Lecture_5_Jan_13_four_slides_per_page_

Lecture_5_Jan_13_four_slides_per_page_ - Membrane Proteins...

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1 Reading Assignment For the 5 th Ed: 636-648 For the 4 th Ed: 598-612 Membrane Proteins different types of membrane proteins how to analyze different types of membrane proteins (methods used to predict or distinguish between integral and peripheral membrane roteins are all based on their differential interaction with membranes) how to study membrane proteins proteins are all based on their differential interaction with membranes) Hydropathy Plot: a method to predict the highly non-polar transmembrane domain of a protein 1. Each a.a. is first assigned a “hydrophobicity index” value (the more ydrophobic an a a is the more positive the value is; the more hydrophilic How to make a hydropathy plot of a protein? How to predict the type of membrane association? hydrophobic an a.a. is, the more positive the value is; the more hydrophilic an a.a. is, the more negative the value is) hydrophilic hydrophobic Hydrophobicity of Amino Acids (determined by the side chains) a.a. with negative hydrophobicity index a.a. with positive hydrophobicity index
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2 Hydropathy Plot: a method to predict the highly non-polar transmembrane domain 1. Each a.a. is first assigned a “hydrophobicity index” value (the more ydrophobic an a a is the more positive the value is; the more hydrophilic How to make a hydropathy plot of a protein? How to predict the type of membrane association? 2. Starting from a.a. 1, a “window” of 20 (i.e. from a.a. 1-20) contiguous residues is taken as a group, and the average “hydrophobicity index” is calculated for this 20 a.a. window hydrophobic an a.a. is, the more positive the value is; the more hydrophilic an a.a. is, the more negative the value is) Then move down one residue to calculate the 3. Then move down one residue to calculate the “hydrophobicity index” of next window (i.e. from a.a. 2-21)
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This note was uploaded on 02/01/2010 for the course MCDB 103 taught by Professor Staff during the Winter '08 term at UCSB.

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Lecture_5_Jan_13_four_slides_per_page_ - Membrane Proteins...

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