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In computational biology, protein pK a calculations are used to estimate the pK a values of amino acids as they exist within proteins.These calculations complement the pK a values reported for amino acids in their free state, and are used frequently within the fields of molecular modeling, structural bioinformatics, and computational biology.
Also, amino acid side chain affinity for water was measured using vapor phases. [14] Vapor phases represent the simplest non polar phases, because it has no interaction with the solute. [ 18 ] The hydration potential and its correlation to the appearance of amino acids on the surface of proteins was studied by Wolfenden.
Example Bjerrum plot: Change in carbonate system of seawater from ocean acidification.. A Bjerrum plot (named after Niels Bjerrum), sometimes also known as a Sillén diagram (after Lars Gunnar Sillén), or a Hägg diagram (after Gunnar Hägg) [1] is a graph of the concentrations of the different species of a polyprotic acid in a solution, as a function of pH, [2] when the solution is at ...
For instance, if a stretch of about 20 amino acids shows positive for hydrophobicity, these amino acids may be part of alpha-helix spanning across a lipid bilayer, which is composed of hydrophobic fatty acids. On the converse, amino acids with high hydrophilicity indicate that these residues are in contact with solvent, or water, and that they ...
The N-O distance required is less than 4 Å (400 pm). Amino acids greater than this distance apart do not qualify as forming a salt bridge. [11] Due to the numerous ionizable side chains of amino acids found throughout a protein, the pH at which a protein is placed is crucial to its stability.
In cell biology, protein kinase A (PKA) is a family of serine-threonine kinase [1] whose activity is dependent on cellular levels of cyclic AMP (cAMP). PKA is also known as cAMP-dependent protein kinase (EC 2.7.11.11). PKA has several functions in the cell, including regulation of glycogen, sugar, and lipid metabolism.
α-Aminoadipic acid is one of the metabolic precursor in the biosynthesis of lysine through α-aminoadipate pathway. Its conjugate base is α-aminoadipate, which is the prevalent form at physiological pH. α-Aminoadipic acid has a stereogenic center and can appear in two enantiomers, L-α-aminoadipate and D-α-aminoadipate.
A weak acid may be defined as an acid with pK a greater than about −2. An acid with pK a = −2 would be 99 % dissociated at pH 0, that is, in a 1 M HCl solution. Any acid with a pK a less than about −2 is said to be a strong acid. Strong acids are said to be fully dissociated.