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Computational studies of intramolecular disulfide bonded catenanes as a novel stabilizing mechanism in thermophilic micr

Computational studies of intramolecular disulfide bonded catenanes as a novel stabilizing mechanism in thermophilic microbes. August 23, 2007 Daniel Park Yeates lab, MBI, UCLA SoCalBSI. Today. Intracellular disulfide abundance in thermophiles/hyperthermophiles

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Computational studies of intramolecular disulfide bonded catenanes as a novel stabilizing mechanism in thermophilic micr

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  1. Computational studies of intramolecular disulfide bonded catenanes as a novel stabilizing mechanism in thermophilic microbes August 23, 2007 Daniel Park Yeates lab, MBI, UCLA SoCalBSI

  2. Today • Intracellular disulfide abundance in thermophiles/hyperthermophiles • P. aerophilum citrate synthase • Searching for catenanes • Results

  3. Importance of studying thermophilic enzymes • Industrial applications • Engineering heat-stable biomolecules • Utilizing those found in nature • Taq DNA polymerase for PCR • Insight into protein folding mechanisms • Evolution of thermostable proteins

  4. Intracellular disulfide bond abundance Mallick et al., 2002 PNAS 99, pp. 9679-9684

  5. Presence of disulfide bonds within the intracellular proteins of P. aerophilum • Both lanes reduced • Presense and absence of iodoacetamide • Large fraction of P. aerophilum proteins contain disulfide bonds Boutz et al., 2007 JMB 368, pp. 1332-1344

  6. Citrate synthase (PaCS) from P. aerophilum Boutz et al., 2007 JMB 368, pp. 1332-1344

  7. Catenane structure of PaCS Boutz et al., 2007 JMB 368, pp. 1332-1344

  8. Disulfide bonds: contribution to the thermostability of PaCS Boutz et al., 2007 JMB 368, pp. 1332-1344

  9. Cysteine abundance at terminal regions

  10. Alignment of thermophilic citrate synthase

  11. Approach

  12. Possible catenanes by temperature

  13. Cysteine abundance at terminal regions

  14. INFORMATION STORAGE AND PROCESSING [J] Translation, ribosomal structure and biogenesis [A] RNA processing and modification [K] Transcription [L] Replication, recombination and repair [B] Chromatin structure and dynamics CELLULAR PROCESSES AND SIGNALING [D] Cell cycle control, cell division, chromosome partitioning [Y] Nuclear structure [V] Defense mechanisms [T] Signal transduction mechanisms [M] Cell wall/membrane/envelope biogenesis [N] Cell motility [Z] Cytoskeleton [W] Extracellular structures [U] Intracellular trafficking, secretion, and vesicular transport [O] Posttranslational modification, protein turnover, chaperones METABOLISM [C] Energy production and conversion [G] Carbohydrate transport and metabolism [E] Amino acid transport and metabolism [F] Nucleotide transport and metabolism [H] Coenzyme transport and metabolism [I] Lipid transport and metabolism [P] Inorganic ion transport and metabolism [Q] Secondary metabolites biosynthesis, transport and catabolism POORLY CHARACTERIZED [R] General function prediction only [S] Function unknown Clusters of orthologous groups (COG) functional classifications

  15. Possible microbial catenanes by function

  16. Possible microbial catenanes by function

  17. Possible thermophilic catenanes by function

  18. Possible thermophilic catenanes further classified by COGs (top 7)

  19. Possible catenane among peroxiredoxin homologs? • [O] COG0450 Peroxiredoxin (7) Thermoanaerobacter tengcongensis MB4 20808569 Methanosaeta thermophila PT 116754713 Pyrobaculum islandicum DSM 4184 119873344 Pyrobaculum islandicum DSM 4184 119871684 Pyrobaculum calidifontis JCM 11548 126458809 Pyrobaculum arsenaticum DSM 13514 145590729 Methanocaldococcus jannaschii DSM 2661 15668917 • [C] COG0372 Citrate synthase (5) Pyrobaculum islandicum DSM 4184 119873179 Pyrobaculum calidifontis JCM 11548 126459178 Pyrobaculum arsenaticum DSM 13514 145592430 Pyrobaculum aerophilum str. IM2 18312809 Aeropyrum pernix K1 14601576

  20. P. islandicum DSM 4184 peroxidase:alignment with homologs

  21. P. islandicum peroxidase homolog

  22. P. islandicum peroxidase homolog

  23. Future directions • MD simulations of possible catenanes • Determine structures of most likely catenanes by X-ray crystallography • Investigate correlation between psychrophilic proteins and disulfide bonding

  24. Todd Yeates Neil King Jason Forse Brian O’Connor Jamil Momand Sandra Sharp Wendie Johnston Nancy Warter-Perez Acknowledgements • SoCalBSI program • Ronnie Cheng • Funded by NIH, NSF, EWD, DOE

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