Constitution and solution conformation of the antibiotic mersacidin determined by NMR and molecular dynamics.
The solution structure of the tetracyclic lantibiotic mersacidin in methanol (CD3OH) has been determined by NMR followed by distance bound driven dynamics and subsequent restrained molecular dynamics simulations combined with an iterative relaxation matrix approach and alternatively by a simulated annealing protocol. The molecular dynamics simulations were performed with the AMBER program system and with the INSIGHT program package. The distance bound driven dynamics calculation was conducted using a modified version of the DISGEO II program. The interproton distance restraints were derived from jump symmetrized rotating-frame Overhauser enhancement and exchange (JS-ROESY) spectra, which yield optimum sensitivity for medium-sized molecules like mersacidin. The connectivities via the sulfide bridges were unambiguously confirmed by heteronuclear NMR techniques (heteronuclear single quantum coherence and heteronuclear multiple bond correlation methods). Due to the tetracyclic structure, mersacidin exhibits a rather rigid globular shape, which neither belongs to the duramycin nor to the nisin structure type lantibiotics. The resulting structures for the simulated annealing protocol of restrained and subsequent free molecular dynamics were compared and found to be very similar.
Prasch
T
T
Institut für Organische Chemie, Johann Wolfgang Goethe-Universität Frankfurt, Germany.
Naumann
T
T
Markert
R L
RL
Sattler
M
M
Schubert
W
W
Schaal
S
S
Bauch
M
M
Kogler
H
H
Griesinger
C
C
D000595:Amino Acid Sequence; D000900:Anti-Bacterial Agents / Q000737:chemistry*; D001407:Bacillus / Q000737:chemistry / Q000235:genetics; D001430:Bacteriocins; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D008969:Molecular Sequence Data; D015394:Molecular Structure; D010455:Peptides; D011487:Protein Conformation; D012984:Software; D012996:Solutions; D013816:Thermodynamics
D000900:Anti-Bacterial Agents; D001430:Bacteriocins; D010455:Peptides; D012996:Solutions; C069959:mersacidin