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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 p K 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 .
N.D.: The pKa value of Pyrrolysine has not been reported. 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.
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.
FEP calculations have been used for studying host–guest binding energetics, pKa predictions, solvent effects on reactions, and enzymatic reactions. Other applications are the virtual screening of ligands in drug discovery , in silico mutagenesis studies [ 2 ] [ 3 ] and antibody affinity maturation. [ 4 ]
These calculations find application in many different areas of chemistry, biology, medicine, and geology. For example, many compounds used for medication are weak acids or bases, and a knowledge of the p K a values, together with the octanol-water partition coefficient , can be used for estimating the extent to which the compound enters the ...
TNP-ATP is a fluorescent molecule that is able to determine whether a protein binds to ATP, and the constants associated with that binding.It is primarily used in fluorescence spectroscopy, but is also very useful as an acceptor molecule in FRET, and as a fluorescent probe in fluorescence microscopy and X-ray crystallography.
Taylor's research group has focused on the structure and function of protein kinases, particularly protein kinase A, since shortly after she began her independent research career. [1] Her group, collaborating with Janusz Sowadski, was the first to solve the crystal structure of a protein kinase when they reported the structure of PKA in 1991. [7]
Protein chemical shift prediction is a branch of biomolecular nuclear magnetic resonance spectroscopy that aims to accurately calculate protein chemical shifts from protein coordinates. Protein chemical shift prediction was first attempted in the late 1960s using semi-empirical methods applied to protein structures solved by X-ray ...