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A pH‐dependent variation in α‐helix structure of the S‐peptide of ribonuclease A studied by Monte Carlo simulated annealing
Author(s) -
Nakazawa Takashi,
Ban Sumiko,
Okuda Yuka,
Masuya Masato,
Mitsutake Ayori,
Okamoto Yuko
Publication year - 2002
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.10055
Subject(s) - chemistry , ribonuclease , salt bridge , peptide , monte carlo method , helix (gastropod) , amino acid , crystallography , residue (chemistry) , stereochemistry , rna , biochemistry , ecology , statistics , mathematics , biology , snail , mutant , gene
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 α‐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 α‐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. © 2002 John Wiley & Sons, Inc. Biopolymers 63: 273–279, 2002; DOI 10.1002/bip.10055