TY - THES T1 - Development of computational methods for predicting structural characteristics of helical membrane proteins A1 - Park,Yungki Y1 - 2007/11/27 N2 - Helical membrane proteins (HMPs) play a crucial role in diverse cellular processes. Given the difficulty in determining their structures by experimental techniques, it is desired to develop computational methods for predicting their structural characteristics. In addition, computational analysis can provide interesting insights into their structure and function that experimental work can not provide. This thesis summarizes years of such computational endeavours, comprising 4 published papers (Paper I ~ IV). In Paper I, it was attempted to model low-resolution tertiary structures of HMPs with a modest number of transmembrane (TM) helices from packing constraints and sequence conservation patterns. In Paper II, a fundamental investigation was undertaken to analyze the degree of correlation between exposure patterns of TM helices to the membrane and their properties such as their hydrophobicities and conservation patterns. In Paper III, on the basis of the work presented in Paper II, an optimal way of deriving the propensity scales of the 20 amino acids to preferentially interact with the membrane as reflected in known HMP structures was presented, which revealed a surprising fact that the architectural principle of HMPs is best captured by the partial specific volumes of the amino acids. In Paper IV, the development of TMX (TransMembrane eXposure), a novel computational method for predicting the lipid accessibility of TM residues of HMPs, was described, which significantly outperforms other existing methods. A web interface for TMX is available at http://service.bioinformatik.uni-saarland.de/tmx. KW - Bioinformatik KW - Membranproteine KW - Helicität KW - Strukturaufklärung KW - Prognose CY - Saarbrücken PB - Universitäts- und Landesbibliothek AD - Postfach 151141, 66041 Saarbrücken UR - http://scidok.sulb.uni-saarland.de/volltexte/2007/1349 ER -