Efficiency of the multicanonical simulation method as applied to peptides of increasing size : the heptapeptide deltorphin
Copyright 2002 Wiley Periodicals, Inc. J Comput Chem 23: 1127-1134, 2002
| Veröffentlicht in: | Journal of computational chemistry. - 1984. - 23(2002), 12 vom: 01. Sept., Seite 1127-34 |
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| 1. Verfasser: | |
| Weitere Verfasser: | , , , |
| Format: | Aufsatz |
| Sprache: | English |
| Veröffentlicht: |
2002
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| Zugriff auf das übergeordnete Werk: | Journal of computational chemistry |
| Schlagworte: | Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, P.H.S. Oligopeptides Peptides deltorphin 119975-64-3 Enkephalin, Leucine 58822-25-6 |
| Zusammenfassung: | Copyright 2002 Wiley Periodicals, Inc. J Comput Chem 23: 1127-1134, 2002 The advantage of the multicanonical (MUCA) simulation method of Berg and coworkers over the conventional Metropolis method is in its ability to move a system effectively across energy barriers thereby providing results for a wide range of temperatures. However, a MUCA simulation is based on weights (related to the density of states) that should be determined prior to a production run and their calculation is not straightforward. To overcome this difficulty a procedure has been developed by Berg that calculates the MUCA weights automatically. In a previous article (Yaşar et al. J Comput Chem 2000, 14, 1251-1261) we extended this procedure to continuous systems and applied it successfully to the small pentapeptide Leu-enkephalin. To investigate the performance of the automated MUCA procedure for larger peptides, we apply it here to deltorphin, a linear heptapeptide with bulky side chains (H-Tyr(1)-D-Met(2)-Phe(3)-His(4)-Leu(5)-Met(6)-Asp(7)-NH(2)). As for Leu-enkephalin, deltorphin is modeled in vacuum by the potential energy function ECEPP. MUCA is found to perform well. A weak second peak is seen for the specific heat, which is given a special attention. By minimizing the energy of structures along the trajectory it is found that MUCA provides a good conformational coverage of the low energy region of the molecule. These latter results are compared with conformational coverage obtained by the Monte Carlo minimization method of Li and Scheraga |
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| Beschreibung: | Date Completed 17.12.2002 Date Revised 14.11.2007 published: Print Citation Status MEDLINE |
| ISSN: | 1096-987X |