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prot pi – protein isoelectric point — an online program for calculating pI of proteins (include multiple subunits and posttranslational modifications) CurTiPot — a suite of spreadsheets for computing acid-base equilibria (charge versus pH plot of amphoteric molecules e.g., amino acids)
Structure of a typical L-alpha-amino acid in the "neutral" form. Amino acids are organic compounds that contain both amino and carboxylic acid functional groups. [1] Although over 500 amino acids exist in nature, by far the most important are the 22 α-amino acids incorporated into proteins. [2]
A pi helix (or π-helix) is a type of secondary structure found in proteins. Discovered by crystallographer Barbara Low in 1952 [ 1 ] and once thought to be rare, short π-helices are found in 15% of known protein structures and are believed to be an evolutionary adaptation derived by the insertion of a single amino acid into an α-helix . [ 2 ]
A table comparing four different scales for the hydrophobicity of an amino acid residue in a protein with the most hydrophobic amino acids on the top. 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]
The table below lists the abundance of amino acids in E.coli cells and the metabolic cost (ATP) for synthesis of the amino acids. Negative numbers indicate the metabolic processes are energy favorable and do not cost net ATP of the cell. [12] The abundance of amino acids includes amino acids in free form and in polymerization form (proteins).
Protein structure is the three-dimensional arrangement of atoms in an amino acid-chain molecule. Proteins are polymers – specifically polypeptides – formed from sequences of amino acids, which are the monomers of the polymer. A single amino acid monomer may also be called a residue, which indicates a
Aspartic acid (symbol Asp or D; [4] the ionic form is known as aspartate), is an α-amino acid that is used in the biosynthesis of proteins. [5] The L-isomer of aspartic acid is one of the 22 proteinogenic amino acids, i.e., the building blocks of proteins. D-aspartic acid is one of two D-amino acids commonly found in mammals.
Short pieces of left-handed helix sometimes occur with a large content of achiral glycine amino acids, but are unfavorable for the other normal, biological L-amino acids. The pitch of the alpha-helix (the vertical distance between consecutive turns of the helix) is 5.4 Å (0.54 nm), which is the product of 1.5 and 3.6.