title: On the pH-conformational dependence of the unblocked SYPYD peptide.
abstract: Simulations were carried out for an unblocked pentapeptide with the sequence Ser-Tyr-Pro-Tyr-Asp (SYPYD) with explicit consideration of the coupling between the conformation of the molecule and the ionization equilibria at a given pH. The available NMR experimental data indicate a high preference for the cis isomeric turn-like form of Tyr-Pro at intermediate pH (approximately 6) and a destabilization of the cis form at both high (approximately 9) and low (approximately 3) pH. In order to identify the source of the stability of the conformation of this pentapeptide as a function of pH, Monte Carlo simulations were used to generate an ensemble of low-energy conformations at different pH values (viz. 3, 6 and 9). The total free energy function used in these calculations includes terms that account for the solvation free energy and free energy of ionization. These terms are evaluated by means of a fast multigrid boundary element (MBE) method. In good qualitative agreement with the experiments, our results indicate that the Boltzmann averaged population of the cis isomeric form of the pentapeptide has a maximum (45 %) at pH 6 and is significantly smaller (25 % and 23 %) for higher and lower pH values, respectively, following the trend of the experimental data. Also, the degree of charge for the lowest-energy conformations, as well as the contribution of electrostatic interactions to the stability of the preferred conformations, vary widely at the different pH values. Different kinds of packing of the aromatic side-chains of Tyr2 and Tyr4 against the proline ring are observed at different pH values, indicating that their contribution to the stability of the low-energy conformations is also pH-dependent. In summary, our results provide a basis for discussing the nature of the interactions that stabilize turn-like conformations of the peptide SYPYD as a function of pH.
authors.affiliation: Cornell Theory Center, Cornell University, Ithaca, NY 14853-3801, USA.
authors.forename: D R
authors.initials: DR
authors.lastname: Ripoll
authors.forename: J A
authors.initials: JA
authors.lastname: Vila
authors.forename: M E
authors.initials: ME
authors.lastname: Villegas
authors.forename: H A
authors.initials: HA
authors.lastname: Scheraga
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D006863:Hydrogen-Ion Concentration; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D009010:Monte Carlo Method; D009842:Oligopeptides / Q000737:chemistry*; D011487:Protein Conformation; D055672:Static Electricity; D013816:Thermodynamics
chemical_list: D009842:Oligopeptides; C121858:seryl-tyrosyl-prolyl-tyrosyl-aspartic acid