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Figure 5
Molecular-dynamics simulation of the MbnF crystal structure with MbnA (red) docked in the active-site channel. This simulation shows that the channel is large enough to accommodate the MB peptide without clashes. However, further analysis of the contacts between MnbF and MbnA would be unreliable due to the short length of the simulation. The MD simulation was run in GROMACS using the AMBER99SB force field and the SPC/E water model. The structure was equilibrated with 100 ps NVT and NPT calculations followed by a 10 ns production run. The average r.m.s.d. was relatively flat by 4 ns.

Journal logoSTRUCTURAL BIOLOGY
COMMUNICATIONS
ISSN: 2053-230X
Volume 79| Part 5| May 2023| Pages 111-118
https://doi.org/10.1107/S2053230X23003035
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