title: A pH-dependent variation in alpha-helix structure of the S-peptide of ribonuclease A studied by Monte Carlo simulated annealing.
abstract: Low-energy conformations of the S-peptide fragment (20 amino acid residues long) of ribonuclease A were studied by Monte Carlo simulated annealing. The obtained lowest-energy structures have alpha-helices with different size and location, depending distinctively on the ionizing states of acidic amino acid residues. The simulation started from completely random initial conformation and was performed without any bias toward a particular structure. The most conspicuous alpha-helices arose from the simulation when both Glu 9 and Asp 14 were assumed to be electrically neutral, whereas the resulting conformations became much less helical when Asp 14 rather than Glu 9 was allowed to have a negative charge. Together with experimental evidence that the alpha-helix in the S-peptide is most stable at pH 3.8, we consider the helix formation need the carboxyl group of Asp 14 to be electrically neutral in this weakly acidic condition. In contrast, a negative charge at Asp 14 appears to function in support of a view that this residue is crucial to helix termination owing to its possibility to form a salt bridge with His 12. These results indicate that the conformation of the S-peptide depends considerably on the ionizing state of Asp 14.
authors.affiliation: Department of Chemistry, Nara Women's University, Nara 630-8506, Japan. t.nakazawa@cc.nara-wu.ac.jp
authors.forename: Takashi
authors.initials: T
authors.lastname: Nakazawa
authors.forename: Sumiko
authors.initials: S
authors.lastname: Ban
authors.forename: Yuka
authors.initials: Y
authors.lastname: Okuda
authors.forename: Masato
authors.initials: M
authors.lastname: Masuya
authors.forename: Ayori
authors.initials: A
authors.lastname: Mitsutake
authors.forename: Yuko
authors.initials: Y
authors.lastname: Okamoto
mesh_terms: D000595:Amino Acid Sequence; D001704:Biopolymers / Q000737:chemistry; D003198:Computer Simulation; D006863:Hydrogen-Ion Concentration; D008969:Molecular Sequence Data; D009010:Monte Carlo Method; D010446:Peptide Fragments / Q000737:chemistry; D017433:Protein Structure, Secondary; D012259:Ribonuclease, Pancreatic / Q000737:chemistry*; D055672:Static Electricity; D013816:Thermodynamics
chemical_list: D001704:Biopolymers; D010446:Peptide Fragments; D012259:Ribonuclease, Pancreatic