Chapter 23, Problem 22EQ

Summary Introduction

To analyze:

Transmembrane domains that span the membrane in a $\text{α-helical}$ form are frequently needed for membrane proteins. Length of these transmembrane domains is around twenty amino acids and usually has amino acids with hydrophobic amino acid side chains. Investigators can project whether a polypeptide sequence has transmembrane domains based on the presence of domains that have $\text{20}$ hydrophobic amino acids. To do so, on the basis of chemistry of transmembrane domains amino acid side chain, each amino acid is given a hydropathy value. Amino acids with precise hydrophobic side chains are given a high ($\text{+ve}$) value, in other hand amino acids that are charged and/or polar are given low ($\text{-ve}$) values. Generally, the range of hydropathy values is around $\text{+4 to -4}$

To scan the amino acid arrangement of a polypeptide and compute values based on the hydropathy values of the amino acid side chains, computer programs have been developed. The program generally scans a frame of seven amino acids and gives an average hydropathy value. For instance, the program would scan amino acids $\text{1–7}$ and give an average value; then it would scan $\text{2–8}$ and give a value, then it would scan $\text{3–9}$ and give value, and so on, till it touched the end (Carboxyl terminus) of the polypeptide sequence.

A figure termed as a hydropathy plot is produced by the computer program, which defines the average hydropathy values in the complete polypeptide arrangement.

An example of a hydropathy plot is as follows,

On the basis of above information following questions is asked.

Question asked to estimate the numbers of possible transmembrane segments in this polypeptide.

Considering that the amino terminus is found in the cytoplasm of the cell. Question asked to draw the structure of this polypeptide if it is inserted in the plasma membrane.

Introduction:

Membrane proteins are secretory proteins that are synthesized on the membrane of endoplasmic reticulum. At the time of synthesis N-terminus of polypeptide is present on exoplasmic side of ER membrane. That’s why after transporting to plasma membrane N-terminus of membrane spanning polypeptide is oriented to the cytoplasmic side of cell. The size of the hydrophobic patch of plasma membrane is ${\text{30A}}^{\text{0}}$, the distance between two amino acids in polypeptide is $\text{1}{\text{.5A}}^{\text{0}}$ $\left(\text{1}{\text{.5A}}^{\text{0}}\text{ × 20 a}{\text{.a = 30A}}^{\text{0}}\right)$ and to span plasma membrane polypeptideshould possess at least twenty hydrophobic (Non-polar) amino acids sequentially.