Dear Modellers.
I am trying to model MHC class I molecules and have come across a problem which appears to be related to the alignment. MHC molecules consist of three individual peptide chains and I have therefore specified my input sequence in the alignment file with the chain break character / (see alignment file below). When modelled, this gives rise to a model with a serious flaw: It appears that the chain break character is interpreted by MODELLER as a kind of "dummy residue". The result is that the first chain is modelled nicely, but the second and third chains are shifted by one and two residues, respectively. This is a BIG problem, especially as I am interested in the exact interactions of the third chain (a small oligopeptide) with the rest of the molecule. I have come up with a temporary "solution" (hopefully) where I simply delete the last residue of the first and second chain in order to make room for the "dummy residue". This produces nice models (which are lacking two residues), but I would like to be able to model the entire molecule.
This is my alignment file which is modelled by the model.top routine:
>P1;1hhi structureX:1hhi: 1:A : 9:C : MHC I: HLA-A0201: * >P1;1A11 sequence:1A11: 1:A : @:@ : MHC I: HLA-A1101: GSHSMRYFYTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAP WIEQEGPEYWDQETRNVKAQSQTDRVDLGTLRGYYNQSEDGSHTIQIMYG CDVGPDGRFLRGYRQDAYDGKDYIALNEDLRSWTAADMAAQITKRKWEAA HAAEQQRAYLEGRCVEWLRRYLENGKETLQRTDPPKTHMTHHPISDHEAT LRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDGTFQKWAAVVVP SGEEQRYTCHVQHEGLPKPLTLRWE/ MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKV EHSDLSFSKDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM /GILGFVFTK
*
I've probably forgotten something essential, but I don't see what it is. I would be happy for any comments and suggestions.
Many thanks.
Thomas
--------------------------------------------------------------------------- Thomas Blicher, Department of Chemistry, Universitetsparken 5, Copenhagen University, 2100 Copenhagen Denmark. phone: 45-35320280, fax: 45-35320299 E-mail: thomas@kage.ki.ku.dk