The ligand-protein complex from the docking study was subjected to MD simulation performed using Desmond program (Schrödinger, LLC, New York, NY, 2016) [12 (link), 13 (link)]. The complex was solvated with the TIP3P water model [14 ] in a 10Å ×10Å×10Å orthorhombic box. The simulation was carried out with Optimized Potential for Liquid Simulations (OPLS) force field. The default Desmond protocol was applied to equilibrate the prepared system and was followed by a 50ns NPT simulation to equilibrate the system. The equilibrated system was saved every 5 ps of time intervals. Potential energy of the entire system was calculated. Stability of the docked complex was evaluated from their root mean square deviation (RMSD) plots. A root mean square fluctuation (RMSF) plot of the backbone atoms of each residue was also created. A snapshot of the protein-peptide complexes were generated using PyMOL (The PyMOL Molecular Graphics System, Version 1.8 Schrödinger, LLC.).
Desmond program
Manufactured by Schrödinger
The Desmond program is a molecular dynamics simulation software developed by Schrödinger. It provides a platform for the simulation and analysis of biomolecular systems. The core function of Desmond is to enable the computation and modeling of the behavior and interactions of complex molecular structures.
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6 protocols using desmond program
1
Molecular Dynamics Simulation of Ligand-Protein Complex
2
Molecular Dynamics of Protein-Ligand Complexes
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We performed four independent MD simulations using the Desmond program (Bowers et al., 2006 ) in Schrödinger suite 2019‐2. Each protein–ligand complex was inserted in a POPC membrane of 140 × 140 Å (approximate) and solvated using explicit TIP3P water models and an orthorhombic box with periodic boundary conditions. All complexes were neutralized with 0.15 mol·L−1 of NaCl and parametrized with OPLSe force field. Each simulation was performed for a total of 500 ns with a recording interval of 100 ps. NPT ensemble at standard conditions of T = 310.15 K and P = 1 atm was used. Ligand interaction diagrams were performed using the “simulation interaction diagram program” module of Schrodinger maestro.
3
Molecular Dynamics Simulation of MurF Inhibitors
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The Desmond program of Schrodinger software (version 2021-2) (Bowers, 2006 ) was used for the explicit solvent molecular dynamics simulation of the selected NPs. The OPLS4 force field (Jorgensen et al., 1996 (link)) was used to model protein-ligand interactions. A simulated triclinic periodic boundary box with an extension of 10 Å in each direction was made to help solve the structures of the A. baumannii MurF target protein. Explicit solvation models (Monte-Carlo equilibrated SPC, the transferable intermolecular potential 3 points) were used for each system. (Jorgensen et al., 1983 (link)). Lennard Jones (LJ) interactions (with cut-off value = 10) (Shaik et al., 2010 (link)) and the SHAKE algorithm (Kräutler et al., 2001 (link)) were applied to standardize the mobility of all Bonds (covalent and hydrogen bonds). The system was solvated with additional counter ions (0.15 M of Na + Cl) to neutralize the system. The protein-ligand complex was energy minimized using the steepest descent algorithm until the gradient threshold of 25 kcal/mol/Å was reached. The complex was subjected to molecular dynamics simulation in NPT ensemble class at 300 K and 1 bar pressure using default parameters of the Desmond program. The simulation was run for a total of 200 nanoseconds, with a time step of 2 fs, and data were collected every 20 ps.
4
Molecular Dynamics Simulation of Ligand-Protein Interactions
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MD simulation analysis was carried out using the Desmond program of Schrodinger software [40 ]. The docked ligand complex with the highest binding energy was selected for the MD simulation study with OPLS 2005 force-field parameters. The docked complex was centered on the orthorhombic box of the predefined TIP3P water system. The box’s volume was minimized and the net charge of the system was neutralized by incorporating 0.15 M NaCl into each system to mimic the physiological state [41 ]. The temperature and pressure were kept constant at 300 K and 1.01325 bar using the Nose–Hoover thermostat and Martyna–Tobias–Klein barostat methods. Simulation analysis was performed through the NPT ensembles by considering heavy atoms, time intervals, and pressure [42 ]. Exactly 10 ns of the flexible system was carried out with NPT ensembles and the long-range electrostatic interactions were computed using the Particle–Mesh–Ewald algorithm. The trajectories were recorded at 4.8 ps intervals and the protein–ligand interaction, stability, and behavior were performed using the Desmond simulation interaction diagram in maestro [40 ].
5
Molecular Dynamics of GLRX Protein Variants
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Using the crystal structure of GLRX (PDB ID: 4RQR, Uniprot ID: P35754), we constructed models of GLRX wild type and mutants (C83S, C8S, and C79S) as well as the GLRX dimers for molecular dynamics (MD) simulations, using Protein Preparation Wizard (Pymol, Schrödinger, Inc.) and the relaxation strategy in our prior work52 (link). The simulation box was built with the SPC water model and the OPL3e force field53 (link). All the NPT simulations (300 K, 1 atm) were carried out in the Desmond program (Schrödinger, LLC) on graphics processing units (GPUs), with a recording interval of 9.6 ps and the van der Waals and short-range electrostatics cut off at 9 Å. Each GLRX wild type or mutant has two 400-ns simulation replicas while each GLRX multimer was simulated with two replicas, 200 ns each (Supplementary Table 3 ). The multimer conformations were obtained from alignment to a dimer crystal structure (PDB ID: 3UIW) or self-assembly of free monomers. All these simulations were analyzed using the Simulation Event Analysis tool implemented in Maestro.
6
Molecular Dynamics Simulations of Protein
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For Molecular Dynamics (MD) simulations the Desmond program (Schrödinger, LLC) and OPLS3e (Harder et al., 2016) force field was used , with a simulation time set to 1000 ns for monomer and 200ns for dimer. For the simulations temperature was 300 K, pressure was 1.0325 bar, while cut off radius was set to 10 Å. The whole system was considered as isothermal-isobaric (NPT) ensemble class. TIP3P model (Berendsen et al., 1981) was used for modelling of the solvent. MD system consisted of one molecule of the protein placed into the cubic box. Input and output files in the case used were prepared on protein preparation wizard (Madhavi Sastry et al., 2013) , analyzed and visualized with Maestro (Schrödinger, LLC) graphical user interface (GUI).
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