Chapter 1-1. Hydrophobic Index of Biomacromolecules
Recommended Reading: 【Biology】 Chapter 1. Composition of Living Organisms
1. Type 1. Integral Membrane Protein and Hydropathy Plot
2. Type 2. Hydrophilic-Lipophilic Balance
1. Type 1. Integral Membrane Protein and Hydropathy Plot
⑴ Overview
① Integral membrane protein: A membrane protein that penetrates into the hydrophobic core of the cell membrane.
② Hydropathy plot: Also called hydrophobic coordinates.
③ Transmembrane region: Generally, the transmembrane region consists of about 20 hydrophobic amino acids.
⑵ Hydrophobicity Coefficient (HI) of Amino Acids: The larger the value, the higher the hydrophobicity of the amino acid.
Table 1. Abbreviations for Amino Acids
○ A: 1.8
○ C: 2.5
○ D: -3.5
○ E: -3.5
○ F: 2.8
○ G: -0.4
○ H: -3.2
○ I: 4.5
○ K: -3.9
○ L: 3.8
○ M: 1.9
○ N: -3.5
○ P: -1.6
○ Q: -3.5
○ R: -4.5
○ S: -0.8
○ T: -0.7
○ V: 4.2
○ W: -0.9
○ Y: -1.3
⑶ Analysis Method
① Step 1. Set 19 amino acids corresponding to the size of a transmembrane segment to the window size.
② Step 2. Define the 19 amino acids at the N-terminal of X as Segment 1 and calculate the average HI.
③ Step 3. Move Segment 1 toward the C-terminal by one amino acid to define Segment 2 and calculate the average HI.
④ Step 4. Repeat Step 3 until reaching the C-terminal of X.
⑤ Step 5. Plot the average HI of each segment on a graph.
⑥ Step 6. Infer the transmembrane region as the segment with a high hydrophobic region (i.e., high average HI value).
2. Type 2. Hydrophilic-Lipophilic Balance (HLB)
⑴ Griffin’s Calculation Method
① Mh: Mass of the hydrophilic portion within the molecule
② M: Total mass of the molecule
③ Produces a value between 0 and 20.
④ HLB values for different types of surfactants
Figure 1. HLB Values for Different Types of Surfactants
⑵ Davies’ Calculation Method
① m: Number of hydrophilic groups in the molecule
② Hi: H coefficient of the i-th hydrophilic group
③ n: Number of lipophilic groups in the molecule
Input: 2019.03.12 14:42