Table 2.
Studies that use MD simulations to investigate phenomena related to the synthesis and transport of LPS.a,b
| System | Production simulation software | Force field | Molecular representation | Enhanced sampling |
Binding/process free energy |
Year | Ref. |
|---|---|---|---|---|---|---|---|
| Apo K. pneumoniae LptDE embedded in bilayer (OL: re-LPS; IL: CDL, POPG, POPE) | GROMACS 2018.6 or 2019.1 |
MARTINI 2.2 EN CHARMM36 |
AA or CG/AA (*1) |
With or without PLUMED(*2) (*3) |
(-) | 2021 | [118] |
| Re-LPS-bound K. pneumoniae LptDE embedded in bilayer (OL: Re-LPS; IL: CDL, POPG, POPE) | |||||||
| Thanatin-bound K. pneumoniae LptDE embedded in bilayer (OL: re-LPS; IL: CDL, POPG, POPE) | |||||||
| A. baumanii KdsC/top 3 molecules from Asinex database | AMBER 16 | AMBER ff03.r1 GAFF |
AA | (-) | MM-GBSA MM-PBSA |
2020 | [24] |
| Apo S. flexneri LptDE embedded in DMPE bilayer | Anton 1 AMBER n.s. |
CHARMM36 | AA | SMD | REUS (PMF, WHAM) | 2020 | [4] |
| S. flexneri LptDE embedded in DMPE bilayer with LPS bound in the N-terminal domain of LptD | |||||||
| P. aeruginosa LptDE embedded in DMPE bilayer | (-) | (-) | |||||
| P. aeruginosa LptDE embedded in OM model (OL: E. coli Ra-LPS; IL: POPE) | |||||||
| A. ferrooxidans GnnA/UDP-GlcNAc/NAD+ | AMBER 18 | GAFF2 | AA | (-) | (-) | 2020 | [124] |
| Apo K. pneumoniae HEP-III | GROMACS 5.1.4 |
AMBER ff99SB |
AA | (-) | (-) | 2019 | [34] |
| K. pneumoniae HEP-III/ADP | MM-PBSA | ||||||
| K. pneumoniae HEP-III/top 2 molecules from Asinex database | |||||||
| N. meningitidis KDO8P synthase/3 biphosphate inhibitors (one inhibitor per system) | AMBER 16 |
AMBER ff14SB |
AA |
(-) |
MM-PBSA MM-GBSA SIE |
2019 |
[101] |
| P. aeruginosa LpxH/Lipid X |
AMBER 14 |
AMBER ff14SB GAFF |
AA |
(-) |
(-) | 2018 | [125] |
| P. aeruginosa LpxH F82G/L83G mutant | |||||||
| Apo P. aeruginosa LpxH from apo and Lipid X bound crystal structures (in separate systems) | |||||||
| WT E. coli LptC dimer | Desmond n.s. |
n.s. | AA |
(-) |
(-) |
2018 | [126] |
| Mutated E. coli LptC dimer | |||||||
| Apo E. coli HepI | Desmond n.s. |
OPLS-AA 2005 | AA | (-) | (-) | 2017 | [20] |
(*1) The original publication does not explicitly indicate the molecular representation for each studied system. (*2) The original publication does not explicitly indicate in which of the studied systems PLUMED was used. (*3) When the PLUMED plugin was used, the specific enhanced sampling method has not been detailed. For specific information about the PLUMED plugin, the reader is directed to Ref. [127].
n.s.: Not specified.
For the sake of clarity, the abbreviations and acronyms cited in this Table have been included and defied in the “List of abbreviations and acronyms” at the beginning of the manuscript.
The force fields included in this Table encompass all of them used in the study, but the force fields used for each system have not been specified.