Molecular simulation model of C. ammoniagenes FAD synthase in complex with ATP/Mg²⁺ and FMN

Briefly, the protocol was:

• Minimization of solvent+ions receptor:ATP:Mg2+:FMN with position restraints (on AMP portion of ATP and FMN)
• 100 ps of NVT md with restraints
• Re-minimize without restraints
• 100 ps of NVT md without restraints
• 200 ps of NPT md without restraints
• Final minimization without restraints

Files

• em_final.gro - final minimized configuration GROMACS *.gro format
• em_final.pdb - final minimized configuration PDB format
• em_final_noSOL_noIONS.gro - solvent and ions removed GROMACS *.gro format
• em_final_noSOL_noIONS.pdb - solvent and ions removed PDB format

System preparation

• build_topologies - contains work to build AMBER topologies for use with the GROMACS simulation package
• solvation_equilibration - steps to add Mg2+, add solvent and ions, minimize and equilibrate

Methods

All structural models were mimimized and equilibrated using the GROMACS simulation software, version 2020.4 (Abraham 2015). Input coordinates were taken from the molecular docking model of C. ammoniagenes FAD synthase in complex with adenosine monophosphate (AMP) and flavin mononucleotide (FMN), based on the published by ??????. The GROMACS tool pdb2gmx was used to protonate the receptor at pH 7.0 and prepare its topology using the AMBER ff99SB force field (). AMBER-compatible simulation parameters for adenosine triphosphate (ATP) and FMN (fully oxidized) were taken from Meager et al. (2003) and Schneider et al (1999), respectively.

References

Lans, Isaias, Juan Seco, Ana Serrano, Ricardo Burbano, Pilar Cossio, Martha C. Daza, and Milagros Medina. “The Dimer-of-Trimers Assembly Prevents Catalysis at the Transferase Site of Prokaryotic FAD Synthase.” Biophysical Journal 115, no. 6 (September 2018): 988–95. https://doi.org/10.1016/j.bpj.2018.08.011.

Abraham, Mark James, Teemu Murtola, Roland Schulz, Szilárd Páll, Jeremy C. Smith, Berk Hess, and Erik Lindahl. “GROMACS: High Performance Molecular Simulations through Multi-Level Parallelism from Laptops to Supercomputers.” SoftwareX 1–2 (September 2015): 19–25. https://doi.org/10.1016/j.softx.2015.06.001.

Meagher, Kristin L., Luke T. Redman, and Heather A. Carlson. “Development of Polyphosphate Parameters for Use with the AMBER Force Field.” Journal of Computational Chemistry 24, no. 9 (July 15, 2003): 1016–25. https://doi.org/10.1002/jcc.10262.

Schneider, C., and J. Sühnel. “A Molecular Dynamics Simulation of the Flavin Mononucleotide-RNA Aptamer Complex.” Biopolymers 50, no. 3 (September 1999): 287–302. https://doi.org/10.1002/(SICI)1097-0282(199909)50:3<287::AID-BIP5>3.0.CO;2-G.