Assessment of Two Theoretical Methods to Estimate Potentiometric Titration Curves of Peptides:  Comparison with Experiment

Abstract

We compared the ability of two theoretical methods of pH-dependent conformational calculations to reproduce experimental potentiometric-titration curves of two models of peptides: Ac-K 5 -NHMe in 95% methanol (MeOH)/5% water mixture and Ac-XX(A) 7 OO-NH 2 (XAO) (where X is diaminobutyric acid, A is alanine, and O is ornithine) in water, methanol (MeOH) and dimethylsulfoxide (DMSO), respectively. The titration curve of the former was taken from the literature, and the curve of the latter was determined in this work. The first theoretical method involves a conformational search using the Electrostatically Driven Monte Carlo (EDMC) method with a low-cost energy function (ECEPP/3 plus the SRFOPT surface-solvation model, assumming that all titratable groups are uncharged) and subsequent reevaluation of the free energy at a given pH with the Poisson-Boltzmann equation, considering variable protonation states. In the second procedure, MD simulations are run with the AMBER force field and the Generalized-Born model of electrostatic solvation, and the protonation states are sampled during constant-pH MD runs. In all three solvents, the first pK a of XAO is strongly downshifted compared to the value for the reference compounds (ethyl amine and propyl amine, respectively); the water and methanol curves have one, and the DMSO curve has two jumps characteristic of remarkable differences in the dissociation constants of acidic groups. The predicted titration curves of Ac-K 5 -NHMe are in good agreement with the experimental ones; better agreement is achieved with the MD-based method. The titration curves of XAO in methanol and DMSO, calculated using the MD-based approach, trace the shape of the experimental curves, reproducing the pH jump, while those calculated with the EDMC-based approach, and the titration curve in water calculated using the MD-based approach, have smooth shapes characteristic of the titration of weak multifunctional acids with small differences between the dissociation constants. Nevertheless, quantitative agreement between theoretically predicted and experimental titration curves is not achieved in all three solvents even with the MD-based approach which is manifested by a smaller pH range of the calculated titration curves with respect to the experimental curves. The poorer agreement obtained for water than for the non-aqueous solvents suggests a significant role of specific solvation in water, which cannot be accounted for by the meanfield solvation models.

Like‐charged residues at the ends of oligoalanine sequences might induce a chain reversal

“…This result was in agreement with an earlier small‐angle X‐ray diffraction study (SAXS) of Pande and coworkers,27 which indicated a small radius of gyration, R g = 7.4 Å, in agreement with that calculated based on our conformational studies 25, 26. Further support was gained from our potentiometric study of this peptide, in which the value of p K a1 = 2.3 is extraordinarily low, which demonstrates that all four charged groups are very close toeach other, which is possible only if there is a chain reversal 28…”

“…In our earlier work,25, 26, 28, 29 we noticed that all‐α‐helical conformations are often formed if anti‐ROE restraints are not imposed, even though there are no ROE signals characteristic of α‐helical contacts. Including anti‐ROE restraints along with ROE restraints, therefore, is necessary.…”

Thermodynamics of the Protonation Equilibria of Two Fragments of N-Terminal β-Hairpin of FPB28 WW Domain

“…For D9, pK a1 can be assigned to Asp15, pK a2 and pK a3 can correspond to either of the two lysine residues, and pK a4 and pK a5 can be assigned to either of the two tyrosine residues. On the basis of our earlier simulation studies of the coupling between the conformation and acidÀbase equilibria, 35 it can be noted that each of pK a2 and pK a3 (for D7 and D9), as well as pK a4 and pK a5 (for D9), as a value averaged over conformations, has contributions from either lysine (pK a2 and pK a3 ) or tyrosine (pK a4 and pK a5 ) residue. It can be seen that, for both peptides at room temperature (t = 25°C), pK a1 is lower than that of acetic acid (4.76 47 ) and pK a2 and pK a3 are significantly lower than those of n-butylamine (10.5 27 ), which can be considered a reference compound for the side chain of lysine.…”

Hair Whorls in the Dog (Canis familiaris), Part II: Asymmetries

“…It should be noted that the most populated conformations of XAO4, 5 have a bent shape, although both ends of this peptide are positively charged as for KAK; the bent shape is supported by the presence of long‐range ROE connectivities 4. As for OAD, the bent shape of XAO is confirmed by an unusually low value of p K a1 ,3 which is only 2.72 in water, compared to 8.9 for KAK and to p K a ref = 10.87 for ethylamine, which models the isolated side chain of ornithine 3. From the data of ref.…”

“…Recently,3–5 we studied the conformation of Ac‐XX‐A 7 ‐OO‐NHMe, XAO (where A, O, and X denote alanine, ornithine, and diaminobutyric acid residues, respectively) by NMR and Circular dichroism (CD) spectroscopy and theoretical calculations. Earlier, Kallenbach and coworkers6, 7 provided some experimental evidence for the presence of a polyproline II (P II ) stretch in this peptide, and also in other alanine‐based peptides8, 9; this conclusion was extended further by these researchers by stating that the P II conformation is characteristic of the unfolded state of proteins.…”