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...
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| Main Authors: | , |
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| Format: | Article (Journal) |
| Language: | English |
| Published: |
February 17, 1999
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| In: |
The journal of physical chemistry. B, Biophysics, biomaterials, liquids, and soft matter
Year: 1999, Volume: 103, Issue: 9, Pages: 1586-1594 |
| ISSN: | 1520-5207 |
| DOI: | 10.1021/jp983674t |
| Online Access: | Verlag, Volltext: http://dx.doi.org/10.1021/jp983674t
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| Author Notes: | Dan Mihailescu and Jeremy C. Smith |
| Summary: | 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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| Item Description: | Gesehen am 05.10.2017 |
| Physical Description: | Online Resource |
| ISSN: | 1520-5207 |
| DOI: | 10.1021/jp983674t |