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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.
In particular, the pH of a solution can be predicted when the analytical concentration and pK a values of all acids and bases are known; conversely, it is possible to calculate the equilibrium concentration of the acids and bases in solution when the pH is known. These calculations find application in many different areas of chemistry, biology ...
Note: The pKa value of an amino-acid residue in a small peptide is typically slightly different when it is inside a protein. Protein pKa calculations are sometimes used to calculate the change in the pKa value of an amino-acid residue in this situation.
The isoionic point is the pH value at which a zwitterion molecule has an equal number of positive and negative charges and no adherent ionic species. It was first defined by S.P.L. Sørensen, Kaj Ulrik Linderstrøm-Lang and Ellen Lund in 1926 [1] and is mainly a term used in protein sciences.
Serine (symbol Ser or S) [3] [4] is an α-amino acid that is used in the biosynthesis of proteins. It contains an α-amino group (which is in the protonated − NH +3 form under biological conditions), a carboxyl group (which is in the deprotonated − COO −
For an amino acid with only one amine and one carboxyl group, the pI can be calculated from the mean of the pKas of this molecule. [4]= + The pH of an electrophoretic gel is determined by the buffer used for that gel.
A simple buffer solution consists of a solution of an acid and a salt of the conjugate base of the acid. For example, the acid may be acetic acid and the salt may be sodium acetate . The Henderson–Hasselbalch equation relates the pH of a solution containing a mixture of the two components to the acid dissociation constant , K a of the acid ...
Strong acids, such as sulfuric or phosphoric acid, have large dissociation constants; weak acids, such as acetic acid, have small dissociation constants. The symbol K a , used for the acid dissociation constant, can lead to confusion with the association constant , and it may be necessary to see the reaction or the equilibrium expression to ...