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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 .
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 ]
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.
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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]
Cation–π interactions can tune the pKa of nitrogenous side-chains, increasing the abundance of the protonated form; this has implications for protein structure and function. [15] While less studied in this context, the DNA bases are also able to participate in cation–π interactions. [16] [17]
Calculating contacts is an important task in structural bioinformatics, being important for the correct prediction of protein structure and folding, thermodynamic stability, protein-protein and protein-ligand interactions, docking and molecular dynamics analyses, and so on.