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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 p K a value, and knowledge of the pKa ...
Peptide bond formation via dehydration reaction. When two amino acids form a dipeptide through a peptide bond, [1] it is a type of condensation reaction. [2] In this kind of condensation, two amino acids approach each other, with the non-side chain (C1) carboxylic acid moiety of one coming near the non-side chain (N2) amino moiety of the other.
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.
Other recent approaches are based on a support vector machine algorithm [10] and pKa optimization against experimentally known protein/peptide isoelectric points. [11] Moreover, experimentally measured isoelectric point of proteins were aggregated into the databases.
Pauling's second rule is that the value of the first pK a for acids of the formula XO m (OH) n depends primarily on the number of oxo groups m, and is approximately independent of the number of hydroxy groups n, and also of the central atom X. Approximate values of pK a are 8 for m = 0, 2 for m = 1, −3 for m = 2 and < −10 for m = 3. [28]
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.
GLP-1s (glucagon-like peptide-1 receptor agonists) are medications used to treat type 2 diabetes and obesity. You’ve probably heard of them under brand names like Ozempi c® and Wegovy ...
2,5-Diketopiperazine is an organic compound with the formula (NHCH 2 C(O)) 2. The compound features a six-membered ring containing two amide groups at opposite positions in the ring. It was first compound containing a peptide bond to be characterized by X-ray crystallography in 1938. [ 1 ]