Homology models of the Hs β-cardiac myosin-2 motor domain (residues 1–800) were built using Modeller (Sali and Blundell, 1993 (link)) and the X-ray crystal structure of Gg myosin-2 Subfragment-1 (PDB code: 2MYS ) as template. Prior to molecular docking, the protein models were subjected to geometry optimization using MacroModel (MacroModel, version 9.9; Schrödinger, LLC, New York, NY, 2011) and the OPLS2005 force field. Blind and local docking of EMD 57033 was carried out using Autodock4 (Morris et al., 1998 (link)), employing the Lamarckian Genetic Algorithm. The ligand was prepared and energy-minimized using MacroModel (MacroModel, version 9.9; Schrödinger, LLC, New York, NY, 2011) and the OPLS2005 force field, as well as AutodockTools (Sanner, 1999 (link); Morris et al., 2009 (link)). During flexible docking, the side chains of Arg29 and Lys34 were allowed full conformational flexibility. In addition, local docking was performed using models that are based on the X-ray structure of Hs β-cardiac myosin-2 experimentally solved by the laboratory of I Rayment (PDB code: 4DB1 ).
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Maestro, by Schrödinger (20 mentions)
Ligprep, by Schrödinger (15 mentions)
Protein preparation wizard, by Schrödinger (6 mentions)
Ligprep module, by Schrödinger (4 mentions)
Maestro 11, by Schrödinger (4 mentions)
Jaguar, by Schrödinger (3 mentions)
Modeller, by Schrödinger (3 mentions)
Prism 8, by GraphPad (3 mentions)
Biologics, by Schrödinger (2 mentions)
Autodocktools, by Schrödinger (2 mentions)
Maestro suite, by Schrödinger (2 mentions)
Facsdiva software, by BD (2 mentions)
Protein preparation wizard 2015 4, by Schrödinger (2 mentions)
Mmff94, by Schrödinger (2 mentions)
Sigmaplot 14, by Merck Group (1 mentions)
Chem3d ultra, by PerkinElmer (1 mentions)
Phase module, by Schrödinger (1 mentions)
Confgen, by Schrödinger (1 mentions)
Chembiodraw, by Revvity Signals Software (1 mentions)
Maestro module, by Schrödinger (1 mentions)
108 protocols using macromodel
1
Modeling and Docking of Cardiac Myosin-2 Motor
2
Docking Simulation of Topoisomerase I
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For the docking simulation, the Homo sapiens topoisomerase I protein (PDB: 1TBI) was prepared using the protein preparation module in Maestro 11.0 (Maestro, Schrödinger, LLC, New York, NY, USA, 2019). Water molecules as well as the camptothecin ligand were removed from the active site. Hydrogen bonds were optimized using default value and an energy minimization was performed only on the protein hydrogens in Macro-Model (MacroModel, Schrödinger, LLC, New York, NY, USA, 2019). A large enough grid encompassing the active site was generated and the ligands prepared with protonation state at pH7.4 were docked using Glide (Glide, Schrödinger, LLC, New York, NY, USA, 2019) extra-precision mode without any constraints.
3
Energy Minimization Using OPLS3 Force Field
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The resultant model was energy minimized using the protocol previously reported in our lab [45 ]. The minimization protocol used the OPLS3 [42 (link),43 (link),44 (link)] all atom force field in Macromodel (Schrödinger 2017-4: Macromodel, Schrödinger, LLC, New York, NY, USA, 2017). An extended Van der Waals cutoff (8.0 Å, updated every 10 steps), a 20.0 Å electrostatic cutoff, and a 4.0 Å hydrogen bond cutoff were used in each stage of the calculation.
4
Computational Modeling of E-Z Isomerization
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The entire computational work presented here, including quantum chemical calculations and force-field-based analyses, was performed utilizing Schrödinger Materials Science Suite (Version 2.2). Quantum chemical simulations for potential energy surfaces of E-Z isomerization were run by the suite’s quantum chemistry package Jaguar (Version 9.1)48 (link). Force-field-based static and dynamic simulations were carried out using the suite’s molecular mechanics and molecular dynamics packages: MacroModel (Schrödinger Release 2016-4: MacroModel) and Desmond Molecular Dynamics System (Schrödinger Release 2016-4: Desmond Molecular Dynamics System, Maestro-Desmond Interoperability Tools), respectively. OPLS2005 force field was used to describe the structure-energy relationship throughout the force-field-based simulations40 (link),49 (link).
5
Energy Minimization of Molecular Structures
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The resultant model was energy minimized using the protocol previously reported by our lab [51 (link)]. The minimization protocol used the OPLS3e [71 (link),72 (link),73 (link),74 (link)] all-atom force field in Macromodel (Schrödinger 2017-4: Macromodel, Schrödinger, LLC, New York, NY, USA, 2017). An extended Van der Waals cutoff (8.0 Å, updated every 10 steps), a 20.0 Å electrostatic cutoff, and a 4.0 Å hydrogen bond cutoff were used in each stage of the calculation.
6
Modeling Epo Glycosylation and Receptor Interactions
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The models of Epo glycosylated were generated using the crystallographic structure of human Epo (PDB code: 1EER), where mutations K24N, K38N and K83N were created to restore the glycosylation sites in Epo using Modeller 9.15 [40] . The oligosaccharides tetra- and di-antennary for the Epo wild type (Epo) and L-glycosylation (EpoL), respectively, were created by SWEET2 (http://www.glycosciences.de/modeling/sweet2/doc/index.php ). The N-linked glycosylation process for each Epo variant was performed using Maestro (Schrödinger, LLC, New York, NY, 2016), and the resulting models were minimized energetically in a conjugate gradient (Polak-Ribiere) utilizing MacroModel (Schrödinger, LLC, New York, NY, 2016). The NonHem-EpoR was created conserving one chain from the EpoR complemented with the β common receptor chain (PDB code: 2GYS). The complexes Epo-EpoR and Epo-NonHem-EpoR were generated by a rigid docking using ZDock [41] , optimized in MacroModel, and finally analyzed energetically with Prime (Schrödinger, LLC, New York, NY, 2016). The interaction surface analysis was performed using InterSurfPro (http://curie.utmb.edu/usercomplex.html ). Images and molecular surfaces were created by PyMol (version 1.5, DeLano Scientific LLC).
7
Peptide Ligand Optimization for Pin1 and Pin4
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Ligands and protein preparations: Peptides were generated using tools available in Maestro (Maestro release 2018, Schrödinger, LLC, New York, NY, 2018) and minimized by MacroModel (MacroModel release 2018, Schrödinger, LLC, New York, NY, 2018) employing OPLSAA 2005 as force field.[28] For simulating the effects derived by the solvent the GB/SA model was employed, selecting ‘‘no cutoff’’ for non‐bonded interactions. PRCG technique with 5000 maximum iterations (threshold for gradient convergence=0.001) was used. The resulting structures were treated by LigPrep (LigPrep release 2018, Schrödinger, LLC, New York, NY, 2018) for identifying the most probable ionization state at cellular pH value (7.4±0.5). The 3D structures of human Pin1 and Pin4 were downloaded from the Protein Data Bank (PDB IDs 2XP4[29] and 3UI5,[30] respectively) and imported in Maestro suite 2018. Water molecules, ions and compounds used for crystallization were removed, while the ligands were kept. The resulting structures were prepared using protein preparation wizard protocol to obtain suitable starting structures for further computational experiments as described previously.[31 , 32 ]
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Ligands and protein preparations: Peptides were generated using tools available in Maestro (Maestro release 2018, Schrödinger, LLC, New York, NY, 2018) and minimized by MacroModel (MacroModel release 2018, Schrödinger, LLC, New York, NY, 2018) employing OPLSAA 2005 as force field.
8
Molecular Docking of TWIK-1 Channel Ligand
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A TASK-1 homology model based on TWIK-1 channel (PDB ID: 3UMK) was used for docking calculations, as previously described [28] . The molecular docking calculation was performed using Glide v.7.4 with the standard precision (SP) mode [29] . Docking grid was centered on residues that significantly affects the conduction of the channel (Q126, L239, N240) and a cubic box with the axial length of 25Å was used. The A293 ligand in its neutral state was prepared using LigPrep module (LigPrep, Schrödinger, LLC, New York, NY, USA, 2017). Energy minimization in the gas phase using Macromodel (Macromodel, Schrodinger, LLC, New York, NY, USA, 2017) with the OPLS2005 force field was performed. Twenty conformers of the ligand previously optimized were generated using ConfGen tool [30] . For the poses generation, it was enabled the strain correction for the GlideScore. Finally, one hundred poses were generated (five poses per conformer).
9
Modeling Asymmetric MexY Homotrimer
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The amino acid sequences of the MexY from P. aeruginosa PAO1, PA7 and PA14 were retrieved from The Pseudomonas Genome Database66 (link) (accession codes GCF_000006765.1, GCF_000017205.1, and GCF_000404265.1, respectively) and a homology model of an asymmetric MexY homotrimer was constructed using the cryo-EM structure of MexB as the template (PDB 6IOL chain B or 6TA6 chain C) on the Swiss Model server (https://swissmodel.expasy.org ). Models built with the Swiss Model server were minimized in MacroModel (Schrödinger LLC 2022–3) using the OPLS4 force field and Polak-Ribier Conjugate Gradient (PRCG) minimization method with 2500 iterations. A MexYPAO1 model was also generated with the transmembrane regions removed and the remaining periplasmic components joined with Gly/Ser linker (“MexY-per”, comprising residues: MexY1−38-GSGSGGSGGS (linker)-MexY558−863). The MexY-per model was constructed using the full P. aeruginosa PAO1 MexY homology model as the starting template in Biologics (Schrödinger LLC 2022–3) and with enhanced loop sampling for the linker region.
10
Structural Modeling of MexY Efflux Pump
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The amino acid sequences of the MexY from P. aeruginosa PAO1, PA7 and PA14 were retrieved from The Pseudomonas Genome Database67 (link) (accession codes GCF_000006765.1, GCF_000017205.1, and GCF_000404265.1, respectively). Homology models of the asymmetric MexY homotrimer were constructed using two independent cryo-EM structures of MexB as the template (PDB 6IOL chains E, F and G, and 6TA6 chains J, K and L) on the Swiss Model server (https://swissmodel.expasy.org ). Although at modest resolution compared to some other available structures of MexB alone, these templates were selected with the expectation that the trimeric MexB structure within the full efflux pump would best represent the relevant conformational states of the transporter protein68 . Models built with the Swiss Model server were minimized in MacroModel (Schrödinger LLC 2022–3) using the OPLS4 force field and Polak-Ribier Conjugate Gradient (PRCG) minimization method with 2500 iterations. A MexYPAO1 model was also generated with the transmembrane regions removed and the remaining periplasmic components joined with Gly/Ser linker (“MexY-per”, comprising residues: MexY1−38-GSGSGGSGGS (linker)-MexY558−863). The MexY-per model was constructed using the full P. aeruginosa PAO1 MexY homology model as the starting template in Biologics (Schrödinger LLC 2022–3) and with enhanced loop sampling for the linker region.
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