Amino acids titration

The intrinsic pKa thus represents the pK of the group in the protein with all other titratable amino acids in their neutral state. Finally, the interaction energy, between the sites i and j, is... 

Sampling of the biomolecular conformations is usually performed using MD simulations or Monte Carlo methods (61, 62). The protonation state of titrateable amino acids can be treated with constant pH dynamics, QM/MM calculations, or continuum electrostatics methods (61, 62). Formation of a protein-protein encounter complex is often studied using Brownian dynamics (63). Studies of protein-protein docking involve electrostatic potential analysis and, more recently, protein flexibility models, for example normal mode analysis (64). 

The intrinsic pK thus represents the of a group in the protein when all other titratable amino acids are in their neutral state. Sometimes, it is useful to have all sites deprotonated as the reference state for the system in this case the free energy of the molecule with the protonation state (ar j,. . . , of the whole molecule is... 

It can be seen from Table 2 that the intrinsic values of the pK s are close to the model compound value that we use for Cys(8.3), and that interactions with surrounding titratable residues are responsible for the final apparent values of the ionization constants. It can also be seen that the best agreement with the experimental value is obtained for the YPT structure suplemented with the 27 N-terminal amino acids, although both the original YPT structure and the one with the crystal water molecule give values close to the experimentally determined one. Minimization, however, makes the agreement worse, probably because it w s done without the presence of any solvent molecules, which are important for the residues on the surface of the protein. For the YTS structure, which refers to the protein crystallized with an SO4 ion, the results with and without the ion included in the calculations, arc far from the experimental value. This may indicate that con-... 

Method. An amino-acid such as glycine, NHjCH,COOH, cannot be estimated by direct titration with standard alkali solution, owing to the opposing effects of the basic and the acidic groups. If, however, the amino-acid is first... 

Many pharmaceutical compounds are weak acids or bases that can be analyzed by an aqueous or nonaqueous acid-base titration examples include salicylic acid, phenobarbital, caffeine, and sulfanilamide. Amino acids and proteins can be analyzed in glacial acetic acid, using HCIO4 as the titrant. For example, a procedure for determining the amount of nutritionally available protein has been developed that is based on an acid-base titration of lysine residues. ... 

The potentiometric titration curve shown here was recorded on a 0.4300-g sample of a purified amino acid that was dissolved in 50.00 ml of water and titrated with 0.1036 M NaOH. Identify the amino acid from the possibilities listed in the following table. 

If a sample contains groups that can take up or lose a proton, (N//, COO//), then one must expect the pH and the concentration to affect the chemical shift when the experiment is carried out in an acidic or alkaline medium to facilitate dissolution. The pH may affect the chemical shift of more distant, nonpolar groups, as shown by the amino acid alanine (38) in neutral (betaine form 38a) or alkaline solution (anion 38b). The dependence of shift on pH follows the path of titration curves it is possible to read off the pK value of the equilibrium from the point of inflection... 

FIGURE 4.6 The ionic forms of the amino acids, shown without consideration of any ionizations on the side chain. The cationic form is the low pH form, and the titration of the cationic species with base yields the zwitterion and finally the anionic form. (Irving Geis)... 

Typical values for pAlg are in the range of 9.0 to 9.8. At physiological pH, the a-carboxyl group of a simple amino acid (with no ionizable side chains) is completely dissociated, whereas the a-amino group has not really begun its dissociation. The titration curve for such an amino acid is shown in Figure 4.7. 

Look carefully at the titration curve in Figure 26.1. In acid solution, the amino acid is protonated and exists primarily as a cation. In basic solution, the amino acid is deprotonated and exists primarily as an anion. In between the two is an intermediate pH at which the amino acid is exactly balanced between anionic and cationic forms and exists primarily as the neutral,... 

Overproduction of the chromosomal genes for the dihydrofolate reductase (DHFR) and the dihydroptero-ate synthase (DHPS) leads to a decreased susceptibility to trimethoprim and sulfamethoxazol, respectively. This is thought to be the effect of titrating out the antibiotics. However, clinically significant resistance is always associated with amino acid changes within the target enzymes leading to a decreased affinity of the antibiotics. 

Example 36 Four batches. A, B, C, and D, of an amino acid hydrochloride were investigated four different titration techniques were applied to every sample ... 

Figure 2.21. Results of 96 titrations of an amino acid. (See Table 2.17.)...

C18-0103. When a solution of leucine (an amino acid) in water is titrated with strong base, the pH before titration is 1.85, the pH at the midpoint of the titration is 2.36, and the pH at the stoichiometric point is 6.00. Determine the value of K. for leucine. 

C18-0142. The amine group of an amino acid readily accepts a proton, and the protonated form of an amino acid can be viewed as a diprotic acid. The p Zg values for serine (H2 NCHRCO2 H, i = CH2 OH) are p ra(H3 N"") =9.1 and p (002 H) - 2.2. (a) What is the chemical formula of the species that forms when serine dissolves in pure water (b) If this species is titrated with strong acid, what reaction occurs (c) 10.00 mL of 1.00 M HCl is added to 200. mL of 0.0500 M serine solution. This mixture is then titrated with 0.500 M NaOH. Draw the titration curve, indicating the pH at various stages of this titration. 

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