Transmembrane beta-barrels (TMBB) are a special structural class of proteins predominately found in the outer membranes of Gram-negative bacteria, mitochondria, and chloroplasts. TMBBs are surface-accessible proteins that perform a variety of functions ranging from iron acquisition to osmotic regulation. These properties make TMBBs tempting targets for vaccine or drug therapy development A prediction method based on the physicochemical properties of experimentally characterized TMBB structures was developed to predict TMBB-encoding genes from genomic databases. The algorithm's prediction efficiency was tested using a non-redundant set of sequences from proteins of known structure. The algorithm was based on the work of Wimley (2002), but was improved because of its disappointingly high false-positive prediction rate. The improved prediction algorithm developed in this study was shown to be more accurate than previously published prediction methods. Its accuracy is near 99% when using the most efficient prediction criteria, i.e. where the most known TMBBs are correctly predicted and the most non-TMBBs are correctly excluded. The improved algorithm was used to predict the abundance of TMBBs in 611 chromosomes from Gram-negative and acid-fast bacteria. The average predicted abundance of genomic TMBBs was 3%, which is consistent with previous estimates Predicted outer membrane protein L (OmpL) from Salmonella typhimurium LT2, was tested as a model for validating the prediction method. All of the physicochemical and spectroscopic properties exhibited by OmpL are consistent with other known TMBBs. Recombinant OmpL localizes to the outer membrane when expressed in Escherichia coli; has a beta-sheet-rich secondary structure with stable tertiary contacts in the presence of either detergent micelles or a lipid bilayer; OmpL also forms a pore through which small hydrophilic solutes can diffuse. Together, this data proves that OmpL is a true TMBB, which supports the computational prediction. This work significantly contributes to the advancement of TMBB research / acase@tulane.edu
| Identifer | oai:union.ndltd.org:TULANE/oai:http://digitallibrary.tulane.edu/:tulane_27522 |
| Date | January 2009 |
| Contributors | Freeman, Thomas C., Jr (Author), Landry, Samuel J (Thesis advisor) |
| Publisher | Tulane University |
| Source Sets | Tulane University |
| Language | English |
| Detected Language | English |
| Rights | Access requires a license to the Dissertations and Theses (ProQuest) database., Copyright is in accordance with U.S. Copyright law |
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