Hydrophobicity of Amino Acids and Types

The hydrophobicity of an amino acid refers to its tendency to avoid water molecules and instead prefer to mix with other hydrophobic molecules. 

This property plays an important role in protein structure and function, as it affects how amino acids are arranged in the protein's three-dimensional structure and how the protein interacts with its environment.

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Types of Hydrophobicity Amino Acids

There are 20 different types of amino acids that make up proteins, and they differ in their hydrophobicity. In general, amino acids with non-polar side chains are more hydrophobic than amino acids with polar or charged side chains. 

The following is a list of amino acids in order from most hydrophobic to least hydrophobic:

1. Tryptophan (Trp)
2. Phenylalanine (Phe)
3. Leucine (Leu)
4. Isoleucine (Ile)
5. Methionine (Met)
6. Valine (Val)
7. Proline (Pro)
8. Alanine (Ala)
9. Glycine (Gly)
10. Cysteine (Cys)
11. Serine (Ser)
12. Threonine (Thr)
13. Tyrosine (Tyr)
14. Asparagine (Asn)
15. Glutamine (Gln)
16. Histidine (His)
17. Lysine (Lys)
18. Arginine (Arg)
19. Aspartic acid (Asp)
20. Glutamic acid (Glu)

This is a general ranking, and the hydrophobicity of amino acids can vary depending on the specific environment and context in which they are found.

Hydrophilic amino acids are usually located on the surface of proteins, where they can interact with water molecules and other polar molecules. This allows them to form hydrogen bonds and other interactions that help stabilize the protein's structure and facilitate its interactions with other molecules.

Applications of Hydrophilic Amino Acids

The hydrophobicity of amino acids has applications in fields such as biochemistry, biophysics, and molecular biology. For example, researchers use hydrophobic interactions to purify proteins from complex mixtures by selectively binding them to hydrophobic surfaces. Hydrophobicity is also used to predict the location of amino acids in proteins and to design new proteins with specific properties.

Hydrophobicity scales

Hydrophobicity scales are used to quantify the relative hydrophobicity or hydrophilicity of different molecules or parts of molecules, such as amino acids or protein domains. These are based on experimental measurements or computational models of the propensity of a molecule or group to interact with water.

One of the earliest and most widely used hydrophobicity scales is the Kite–Doolittle scale, created in the 1980s based on the observation that amino acids with nonpolar side chains in the interior of proteins are located away from the surrounding aquatic environment. 

The Kyte–Doolittle scale assigns each amino acid a numerical value based on its relative hydrophobicity or hydrophilicity, with more positive values indicating greater hydrophobicity.

Hydrophilicity plot

A hydrophilicity plot is a graphical representation of the relative hydrophilicity or hydrophobicity of a protein or protein region. It is often used to identify potential transmembrane domains or other hydrophobic regions in a protein sequence.

The plot is usually made by computing the average hydrophobicity or hydrophilicity of a sliding window of amino acids along the protein sequence and plotting the resulting values in a curve. Hydrophilic regions of the protein appear as peaks in the plot, while hydrophobic regions appear as valleys.

>Amino Acids- Definition, Properties, Structure, Classification, Functions