Ace The Race BioSmart Publications
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Suman Patra
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How can I calculate the no. of residues in a transmembrane alpha -helix considering the thickness of membrane?
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Several simple methods of analyzing amino acid sequences have been found to yield reasonably accurate predictions of secondary structure for transmembrane proteins. The relative polarity of each of the 20 amino acids has been determined experimentally by measuring the free-energy change of moving a given residue from a hydrophobic solvent into water. This f’ree energy of transfer ranges from very exergonic for charged or polar residues to very endergonic for amino acids with aromatic or aliphatic hydrocarbon side chains. To estimate the overall hydrophobicity of a sequence of amino acids, one sums the free energies of transfer for those residues, obtaining a hydropathy index for that region. To search a sequence for potential membrane-spanning segments, one calculates the hydropathy index for successive segments of a given size (a “window,” which may be from 7 to 20 residues). For a window of 7 residues, the indexes for residues 1 to 7, 2 to 8, 3 to 9, and so on, are plotted as in Figure l. A region of about 20 residues of high hydropathy index is presumed to be a transmembrane segment. When the sequences of membrane proteins of known three-dimensional structure are scanned in this way, a reasonably good correspondence is found between predicted and known membrane-spanning segments. Hydropathy analysis predicts a single hydrophobic helix for glycophorin (Fig. a, five for the M subunit of the photosynthetic reaction center protein (Fig. b), seven transmembrane segments for bacteriorhodopsin (Fig. c), and twelve segments for the chloride-bicarbonate exchanger (Fig. d).