β-sheet formation in BPTI(16–36) by Monte Carlo simulated annealing

Structures of a peptide fragment of β2-microglobulin studied by replica-exchange molecular dynamics simulations - Towards the understanding of the mechanism of amyloid formation

We investigate in detail the structural properties of the monomeric peptide fragment that corresponds to residues 21-31 of beta(2)-microglobulin. As a first step towards the understanding of the mechanism of the amyloid formation, we have performed a replica-exchange molecular dynamics simulation of this peptide with explicit water molecules. We analyze various structural properties as functions of temperature. Although the corresponding part of the native protein is a fully extended beta-strand, our results show that beta-hairpin structures are formed with high frequency around 310 K. We conjecture that this beta-hairpin formation is closely related to the amyloid fibrillogenesis.

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.

New Monte Carlo algorithms for protein folding

Over the past three decades, a number of powerful simulation algorithms have been introduced to the protein folding problem. For many years, the emphasis has been placed on how to both overcome the multiple minima problem and find the conformation with the global minimum potential energy. Since the new view of the protein folding mechanism (based on the free energy landscape of the protein system) arose in the past few years, however, it is now of interest to obtain a global knowledge of the phase space, including the intermediate and denatured states of proteins. Monte Carlo methods have proved especially valuable for these purposes. As well as new, powerful optimization techniques, novel algorithms that can sample much a wider phase space than conventional methods have been established.