patel TR, Chojnowski G, Koul A, Dzananovic E, McEleney K, Bujnicki JM, McKenna SA

Characterization of the termini of the West Nile virus genome and their interactions with the small isoform of the 2' 5'-Oligoadenylate Synthetase family

Glow D, Pianka D, Sulej A, Kozlowski L, Czarnecka J, Chojnowski G, Skowronek KJ, Bujnicki JM

Sequence-specific cleavage of dsRNA by Mini-III RNase

Liu S, Mozaffari-Jovin S, Wollenhaupt J, Santos KF, Theuser M, Dunin-Horkawicz S, Fabrizio P, Bujnicki JM, Lührmann R, Wahl MC

A composite double-/single-stranded RNA-binding region in protein Prp3 supports tri-snRNP stability and splicing

Miao Z, Adamiak RW, Blanchet MF, Boniecki M, Bujnicki JM, Chen SJ, Cheng C, Chojnowski G, Chou FC, Cordero P, Cruz JA, Ferré-D'amaré AR, Das R, Ding F, Dokholyan NV, Dunin-Horkawicz S, Kladwang W, Krokhotin A, Lach G, Magnus M, Major F, Mann TH, Masquida B, Matelska D, Meyer M, Peselis A, Popenda M, Purzycka KJ, Serganov A, Stasiewicz J, Szachniuk M, Tandon A, Tian S, Wang J, Xiao Y, Xu X, Zhang J, Zhao P, Zok T, Westhof E

RNA-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structures

Philips A, Lach G, Bujnicki JM

Computational methods for prediction of RNA interactions with metal ions and small organic ligands

Plotka M, Kaczorowska AK, Morzywolek A, Makowska J, Kozlowski LP, Thorisdottir A, Skírnisdottir S, Hjörleifsdottir S, Fridjonsson OH, Hreggvidsson GO, Kristjansson JK, Dabrowski S, Bujnicki JM, Kaczorowski T

Biochemical Characterization and Validation of a Catalytic Site of a Highly Thermostable Ts2631 Endolysin from the Thermus scotoductus Phage vB_Tsc2631

Tuszynska I, Magnus M, Jonak K, Dawson W, Bujnicki JM

NPDock – a web server for protein-nucleic acid docking

Zheng H, Shabalin I, Handing K, Bujnicki JM, Minor M

Magnesium binding architectures in RNA crystal structures: validation binding preferences, classification, and motif detection

The RNAcentral Consortium (Petrov AI et al within Bujnicki JM)

RNAcentral: a comprehensive database of non-coding RNA sequences

Machnicka AM, Kaminska KH, Dunin-Horkawicz S, Bujnicki JM.

Phylogenomics and sequence-structure-function relationships in the GmrSD family of Type IV restriction enzymes.

2014

Sierocka I, Kozlowski LP, Bujnicki JM, Jarmolowski A, Szweykowska-Kulinska Z

Female-specific gene expression in dioecious liverwort Pellia endiviifolia is developmentally regulated and connected to archegonia production

Ramos-Molina B, Lambertos A, Lopez-Contreras AJ, Kasprzak JM, Czerwoniec A, Bujnicki JM, Cremades A, Penafiel R

Structural and degradative aspects of ornithine decarboxylase antizyme inhibitor 2

Walen T, Chojnowski G, Gierski P,Bujnicki JM,

ClaRNA: a classifier of contacts in RNA 3D structures based on a comparative analysis of various classification schemes

Grabowska AD, Wywiał E, Dunin-Horkawicz S , Lasica AM, Wösten MM, Nagy-Staroń A, Godlewska R, Bocian-Ostrzycka K, Pieńkowska K, Laniewski P, Bujnicki JM, van Putten JP, Jagusztyn-Krynicka EK

Functional and bioinformatics analysis of two Campylobacter jejuni homologs of the thiol-disulfide oxidoreductase, DsbA

Szczepaniak K, Lach G, Bujnicki JM, Dunin-Horkawicz S

Designability landscape reveals sequence features that define axial helix rotation in four-helical homo-oligomeric antiparallel coiled-coil structures

Tuszynska I, Matelska D, Magnus M, Chojnowski G, Kasprzak JM, Kozlowski LP, Dunin-Horkawicz S, Bujnicki JM

Computational modeling of protein-RNA complex structures

Plotka M, Kaczorowska AK, Stefanska A, Morzywolek A, Fridjonsson OH, Dunin-Horkawicz S, Kozlowski L, Hreggvidsson GO, Kristjansson JK, Dabrowski S, Bujnicki JM, Kaczorowski T

Novel Highly Thermostable Endolysin from Thermus scotoductus MAT2119 Bacteriophage Ph2119 with Amino Acid Sequence Similarity to Eukaryotic Peptidoglycan Recognition Proteins

Dzananovic E, Patel TR, Chojnowski G, Boniecki MJ, Deo S, McEleney K, Harding SE, Bujnicki JM, McKenna SA

Solution conformation of Adenovirus Virus Associated RNA-I and its interaction with PKR

Chojnowski G, Walen T, Bujnicki JM

RNA Bricks - a database of RNA 3D motifs and their interactions

Smietanski M, Werner M, Purta E, Kaminska KH, Stepinski J, Darzynkiewicz E, Nowotny M, Bujnicki JM

Structural analysis of human 2′-O-ribose methyltransferases involved in mRNA cap structure formation

Crochemore M, Iliopoulos CS, Kubica M, Radoszewski J, Rytter W, Stencel K, Walen T

New simple efficient algorithms computing powers and runs in strings

Sadowski Ł, Jastrzębski K, Purta E, Hellberg C, Miaczynska M

Labeling of platelet-derived growth factor by reversible biotinylation to visualize its endocytosis by microscopy

Toczyłowska-Mamińska R, Olszewska A, Laskowski M, Bednarczyk P, Skowronek K, Szewczyk A

Potassium channel in the mitochondria of human keratinocytes

Majorek KA, Dunin-Horkawicz S, Steczkiewicz K, Muszewska A, Nowotny M, Ginalski K, Bujnicki JM

The RNase H-like superfamily: new members, comparative structural analysis and evolutionary classification

Byszewska M, Smietanski M, Purta E, Bujnicki JM.

RNA methyltransferases involved in 5' cap biosynthesis.

Machnicka M, Olchowik A, Grosjean H, Bujnicki JM.

Distribution and frequencies of post-transcriptional modifications in tRNAs.

Mierzejewska K, Siwek W, Czapinska H, Kaus-Drobek M, Radlinska M, Skowronek K, Bujnicki JM, Dadlez M, Bochtler M

Structural basis of the methylation specificity of R.DpnI

Rother K, Rother M, Skiba P, Bujnicki JM

Automated modeling of RNA 3D structure

Magnus M, Matelska D, Lach G, Chojnowski G, Boniecki MJ, Purta E, Dawson W, Dunin-Horkawicz S, Bujnicki JM

Computational modeling of RNA 3D structures, with the aid of experimental restraints

2013

Machnicka MA, Milanowska K, Osman Oglou O, Purta E, Kurkowska M, Olchowik A, Januszewski W, Kalinowski S, Dunin-Horkawicz S, Rother KM, Helm M, Bujnicki JM, Grosjean H

MODOMICS: a database of RNA modification pathways: 2013 update

Milanowska K, Mikolajczak K, Lukasik A, Skorupski M, Balcer Z, Machnicka MA, Nowacka M, Rother KM, Bujnicki JM

RNApathwaysDB – a database of RNA maturation and decay pathways

Nowak E, Potrzebowski W, Konarev PV, Rausch JW, Bona MK, Svergun DI, Bujnicki JM, Le Grice SF, Nowotny M

Structural analysis of monomeric retroviral reverse transcriptase in complex with an RNA/DNA hybrid

Puton T, Kozlowski LP, Rother KM, Bujnicki JM

CompaRNA: a server for continuous benchmarking of automated methods for RNA secondary structure prediction

Bujnicki JM, Tiuryn J

Bioinformatics and computational biology in Poland

Lukasiak P, Antczak M, Ratajczak T, Bujnicki JM, Szachniuk M, Adamiak RW, Popenda M, Blazewicz J

RNAlyzer--novel approach for quality analysis of RNA structural models

Pawlowski M, Bogdanowicz A, Bujnicki JM

QA-RecombineIt: a server for quality assessment and recombination of protein models

Crochemore M, Iliopoulos C.S, Kociumaka T, Kubica M, Pachocki J, Radoszewski J, Rytter W,Tyczyński W, Waleń T

A note on efficient computation of all Abelian periods in a string

Bednarczyk P, Wieckowski MR, Broszkiewicz M, Skowronek K, Siemen D, Szewczyk A

Putative Structural and Functional Coupling of the Mitochondrial BKCa Channel to the Respiratory Chain

Kubica M, Kulczyńskia T, Radoszewskia J, Rytter W,Walen T

A linear time algorithm for consecutive permutation pattern matching

Matelska D, Purta E, Panek S, Boniecki MJ, Bujnicki JM, Dunin-Horkawicz S

S6:S18 ribosomal protein complex interacts with a structural motif present in its own mRNA

Czeredys M, Samluk L, Michalec K, Tułodziecka K, Skowronek K, Nałęcz KA

Caveolin-1 - a novel interacting partner of organic cation/carnitine transporter (octn2): effect of protein kinase C on this interaction in rat astrocytes.

Philips A, Milanowska K, Lach G, Bujnicki JM

LigandRNA: computational predictor of RNA-ligand interactions

Xu C, Liu R, Mehta AK, Guerrero-Ferreira RC, Wright ER, Dunin-Horkawicz S, Morris K, Serpell LC, Zuo X, Wall JS, Conticello VP

Rational design of helical nanotubes from self-assembly of coiled-coil lock washers

2012

Philips A, Milanowska K, Lach G, Boniecki M, Rother K, Bujnicki JM

MetalionRNA: computational predictor of metal-binding sites in RNA structures

Kennaway CK, Taylor JE, Song CF, Potrzebowski W, Nicholson W, White JH, Swiderska A,Obarska-Kosinska A, Callow P, Cooper LP, Roberts GA, Artero JB,Bujnicki JM, Trinick J, Kneale GG, Dryden DT

Structure and operation of the DNA-translocating type I DNA restriction enzymes

Rother K, Potrzebowski W, Puton T, Rother M, Wywial E, Bujnicki JM

A toolbox for developing bioinformatics software

Puton T, Kozlowski L, Tuszynska I, Rother K, Bujnicki JM

Computational methods for prediction of protein-RNA interactions

Nakagome S, Mano S, Kozlowski L, Bujnicki JM, Shibata H, Fukumaki Y, Kidd JR, Kidd KK, Kawamura S, Oota H

Crohn's Disease Risk Alleles on the NOD2 Locus Have Been Maintained by Natural Selection on Standing Variation

Roovers M, Oudjama Y, Fislage M, Bujnicki JM, Versées W, Droogmans L

The open reading frame TTC1157 of Thermus thermophilus HB27 encodes the methyltransferase forming N2-methylguanosine at position 6 in tRNA

Zylicz-Stachula A, Zolnierkiewicz O, Lubys A, Ramanauskaite D, Mitkaite G, Bujnicki JM, Skowron P

Related bifunctional restriction endonuclease-methyltransferase triplets: TspDTI, Tth111II/TthHB27I and TsoI with distinct specificities

Chojnowski G, Bujnicki JM, Bochtler M

RIBER/DIBER: a software suite for crystal content analysis in the studies of protein-nucleic acid complexes

Cruz JA, Blanchet MF, Boniecki M, Bujnicki JM, Chen SJ, Cao S, Das R, Ding F, Dokholyan NV, Flores SC, Huang L, Lavender CA, Lisi V, Major F, Mikolajczak K, Patel DJ, Philips A, Puton T, Santalucia J, Sijenyi F, Hermann T, Rother K, Rother M, Serganov A, Skorupski M, Soltysinski T, Sripakdeevong P, Tuszynska I, Weeks KM, Waldsich C, Wildauer M, Leontis NB, Westhof E

RNA-Puzzles: A CASP-like evaluation of RNA three-dimensional structure prediction

Fislage M, Roovers M, Tuszynska I, Bujnicki JM, Droogmans L, Versées W

Crystal structures of the tRNA:m(2)G6 methyltransferase Trm14/TrmN from two domains of life

Lach G, DeKievet M, Jentschura UD

Einstein–Hopf drag, Doppler shift of thermal radiation and blackbody drag: Three perspectives on quantum friction

Malenda A, Skrobanska A, Issat T, Winiarska M, Bil J, Oleszczak B, Sinski M, Firczuk M, Bujnicki JM, Chlebowska J, Staruch AD, Glodkowska-Mrowka E, Kunikowska J, Krolicki L, Szablewski L, Gaciong Z, Koziak K, Jakobisiak M, Golab J, Nowis DA

Statins Impair Glucose Uptake in Tumor Cells

Samluk L, Czeredys M, Skowronek K, Nałęcz KA

Protein kinase C regulates amino acid transporter ATB

Siwek W, Czapinska H, Bochtler M, Bujnicki JM, Skowronek K

Crystal structure and mechanism of action of the N6-methyladenine dependent type IIM restriction endonuclease

Pietal MJ, Szostak N, Rother KM, Bujnicki JM

RNAmap2D -- calculation, visualization and analysis of contact and distance maps for RNA and protein-RNA complex structures

Pawlowski M, Bujnicki JM

The utility of comparative models and the local model quality for protein crystal structure determination by Molecular Replacement

Sulej AA, Tuszynska I, Skowronek KJ, Nowotny M, Bujnicki JM

Sequence-specific cleavage of the RNA strand in DNA-RNA hybrids by the fusion of ribonuclease H with a zinc finger

Drozdz M, Piekarowicz A, Bujnicki JM, Radlinska M

Novel non-specific DNA adenine methyltransferases

Korneta I, Magnus M, Bujnicki JM

Structural bioinformatics of the human spliceosomal proteome

Poleszak K, Kaminska KH, Dunin-Horkawicz S, Lupas A, Skowronek KJ, Bujnicki JM

Delineation of structural domains and identification of functionally important residues in DNA repair enzyme Exonuclease VII

Skowronek K, Boniecki MJ, Kluge B, Bujnicki JM

Rational engineering of sequence specificity in R.MwoI restriction endonuclease

Magnus M, Pawlowski M, Bujnicki JM

MetaLocGramN: A meta-predictor of protein subcellular localization for Gram-negative bacteria

Al-Haggar M, Madej-Pilarczyk A, Kozlowski L, Bujnicki JM, Yahia S, Abdel-Hadi D, Shams A, Ahmad N, Hamed S, Puzianowska-Kuznicka M

A novel homozygous p.Arg527Leu LMNA mutation in two unrelated egyptian families causes overlapping mandibuloacral dysplasia and progeria syndrome

Roszczenko P, Radomska KA, Wywial E, Collet JF, Jagusztyn-Krynicka EK

A novel insight into the oxidoreductase activity of Helicobacter pylori HP0231 protein

Kusio-Kobialka M, Wolanin K, Podszywalow-Bartnicka P, Sikora E, Skowronek K, McKenna SL, Ghizzoni M, Dekker FJ, Piwocka K

Increased acetylation of lysine 317/320 of p53 caused by BCR-ABL protects from cytoplasmic translocation of p53 and mitochondria-dependent apoptosis in response to DNA damage

Korneta I, Bujnicki JM

Intrinsic disorder in the human spliceosomal proteome

Kasprzak JM, Czerwoniec A, Bujnicki JM

Molecular evolution of dihydrouridine synthases

Kozlowski LP, Bujnicki JM

MetaDisorder: A meta-server for the prediction of intrinsic disorder in proteins

Rother K, Rother M, Boniecki M, Puton T, Tomala K, Lukasz P, Bujnicki JM

Template-based and template-free modeling of RNA 3D structure: inspirations from protein structure modeling In "RNA Structure Prediction and Modelling"

Kozlowski L, Orlowski J, Bujnicki JM

Structure prediction of alternatively spliced proteins In „Alternative pre-mRNA Splicing: Theory and Protocols: The Complete Guide for Biomedical Scientists”

2011

Milanowska K, Krwawicz J, Papaj G, Kosinski J, Poleszak K, Lesiak J, Osinska E, Rother K, Bujnicki JM

REPAIRtoire-a database of DNA repair pathways

Rother K, Rother M, Boniecki M, Puton T, Bujnicki JM

RNA and protein 3D structure modeling: similarities and differences

Rother M, Milanowska K, Puton T, Jeleniewicz J, Rother K, Bujnicki JM

ModeRNA server: an online tool for modeling RNA 3D structures

Tuszynska I, Bujnicki JM

DARS-RNP and QUASI-RNP: New statistical potentials for protein-RNA docking

Werner M, Purta E, Kaminska KH, Cymerman IA, Campbell DA, Mittra B, Zamudio JR, Sturm NR, Jaworski J, Bujnicki JM

2'-O-ribose methylation of cap2 in human: function and evolution in a horizontally mobile family

Rother M, Rother K, Puton T, Bujnicki JM

ModeRNA: a tool for comparative modeling of RNA 3D structure

Bateman A, Agrawal S, Birney E, Bruford EA, Bujnicki JM, Cochrane G, Cole JR, Dinger ME, Enright AJ, Gardner PP, Gautheret D, Griffiths-Jones S, Harrow J, Herrero J, Holmes IH, Huang HD, Kelly KA, Kersey P, Kozomara A, Lowe TM, Marz M, Moxon S, Pruitt KD, Samuelsson T, Stadler PF, Vilella AJ, Vogel JH, Williams KP, Wright MW, Zwieb C

RNAcentral: A vision for an international database of RNA sequences

Czerwoniec A, Bujnicki JM

Identification and modeling of a phosphatase-like domain in a tRNA 2'-O-ribosyl phosphate transferase Rit1p

Liu J, Ganapathy K, Wywial E, Bujnicki JM, Nwogwugwu CA, Nes WD

Effect of substrate features and mutagenesis of active site tyrosine residues on the reaction course catalysed by Trypanosoma brucei sterol C-24-methyltransferase

Milanowska K, Rother K, Bujnicki JM

Databases and bioinformatics tools for the study of DNA repair

Rother M, Rother K, Puton T, Bujnicki JM

RNA tertiary structure prediction with ModeRNA

Sikorski K, Czerwoniec A, Bujnicki JM, Wesoly J, Bluyssen HAR

STAT1 as a novel therapeutical target in pro-atherogenic signal integration of IFNg, TLR4 and IL-6 in vascular disease

Bielska E, Lucas X, Czerwoniec A, Kasprzak JM, Kaminska KH, Bujnicki JM

Virtual screening strategies in drug design - methods and applications

Abrahams JP, Apweiler R, Balling R, Bertero MG, Bujnicki JM, Chayen NE, Chène P, Corthals GL, Dyląg T, Förster F, Heck AJ, Henderson PJ, Herwig R, Jehenson P, Kokalj SJ, Laue E, Legrain P, Martens L, Migliorini C, Musacchio A, Podobnik M, Schertler GF, Sc

"4D Biology for health and disease" workshop report

Husain N, Obranic S, Koscinski L, Seetharaman J, Babic F, Bujnicki JM, Maravic-Vlahovicek G, Sivaraman J

Structural basis for the methylation of A1408 in 16S rRNA by a panaminoglycoside resistance methyltransferase NpmA from a clinical isolate and analysis of the NpmA interactions with the 30S ribosomal subunit

Kozlowski L, Orlowski J, Bujnicki JM

Structure prediction of alternatively spliced proteins

Rother K, Rother M, Boniecki M, Puton T, Tomala K, Lukasz P, Bujnicki JM

Template-based and template-free modeling of RNA 3D structure: inspirations from protein structure modeling

Tesfazgi Mebrhatu M, Wywial E, Ghosh A, Michiels CW, Lindner AB, Taddei F, Bujnicki JM, Van Melderen L, Aertsen A

Evidence for an evolutionary antagonism between Mrr and Type III modification systems.

Spears JL, Rubio MA, Gaston KW, Wywial E, Strikoudis A, Bujnicki JM, Papavasiliou FN, Alfonzo JD

A single zinc ion is sufficient for an active Trypanosoma brucei tRNA editing deaminase

2010

Gajda MJ, Tuszynska I, Kaczor M, Bakulina AY, Bujnicki JM

FILTREST3D: discrimination of structural models using restraints from experimental data.

Chua TK, Seetharaman J, Kasprzak JM, Ng C, Patel BK, Love C, Bujnicki JM, Sivaraman J

Crystal structure of a fructokinase homolog from Halothermothrix orenii

Kosinski J, Hinrichsen I, Bujnicki JM, Friedhoff P, Plotz G

Identification of Lynch syndrome mutations in the MLH1-PMS2 interface that disturb dimerization and mismatch repair.

Husain N, Tkaczuk KL, Tulsidas SR, Kaminska KH, Cubrilo S, Maravić-Vlahovicek G, Bujnicki JM, Sivaraman J

Structural basis for the methylation of G1405 in 16S rRNA by aminoglycoside resistance methyltransferase Sgm from an antibiotic producer: a diversity of active sites in m7G methyltransferases.

Kempenaers M, Roovers M, Oudjama Y, Tkaczuk KL, Bujnicki JM, Droogmans L

New archaeal methyltransferases forming 1-methyladenosine or 1-methyladenosine and 1-methylguanosine at position 9 of tRNA.

Pukszta S, Schilke B, Dutkiewicz R, Kominek J, Moczulska K, Stepien B, Reitenga KG, Bujnicki JM, Williams B, Craig EA, Marszalek J

Co-evolution-driven switch of J-protein specificity towards an Hsp70 partner.

Zhang Z, Theler D, Kaminska KH, Hiller M, de la Grange P, Pudimat R, Rafalska I, Heinrich B, Bujnicki JM, Allain FH, Stamm S

The YTH domain is a novel RNA binding domain.

Pukáncsik M, Békési A, Klement E, Hunyadi-Gulyás E, Medzihradszky KF, Kosinski J, Bujnicki JM, Alfonso C, Rivas G, Vértessy BG

Physiological truncation and domain organization of a novel uracil-DNA-degrading factor.

Zhou X, Chua TK, Tkaczuk KL, Bujnicki JM, Sivaraman J

The crystal structure of Escherichia coli spermidine synthase SpeE reveals a unique substrate-binding pocket.

Kaminska KH, Purta E, Hansen LH, Bujnicki JM, Vester B, Long KS

Insights into the structure, function and evolution of the radical-SAM 23S rRNA methyltransferase Cfr that confers antibiotic resistance in bacteria.

Tuszynska I, Bujnicki JM

Predicting atomic details of the unfolding pathway for YibK, a knotted protein from the SPOUT superfamily

Khan F, Furuta Y, Kawai M, Kaminska KH, Ishikawa K, Bujnicki JM, Kobayashi I

A putative mobile genetic element carrying a novel type IIF restriction-modification system (PluTI).

Rother K, Hoffmann S, Bulik S, Hoppe A, Gasteiger J, Holzhütter HG

IGERS: inferring Gibbs energy changes of biochemical reactions from reaction similarities

Tkaczuk KL

Trm13p, the tRNA:Xm4 modification enzyme from Saccharomyces cerevisiae is a member of the Rossmann-fold MTase superfamily: prediction of structure and active site

Bhagat J, Tanoh F, Nzuobontane E, Laurent T, Orlowski J, Roos M, Wolstencroft K, Aleksejevs S, Stevens R, Pettifer S, Lopez R, Goble CA

BioCatalogue: a universal catalogue of web services for the life sciences

2009

Leski TA, Caswell CC, Pawlowski M, Klinke DJ, Bujnicki JM, Hart SJ, Lukomski S

Identification and classification of bcl genes and proteins of Bacillus cereus group organisms and their application in Bacillus anthracis detection and fingerprinting.

Kolmos E, Nowak M, Werner M, Fischer K, Schwarz G, Mathews S, Schoof H, Nagy F, Bujnicki JM, Davis SJ

Integrating ELF4 into the circadian system through combined structural and functional studies.

Pena V, Jovin SM, Fabrizio P, Orlowski J, Bujnicki JM, Lührmann R, Wahl MC

Common design principles in the spliceosomal RNA helicase Brr2 and in the Hel308 DNA helicase.

Palfi Z, Jaé N, Preusser C, Kaminska KH, Bujnicki JM, Lee JH, Günzl A, Kambach C, Urlaub H, Bindereif A

SMN-assisted assembly of snRNP-specific Sm cores in trypanosomes.

Zylicz-Stachula A, Bujnicki JM, Skowron PM

Cloning and analysis of a bifunctional methyltransferase/restriction endonuclease TspGWI, the prototype of a Thermus sp. enzyme family.

Pawłowski M, Lasica AM, Jagusztyn-Krynicka EK, Bujnicki JM

AAN82231 protein from uropathogenic E. coli CFT073 is a close paralog of DsbB enzymes and does not belong to the DsbI family

Purta E, O'Connor M, Bujnicki JM, Douthwaite S

YgdE is the 2'-O-ribose methyltransferase RlmM specific for nucleotide C2498 in bacterial 23S rRNA.

Bauer RA, Rother K, Moor P, Reinert K, Steinke T, Bujnicki JM

Fast Structural Alignment of Biomolecules Using a Hash Table, N-Grams and String Descriptors

Matsumoto Y, Oota H, Asaoka Y, Nishina H, Watanabe K, Bujnicki JM, Oda S, Kawamura S, Mitani H

Medaka: a promising model animal for comparative population genomics.

Pierechod M, Nowak A, Saari A, Purta E, Bujnicki JM, Konieczny I

Conformation of a plasmid replication initiator protein affects its proteolysis by ClpXP system

Kennaway CK, Obarska-Kosinska A, White JH, Tuszynska I, Cooper LP, Bujnicki JM, Trinick J, Dryden DT

The structure of M.EcoKI Type I DNA methyltransferase with a DNA mimic antirestriction protein

Nakonieczna J, Kaczorowski T, Obarska-Kosinska A, Bujnicki JM

Functional analysis of MmeI from methanol utilizer Methylophilus methylotrophus, a subtype IIC restriction-modification enzyme related to type I enzymes.

Czerwoniec A, Dunin-Horkawicz S, Purta E, Kaminska KH, Kasprzak JM, Bujnicki JM, Grosjean H, Rother K

MODOMICS: a database of RNA modification pathways. 2008 update

Fink G, Hajdo L, Skowronek KJ, Reuther C, Kasprzak AA, Diez S

The mitotic kinesin-14 Ncd drives directional microtubule-microtubule sliding.

Majorek KA, Bujnicki JM

Modeling of Escherichia coli Endonuclease V structure in complex with DNA.

2008

Orlowski J, Mebrhatu MT, Michiels CW, Bujnicki JM, Aertsen A

Mutational analysis and a structural model of methyl-directed restriction enzyme Mrr.

Gyrd-Hansen M, Darding M, Miasari M, Santoro MM, Zender L, Xue W, Tenev T, da Fonseca PC, 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.

Purta E, O\'Connor M, Bujnicki JM, Douthwaite S

YccW is the m5C methyltransferase specific for 23S rRNA nucleotide 1962

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.

Sunita S, Tkaczuk KL, Purta E, Kasprzak JM, 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.

Pawlowski M, Gajda MJ, Matlak R, Bujnicki JM

MetaMQAP: a meta-server for the quality assessment of protein models.

Purta E, Kaminska KH, Kasprzak JM, Bujnicki JM, Douthwaite S

YbeA is the m3Psi methyltransferase RlmH that targets nucleotide 1915 in 23S rRNA.

Kosinski J, Plotz G, Guarné A, Bujnicki JM, Friedhoff P

The PMS2 subunit of human MutLalpha contains a metal ion binding domain of the iron-dependent repressor protein family.

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.

Orlowski J, Bujnicki JM

Structural and evolutionary classification of Type II restriction enzymes based on theoretical and experimental analyses.

Roovers M, Kaminska KH, Tkaczuk KL, Gigot D, Droogmans L, Bujnicki JM

The YqfN protein of Bacillus subtilis is the tRNA: m1A22 methyltransferase (TrmK).

Chua TK, Bujnicki JM, Tan TC, Huynh F, Patel BK, Sivaraman J

The structure of sucrose phosphate synthase from Halothermothrix orenii reveals its mechanism of action and binding mode.

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.

Cymerman IA, Chung I, Beckmann BM, Bujnicki JM, Meiss G

EXOG, a novel paralog of Endonuclease G in higher eukaryotes.

Bhagwat AS, Carpenter MA, Bujnicki JM

Is AID a monomer in solution?

Feder M, Purta E, Koscinski L, Cubrilo S, Maravic Vlahovicek G, Bujnicki JM

Virtual screening and experimental verification to identify potential inhibitors of the ErmC methyltransferase responsible for bacterial resistance against macrolide antibiotics.

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

Kaminska KH, Bujnicki JM

Bacteriophage Mu Mom protein responsible for DNA modification is a new member of the acyltransferase superfamily.

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 last two steps in the biosynthesis of hypermodified nucleoside mnm5s2U in tRNA.

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 ms(2)io(6)A37 in tRNA.

Vasu K, Saravanan M, Bujnicki JM, Nagaraja V

Structural integrity of the beta beta alpha-Metal finger motif is required for DNA binding and stable protein-DNA complex formation in R.KpnI.

Maravić Vlahovicek 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.

2007

Chovancová E, Kosinski J, Bujnicki JM, Damborský J

Phylogenetic analysis of haloalkane dehalogenases.

Ibryashkina EM, Zakharova MV, Baskunov VB, Bogdanova ES, Nagornykh MO, Den\'mukhamedov MM, Melnik BS, Kolinski A, Gront D, Feder M, Solonin AS, Bujnicki JM

Type II restriction endonuclease R.Eco29kI is a member of the GIY-YIG nuclease superfamily.

Jakubauskas A, Giedriene J, Bujnicki JM, Janulaitis A

Identification of a single HNH active site in type IIS restriction endonuclease Eco31I

Koscinski L, Feder M, Bujnicki JM

Identification of a missing sequence and functionally important residues of 16S rRNA:m(1)A1408 methyltransferase KamB that causes bacterial resistance to aminoglycoside antibiotics.

Kosinski J, Kubareva E, 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.

Kudan EV, Brevnov MG, Subach OM, Rechkoblit OA, Buĭnitskiĭ IaM, Gromova ES

[Probing of contacts between EcoRII DNA methyltransferase and DNA using substrate analogs and molecular modeling].

Liu Y, Li Z, Lin Q, Kosinski J, Seetharaman J, Bujnicki JM, Sivaraman J, Hew CL

Structure and evolutionary origin of Ca(2+)-dependent herring type II antifreeze protein.

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.

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

Ozanick SG, Bujnicki JM, Sem DS, Anderson JT

Conserved amino acids in each subunit of the heteroligomeric tRNA m1A58 Mtase from Saccharomyces cerevisiae contribute to tRNA binding.

Pena V, Liu S, Bujnicki JM, Lührmann R, Wahl MC

Structure of a multipartite protein-protein interaction domain in splicing factor prp8 and its link to retinitis pigmentosa.

Pietal MJ, Tuszynska I, Bujnicki JM

PROTMAP2D: visualization, comparison and analysis of 2D maps of protein structure.

Sabates-Bellver J, Van der Flier LG, de Palo M, Cattaneo E, Maake C, Rehrauer H, Laczko E, Kurowski MA, Bujnicki JM, Menigatti M, Luz J, Ranalli TV, Gomes V, Pastorelli A, Faggiani R, Anti M, Jiricny J, Clevers H, Marra G

Transcriptome profile of human colorectal adenomas.

Sasin JM, Godzik A, Bujnicki JM

SURF'S UP! - protein classification by surface comparisons

Schäfer 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.

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.

Tkaczuk KL, Dunin-Horkawicz S, Purta E, Bujnicki JM

Structural and evolutionary bioinformatics of the SPOUT superfamily of methyltransferases.

Zamudio JR, Mittra B, Foldynová-Trantírková S, Zeiner GM, Lukes J, Bujnicki JM, Sturm NR, Campbell DA

The 2'-O-ribose methyltransferase for cap 1 of spliced leader RNA and U1 small nuclear RNA in Trypanosoma brucei

2006

Dunin-Horkawicz S, Czerwoniec A, Gajda MJ, Feder M, Grosjean H, Bujnicki JM

MODOMICS: a database of RNA modification pathways.

Bheemanaik S, Bujnicki JM, Nagaraja V, Rao DN

Functional analysis of amino acid residues at the dimerisation interface of KpnI DNA methyltransferase.

Bujnicki JM

Protein-structure prediction by recombination of fragments.

Carpenter M, Divvela P, Pingoud V, Bujnicki J, Bhagwat AS

Sequence-dependent enhancement of hydrolytic deamination of cytosines in DNA by the restriction enzyme PspGI.

Chiang PK, Bujnicki JM, Su X, Lanar DE

Malaria: therapy, genes and vaccines.

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

Dunin-Horkawicz S, Feder M, Bujnicki JM

Phylogenomic analysis of the GIY-YIG nuclease superfamily.

Gabant G, Auxilien S, Tuszynska I, Locard M, Gajda MJ, Chaussinand G, Fernandez B, Dedieu A, Grosjean H, Golinelli-Pimpaneau B, Bujnicki JM, Armengaud J

THUMP from archaeal tRNA:m22G10 methyltransferase, a genuine autonomously folding domain.

Godlewska R, Dzwonek A, Mikuła M, Ostrowski J, Pawłowski M, Bujnicki JM, Jagusztyn-Krynicka EK

Helicobacter pylori protein oxidation influences the colonization process.

Gros L, Renodon-Cornière 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.

Han R, Caswell CC, Lukomska E, Keene DR, Pawlowski M, Bujnicki JM, Kim JK, Lukomski S

Binding of the low-density lipoprotein by streptococcal collagen-like protein Scl1 of Streptococcus pyogenes.

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.

Metz J, Wächter A, Schmidt B, Bujnicki JM, Schwappach B

The yeast Arr4p ATPase binds the chloride transporter Gef1p when copper is available in the cytosol.

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.

Obarska A, Blundell A, Feder M, Vejsadová S, Sisáková E, Weiserová M, Bujnicki JM, Firman K

Structural model for the multisubunit Type IC restriction-modification DNA methyltransferase M.EcoR124I in complex with DNA.

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.

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.

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 DNA fragmentation factor 40/caspase-activated DNase endonuclease in human Jurkat cells.

Skowronek KJ, Kosinski J, Bujnicki JM

Theoretical model of restriction endonuclease HpaI in complex with DNA, predicted by fold recognition and validated by site-directed mutagenesis.

Tkaczuk KL, Obarska A, Bujnicki JM

Molecular phylogenetics and comparative modeling of HEN1, a methyltransferase involved in plant microRNA biogenesis.

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.

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.

2005

Armalyte E, Bujnicki JM, Giedriene J, Gasiunas G, Kosiński J, Lubys A

Mva1269I: a monomeric type IIS restriction endonuclease from Micrococcus varians with two EcoRI- and FokI-like catalytic domains.

Bujnicki J.M.

Przewidywanie struktury bialek: Boltzmann i Darwin

Chmiel AA, Bujnicki JM, Skowronek KJ

A homology model of restriction endonuclease SfiI in complex with DNA

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.

Cymerman IA, Meiss G, Bujnicki JM

DNase II is a member of the phospholipase D superfamily.

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.

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

Koliński A, Bujnicki JM

Generalized protein structure prediction based on combination of fold-recognition with de novo folding and evaluation of models.

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.

Kosinski J, Steindorf I, Bujnicki JM, Giron-Monzon L, Friedhoff P

Analysis of the quaternary structure of the MutL C-terminal domain.

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

Pingoud V, Geyer H, Geyer R, Kubareva E, Bujnicki JM, Pingoud A

Identification of base-specific contacts in protein-DNA complexes by photocrosslinking and mass spectrometry: a case study using the restriction endonuclease SsoII

Pingoud V, Sudina A, Geyer H, Bujnicki JM, Lurz R, Lüder 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

Purushothaman SK, Bujnicki JM, Grosjean H, Lapeyre B

Trm11p and Trm112p are both required for the formation of 2-methylguanosine at position 10 in yeast tRNA.

Purta E, van Vliet F, Tricot C, De Bie LG, Feder M, Skowronek K, Droogmans L, Bujnicki JM

Sequence-structure-function relationships of a tRNA (m7G46) methyltransferase studied by homology modeling and site-directed mutagenesis.

Raczko AM, Bujnicki JM, Pawlowski M, Godlewska R, Lewandowska M, Jagusztyn-Krynicka EK

Characterization 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.

Radlinska M, Kondrzycka-Dada A, Piekarowicz A, Bujnicki JM

Identification of amino acids important for target recognition by the DNA:m5C methyltransferase M.NgoPII by alanine-scanning mutagenesis of residues at the protein-DNA interface.

Radlińska M, Piekarowicz A, Galimand M, Bujnicki JM

Cloning and preliminary characterization of a GATC-specific beta2-class DNA:m6A methyltransferase encoded by transposon Tn1549 from Enterococcus spp.

Tkaczuk KL, Bujnicki JM, Bialkowska A, Bielecki S, Turkiewicz M, Cieslinski H, Kur J

Molecular modeling of a psychrophilic β-galactosidase

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.

Kosinski J, Steindorf I, Bujnicki JM, Giron-Monzon L, Friedhoff P

Analysis of the quaternary structure of the MutL C-terminal domain.

Purushothaman SK, Bujnicki JM, Grosjean H, Lapeyre B

Trm11p and Trm112p are both required for the formation of 2-methylguanosine at position 10 in yeast tRNA.

Raczko AM, Bujnicki JM, Pawlowski M, Godlewska R, Lewandowska M, Jagusztyn-Krynicka EK

Characterization 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.

Radlinska M, Kondrzycka-Dada A, Piekarowicz A, Bujnicki JM

Identification of amino acids important for target recognition by the DNA:m5C methyltransferase M.NgoPII by alanine-scanning mutagenesis of residues at the protein-DNA interface.

Radlińska M, Piekarowicz A, Galimand M, Bujnicki JM

Cloning and preliminary characterization of a GATC-specific beta2-class DNA:m6A methyltransferase encoded by transposon Tn1549 from Enterococcus spp.

2004

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, S-adenosylmethionine-dependent methyltransferase, conserved in Archaea and Eukaryota.

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.

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.

Koudan EV, Bujnicki JM, Gromova ES

Homology modeling of the CG-specific DNA methyltransferase SssI and its complexes with DNA and AdoHcy.

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, S-adenosylmethionine-dependent methyltransferase, conserved in Archaea and Eukaryota.

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.

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.

Koudan EV, Bujnicki JM, Gromova ES

Homology modeling of the CG-specific DNA methyltransferase SssI and its complexes with DNA and AdoHcy.

Maravić G, Bujnicki JM, Flögel M

Mutational analysis of basic residues in the N-terminus of the rRNA:m6A methyltransferase ErmC'

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.

Paziewska A, Wyrwicz LS, Bujnicki JM, Bomsztyk K, Ostrowski J

Cooperative binding of the hnRNP K three KH domains to mRNA targets.

Potluri S, Khan AA, Kuzminykh A, Bujnicki JM, Friedman AM, Bailey-Kellogg C

Geometric analysis of cross-linkability for protein fold discrimination.

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

Saravanan M, Bujnicki JM, Cymerman IA, Rao DN, Nagaraja V

Type II restriction endonuclease R.KpnI is a member of the HNH nuclease superfamily.

Sasin JM, Bujnicki JM

COLORADO3D, a web server for the visual analysis of protein structures.

Schäfer 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.

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.

2003

Maravić G, Feder M, Pongor S, Flögel M, Bujnicki JM

Mutational analysis defines the roles of conserved amino acid residues in the predicted catalytic pocket of the rRNA:m6A methyltransferase ErmC'

Mouaikel J, Bujnicki JM, Tazi J, Bordonné R

Sequence-structure-function relationships of Tgs1, the yeast snRNA/snoRNA cap hypermethylase

Pingoud V, Conzelmann C, Kinzebach S, Sudina A, Metelev V, Kubareva E, Bujnicki JM, Lurz R, Lüder G, Xu SY, Pingoud A

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

Sasin JM, Kurowski MA, Bujnicki JM

STRUCLA: a WWW meta-server for protein structure comparison and evolutionary classification.

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.

Coker JA, Sheridan PP, Loveland-Curtze J, Gutshall KR, Auman AJ, Brenchley JE

Biochemical characterization of a beta-galactosidase with a low temperature optimum obtained from an Antarctic arthrobacter isolate.

Coker JA, Sheridan PP, Loveland-Curtze J, Gutshall KR, Auman AJ, Brenchley JE

Biochemical characterization of a beta-galactosidase with a low temperature optimum obtained from an Antarctic arthrobacter isolate.

Bujnicki JM

Crystallographic and bioinformatic studies on restriction endonucleases: inference of evolutionary relationships in the "midnight zone" of homology

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.

Bujnicki JM, Prigge ST, Caridha D, Chiang PK

Structure, evolution, and inhibitor interaction of S-adenosyl-L-homocysteine hydrolase from Plasmodium falciparum.

De Bie LG, 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.

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.

Feder M, Pas J, Wyrwicz LS, Bujnicki JM

Molecular phylogenetics of the RrmJ/fibrillarin superfamily of ribose 2'-O-methyltransferases

Gordon RK, Ginalski K, Rudnicki WR, Rychlewski L, Pankaskie MC, Bujnicki JM, Chiang PK

Anti-HIV-1 activity of 3-deaza-adenosine analogs. Inhibition of S-adenosylhomocysteine hydrolase and nucleotide congeners.

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

Kurowski MA, Bhagwat AS, Papaj G, Bujnicki JM

Phylogenomic identification of five new human homologs of the DNA repair enzyme AlkB.

Kurowski MA, Bujnicki JM

GeneSilico protein structure prediction meta-server.

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.

Maravić G, Bujnicki JM, Feder M, Pongor S, Flögel M

Alanine-scanning mutagenesis of the predicted rRNA-binding domain of ErmC' redefines the substrate-binding site and suggests a model for protein-RNA interactions

2002

Bujnicki JM

Sequence permutations in the molecular evolution of DNA methyltransferases

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

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:m(6)A methyltransferase

Bujnicki JM, Feder M, Rychlewski L, Fischer D

Errors in the D. radiodurans large ribosomal subunit structure detected by protein fold-recognition and structure validation tools

Bujnicki JM, Leach RA, Debski J, Rychlewski L

Bioinformatic analyses of the tRNA: (guanine 26, N2,N2)-dimethyltransferase (Trm1) family

Bujnicki JM, Rychlewski L

Fold-recognition analysis predicts that the Tag protein family shares a common domain with the helix-hairpin-helix DNA glycosylases

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

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

Bujnicki J, Rychlewski L, Fischer D

Fold-recognition detects an error in the Protein Data Bank

Godlewska R, Bujnicki JM, Ostrowski J, Jagusztyn-Krynicka EK

The hppA gene of Helicobacter pylori encodes the class C acid phosphatase precursor

Pingoud V, Kubareva E, Stengel G, Friedhoff P, Bujnicki JM, Urbanke C, Sudina A, Pingoud A

Evolutionary relationship between different subgroups of restriction endonucleases.

Pintard L, Bujnicki JM, Lapeyre B, Bonnerot C

MRM2 encodes a novel yeast mitochondrial 21S rRNA methyltransferase

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

Xu Y, Keene DR, Bujnicki JM, Höök M, Lukomski S

Streptococcal Scl1 and Scl2 proteins form collagen-like triple helices.

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

2001

Bujnicki JM

In silico analysis of the tRNA:m1A58 methyltransferase family: homology-based fold prediction and identification of new members from Eubacteria and Archaea

Bujnicki JM

Understanding the evolution of restriction-modification systems: clues from sequence and structure comparisons.

Bujnicki JM

A model of structure and action of Sau3AI restriction endonuclease that comprises two MutH-like endonuclease domains within a single polypeptide.

Bujnicki JM, Elofsson A, Fischer D, Rychlewski L

Structure prediction meta server

Bujnicki JM, Elofsson A, Fischer D, Rychlewski L

LiveBench-1: continuous benchmarking of protein structure prediction servers

Bujnicki JM, Elofsson A, Fischer D, Rychlewski L

LiveBench-2: large-scale automated evaluation of protein structure prediction servers.

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

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

Bujnicki JM, Radlinska M, Rychlewski L

Polyphyletic evolution of type II restriction enzymes revisited: two independent sources of second-hand folds revealed

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

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.

Bujnicki JM, Rychlewski L

Sequence analysis and structure prediction of aminoglycoside-resistance 16S rRNA:m7G methyltransferases

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

Bujnicki JM, Rychlewski L

Unusual evolutionary history of the tRNA splicing endonuclease EndA: relationship to the LAGLIDADG and PD-(D/E)XK deoxyribonucleases.

Bujnicki JM, Rychlewski L

Reassignment of specificities of two cap methyltransferase domains in the reovirus lambda 2 protein

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.

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.

Lundström J, Rychlewski L, Bujnicki J, Elofsson A

Pcons: a neural-network-based consensus predictor that improves fold recognition

Radlinska M, Bujnicki JM

Cloning of enterohemorrhagic Escherichia coli phage VT-2 dam methyltransferase

Radlinska M, Bujnicki JM

Site-directed mutagenesis defines the catalytic aspartate in the active site of the atypical DNA: m4C methyltransferase M.NgoMXV

2000

Bujnicki JM

Phylogenomic analysis of 16S rRNA:(guanine-N2) methyltransferases suggests new family members and reveals highly conserved motifs and a domain structure similar to other nucleic acid amino-methyltransferases.

Bujnicki JM

Sequence, structural, and evolutionary analysis of prokaryotic ribosomal protein L11 methyltransferases.

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 betabetaalphaMe endonucleases

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

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.