Theoretical study of the packing of alpha-helices into possible transmembrane bundles. Sequences including alanines, leucines and serines.
Energy optimizations are carried out on packages of two and five alpha-helices containing leucines on their faces of contact and made otherwise of alanines. The effect of these bulky side-chains on the optimal arrangements is analysed and compared to the results previously obtained for pure poly(L-alanine) packages; the essential pairing properties are conserved (near antiparallelism, preponderous role of the non-bonded interactions, possibility of existence of parallel pairs); five alpha-helices made of 8 alanines and 6 leucines (three on each interface) can pack in different stable P5L bundles including various holes, according to the tilt and relative sliding of the helices. Substitution of serines to the alanines lying on the inner wall affects very little the interhelix packing. The seryl side chains adapt their conformation at best to their surroundings. The P5L packages can be used to represent individual subunits arranged in 'superbundles' around a central pit in a channel-forming protein.
D000409:Alanine; D000595:Amino Acid Sequence; D055598:Chemical Phenomena; D002627:Chemistry, Physical; D004563:Electrochemistry; D007473:Ion Channels; D007930:Leucine; D008565:Membrane Proteins; D011487:Protein Conformation; D012694:Serine; D013816:Thermodynamics
D007473:Ion Channels; D008565:Membrane Proteins; D012694:Serine; D007930:Leucine; D000409:Alanine