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Figure 4. Comparison of a MTB ImuA’ (Rv3395c) model with the RecA crystal structure. ImuA’ appears to be a “crippled” RecA homolog. It lacks the C-terminal subdomain and ATP-binding site. Previously, these genes were identified as putative mycobacterial components of an imuA’-imuB-dnaE2 mutagenic cassette widespread in bacteria. Using computational techniques we have generated models for all three Mtb proteins. Combining these models with sequence analysis we showed that although Rv3394c is related to Y-family DNA polymerase, it cannot function as a polymerase, because it lacks the essential active site residues. The computational analysis also identified a substantial disorder within the C-terminal region, suggesting its participation in protein-protein interactions. The subsequent experiments in the Prof. V. Mizrahi’s lab directly confirmed computational findings. In turn, a computational model of Rv3395c (Fig. 5) allowed the design of its truncation variants that subsequently were used to map the Rv3395c regions important for its interaction with Rv3394c. A computational model of the DnaE2 polymerase, which was shown to be directly responsible for the mutagenic translesion synthesis (TLS), provided clues as to its functional specialization. Compared with the main replicative polymerase (DnaE1), DnaE2 lacks the C-terminal domain, which mediates interaction with the polIII t-subunit. The t-subunit is coordinating leading and lagging DNA strand synthesis during replication. The absence of the t-interacting domain suggests that DnaE2 is unable to substitute DnaE1 within the replisome. In addition, the absence of key histidine and aspartate residues in the PHP domain of DnaE2 hints at compromised proofreading function. Taken together, these computational results played an important role in revealing individual roles of the DnaE2-Rv3394c-Rv3395c “mutagenic complex” components as well as mapping their interaction regions. Results of the study have been reported in Proceedings of the National Academy of Sciences of the USA [6]. Rv3394c S.Solfataricus Dpo4 Figure 5. Structurally, MTB ImuB (Rv3394c) is very similar to a Y-family polymerase (Dpo4), but it lacks polymerase active site residues. 35 th anniversary 52
53 International collaboration Prof. Penny Beuning, Northeastern University, Boston, MA, USA Dr. Daniel Barsky, Lawrence Livermore National Laboratory, Livermore, CA, USA Prof. Valerie Mizrahi, University of the Witwatersrand, Johannesburg, South Africa Prof. Martin Kupiec, Tel Aviv University, Israel Dr. Lajos Haracska, Biological Research Center, Hungarian Academy of Sciences, Szeged, Hungary Grants Howard Hughes Medical Institute Research Council of Lithuania JOURNAL ARTICLES 1. Repšys V, Margelevičius M, Venclovas Č. Re-searcher: a system for recurrent detection of homologous protein sequences. BMC Bioinformatics 2008, 9:296. 2. Venclovas Č, Margelevičius M. The use of automatic tools and human expertise in template-based modeling of CASP8 target proteins. Proteins 2009, 77 Suppl 9:81-8. 3. Margelevičius M, Venclovas Č. Detection of distant evolutionary relationships between protein families using theory of sequence profileprofile comparison. BMC Bioinformatics 2010, 11:89. 4. Margelevičius M, Laganeckas M, Venclovas Č. COMA server for protein distant homology search. Bioinformatics 2010, 26(15):1905-6. 5. McCauley MJ, Shokri L, Sefcikova J, Venclovas Č, Beuning PJ, Williams MC. Distinct double- and single-stranded DNA binding of E. coli replicative DNA polymerase III α subunit. ACS Chem Biol 2008, 3(9):577-87. 6. Warner DF, Ndwandwe DE, Abrahams GL, Kana BD, Machowski EE, Venclovas Č, Mizrahi V. Essential roles for imuA'- and imuB-encoded accessory factors in DnaE2-dependent mutagenesis in Mycobacterium tuberculosis. Proc Natl Acad Sci U S A 2010, 107(29):13093-8. 7. Laganeckas M, Margelevičius M, Venclovas Č. Identification of new homologs of PD-(D/E)XK nucleases by support vector machines trained on data derived from profile-profile alignments. Nucleic Acids Res 2010, doi:10.1093/nar/gkq958. 8. Zubrienė A, Gutkowska M, Matulienė J, Chaleckis R, Michailovienė V, Voroncova A, Venclovas Č, Zylicz A, Zylicz M, Matulis D. Thermodynamics of radicicol binding to human Hsp90 alpha and beta isoforms. Biophys Chem 2010, 152(1-3):153-63. BOOK CHAPTER 1. Barsky, D., Lawrence, T.A. and Venclovas, Č. How proteins slide on DNA. In Williams, M. C. and Maher, L. J. III (eds.), Biophysics of DNA- Protein Interactions. Springer Science+Business Media, LLC., In press.
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35 th anniversary Report 2008 - 201
Page 3 and 4: 35 th anniversary Report 2008 - 201
Page 5 and 6: 3 Director’s note This triennial
Page 8 and 9: INSTITUTE OF BIOTECHNOLOGY: The his
Page 10 and 11: IBT citations in 1991 - 2009 ISI We
Page 12 and 13: Grants 1995-2010 FRAMEWORK 7 PROGRA
Page 14 and 15: 1997 1999 2000 2001 2002 2004 Docto
Page 16 and 17: Strengthening and Sustaining the Eu
Page 18 and 19: Lab Leader Virginijus Šikšnys, Ph
Page 20 and 21: Structure and function of restricti
Page 22 and 23: Time-resolved fluorescence studies
Page 24 and 25: Lab Leader Saulius Klimašauskas, P
Page 26 and 27: HPLC-MS analysis performed by Zita
Page 28 and 29: Archaeal C/D box RNPs: towards prog
Page 30 and 31: Lab leader Gintautas Žvirblis, PhD
Page 32 and 33: In conclusion, the dual potential o
Page 34 and 35: For that purpose 93 serum samples w
Page 36 and 37: International Collaboration Prof. D
Page 38 and 39: Lab Leader Aurelija Žvirblienė, P
Page 40 and 41: Master student V.Žilaitytė, Dr. A
Page 42 and 43: Until recently, IS6110-RFLP and spo
Page 44 and 45: Lab Leader Daumantas Matulis, PhD L
Page 46 and 47: Here at the LBDD we have cloned and
Page 48 and 49: CONFERENCES AND COLLABORATION The L
Page 50 and 51: Lab Leader Česlovas Venclovas, PhD
Page 52 and 53: COMA has been implemented as a stan
Page 56 and 57: DNA Sequencing Center Eglė Rudokie
Page 58 and 59: Design by UAB Idea Artis Printed by
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