Hydropathy plot, a plot that is used for the determination of the hydrophilicity and hydrophobicity of protein’s amino acid.
It is employed to describe or pinpoint a protein’s potential structure or domains. The plot’s y-axis represents the degree of hydrophilicity and hydrophobicity, while the x-axis represents a protein’s amino acid sequence.
Membrane proteins like rhodopsin with alpha-helical regions of 20-25 amino acids span the lipid bilayer, around 30 A thick. Many amino acids under this region are non-polar and uncharged, making them easier to interact with hydrophobic membranes. So by analyzing this amino acid sequence, we can create a hydropathy plot to identify the position and number of transmembrane domains. This plot is also known as the hydrophobicity plot.
The hydrophobic segment has a positive hydropathy index indicating that energy is necessary to transfer to water. The number of the hydrophobic segment indicates the number of transmembrane domains.
The negative value of the hydropathy plot indicates the hydrophilic portion.
Importance of Hydropathy Plot
- By examining the hydrophilic and hydrophobic regions we Can identify the protein structure and orientations.
- This plot helps to identify the hydrophobic regions that are likely to span the lipid bilayer.
- This is helpful in protein engineering to produce a protein with specific functions associated with the membrane.
- This helps to study protein families and evolutionary relationships by comparing different proteins.
References
- https://www.cliffsnotes.com/study-notes/599249
- https://www.biophysics.org/Portals/0/BPSAssets/Education/Documents/Lecture%2018%20Neher.pdf
- https://www.wizeprep.com/online-courses/4694/chapter/2/core
