Hydrophilicity plot
Encyclopedia
A hydrophilicity plot is a quantitative analysis
of the degree of hydrophobicity or hydrophilicity of amino acid
s of a protein
. It is used to characterize or identify possible structure or domains of a protein.
The plot has amino acid sequence of a protein on its x-axis, and degree of hydrophobicity and hydrophilicity on its y-axis. There are a number of methods to measure the degree of interaction of polar solvents such as water with specific amino acids. For instance, the Kyte-Doolittle scale indicates hydrophobic amino acids, while the Hopp-Woods scale
measures hydrophilic residues.
Analyzing the shape of the plot gives information about partial structure of the protein. For instance, if a stretch of about 20 amino acids shows positive for hydrophobicity, then this indicates that these amino acids may be part of alpha-helix spanning across a lipid bilayer
, which is composed of hydrophobic fatty acids. Conversely, amino acids with high hydrophilicity indicate that these residues are in contact with solvent, or water, and that they are therefore likely to reside on the outer surface of the protein.
Quantitative analysis (chemistry)
In chemistry, quantitative analysis is the determination of the absolute or relative abundance of one, several or all particular substance present in a sample....
of the degree of hydrophobicity or hydrophilicity of amino acid
Amino acid
Amino acids are molecules containing an amine group, a carboxylic acid group and a side-chain that varies between different amino acids. The key elements of an amino acid are carbon, hydrogen, oxygen, and nitrogen...
s of a protein
Protein
Proteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form, facilitating a biological function. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of...
. It is used to characterize or identify possible structure or domains of a protein.
The plot has amino acid sequence of a protein on its x-axis, and degree of hydrophobicity and hydrophilicity on its y-axis. There are a number of methods to measure the degree of interaction of polar solvents such as water with specific amino acids. For instance, the Kyte-Doolittle scale indicates hydrophobic amino acids, while the Hopp-Woods scale
Hopp-Woods scale
The Hopp–Woods hydrophilicity scale of amino acids is a method of ranking the amino acids in a protein according to their water solubility in order to search for surface locations on proteins, and especially those locations that tend to form strong interactions with other macromolecules such as...
measures hydrophilic residues.
Analyzing the shape of the plot gives information about partial structure of the protein. For instance, if a stretch of about 20 amino acids shows positive for hydrophobicity, then this indicates that these amino acids may be part of alpha-helix spanning across a lipid bilayer
Lipid bilayer
The lipid bilayer is a thin membrane made of two layers of lipid molecules. These membranes are flat sheets that form a continuous barrier around cells. The cell membrane of almost all living organisms and many viruses are made of a lipid bilayer, as are the membranes surrounding the cell nucleus...
, which is composed of hydrophobic fatty acids. Conversely, amino acids with high hydrophilicity indicate that these residues are in contact with solvent, or water, and that they are therefore likely to reside on the outer surface of the protein.