Molecular dynamics simulation of the cyclic decapeptide antibiotic, gramicidin S, in dimethyl sulfoxide solution
We report on a 5 ns molecular dynamics simulation of the decapeptide antibiotic, gramicidin S (cyclo-(Leu-DPhe-Pro-Val-Orn)2) in dimethyl sulfoxide solution. Throughout the simulation the backbone ring maintains an antiparallel β-pleated sheet conformation with two type II‘ β-turns. The backbone dih...
Gespeichert in:
| Hauptverfasser: | , |
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| Dokumenttyp: | Article (Journal) |
| Sprache: | Englisch |
| Veröffentlicht: |
February 17, 1999
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| In: |
The journal of physical chemistry. B, Biophysics, biomaterials, liquids, and soft matter
Year: 1999, Jahrgang: 103, Heft: 9, Pages: 1586-1594 |
| ISSN: | 1520-5207 |
| DOI: | 10.1021/jp983674t |
| Online-Zugang: | Verlag, Volltext: http://dx.doi.org/10.1021/jp983674t
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| Verfasserangaben: | Dan Mihailescu and Jeremy C. Smith |
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| 245 | 1 | 0 | |a Molecular dynamics simulation of the cyclic decapeptide antibiotic, gramicidin S, in dimethyl sulfoxide solution |c Dan Mihailescu and Jeremy C. Smith |
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| 520 | |a We report on a 5 ns molecular dynamics simulation of the decapeptide antibiotic, gramicidin S (cyclo-(Leu-DPhe-Pro-Val-Orn)2) in dimethyl sulfoxide solution. Throughout the simulation the backbone ring maintains an antiparallel β-pleated sheet conformation with two type II‘ β-turns. The backbone dihedrals are relatively inflexible and do not undergo any conformational transitions. The simulation reproduces the Φ and Ψ angles derived from nuclear magnetic resonance spectroscopy to within 18° standard deviation on average. Correlations between the backbone dihedral angles are found. The side chain dihedrals are much more flexible, and the multiple conformational states of these are classified using a clustering technique. Side chain hydrogen-bonding involving the ornithine and phenylalanine residues is analyzed and discussed in the context of previous work. | ||
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