Search results
Results from the WOW.Com Content Network
FDPB-based methods calculate the change in the pK a value of an amino acid side chain when that side chain is moved from a hypothetical fully solvated state to its position in the protein. To perform such a calculation, one needs theoretical methods that can calculate the effect of the protein interior on a pK a value, and knowledge of the pKa ...
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 ...
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.
In chemistry, biochemistry, and pharmacology, a dissociation constant (K D) is a specific type of equilibrium constant that measures the propensity of a larger object to separate (dissociate) reversibly into smaller components, as when a complex falls apart into its component molecules, or when a salt splits up into its component ions.
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]
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]
The G s alpha subunit slowly catalyzes the hydrolysis of GTP to GDP, which in turn deactivates the G s protein, shutting off the cAMP pathway. The pathway may also be deactivated downstream by directly inhibiting adenylyl cyclase or dephosphorylating the proteins phosphorylated by PKA. Molecules that inhibit the cAMP pathway include:
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.