Question

You are provided with the amino acid sequence of an important human protein that is suspected to be membrane protein. How can you analyze the amino acid sequence to try to find out more information on the transmembrane nature of this protein and the region of the protein that is likely to be in the membrane?

Answer 1

Based on the sequence analysis,  the identification of integral membrane protein (IMPs) can be solved by sequence or profile alignment techniques that detect relatives of known IMPs. Alternatively, we can search motif databases such as  PROSITE, PRINTS to identify functional motifs that are characteristic of IMPs and use these motifs to extend the database searches. Prediction of TM segments, kinks, functional residues and motifs can all help in elucidating the target structural and functional features of protein.

Generally protein which span in the membrane as transmembrane have hydropobic sequence i.e. is non polar amino acid and almost with no charge over them.This hydrophobicity can be analyse through hydropathy plot. the information is used to analyse the region of protein spanning in membrane. Hydropathy plots allow for the visualization of hydrophobicity over the length of a peptide sequence. A hydropathy scale which is based on the hydrophobic and hydrophilic properties of the 20 amino acids is used. A moving "window" determines the summed hydropathy at each point in the sequence (Y coordinate). These sums are then plotted against their respective positions (X coordinate). Such plots are useful in determining the hydrophobic interior portions of globular proteins as well as determining membrane spanning regions of membrane bound proteins. Another method is Discrete wavelet transform (DWT) has been developed to predict the number and location of transmembrane helix (TMHs ) in membrane proteins based on sequence.