Molecular mechanics calculations were used to determine the lipid favourable surfaces of transmembrane helices. The symmetric hydrophobic dodecane molecule was chosen as a lipophilic probe, since it has no polar groups, and only van der Waals interaction would be encountered. To evaluate the effectiveness of this approach the transmembrane helices of bacteriorhodopsin (BR) were chosen as the model system since both its helix - helix and lipid - helix interfaces have been structurally defined by crystallography. The ideal alpha-helix geometry of the TM helices of the BR, mimicking the transmembrane helices, were used to study the interaction with the lipophilic probe and hence to map the surface as a test case. The calculated lipid facing surfaces of three TM helices substantially agreed with lipid observed interacting surfaces of TM helices in the crystal structure. The two lipophilic surfaces were predicted for the other four TM helices. One surface for each of those helices was in excellent agreement with lipid facing surfaces determined by crystallography data. The other surface was poor prediction of the lipid facing surface, but the rest of the surface could be assigned as a helix - helix interfaces. These will be used the study of more complex helices and lipids in the same way. The results for the interaction of dodecane with BR were encouraging and it should provide a basis for obtaining extra information in determination of lipid favourable surfaces of helices of other integral membrane proteins with unknown three-dimensional structure.
|Number of pages||31|
|Journal||Internet Journal of Chemistry|
|Publication status||Published - 23 Apr 2003|
- molecular mechanics