I am working on a bioinformatics project with HMMs and want to write some initiation probabilities for the location of amino acid residues. I know for different transmembrane proteins there will be different cases, but, in general, which regions of the protein would correspond to more AA residues: intracellular or extracellular? Or is there no general pattern?
Yes ,there are some patterns. First you have to determine which group of membrane proteins you're talking about. According to Molecular Cell Biology Lodish et al 8th ed chapter 13, there are 6 types of ER membrane proteins ( and therefore in the cell membrane)
The 6 types are type 1,type 2 ,type 3 , type 4,Tail anchored proteins ,GPI anchored proteins. Nearly all AA residues in type 3 or the tail-anchored type are located in the cytosolic side of the membrane ( their difference is in their N/C terminus orientation) whereas GPI anchored type has almost its entire AA residues in the exoplasmic side.
For other types there may not be a general pattern.
See E. Hartmann et al., 1989, P. Natl. Acad. Sci. USA 86:5786, and C. A. Brown and S. D. Black, 1989, J. Biol. Chem. 264:4442.
By the way , you can also think of it in another way. Antigens , Hormone Receptors , Structral proteins in exoplasmic leaflet of membrane usually have more AA in the exoplasmic side.