Computational Assembly of Beta Barrel Membrane Protein

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DESCRIPTION (provided by applicant): Beta-barrels are one of the two classes of membrane proteins. They are found in gram-negative bacteria, acid-fast gram-positive bacteria, pore-forming exotoxins, and mitochondria, and are an important class of therapeutic targets for infectious diseases. Knowledge of the three-dimensional structures of membrane beta-barrels will be critical for developing effective anti-bacterial drugs. Studying how beta-barrels organize in membranes will also provide important lessons on how membrane proteins fold in general. The goal of the proposed project is two-fold: 1) to gain understanding on how beta-barrel proteins are assembled in membrane environments through computational studies, and 2) to predict at genomic scale a large number of accurate structures. We plan to develop a multi-pronged approach to achieve these goals. The specific aims of this project are: a) identification of sequence and spatial motifs and anti-motifs in beta-barrel proteins for stability analysis, b) evolutionary analysis of beta-barrel membrane proteins for detection of remote structural homologs and functional regions, and c) large scale prediction of three-dimensional structures and assembly of beta-barrel proteins. This project complements experimental work by providing additional interpretation and explanation of experimental results. It will also generate further testable hypotheses for experimental investigations. The outcome of the proposed research includes novel sequence and spatial motifs useful for protein design, membrane beta-barrel-specific scoring matrices useful for remote homology detection, empirical potential functions for assessing beta-barrel stabilities, and a large number of predicted structures. In addition, it will produce computational algorithms, software, and databases that will be made publicly available for further studies. Many emerging infectious diseases pose serious threats to public health, including hospital-acquired pneumonia due to gram-negative bacteria, meningococcal meningitis, anthrax, and staphylococcal infections such as surgical wound and burn infections. We do not have adequate treatments to counter possible outbreaks of these infections, and it is urgent to develop antimicrobial drugs and vaccines to combat these threats. Because beta-barrel proteins play key roles in the pathogenesis of these infectious diseases, our proposed research will lead to new targets and new strategies in the development of drugs and vaccines.