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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 ...
In chemistry and biochemistry, the Henderson–Hasselbalch equation = + ([] []) relates the pH of a chemical solution of a weak acid to the numerical value of the acid dissociation constant, K a, of acid and the ratio of the concentrations, [] [] of the acid and its conjugate base in an equilibrium.
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]
It will only calculate selective pressure within protein coding regions. In addition, selection that does not cause differences at an amino acid level—for instance, balancing selection—cannot be detected by these techniques. [1] Another issue is that heterogeneity within a gene can make a result hard to interpret.
Carbonic acid is a chemical compound with the chemical formula H 2 C O 3.The molecule rapidly converts to water and carbon dioxide in the presence of water. However, in the absence of water, it is quite stable at room temperature.
The concentration of the species LH is equal to the sum of the concentrations of the two micro-species with the same chemical formula, labelled L 1 H and L 2 H. The constant K 2 is for a reaction with these two micro-species as products, so that [LH] = [L 1 H] + [L 2 H] appears in the numerator, and it follows that this macro-constant is equal ...
The buffering region is dependent upon the pKa, and is typically +/- 1.0 pH units of the pKa. The pKa of KHP is 5.4, so its pH buffering range would be 4.4 to 6.4; however, due to the presence of the second acidic group that bears the potassium ion, the first pKa also contributes to the buffering range well below pH 4.0, which is why KHP is a ...
A speciation calculation is one in which concentrations of all the species in an equilibrium system are calculated, knowing the analytical concentrations, T A, T B etc. of the reactants A, B etc. This means solving a set of nonlinear equations of mass-balance