Hydropathic plots

Hydropathic plotsWhat is a protein hydropathicity plot?

It is a method to display the hydrophobic and hydrophilic regions of a protein sequence and predict the structure based on these regions.Hydrophobic- water fearingNonpolar regions and unable to interact with waterLocated on the inside of the membraneUsually membrane-spanning proteins: channels or poresMust have a stretch of 18-20 amino acids to cross the membrane

Hydrophilic- water lovingPolar regions and able to interact with waterLocated on the outside of the membraneUsually peripheral proteins: antigens or receptorsIt gives you information about the structure of the protein based on its hydrophobicity and hydrophilicity.

Hydropathy plots allow for the visualization of hydrophobicity over the length of a peptide sequence. A hydropathy scale which is based on the hydrophobic and hydrophilic properties of the 20 amino acids is used. A moving "window" determines the summed hydropathy at each point in the sequence (Y coordinate). These sums are then plotted against their respective positions (X coordinate). Such plots are useful in determining the hydrophobic interior portions of globular proteins as well as determining membrane spanning regions of membrane bound proteins.

How it works

To make a hydropathicity plot, a protein sequence and window size are chosen. A protein sequence can be obtained from a database. A window size refers to the number of amino acids scored at once.If three are examined at once, the first number plotted will be an average of those three. The window moves down one amino acid each time, and each set receives a score that is plotted.After the whole sequence has been plotted, you can determine the hydrophobic or hydrophilic regions by examining the plot. For example, if you are using the Kyte-Doolittle method that shows hydrophobicity, the peaks of the plot are hydrophobic regions.At each position, the average hydrophobic or hydrophilic (depending on method used) index of the amino acids within the window is calculated.Each amino acid has a score depending on the method you are using.Each amino acid has an R group that determines whether the protein is hydrophobic or hydrophilic.These scales for the amino acids have been developed experimentally.

This value is plotted on a graph.X-axis is the window size.Y-axis is the hydrophobicity or hydrophilicity

Methods:Kyte-DoolittleHydrophobicity plotWindow size= 19-21>0 means hydrophobic regionHopp-WoodsHydrophilicity plotWindow size= 5-7>0 means hydrophilic regionThe structure of proteins define their function. Using hydropathicity plots, we can make predictions about the structure, which will enable us to make predictions about functions of proteins.