Analysis of the Secondary Structure of the Transmembrane Domain of SARS CoV E Protein using FTIR Spectroscopy
قاسم موسى هاشم أبو رميله
Qassem Mussa Hashem Abu Rmeleh
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One of the major obstacles facing the field of structural biology in the postgenomic era is the inherent difficulty of solving the structure of membrane proteins under native conditions. Membrane proteins share a common property; part of their structure is embedded in the lipid bilayer. This feature makes them attractive drug targets, which requires a detailed knowledge of the secondary structure of their transmembrane domain. Both crystallography and NMR still encounter difficulties in handling membrane proteins, so there is an urgent need for new biophysical methods and new insights in the biophysics of membrane proteins to solve the secondary structure of such proteins. The outbreak of the severe acute respiratory syndrome (SARS) virus, July 2003, has presented a formidable challenge for the scientific community. As part of that effort, we decided to study the high resolution backbone structure of E transmembrane proteins of the SARS coronavirus, by Attenuated Total Internal Reflection (ATR) FTIR of eighteen of isotopically labeled sites with ( 13C=18O) of the synthesized sequence for the SARS coronavirus E protein transmembrane domain. ATR-FTIR spectroscopy is a wellestablished method for generating precise structural information on isotopically labeled membrane proteins embedded in a lipid bilayer. We used the new biophysical method site specific infrared dichroism (SSID), to investigate the structure and orientation of transmembrane. α-helical bundles We postulate in this work that the E protein of SARS CoV is α-helix, and it has 26 residues embedded in the lipid bilayer, and the SARS CoV E protein is not a regular helix, but it adopts a unique transmembrane helical hairpin model, and the E protein has two possible kinks at residue No. 26 and 31 Phe and Leu respectively within the lipid bilayer, which isreported for the first time in this thesis. And it also has a possible kink in residue No 15 too. All the results were confirmed experimentally.