A pH-dependent variation in α-helix structure of the S-peptide of ribonuclease a studied by Monte Carlo simulated annealing

Takashi Nakazawa, Sumiko Ban, Yuka Okuda, Masato Masuya, Ayori Mitsutake, Yuko Okamoto

Research output: Contribution to journalArticle

2 Citations (Scopus)

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 α-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 a-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 a-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.

Original languageEnglish
Pages (from-to)273-279
Number of pages7
JournalBiopolymers
Volume63
Issue number4
DOIs
Publication statusPublished - 2002 Apr 5
Externally publishedYes

Fingerprint

Simulated annealing
Peptides
Conformations
Acidic Amino Acids
Pancreatic Ribonuclease
Peptide Fragments
Amino acids
Salts
Amino Acids
ribonuclease S-peptide
Ribonucleases

Keywords

  • Energy minimization
  • Monte Carlo simulating annealing
  • S-peptide
  • Tertiary structure prediction

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Biochemistry
  • Biophysics

Cite this

A pH-dependent variation in α-helix structure of the S-peptide of ribonuclease a studied by Monte Carlo simulated annealing. / Nakazawa, Takashi; Ban, Sumiko; Okuda, Yuka; Masuya, Masato; Mitsutake, Ayori; Okamoto, Yuko.

In: Biopolymers, Vol. 63, No. 4, 05.04.2002, p. 273-279.

Research output: Contribution to journalArticle

Nakazawa, Takashi ; Ban, Sumiko ; Okuda, Yuka ; Masuya, Masato ; Mitsutake, Ayori ; Okamoto, Yuko. / A pH-dependent variation in α-helix structure of the S-peptide of ribonuclease a studied by Monte Carlo simulated annealing. In: Biopolymers. 2002 ; Vol. 63, No. 4. pp. 273-279.
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AU - Mitsutake, Ayori

AU - Okamoto, Yuko

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