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Evolution von Double-PSI-Beta-Barrel-Proteinen und Aspartatproteasen

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Hulko,  M
Department Protein Evolution, Max Planck Institute for Developmental Biology, Max Planck Society;

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Citation

Hulko, M. (2006). Evolution von Double-PSI-Beta-Barrel-Proteinen und Aspartatproteasen. PhD Thesis, Eberhard Karls Universität, Tübingen, Germany.


Cite as: https://hdl.handle.net/21.11116/0000-000B-B583-4
Abstract
In three parts the evolution of double psi beta-barrel proteins and aspartic proteases was analyzed. The first part was about the folds double psi beta-barrel to which representatives of N-terminal domains of AAA-ATPases like Vat or Cdc48 belong to, and acid proteases like the aspartic proteases pepsin and HIV-1 protease. Even though these folds have been recognized and described as structurally very similar they are regarded so far to be analogous with convergent development. These assumptions were based on the missing sequence similarity and differences in the connections of their beta-strands. This work suggests a common ancestry based on newly discovered functional similarities. Chaperone assays have been done for that which revealed the prevention of protein aggregation as a common trait. This supplies one more example in which folds changed in the course of divergent evolution. One additional aspect in this part was to examine if the domains of the different folds are interchangeable within their domain context. The second part dealt with the folds double psi bet-barrel and swapped hairpin-barrel. Homology of those has been suspected already due to characteristic structural similarities. However, a low sequence similarity could not support this notion clearly. This homology would be one more example of fold changes during evolution but a evolutionary mechanism had been missing. The structures of the proteins PhS018 from Pyrococcus horikoshii and Af1504 from Archaeoglobus fulgidus were the subject of this work. A new fold has been discovered by solving the solution structure of PhS018: the RIFT-barrels. This fold is intermediate between double psi bet-barrel and swapped hairpin-barrel and provides a plausible evolutionary mechanism for the development of these folds. Moreover, a structurally highly conserved beta/alpha/beta-element could be identified with which an evolutionary scenario from antecedent peptides made of supersecondary structure elements could be proposed. Besides PhS018, the potential double psi beta-barrel protein Af1504 was characterized biochemically. The third part dealt with the function of an operon from A. fulgidus. The protein Af1504 is encoded in it together with the proteins Af1502, Af1503 and Af1505. A HAMP-domain had already been predicted for the transmembrane protein Af1503, which are abundant domains in prokaryotic signal transduction proteins. As the first structure of a HAMP domain ever, the solution structure of the HAMP-domain from Af1503 was solved by NMR spectroscopy. The HAMP domain shows a coiled coil conformation that had never been observed before in a native protein: complementary x-da conformation. Out of this peculiarity, a molecular signal transduction mechanism could be suggested for prokaryotic transmembrane receptors. This mechanism bases on the cogwheel-like rotation of alpha-helices. Another aspect in this part was the search for potential ligands of Af1503. Calcium was suggested to be a ligand and its interaction with Af1503 was investigated and characterized by calorimetry. Finally, a functional interaction of the proteins of this operon and a function of this operon for the archaeon A. fulgidus has been proposed and discussed.