Ayori Mitsutake | PubMed Health

PubMed2004

Replica-exchange extensions of simulated tempering method.

In this paper we consider combinations of two well-known generalized-ensemble algorithms, namely, simulated tempering and replica-exchange method. We discuss two examples of such combinations. One is the replica-exchange simulated tempering and the other is the simulated tempering replica-exchange method. In the former method, a short replica-exchange simulation is first performed and the simulated tempering weight factor is obtained by the multiple-histogram reweighting techniques. This process of simulated tempering weight factor determination is faster and simpler than that in the usual iterative process. A long simulated tempering production run is then performed with this weight factor. The latter method is a further extension of the former in which a simulated tempering replica-exchange simulation is performed with a small number of replicas. These algorithms are particularly useful for studying frustrated systems with rough energy landscape. We give the formulations of these two methods in detail and demonstrate their effectiveness taking the example of the system of a 17-residue helical peptide.

Journal Article↗

PubMed2002

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

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.

Amino Acid Sequence↗