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List of publications related to the project
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Berlin (Reuter & Krüger)
1. Wagenführ K, Pieper S, Mackeldanz P, Linscheid M, Krüger DH, Reuter M (2007) Structural domains in the type III restriction endonuclease EcoP15I: characterization by limited proteolysis, mass spectrometry and insertional mutagenesis. J Mol Biol 366(1):93-102.
2. Terauchi R, Matsumura H, Ito A, Fujisawa S, Bin Nasir KH, Saitoh H, Kamoun S, Winter P, Kahl G, Reuter M, Krüger DH (2006) SuperSAGE, a potent tool to dissect plant-microbe interactions. In: Sanchez F et al. (eds.), Biology of Plant-Microbe Interactions, Vol. 5, International Society for Molecular Plant-Microbe Interactions, St. Paul, MN, USA, 2006, pp. 569-575.
3. Terauchi R, Matsumura H, Krüger DH, Kahl G (2008) The SAGE family: SAGE, LongSAGE, SuperSAGE. In: Kahl G, Meksem K (eds.), The Handbook of Plant Functional Genomics. Wiley-VCH, Weinheim.
4. Matsumura H, Reuter M, Krüger DH, Winter P, Kahl G and Terauchi R. (2008) SuperSAGE. Methods Mol. Biol. 387, 55-70.
5. Matsumura H, Bin Nasir KH, Yoshida K, Ito A, Kahl G, Krüger DH, Terauchi R (2006) SuperSAGE array: the direct use of 26-base-pair transcript tags in oligonucleotide arrays. Nat. Methods 3, 469-474.
6. Möncke-Buchner E, Rothenberg M, Reich S, Wagenführ K, Matsumura H, Terauchi R, Krüger DH and Reuter M (2009) Functional characterization and modulation of the DNA cleavage efficiency of Type III restriction endonuclease EcoP15I in its interaction with two sites in the DNA target. J. Mol. Biol. 387, 1309-1319.
7. Szczepek M, Mackeldanz P, Möncke-Buchner E, Alves J, Krüger DH and Reuter M (2009) Molecular analysis of restriction endonuclease EcoRII from Escherichia coli reveals precise regulation of its enzymatic activity by autoinhibition. Mol. Microbiol. 72, 1011-1021.
8. Raftery MJ, Möncke-Buchner E, Matsumura H, Giese T, Winkelmann A, Reuter M, Terauchi R, Schönrich G and Krüger DH (2009) Unravelling the interaction of HCMV with dendritic cells using SuperSAGE. J. Gen. Virol. 90, 2221-2233.
9. Pingoud V, Wende W, Friedhoff P, Reuter M, Alves J, Jeltsch A, Mones L, Fuxreiter M, and Pingoud A (2009) On the divalent metal ion dependence of DNA cleavage by restriction endonucleases of the EcoRI family. J. Mol. Biol. 393, 140-160. (joined)
10. Wyszomirski KH, Mackeldanz P, Möncke-Buchner E, Schutkowski M, Krüger DH and Reuter M (2009) Analysis of the translocase domain of Type III restriction endonuclease EcoP15I Res subunit proves its strong DNA binding capability. (submitted)
Bristol (Halford)
1. Bellamy SR, Milsom SE, Kovacheva YS, Sessions RB, Halford SE (2007) A switch in the mechanism of communication between the two DNA-binding sites in the SfiI restriction endonuclease. J Mol Biol 373(5):1169-83.
2. Marshall JJ, Gowers DM, Halford SE (2007) Restriction endonucleases that bridge and excise two recognition sites from DNA. J Mol Biol 367(2):419-31.
3. Sasnauskas G, Connolly BA, Halford SE & Siksnys V (2008). Template-directed addition of nucleosides to DNA by the BfiI restriction enzyme. Nucleic Acids Res. 36, 3969–3977. (joined)
4. Sasnauskas G, Connolly BA, Halford SE, Siksnys V (2007) Site-specific DNA transesterification catalyzed by a restriction enzyme. Proc Natl Acad Sci USA 104(7):2115-20. (joined)
5. Barman TE, Bellamy SR, Gutfreund H, Halford SE, Lionne C (2006) The identification of chemical intermediates in enzyme catalysis by the rapid quench-flow technique. Cell Mol Life Sci 63(22):2571-83. Review.
6. Catto LE, Ganguly S, Milsom SE, Welsh AJ, Halford SE (2006)Protein assembly and DNA looping by the FokI restriction endonuclease. Nucleic Acids Res 34(6):1711-20.
7. Catto LE, Bellamy SRW, Retter SE & Halford SE (2008). Dynamics and consequences of DNA looping by the FokI restriction endonuclease. Nucleic Acids Res. 36, 2073-2081.
8. Bellamy SRW, Mina P, Retter SE & Halford SE (2008). Fidelity of DNA sequence recognition by the SfiI restriction endonuclease is determined by communications between its two DNA-binding sites. J. Mol. Biol. 384, 557–563.
9. Sanders KL, Catto LE, Bellamy SRW &. Halford SE (2009). Targeting individual subunits of the FokI restriction endonuclease to specific DNA strands. Nucleic Acids Res., 37, 2105–2115.
10. Halford SE (2009). An end to 40 years of mistakes in DNA-protein association kinetics? Biochem. Soc. Trans., 37, 343-348.
11. Bellamy SRW, Kovacheva YS, Haji Zulkipli I &. Halford SE (2009). Differences between Ca2+ and Mg2+ in DNA binding and release by the SfiI restriction endonuclease: implications for DNA looping. Nucleic Acids Res. 37, 5443-5453.
12. Laurens N, Bellamy SRW, Harms AF, Kovacheva YS, Halford SE & Wuite GJL (2009). Dissecting protein-induced DNA looping dynamics in real-time. Nucleic Acids Res. 37, 5454-5464.
13. Marshall JJT & Halford SE (2009). The Type IIB restriction endonucleases. Biochem. Soc. Trans. (in press.)
14. Halford SE (2009). The (billion dollar) consequences of studying why certain isolates of phage l infect only certain strains of E. coli. The Biochemist (in press.)
15. Sasnauskas G, Zakrys L, Zaremba M, Cosstick R, Gaynor, JW, Halford SE & Siksnys V (2009) A novel mechanism for the scission of double-stranded DNA: BfiI cuts DNA strands of opposite polarity by rotating a single active site. Submitted to Nature Chem. Biol. (joined)
Bristol (Szczelkun)
1. Ramanathan SP, van Aelst K, Peakman LJ, Diffin FM, Sears A, Szczelkun MD and Seidel R (2009) Type III restriction enzymes communicate in 1D without looping between their target sites. Proc. Natl. Acad. Sci. (USA), 106, 1748-1753.
2. Sišáková E, Weiserová M, Dekker C, Seidel R, Szczelkun MD (2008) The Interrelationship of Helicase and Nuclease Domains during DNA Translocation by the Molecular Motor EcoR124I. J Mol Biol 384(5):1273-86.
3. Sišáková E, Stanley LK, Weiserová M, Szczelkun MD (2008) A RecB-family nuclease motif in the Type I restriction endonuclease EcoR124I. Nucleic Acids Res 36(12):3939-49.
4. Seidel R, Bloom JG, Dekker C, Szczelkun MD (2008) Motor step size and ATP coupling efficiency of the dsDNA translocase EcoR124I. EMBO J ;27(9):1388-98.
5. Smith AJ, Szczelkun MD, Savery NJ (2007) Controlling the motor activity of a transcription-repair coupling factor: autoinhibition and the role of RNA polymerase. Nucleic Acids Res 35(6):1802-11.
6. Peakman LJ, Szczelkun MD. (2009) S-adenosyl homocysteine and DNA ends stimulate promiscuous nuclease activities in the Type III restriction endonuclease EcoPI. Nucleic Acids Res. 37(12):3934-45.
7. Stanley LK, Szczelkun MD (2006) Direct and random routing of a molecular motor protein at a DNA junction. Nucleic Acids Res. 2006;34(16):4387-94.
8. Stanley LK, Seidel R, van der Scheer C, Dekker NH, Szczelkun MD, Dekker C (2006) When a helicase is not a helicase: dsDNA tracking by the motor protein EcoR124I. EMBO J 25(10):2230-9.
Budapest (Fuxreiter)
1. Mones L, Kulhánek P, Florián J, Simon I, Fuxreiter M (2007) Probing the two-metal ion mechanism in the restriction endonuclease BamHI. Biochemistry 46(50):14514-23.
2. Solt I, Simon I, Császár AG, Fuxreiter M (2007) Electrostatic versus nonelectrostatic effects in DNA sequence discrimination by divalent ions Mg2+ and Mn2+. J Phys Chem B 111(22):6272-9.
3. Németh-Pongrácz V, Barabás O, Fuxreiter M, Simon I, Pichová I, Rumlová M, Zábranská H, Svergun D, Petoukhov M, Harmat V, Klement E, Hunyadi-Gulyás E, Medzihradszky KF, Kónya E, Vértessy BG (2007) Flexible segments modulate co-folding of dUTPase and nucleocapsid proteins. Nucleic Acids Res 35(2):495-505
4. Chuluunbaatar T, Ivanenko-Johnston T, Fuxreiter M, Meleshko R, Raskó T, Simon I, Heitman J, Kiss A (2007) An EcoRI-RsrI chimeric restriction endonuclease retains parental sequence specificity. Biochim Biophys Acta 1774(5):583-94.
5. Mones L, Simon I, Fuxreiter M (2007) Metal-binding sites at the active site of restriction endonuclease BamHI can conform to a one-ion mechanism. Biol Chem 388(1):73-8.
6. Fuxreiter M, Tompa P, Simon I (2007) Local structural disorder imparts plasticity on linear motifs. Bioinformatics 23(8):950-6.
7. Á Tóth-Petróczy, B. Mészáros, I Simon, AK Dunker, VN Uversky and M Fuxreiter (2008) Assessing conservation of disordered regions in proteins. The Open Proteomics Journal 1:46-53.
8. Tompa P, Fuxreiter M (2008) Fuzzy complexes: polymorphism and structural disorder in protein-protein interactions. Trends Biochem Sci 33(1):2-8.
9. M Fuxreiter, P Tompa, I Simon, VN Uversky, JC Hansen, F Asturias (2008) Malleable machines take shape in eukaryotic transcription regulation. Nat Chem Biol 4, 728-737.
10. Á Tóth-Petróczy, CJ Oldfield, I Simon, Y Takagi, AK Dunker, VN Uversky and M. Fuxreiter (2008) Malleable machines take shape in transcription regulation: the mediator complex PloS Comp Biol 4, e1000243.
11. M Fuxreiter and P Tompa (2009) Fuzzy interactome: the limitations of models in molecular biology, Trends in Biochem Sci, 34,3.
12. P Tompa, M Fuxreiter, CJ Oldfield, I Simon, AK Dunker, VN Uversky (2009) Close encounters of the thrid kind: disordered domains and interactions of proteins. Bioessays 31, 328-35.
13. I Solt, P Kulhanek, I Simon, S Winfield, MC Payne, G Csanyi and M Fuxreiter (2009) Evaluating Boundary dependent force errors in QM/MM simulations. J Phys Chem B 113, 5728-35.
14. L Mones, P Kulhanek, I Simon, A Laio and M Fuxreiter (2009) Egap as a universal coordinate for simulating chemical reactions. J Phys Chem B 113, 7867-73.
15. V Pingoud, W Wende, P Friedhoff, M Reuter, J Alves, A Jeltsch, L Mones, M Fuxreiter, A. Pingoud (2009) On the divalent ion dependence of DNA cleavage by restriction endonucleases of the EcoRI family. J Mol Biol 393, 140-160. (joined)
16. A Toth-Petroczy, I Simon M Fuxreiter, Y Levy (2009) Disordered tails of homeodomains facilitate DNA recognition by providing a trade-off between folding and specific binding J Am Chem Soc 131, 15084-15085.
Düsseldorf (Seidel)
1. Al-Soufi W, Reija B, Felekyan S, Seidel CA, Novo M (2008) Dynamics of supramolecular association monitored by fluorescence correlation spectroscopy. Chemphyschem 9(13):1819-27.
2. Neubauer H, Gaiko N, Berger S, Schaffer J, Eggeling C, Verdier L, Seidel CA, Griesinger C, Volkmer A (2007) Structure and dynamics of Rhodamine G attached to DNA: An NMR and fluorescence study. J. Am. Chem. Soc 129(42):12746-55.
3. Antonik M, Felekyan S, Gaiduk A, Seidel CA (2006) Separating structural heterogeneities from stochastic variations in fluorescence resonance energy transfer distributions via photon distribution analysis. J Phys Chem B 110(13):6970-8.
4. Kalinin S, Felekyan S, Valeri A, Seidel CA (2008) Characterizing multiple molecular States in single-molecule multiparameter fluorescence detection by probability distribution analysis. J Phys Chem B 112(28):8361-74.
5. Kalinin S, Felekyan S, Antonik M, Seidel CAM (2007) Probability Distribution Analysis of Single-Molecule Fluorescence Anisotropy and Resonance Energy Transfer. J. Phys. Chem. B 111, 10253-10262.
6. Woźniak AK, Schröder GF, Grubmüller H, Seidel CAM, Oesterhelt F (2008) Single-molecule FRET measures bends and kinks in DNA. Proc. Natl. Acad. Sci. USA 105(47):18337-42.
7. Kalinin S, Felekyan S, Antonik M, Seidel CA (2007) Probability distribution analysis of single-molecule fluorescence anisotropy and resonance energy transfer. J Phys Chem 111(34):10253-62.
8. Neubauer H, Gaiko N, Berger S, Schaffer J, Eggeling C, Tuma J, Verdier L, Seidel CA, Griesinger C, Volkmer A (2007) Orientational and dynamical heterogeneity of rhodamine 6G terminally attached to a DNA helix revealed by NMR and single-molecule fluorescence spectroscopy. J Am Chem Soc 129(42):12746-55.
9. Gaiduk A, Kühnemuth R, Felekyan S, Antonik M, Becker W, Kudryavtsev V, Sandhagen C, Seidel CA (2007) Fluorescence detection with high time resolution: from optical microscopy to simultaneous force and fluorescence spectroscopy. Microsc Res Tech 70(5):433-41.
10. Eggeling C, Widengren J, Brand L, Schaffer J, Felekyan S, Seidel CA (2006) Analysis of photobleaching in single-molecule multicolor excitation and Forster resonance energy transfer measurements. J Phys Chem A 110(9):2979-95.
11. Novo M, Felekyan S, Seidel CA, Al-Soufi W (2007) Dye-exchange dynamics in micellar solutions studied by fluorescence correlation spectroscopy. J Phys Chem B 111(14):3614-24.
12. Widengren J, Chmyrov A, Eggeling C, Löfdahl PA, Seidel CA (2007) Strategies to improve photostabilities in ultrasensitive fluorescence spectroscopy. J Phys Chem A 111(3):429-40.
13. Widengren J, Kudryavtsev V, Antonik M, Berger S, Gerken M, Seidel CA (2006) Single-molecule detection and identification of multiple species by multiparameter fluorescence detection. Anal Chem 78(6):2039-50.
14. Kudryavtsev V, Felekyan S, Woźniak AK, König M, Sandhagen C, Kühnemuth R, Seidel CA, Oesterhelt F (2007) Monitoring dynamic systems with multiparameter fluorescence imaging. Anal Bioanal Chem 387(1):71-82.
15. PJ Rothwell, W Allen, E Sisamakis, S Kalinin, S Felekyan, J Widergren, G Waksman, CAM Seidel (2009) An Open and Closed case: Klentaq 1 fluctuates between an Open and Closed conformation before dNTP selection. (in preparation)
16. Dikić J, Wende W, Seidel CAM, Rothwell PJ, Pingoud A (2009) The conformational dynamics accompanying substrate binding and cleavage by the Type IIP restriction endonuclease BsoBI. (joined, in preparation)
17. Cristóvão M, Sisamakis E, Marx A, Seidel CAM., Rothwell PJ, Friedhoff P (2009) Conformational changes in DNA and MutS during mismatch recognition. (joined, in preparation)
Fermentas (Lubys)
1. Jurenaite-Urbanaviciene S, Serksnaite J, Kriukiene E, Giedriene J, Venclovas C, Lubys A. Generation of DNA cleavage specificities of type II restriction endonucleases by reassortment of target recognition domains. Proc Natl Acad Sci U S A. 2007 Jun 19;104(25):10358-63.
2. 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.
3. 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.
4. Jakubauskas A, Sasnauskas G, Giedriene J, Janulaitis A (2008) Domain organization and functional analysis of type IIS restriction endonuclease Eco31I. Biochemistry 47:8546-56. (joined)
Giessen (Pingoud & Friedhoff & Wende)
1. Kosinski J, Plotz G, Guarné A, Bujnicki JM, Friedhoff P (2008) The PMS2 subunit of human MutLalpha contains a metal ion binding domain of the iron-dependent repressor protein family. J Mol Biol. 382(3):610-27. (joined)
2. Bonnet I, Biebricher A, Porté PL, Loverdo C, Bénichou O, Voituriez R, Escudé C, Wende W, Pingoud A, Desbiolles P (2008) Sliding and jumping of single EcoRV restriction enzymes on non-cognate DNA. Nucleic Acids Res 36(12):4118-27.
3. Ghosh M, Meiss G, Pingoud AM, London RE, Pedersen LC (2007) The nuclease a-inhibitor complex is characterized by a novel metal ion bridge. J Biol Chem 282(8):5682-90.
4. Friedhoff P, Pingoud A (2007) Engineering site-specific endonucleases. Methods Mol Biol. 2007;352:111-23.
5. Silva GH, Belfort M, Wende W, Pingoud A (2006) From monomeric to homodimeric endonucleases and back: engineering novel specificity of LAGLIDADG enzymes. J Mol Biol 361(4):744-54.
6. Plotz G, Welsch C, Giron-Monzon L, Friedhoff P, Albrecht M, Piiper A, Biondi RM, Lengauer T, Zeuzem S, Raedle J (2006) Mutations in the MutSalpha interaction interface of MLH1 can abolish DNA mismatch repair. Nucleic Acids Res 34(22):6574-86.
7. Manelyte L, Urbanke C, Giron-Monzon L, Friedhoff P (2006) Structural and functional analysis of the MutS C-terminal tetramerization domain. Nucleic Acids Res. 2006;34(18):5270-9.
8. Ahrends R, Kosinski J, Kirsch D, Manelyte L, Giron-Monzon L, Hummerich L, Schulz O, Spengler B, Friedhoff P (2006) Identifying an interaction site between MutH and the C-terminal domain of MutL by crosslinking, affinity purification, chemical coding and mass spectrometry. Nucleic Acids Res 34(10):3169-80.
9. Carpenter M, Divvela P, Pingoud V, Bujnicki J, Bhagwat AS (2006) Sequence-dependent enhancement of hydrolytic deamination of cytosines in DNA by the restriction enzyme PspGI. Nucleic Acids Res 34(13):3762-70. (joined)
10. Schäfer P, Cymerman IA, Bujnicki JM, Meiss G (2007) Human lysosomal DNase IIalpha contains two requisite PLD-signature (HxK) motifs: evidence for a pseudodimeric structure of the active enzyme species. Protein Sci 16(1):82-91. (joined)
11. Pingoud A, Silva GH (2007) Precision genome surgery. Nat Biotechnol 25(7):743-4.
12. Pingoud A, Wende W (2007) A sliding restriction enzyme pauses. Structure 15(4):391-3.
13. Rathert P, Raskó T, Roth M, Slaska-Kiss K, Pingoud A, Kiss A, Jeltsch A (2007) Reversible inactivation of the CG specific SssI DNA (cytosine-C5)-methyltransferase with a photocleavable protecting group. Chembiochem 8(2):202-7.
14. Cymerman IA, Chung I, Beckmann BM, Bujnicki JM, Meiss G (2008) EXOG, a novel paralog of Endonuclease G in higher eukaryotes. Nucleic Acids Res. 36(4):1369-79. (joined)
15. Bonnet I, Biebricher A, Porté PL, Loverdo C, Bénichou O, Voituriez R, Escudé C, Wende W, Pingoud A, Desbiolles P (2008) Sliding and jumping of single EcoRV restriction enzymes on non-cognate DNA. Nucleic Acids Res. 36(12):4118-27.
16. Biebricher A, Wende W, Escudé C, Pingoud A, Desbiolles P (2009) Tracking of single quantum dot labeled EcoRV sliding along DNA manipulated by double optical tweezers.Biophys J. 96(8):L50-2.
17. Singh P, Tripathi P, Silva GH, Pingoud A, Muniyappa K (2009) Characterization of Mycobacterium leprae RecA intein, a LAGLIDADG homing endonuclease, reveals a unique mode of DNA binding, helical distortion, and cleavage compared with a canonical LAGLIDADG homing endonuclease. J Biol Chem. 284(38):25912-28.
18. Pingoud V, Wende W, Friedhoff P, Reuter M, Alves J, Jeltsch A, Mones L, Fuxreiter M, Pingoud A (2009) On the divalent metal ion dependence of DNA cleavage by restriction endonucleases of the EcoRI family. J Mol Biol. 393(1):140-60. (joined)
19. Schierling B, Noël A-J, Wende W, Hien LT, Volkov E, Kubareva Elena, Oretskaya T, Kokkinidis , Römpp A, Spengler B, Pingoud A (2009) Controlling the enzymatic activity of a restriction enzyme by light. Proc. Natl. Acad. Sci. (USA) (in revision)
20. Duppatla V, Bodda C, Urbanke C, Friedhoff P, Rao DN. (2009) The C-terminal domain is sufficient for endonuclease activity of Neisseria gonorrhoeae MutL. Biochem J. 423(2):265-77.
21. Heinze RJ, Giron-Monzon L, Solovyova A, Elliot SL, Geisler S, Cupples CG, Connolly BA, Friedhoff P. (2009) Physical and functional interactions between Escherichia coli MutL and the Vsr repair endonuclease. Nucleic Acids Res. 37(13):4453-63. (joined)
22. Kosinski J, Plotz G, Guarné A, Bujnicki JM, Friedhoff P (2008) The PMS2 subunit of human MutLalpha contains a metal ion binding domain of the iron-dependent repressor protein family. J Mol Biol. 382(3):610-27. (joined)
23. Dikić J, Wende W, Seidel CAM, Rothwell PJ, Pingoud A. (2009) The conformational dynamics accompanying substrate binding and cleavage by the Type IIP restriction endonuclease BsoBI. (joined, in preparation)
24. Cristóvão M, Sisamakis E, Marx A, Seidel CAM., Rothwell PJ, Friedhoff P. (2009) Conformational changes in DNA and MutS during mismatch recognition. (joined, in preparation)
Newcastle (Connolly)
1. BA Connolly (2009) Recognition of deaminated bases by archaeal family-B DNA polymerases. Biochem. Soc. Trans. 37, 65-68.
2. SK Jozwiakowski and BA Connolly (2009) Plasmid-based lacZα assay for DNA polymerase fidelity: application to archaeal family-B DNA polymerase. Nucleic Acids Research 37(15):e102.
3. Gill S, O'Neill R, Lewis RJ, Connolly BA (2007) Interaction of the family-B DNA polymerase from the archaeon Pyrococcus furiosus with deaminated bases. J Mol Biol 372(4):855-63.
4. Bhagwat AS, Connolly BA (2006) Interaction of the Escherichia coli Vsr with DNA and Mismatch Repair Proteins. In: DNA damage recognition pp. 483-490 (eds. W. Siede, Y. W. Kow and P. Doetsch) Taylor and Francis, New York and London.
5. R Heinze, L Giron-Monzon, A Solovyova, S Elliot, S Geisler, C Cupples, BA Connolly and P Friedhoff (2009) Physical and functional interactions between Escherichia coli MutL and the Vsr repair endonuclease. Nucleic Acids Research 37, 4453-4463. (joined)
6. HJ Russell, TT Richardson, K Emptage and BA Connolly (2009) The 3'-5' proofreading exonuclease of archaeal family-B DNA polymerase hinders the copying of template strand deaminated bases. Nucleic Acids Research Sep 26. [Epub ahead of print, doi: 10.1093/nar/gkp800].
7. Harvie DR, Andreini C, Cavallero G, Meng W, Connolly BA, Yoshida K, Fujita Y, Harwood CR, Radford DS, Tottey S, J. Cavet JS, Robinson NJ (2006) Predicting metals sensed by ArsR-SmtB repressors: allosteric interference by a non-effector metal. Mol. Microbiol. 59(4):1341-56.
8. Sasnauskas G, Connolly BA, Halford SE, Siksnys V (2007) Site-specific DNA transesterification catalyzed by a restriction enzyme. Proc Natl Acad Sci USA 104(7):2115-20. (joined)
9. K Emptage, R O’Neill, A Solovyova and BA Connolly (2008) Interplay between DNA polymerase and PCNA switches off base excision repair of uracil and hypoxanthine during replication in archaea. J. Mol. Biol 383, 762-771.
10. Firbank SJ, Wardle J, Heslop P, Lewis RJ, Connolly BA (2008) Uracil recognition in archaeal DNA polymerases captured by X-ray crystallography. J Mol Biol 381(3):529-39.
11. Sasnauskas G, Connolly BA, Halford SE & Siksnys V (2008). Template-directed addition of nucleosides to DNA by the BfiI restriction enzyme. Nucleic Acids Res. 36, 3969–3977. (joined)
12. Wardle J, Burgers PM, Cann IK, Darley K, Heslop P, Johansson E, Lin LJ, McGlynn P, Sanvoisin J, Stith CM, Connolly BA (2008) Uracil recognition by replicative DNA polymerases is limited to the archaea, not occurring with bacteria and eukarya. Nucleic Acids Res. 36(3):705-11. (joined)
Odense (Jensen)
1. Dullnig V, Weiss R, Amon S, Rizzi A, Stutz H (2009) Confirmation of immuno-reactivity of the recombinant major birch pollen allergen Bet v 1a by affinity-CIEF, Electrophoresis 30, 2337-2346.
2. Yang J, Valineva T, Hong J, Bu T, Yao Z, Jensen ON, Frilander MJ, Silvennoinen O (2007) Transcriptional co-activator protein p100 interacts with snRNP proteins and facilitates the assembly of the spliceosome. Nucleic Acids Res 35(13):4485-94.
3. Banuelos S, Omaetxebarria MJ, Ramos I, Larsen MR, Arregi I, Jensen ON, Arizmendi JM, Prado A, Muga A (2007) Phosphorylation of both nucleoplasmin domains is required for activation of its chromatin decondensation activity. J Biol Chem 282(29):21213-21.
4. Fierro-Monti I, Mohammed S, Matthiesen R, Santoro R, Burns JS, Williams DJ, Proud CG, Kassem M, Jensen ON, Roepstorff P (2006) Quantitative proteomics identifies Gemin5, a scaffolding protein involved in ribonucleoprotein assembly, as a novel partner for eukaryotic initiation factor 4E. J Proteome Res 5(6):1367-78.
5. Beck HC, Nielsen EC, Matthiesen R, Jensen LH, Sehested M, Finn P, Grauslund M, Hansen AM, Jensen ON (2006) Quantitative proteomic analysis of post-translational modifications of human histones. Mol Cell Proteomics 5(7):1314-25.
6. Kjeldsen F, Hørning OB, Jensen SS, Giessing AM, Jensen ON (2008) Towards liquid chromatography time-scale peptide sequencing and characterization of post-translational modifications in the negative-ion mode using electron detachment dissociation tandem mass spectrometry. J Am Soc Mass Spectrom 19(8):1156-62.
7. Matthiesen R, Jensen ON (2008) Analysis of mass spectrometry data in proteomics. Methods Mol Biol 453:105-22.
8. Jørgensen S, Elvers I, Trelle MB, Menzel T, Eskildsen M, Jensen ON, Helleday T, Helin K, Sørensen CS, Obarska-Kosinska A, Taylor JE, Callow P, Orlowski J, Bujnicki JM, Kneale GG (2008) HsdR subunit of the type I restriction-modification enzyme EcoR124I: biophysical characterisation and structural modelling. J Mol Biol 376(2):438-52. (joined)
9. Zhang X, Ye J, Jensen ON, Roepstorff P (2007) Highly Efficient Phosphopeptide Enrichment by Calcium Phosphate Precipitation Combined with Subsequent IMAC Enrichment. Mol Cell Proteomics 6(11):2032-42.
10. Redlich G, Zanger UM, Riedmaier S, Bache N, Giessing AB, Eisenacher M, Stephan C, Meyer HE, Jensen ON, Marcus K. Pawlowski M, Gajda MJ, Matlak R, Bujnicki JM (2008) MetaMQAP: a meta-server for the quality assessment of protein models. BMC Bioinformatics 9(1):403. (joined)
11. Rand KD, Zehl M, Jensen ON, Jørgensen TJ (2009) Protein hydrogen exchange measured at single-residue resolution by electron transfer dissociation mass spectrometry. Anal Chem. 81(14):5577-84.
12. Balan L, Foltyn VN, Zehl M, Dumin E, Dikopoltsev E, Knoh D, Ohno Y, Kihara A, Jensen ON, Radzishevsky IS, Wolosker H. (2009) Feedback inactivation of D-serine synthesis by NMDA receptor-elicited translocation of serine racemase to the membrane. Proc Natl Acad Sci USA 106(18):7589-94.
13. Zehl M, Rand KD, Jensen ON, Jørgensen TJ (2008) Electron transfer dissociation facilitates the measurement of deuterium incorporation into selectively labeled peptides with single residue resolution. J Am Chem Soc. 130(51):17453-9.
14. Sharief Barends, Martin Zehl, Sylwia Bialek, Ellen de Waal, Bjørn A. Traag, Ole Nørregaard Jensen, Erik Vijgenboo and Gilles P. van Wezel (2009) tmRNA specifically controls the translation of cell-cycle and stress proteins in Streptomyces. EMBO Reports (in press)
15. Amon S, Rizzi A (2009) Matrix-assisted laser desorption/ionization mass spectrometry and capillary gel electrophoresis for rapid characterization of recombinant monoclonal antibodies. (in preparation)
Replizyme (Darley)
1. Firth AG, Fairlamb IJS, Darley K, Baumann CG. Sonogashira alkynylation of unprotected 8-brominated adenosines and guanosines: Fluorescence properties of compact conjugated acetylenes containing a purine ring. Tetrahedron Letters 2006 (49) 3529-3533
Vilnius (Siksnys)
1. Neely RK, Tamulaitis G, Chen K, Kubala M, Siksnys V, Jones AC (2009) Time-resolved fluorescence studies of nucleotide flipping by restriction enzymes. Nucleic Acids Res. 2009 Sep 8. [Epub ahead of print]
2. Tamulaitiene G, Siksnys V (2008) NotI is not boring. Structure 16(4):497-8.
3. Sokolowska M, Kaus-Drobek M, Czapinska H, Tamulaitis G, Siksnys V, Bochtler M (2007) Restriction endonucleases that resemble a component of the bacterial DNA repair machinery. Cell Mol Life Sci 64(18):2351-7.
4. Sokolowska M, Kaus-Drobek M, Czapinska H, Tamulaitis G, Szczepanowski RH, Urbanke C, Siksnys V, Bochtler M (2007) Monomeric restriction endonuclease BcnI in the apo form and in an asymmetric complex with target DNA. J Mol Biol 369(3):722-34.
5. Sukackaite R, Lagunavicius A, Stankevicius K, Urbanke C, Venclovas C, Siksnys V (2007) Restriction endonuclease BpuJI specific for the 5'-CCCGT sequence is related to the archaeal Holliday junction resolvase family. Nucleic Acids Res 35(7):2377-89.
6. Kaus-Drobek M, Czapinska H, Sokołowska M, Tamulaitis G, Szczepanowski RH, Urbanke C, Siksnys V, Bochtler M (2007) Restriction endonuclease MvaI is a monomer that recognizes its target sequence asymmetrically. Nucleic Acids Res 35(6):2035-46.
7. Sasnauskas G, Connolly BA, Halford SE, Siksnys V (2007) Site-specific DNA transesterification catalyzed by a restriction enzyme. Proc Natl Acad Sci USA 104(7):2115-20. (joined)
8. Bhagwat AS, Carpenter MA, Bujnicki JM (2008) Is AID a monomer in solution? DNA Repair (Amst) 7(3):349-50; author reply 351-2.
9. Szczepanowski RH, Carpenter MA, Czapinska H, Zaremba M, Tamulaitis G, Siksnys V, Bhagwat AS, Bochtler M (2008) Central base pair flipping and discrimination by PspGI. Nucleic Acids Res 36(19):6109-17.
10. Tamulaitiene G, Jakubauskas A, Urbanke C, Huber R, Grazulis S, Siksnys V (2006) The crystal structure of the rare-cutting restriction enzyme SdaI reveals unexpected domain architecture. Structure 14(9):1389-400.
11. Bochtler M, Szczepanowski RH, Tamulaitis G, Grazulis S, Czapinska H, Manakova E, Siksnys V (2006) Nucleotide flips determine the specificity of the Ecl18kI restriction endonuclease. EMBO J 25(10):2219-29.
12. Tamulaitis G, Zaremba M, Szczepanowski RH, Bochtler M, Siksnys V (2008) How PspGI, catalytic domain of EcoRII and Ecl18kI acquire specificities for different DNA targets. Nucleic Acids Res. 2008 Sep 27.
13. Tamulaitis G, Sasnauskas G, Mucke M, Siksnys V (2006) Simultaneous binding of three recognition sites is necessary for a concerted plasmid DNA cleavage by EcoRII restriction endonuclease. J Mol Biol 358(2):406-19.
14. Tamulaitis G, Mucke M, Siksnys V (2006) Biochemical and mutational analysis of EcoRII functional domains reveals evolutionary links between restriction enzymes. FEBS Lett 580(6):1665-71.
15. Tamulaitis G, Zaremba M, Szczepanowski RH, Bochtler M, Siksnys V (2007) Nucleotide flipping by restriction enzymes analyzed by 2-aminopurine steady-state fluorescence. Nucleic Acids Res 35(14):4792-9.
16. Shlyakhtenko LS, Gilmore J, Portillo A, Tamulaitis G, Siksnys V, Lyubchenko YL (2007) Direct visualization of the EcoRII-DNA triple synaptic complex by atomic force microscopy. Biochemistry 46(39):11128-36.
17. Zaremba M, Sasnauskas G, Urbanke C, Siksnys V (2006) Allosteric communication network in the tetrameric restriction endonuclease Bse634I. J Mol Biol 363(4):800-12.
18. Golovenko D, Manakova E, Tamulaitiene G, Grazulis S, Siksnys V (2009) Structural mechanisms for the 5'-CCWGG sequence recognition by the N- and C-terminal domains of EcoRII. Nucleic Acids Res. 2009 Oct 6. [Epub ahead of print]
19. Sasnauskas G., Zakrys L., Zaremba M., Cosstick R., Gaynor J. W., Halford S. E., Siksnys V. A novel mechanism for the scission of double-stranded DNA: BfiI cuts DNA strands of opposite polarity by rotating a single active site Submitted to Nature Chem. Biol. (joined)
20. Sasnauskas G, Connolly BA, Halford SE & Siksnys V (2008). Template-directed addition of nucleosides to DNA by the BfiI restriction enzyme. Nucleic Acids Res. 36, 3969–3977. (joined)
21. Gasiunas G, Sasnauskas G, Tamulaitis G, Urbanke C, Razaniene D, Siksnys V (2008) Tetrameric restriction enzymes: expansion to the GIY-YIG nuclease family. Nucleic Acids Res. 36(3):938-49.
22. Sukackaite R, Grazulis S, Bochtler M, Siksnys V (2008) The recognition domain of the BpuJI restriction endonuclease in complex with cognate DNA at 1.3-A resolution. J Mol Biol. 378(5):1084-93.
23. Tamulaitis G, Zaremba M, Szczepanowski RH, Bochtler M, Siksnys V (2008) How PspGI, catalytic domain of EcoRII and Ecl18kI acquire specificities for different DNA targets. Nucleic Acids Res. 36(19):6101-8.
24. Ibryashkina EM, Sasnauskas G, Solonin AS, Zakharova MV, Siksnys V (2009) Oligomeric structure diversity within the GIY-YIG nuclease family. J Mol Biol. 387(1):10-6.
25. Zaremba M, Owsicka A, Tamulaitis G, Sasnauskas G, Shlyakhtenko LS, Lushnikov A, Lyubchenko YL, Laurens N, van den Broek B, Wuite G, Siksnys V (2009) Transient tetramerization and DNA synapsis trigger cleavage by the Ecl18kI restriction enzyme. (submitted)
Warsaw (Bujnicki)
1. Redlich G, Zanger UM, Riedmaier S, Bache N, Giessing AB, Eisenacher M, Stephan C, Meyer HE, Jensen ON, Marcus K. Pawlowski M, Gajda MJ, Matlak R, Bujnicki JM (2008) MetaMQAP: a meta-server for the quality assessment of protein models. BMC Bioinformatics 9(1):403. (joined)
2. Ozanick SG, Bujnicki JM, Sem DS, Anderson JT (2007) Conserved amino acids in each subunit of the heteroligomeric tRNA m1A58 Mtase from Saccharomyces cerevisiae contribute to tRNA binding. Nucleic Acids Res 35(20):6808-19.
1. Cymerman IA, Obarska A, Skowronek KJ, Lubys A, Bujnicki JM (2006) Identification of a new subfamily of HNH nucleases and experimental characterization of a representative member, HphI restriction endonuclease. Proteins 65(4):867-76. (joined)
3. Miyazono K, Watanabe M, Kosinski J, Ishikawa K, Kamo M, Sawasaki T, Nagata K, Bujnicki JM, Endo Y, Tanokura M, Kobayashi I (2007) Novel protein fold discovered in the PabI family of restriction enzymes. Nucleic Acids Res 35(6):1908-18.
4. Orlowski J, Boniecki M, Bujnicki JM (2007) I-Ssp6803I: the first homing endonuclease from the PD-(D/E)XK superfamily exhibits an unusual mode of DNA recognition. Bioinformatics 23(5):527-30.
5. Schäfer P, Cymerman IA, Bujnicki JM, Meiss G (2007) Human lysosomal DNase IIalpha contains two requisite PLD-signature (HxK) motifs: evidence for a pseudodimeric structure of the active enzyme species. Protein Sci 16(1):82-91. (joined)
6. Orlowski J, Bujnicki JM (2008) Structural and evolutionary classification of Type II restriction enzymes based on theoretical and experimental analyses. Nucleic Acids Res 36(11):3552-69.
7. Kaminska KH, Baraniak U, Boniecki M, Nowaczyk K, Czerwoniec A, Bujnicki JM (2008) Structural bioinformatics analysis of enzymes involved in the biosynthesis pathway of the hypermodified nucleoside ms(2)io(6)A37 in tRNA. Proteins 70(1):1-18.
8. Vasu K, Saravanan M, Bujnicki JM, Nagaraja V (2008) Structural integrity of the beta beta alpha-Metal finger motif is required for DNA binding and stable protein-DNA complex formation in R.KpnI. Biochim Biophys Acta 1784(2):269-75.
9. 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 (2007) Type II restriction endonuclease R.Eco29kI is a member of the GIY-YIG nuclease superfamily. BMC Struct Biol 7:48.
10. Obarska A, Blundell A, Feder M, Patel J, Vejsadova S, Sisakova E, Weiserova M, Bujnicki JM, Firman K (2006) Structural model for the multisubunit Type IC restriction-modification DNA methyltransferase M.EcoR124I in complex with DNA. Nucleic Acids Res 34(7):1992-2005.
11. Carpenter M, Divvela P, Pingoud V, Bujnicki J, Bhagwat AS (2006) Sequence-dependent enhancement of hydrolytic deamination of cytosines in DNA by the restriction enzyme PspGI. Nucleic Acids Res 34(13):3762-70. (joined)
12. Kosinski J, Plotz G, Guarné A, Bujnicki JM, Friedhoff P (2008) The PMS2 subunit of human MutLalpha contains a metal ion binding domain of the iron-dependent repressor protein family. J Mol Biol 382(3):610-27. (joined)
13. Sasin JM, Godzik A, Bujnicki JM (2007) SURF'S UP! - protein classification by surface comparisons. J Biosci 32(1):97-100.
14. Dunin-Horkawicz S, Feder M, Bujnicki JM (2006) Phylogenomic analysis of the GIY-YIG nuclease superfamily. BMC Genomics 7(1):98.
15. 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 (2007) Type II restriction endonuclease R.Eco29kI is a member of the GIY-YIG nuclease superfamily. BMC Struct Biol 7:48.
16. Wyszyńska A, Pawłowski M, Bujnicki J, Pawelec D, Van Putten JP, Brzuszkiewicz E, Jagusztyn-Krynicka EK, Kosinski J, Kubareva E, Bujnicki JM (2008) A model of restriction endonuclease MvaI in complex with DNA: a template for interpretation of experimental data and a guide for specificity engineering. Proteins 68(1):324-36.
17. Pietal MJ, Tuszynska I, Bujnicki JM (2007) PROTMAP2D: visualization, comparison and analysis of 2D maps of protein structure. Bioinformatics 23(11):1429-30.
18. Czerwoniec A, Dunin-Horkawicz S, Purta E, Kaminska KH, Kasprzak J, Bujnicki JM, Grosjean H, Rother K (2009) MODOMICS: a database of RNA modification pathways. 2008 update Nucleic Acids Res 37(Database issue):D118-21.
19. Czerwoniec A, Kasprzak JM, Kaminska KH, Rother K, Purta E, Bujnicki JM (2009) Folds and functions of domains in RNA modification enzymes. In "DNA and RNA modification enzymes: comparative structure, mechanism, functions, cellular interactions and evolution". Editor: Grosjean H. Landes Bioscience.
20. Majorek K, Bujnicki JM (2009) Modeling of Escherichia coli Endonuclease V structure in complex with DNA J Mol Model 15(2):173-82.
21. Kennaway CK J, Obarska-Kosinska A, White JK, Tuszynska I, Cooper LP, Bujnicki JM, Trinick J, Dryden DTF (2009) The structure of M.EcoKI Type I DNA methyltransferase with a DNA mimic antirestriction protein. Nucleic Acids Res 37(3):762-70.
22. Jakubauskas A, Giedriene J, Bujnicki JM, Janulaitis A (2007) Identification of a single HNH active site in Type IIS restriction endonuclease Eco31I. J Mol Biol 370(1):157-69. (joined)
23. Koudan EV, Brevnov MG, Subach OM, Rechkoblit OA, Bujnicki JM, Gromova ES (2007) Probing of contacts between EcoRII DNA methyltransferase and DNA using substrate analogs and molecular modeling. Mol Biol (Mosk) 41(5):885-99.
24. Kosinski J, Kubareva EA, Bujnicki JM (2007) A model of restriction endonuclease MvaI in complex with DNA: a template for interpretation of experimental data and a guide for specificity engineering. Proteins 68(1):324-36.
25. Nakonieczna J, Kaczorowski T, Obarska-Kosinska A, Bujnicki JM (2009) Functional analysis of the MmeI restriction-modification enzyme from a methanol utilizer Methylophilus methylotrophus: A subtype IIC enzyme related to Type I enzymes. Appl Environ Microbiol 75(1):212-23.
26. Pierechod M, Nowak A, Saari A, Purta E, Bujnicki JM, Konieczny I (2009) Conformation of a plasmid replication initiator protein affects its proteolysis by ClpXP system. Protein Sci 18(3):637-49.
27. Zylicz-Stachula A, Bujnicki JM, Skowron P (2009) Cloning and analysis of a bifunctional methyltransferase/restriction endonuclease TspGWI, the prototype of a Thermus sp. enzyme family BMC Mol Biol 29;10(1):52.
28. Fukuda E, Kaminska KH, Bujnicki JM, Kobayashi I (2008) Cell death upon epigenetic genome methylation: a novel function of methyl-specific deoxyribonucleases Genome Biol 9(11):R163.
29. Orlowski J, Mebrhatu MT, Michiels CW, Bujnicki JM, Aertsen A (2008) Mutational analysis and a structural model of methyl-directed restriction enzyme Mrr Biochem Biophys Res Commun 377(3):862-6.
30. Sikora E, Bielak-Zmijewska A, Magalska A, Piwocka K, Mosieniak G, Kalinowska M, Widlak P, Cymerman IA, Bujnicki JM (2006) Curcumin induces caspase-3 dependent apoptotic pathway but inhibits DFF40/CAD endonuclease in human Jurkat cells. Mol Cancer Ther 5(4):927-34.
31. Bheemanaik S, Bujnicki JM, Nagaraja V, Rao DN (2006) Functional analysis of amino acid residues in the dimerisation interface of KpnI DNA methyltransferase. Biol Chem 2006 May;387(5):515-23.
32. Samaranayake M, Bujnicki JM, Carpenter M, Bhagwat AS (2006) Evaluation of molecular models for the affinity maturation of antibodies: roles of cytosine deamination by AID and DNA repair. Chem Rev 106(2):700-19.
33. Skowronek KJ, Kosinski J, Bujnicki JM (2006) A theoretical model of restriction endonuclease HpaI in complex with DNA, predicted by fold-recognition and validated by site-directed mutagenesis. Proteins 63(4):1059-68.
34. Skowronek KJ, Bujnicki JM (2007) Restriction and homing endonucleases. Chapter 21 in "Industrial Enzymes. Structure, Function and Applications"; Editors: Polaina J, MacCabe AP. Springer-Verlag, ISBN: 978-1-4020-5376-4.
35. Kaminska KH, Kawai M, Boniecki M, Kobayashi I, Bujnicki JM. (2008) Type II restriction endonuclease R.Hpy188I belongs to the GIY-YIG nuclease superfamily, but exhibits an unusual active site BMC Struct Biol 8(1):48.
36. Bauer RA, Rother K, Bujnicki JM, Preissner R (2008) Suffix techniques as a rapid method for RNA substructure search Genome Inf 20:183-198.
37. Obarska-Kosinska A, Taylor JE, Callow P, Orlowski J, Bujnicki JM, Kneale GG (2008) HsdR subunit of the Type I restriction-modification enzyme EcoR124I: biophysical characterisation and structural modelling J Mol Biol 376(2):438-52.
38. Kaminska KH, Bujnicki JM (2008) Bacteriophage Mu Mom protein responsible for DNA modification is a new member of the acyltransferase superfamily Cell Cycle 7(1):120-1.
39. Jørgensen S, Elvers I, Trelle MB, Menzel T, Eskildsen M, Jensen ON, Helleday T, Helin K, Sørensen CS, Obarska-Kosinska A, Taylor JE, Callow P, Orlowski J, Bujnicki JM, Kneale GG (2008) HsdR subunit of the type I restriction-modification enzyme EcoR124I: biophysical characterisation and structural modelling. J Mol Biol 376(2):438-52. (joined)
40. Kosinski J, Plotz G, Guarné A, Bujnicki JM, Friedhoff P (2008) The PMS2 subunit of human MutLalpha contains a metal ion binding domain of the iron-dependent repressor protein family. J Mol Biol. 382(3):610-27. (joined)
41. Cymerman IA, Chung I, Beckmann BM, Bujnicki JM, Meiss G (2008) EXOG, a novel paralog of Endonuclease G in higher eukaryotes. Nucleic Acids Res. 36(4):1369-79. (joined)
42. Bauer RA, Rother K, Bujnicki JM, Preissner R (2008) Suffix techniques as a rapid method for RNA substructure search. Genome Inform. 20:183-98.
York (Hoggett & Baumann)
1. Firth AG, Fairlamb IJS, Darley K, Baumann CG (2006) Sonogashira alkynylation of unprotected 8-brominated adenosines and guanosines: Fluorescence properties of compact conjugated acetylenes containing a purine ring. Tetrahedron Letters (49) 3529-3533. (joined)
2. KN Sas, J Hoggett Kinetic analysis of interaction and of enhancer binding protein PspF with DNA. (in preparation)
3. KN Sas, A Leech, J Hoggett Nucleotide-dependent oligomerisation of the sigma-54 dependent enhancer binding protein PspF. (in preparation)
4. KN Sas, J Hoggett The kinetics of ATP-dependent binding of the bacterial enhancer binding protein PspF to DNA. (in preparation)
23.04.2008 17:57
