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The pymol molecular graphics system version 1

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The PyMOL Molecular Graphics System, Version 1.8 is a molecular visualization tool. It provides a three-dimensional representation of molecular structures, allowing users to explore and analyze the spatial arrangement of atoms and molecules.

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Ucsf chimera package, by Schrödinger (2 mentions) Pymol 1, by Schrödinger (2 mentions) Pymol v2, by Schrödinger (1 mentions) Vina v, by AutoDock (1 mentions) Prism 6, by GraphPad (1 mentions) Illustrator cs6, by Adobe (1 mentions) Naccess, by Schrödinger (1 mentions) Sigmaplot, by Grafiti LLC (1 mentions) Avance 3 hd spectrometer, by Bruker (1 mentions)

52 protocols using the pymol molecular graphics system version 1

1

Visualizing Structural Conservation of Carboxysome Shell Proteins

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Multiple sequence alignments of subsets of the dataset above were separately created for CcmK1/2 and CcmK3–6. Conservation scores were calculated with the Consurf online tool (Ashkenazy et al., 2010 (link)), and were visualized using Protein Data Bank (pdb) files in the magenta_white_cyan color gradient to display decreasing conservation in pymol (The PyMOL Molecular Graphics System, Version 1.8, Schrödinger, LLC). The pdb entries used as scaffolds on which conservation scores were plotted included 3bn4 (for CcmK1 and the homology model of Nostoc sp. PCC 7524 CcmK6), 3ssr (for CcmK2 and the homology model of Cyanothece sp. PCC7425 CcmK5) and 2a18 (for CcmK4 and the homology model of Syn7942 CcmK3) (Kerfeld et al., 2005 (link); Tanaka et al., 2008 (link); Samborska and Kimber, 2012 (link)). Homology models were built using the SWISS-MODEL online tool (Biasini et al., 2014 (link)). HMM logos for all classes were created using the Skylign online tool with standard settings (observed counts used, full length alignment, letters contain all information) (Wheeler et al., 2014 (link)). HMM logos were manually aligned for comparison.
Sommer M., Cai F., Melnicki M, & Kerfeld C.A. (2017). β-Carboxysome bioinformatics: identification and evolution of new bacterial microcompartment protein gene classes and core locus constraints. Journal of Experimental Botany, 68(14), 3841-3855.
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2

Structural Analysis of Human Glutathione Peroxidase

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For structural analysis of the human GPx1 protein, the crystal structure of the selenocysteine to glycine mutant was used (resolution: 1.5 Å, PDB ID: 2f8a). To enable the representation of the selenocysteine in the human Gpx1 structure in a more appropriate way, the crystal structure of the selenoenzyme glutathione peroxidase from Bos taurus (resolution: 2.0 Å, PDB ID: 1gp1) that includes a selenic acid (residue name: SE7) was superimposed on the human structure with the PyMOL tool (The PyMOL Molecular Graphics System, Version 1.8 Schrödinger, LLC) (RMSD: 0.29 Å). Afterwards, the glycine in the structure of human Gpx1 (2f8a) was replaced by the aligned selenic acid. The distances between the C-alpha atoms of the backbone structure for the respective amino acid residues were calculated using the Visual molecular dynamics (VMD) software support ([21]
http://www.ks.uiuc.edu/Research/vmd/), which was also used for the visualization. The labeled residues K114 and E116 are numbered according to the residue numbering in the UniProt entry with the accession number P07203, and correspond to K112 and E114 in the PDB structure, 2f8a. The inserted selenic acid is at position 49 in the UniProt sequence and position 47 in the PDB file, 2f8a.
Sultan C.S., Saackel A., Stank A., Fleming T., Fedorova M., Hoffmann R., Wade R.C., Hecker M, & Wagner A.H. (2018). Impact of carbonylation on glutathione peroxidase-1 activity in human hyperglycemic endothelial cells. Redox Biology, 16, 113-122.
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3

Structural Determination of Ps01740 Protein

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All X-ray data were collected at the Advanced Light Source beamline 5.0.3 (ALS, Berkeley, CA). The X-ray dataset for the native Ps01740 was collected at a wavelength of 0.97648 Å at 100 K. The data sets were indexed, integrated, and scaled using HKL2000.27 The data collection statistics are summarized in Table 2.
The structure for Ps01740 was determined by molecular replacement (MR) using Phaser-MR28 (link) and Autobuild29 (link) from the PHENIX suite of programs. The Cg10062 structure (PDB entry 3N4G, 26% sequence identity) was used as a search model for the initial phase estimates for Ps01740 structure factors. Structure refinement was performed using Phenix Refine,30 (link) in which TLS parameter refinement was included in the refinement.31 (link) Model structures were evaluated during and after refinement using Molprobity.32 (link) The refinement statistics for the structures are summarized in Table 2. All figures were prepared with PyMol (The PyMOL Molecular Graphics System, Version 1.8 Schrödinger, LLC).33
LeVieux J.A., Baas B.J., Kaoud T.S., Davidson R., Babbitt P.C., Zhang Y.J, & Whitman C.P. (2017). Kinetic and Structural Characterization of a cis-3-Chloroacrylic Acid Dehalogenase Homologue in Pseudomonas sp. UW4: A Potential Step Between Subgroups in the Tautomerase Superfamily. Archives of biochemistry and biophysics, 636, 50-56.
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4

Homology Modeling of CAPN5 Structure

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Homology models of CAPN5’s protease core (PC1—PC2) were generated using MODELLER 9.14 (Eswar et al., 2006 (link)) with CAPN9 as a template as previously described and further refined by conformational sampling based on our previously published SAXS data (Gakhar et al., 2016 (link)). Homology models of CAPN5’s calpain β-sandwich domain (CBSW; DIII) were generated using CAPN2 as a template (PDB: 1KFU, 32% identity, 95% sequence coverage). Homology models of the CAPN5 C2 domain (DIV) were generated using the structure of the Munc13–1 C2 domain (PDB: 2CJT, 30% identity, 59% sequence coverage). Models of the individual domains were assembled using ab initio domain assembly in MODELLER to generate a model of the full-length CAPN5 structure. PyMOL generated all structural figures (The PyMOL Molecular Graphics System, Version 1.8; Schrödinger, LLC).
Wert K.J., Koch S.F., Velez G., Hsu C.W., Mahajan M., Bassuk A.G., Tsang S.H, & Mahajan V.B. (2019). CAPN5 genetic inactivation phenotype supports therapeutic inhibition trials. Human mutation, 40(12), 2377-2392.
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5

Molecular Visualization and Interactions

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The models were visualized using PyMOL v 2.5 (www.pymol.org, accessed on 20 February 2023), a molecular visualization system (The PyMOL Molecular Graphics System, Version 1.8 Schrodinger, LLC, New York, NY, USA). To visualize the atomic interactions Discovery Studio Visualizer V21.1 was used.
Tasleem M., Hussein W.M., El-Sayed A.A, & Alrehaily A. (2023). An In Silico Bioremediation Study to Identify Essential Residues of Metallothionein Enhancing the Bioaccumulation of Heavy Metals in Pseudomonas aeruginosa. Microorganisms, 11(9), 2262.
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6

Structural Insights into Protein Complexes

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Depiction of molecular models were generated using PyMOL (The PyMOL Molecular Graphics System, version 1.8, Schrödinger), the UCSF Chimera package from the Computer Graphics Laboratory, University of California, San Francisco (supported by National Institutes of Health P41 RR-01081) and UCSF ChimeraX developed by the Resource for Biocomputing, Visualization, and Informatics at the University of California, San Francisco, with support from National Institutes of Health R01-GM129325 and the Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases (Pettersen et al., 2004 (link); Goddard et al., 2018 (link)). Protein domains graphs (Figure 1—figure supplement 4; Figure 4) were generated using domainsGraph.py (Patel, 2020 ; copy archived at https://github.com/elifesciences-publications/domainsGraph).
Some of the software packages mentioned above were configured by SBgrid (Morin et al., 2013 (link)).
Patel A.B., Moore C.M., Greber B.J., Luo J., Zukin S.A., Ranish J, & Nogales E. (2019). Architecture of the chromatin remodeler RSC and insights into its nucleosome engagement. eLife, 8, e54449.
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7

Structural Modeling and Docking of Murine P-gp

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Initial structure of murine P‐gp (4XWK[44] was retrieved from Protein Data Bank (www.rcsb.org[50])). Inner missing regions were modeled using Modeller[51] as implemented in UCSF Chimera 1.11.2.[52] The structure was then minimized with Amber force field ff14SB.[53] Molecular docking was carried out with Gold software v. 2020.2.0[45] using default settings. PyMOL was used for analysis and picture rendering (The PyMOL Molecular Graphics System, Version 1.8 Schrödinger, LLC.).
Braconi L., Teodori E., Contino M., Riganti C., Bartolucci G., Manetti D., Romanelli M.N., Perrone M.G., Colabufo N.A., Guglielmo S, & Dei S. (2022). Overcoming Multidrug Resistance (MDR): Design, Biological Evaluation and Molecular Modelling Studies of 2,4‐Substituted Quinazoline Derivatives. Chemmedchem, 17(12), e202200027.
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8

Protein Structure Analysis Workflow

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Protein structural diagrams were prepared by UCSF Chimera and Pymol (The PyMOL Molecular Graphics System, Version 1.8 Schrödinger, LLC, 201561 (link),62 (link)). Surface area, solvation energy and solvation effect calculations were performed using PISA module of CCP4 package63 (link). Ligand Explorer was used to analyse the ligand-protein interaction and to measure distances, which was further validated by NCONT module of CCP464 (link). For protease cleavage site prediction PROSPERous server was used under http://lightning.med.monash.edu/prosperous/ (“PROSPERous: a comprehensive server for predicting protease-specific substrates and cleavage sites using a combination of multiple scoring functions. Submitted for publication”)65 .
Hufnagl K., Ghosh D., Wagner S., Fiocchi A., Dahdah L., Bianchini R., Braun N., Steinborn R., Hofer M., Blaschitz M., Roth G.A., Hofstetter G., Roth-Walter F., Pacios L.F, & Jensen-Jarolim E. (2018). Retinoic acid prevents immunogenicity of milk lipocalin Bos d 5 through binding to its immunodominant T-cell epitope. Scientific Reports, 8, 1598.
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9

Structural Modeling of Human SirT7

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For in silico SirT7 structural model, an initial homology model was constructed for human SirT7 using the coordinates of the determined x-ray crystal structure of human SirT6 (Protein Data Bank ID: 5M6F; 1.87 Å resolution, 42% of sequence identity). Modeller 9.12 was used to model the nondetermined regions of the protein. The side chain conformations for nonconserved residues were positioned according to SCWRL4 (Krivov). The protein was embedded in a TIP3P water box. The initial system was energy-minimized and subjected to 10 ns of molecular dynamics equilibration and, lastly, to a production stage extending to 150 ns. All the simulations were performed with GROMACS 5.0 simulation package. The molecular model of SirT7 was used as the initial model to introduce H187Y and N189A mutations. For comparison purposes, SirT1 to SirT5 structures were superimposed to SirT6 structure and SirT7 structural model using PyMOL (The PyMOL Molecular Graphics System, version 1.8, Schrödinger LLC.).
Simonet N.G., Thackray J.K., Vazquez B.N., Ianni A., Espinosa-Alcantud M., Morales-Sanfrutos J., Hurtado-Bagès S., Sabidó E., Buschbeck M., Tischfield J., De La Torre C., Esteller M., Braun T., Olivella M., Serrano L, & Vaquero A. (2020). SirT7 auto-ADP-ribosylation regulates glucose starvation response through mH2A1. Science Advances, 6(30), eaaz2590.
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10

Structural Analysis of Calpain Protease Domains

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Calpain protease core structures were evaluated by their reported global validation metrics in PDB-REDO (Rfree, Clashscore, Ramachandran outliers, Sidechain outliers, and RSRZ outliers) (Gore et al., 2017 (link); Joosten et al., 2009 (link)). Structures meeting at least 3 out of the 5 metrics, with percentile scores greater than X-ray structures of a similar resolution, were further evaluated. Structures not meeting these criteria were excluded (PDB: 1DF0, 1QXP; 1KFX, 1KFU, and 1U5I). Structures of individual calpain domains (PC1 and PC2) were superimposed using PyMOL to calculate the pairwise RMSD between protein alpha carbon atoms (Cα; The PyMOL Molecular Graphics System, Version 1.8 Schrödinger, LLC). A structural dissimilarity matrix (SDM) was constructed using the Cα RMSD values in order to generate a phylogenetic tree. The phylogenetic tree was constructed using the UPGMA (Unweighted Pair Group Method with Arithmetic Mean) method in MEGA7 (Molecular Evolutionary Genetics Analysis) software (Kumar et al., 2016 (link); Sneath and Sokal, 1973 ).
Velez G., Sun Y.J., Khan S., Yang J., Herrmann J., Chemudupati T., MacLaren R.E., Gakhar L., Wakatsuki S., Bassuk A.G, & Mahajan V.B. (2020). Structural Insights into the Unique Activation Mechanisms of a Non-classical Calpain and Its Disease-Causing Variants. Cell reports, 30(3), 881-892.e5.
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