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A hydrophilicity plot is a quantitative analysis of the degree of hydrophobicity or hydrophilicity of amino acids 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.
A number of different hydrophobicity scales have been developed. [3] [1] [7] [8] [9] The Expasy Protscale website lists a total of 22 hydrophobicity scales. [10] There are clear differences between the four scales shown in the table. [11] Both the second and fourth scales place cysteine as the most hydrophobic residue, unlike the other two ...
This suggests that early ribosomes read the second codon position most carefully, to control hydrophobicity patterns in protein sequences. The first table—the standard table—can be used to translate nucleotide triplets into the corresponding amino acid or appropriate signal if it is a start or stop codon. The second table, appropriately ...
The free energy associated with minimizing interfacial areas is responsible for minimizing the surface area of water droplets and air bubbles in water. This same principle is the reason that hydrophobic amino acid side chains are oriented away from water, minimizing their interaction with water.
An alpha-helix with hydrogen bonds (yellow dots) The α-helix is the most abundant type of secondary structure in proteins. The α-helix has 3.6 amino acids per turn with an H-bond formed between every fourth residue; the average length is 10 amino acids (3 turns) or 10 Å but varies from 5 to 40 (1.5 to 11 turns).
Cystine is the oxidized derivative of the amino acid cysteine and has the formula (SCH 2 CH(NH 2)CO 2 H) 2.It is a white solid that is poorly soluble in water. As a residue in proteins, cystine serves two functions: a site of redox reactions and a mechanical linkage that allows proteins to retain their three-dimensional structure.
Met is essential for humans. Always the first amino acid to be incorporated into a protein, it is sometimes removed after translation. Like cysteine, it contains sulfur, but with a methyl group instead of hydrogen. This methyl group can be activated, and is used in many reactions where a new carbon atom is being added to another molecule.
Hence the hydrophobicity of a compound (as measured by its distribution coefficient) is a major determinant of how drug-like it is. More specifically, for a drug to be orally absorbed, it normally must first pass through lipid bilayers in the intestinal epithelium (a process known as transcellular transport).