Analytical Rebridging Monte Carlo: Application to cis/trans Isomerization in Proline-Containing, Cyclic Peptides

We present a new method, the analytical rebridging scheme, for Monte Carlo simulation of proline-containing, cyclic peptides. The cis/trans isomerization is accommodated by allowing for two states of the amide bond. We apply our method to five peptides that have been previously characterized by NMR...

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Bibliographic Details
Published in:arXiv.org 1999-07
Main Authors: Wu, Minghong G, Deem, Michael W
Format: Article
Language:English
Subjects:
Balancing
Computer simulation
Isomerization
Monte Carlo simulation
NMR
Nuclear magnetic resonance
Peptides
Proline
Online Access:Get full text
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Summary:We present a new method, the analytical rebridging scheme, for Monte Carlo simulation of proline-containing, cyclic peptides. The cis/trans isomerization is accommodated by allowing for two states of the amide bond. We apply our method to five peptides that have been previously characterized by NMR methods. Our simulations achieve effective equilibration and agree well with experimental data in all cases. We discuss the importance of effective equilibration and the role of bond flexibility and solvent effects on the predicted equilibrium properties.
ISSN:2331-8422
DOI:10.48550/arxiv.9904057