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Pymol v2

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PyMOL v2.5.2 is a molecular visualization software that allows users to create high-quality 3D images and animations of molecular structures. It is a powerful tool for understanding the structure and function of proteins, nucleic acids, and other biological molecules.

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93 protocols using pymol v2

1

Structural Analysis of Antibody-Antigen Interactions

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CDR lengths were derived based on IMGT definitions61 (link). Structural figures were made using PyMOL v2.3 (Schrödinger, LLC) or ChimeraX v0.962 (link). Buried surface areas (BSAs) were calculated using PDBePISA63 (link) and a 1.4 Å probe. Potential hydrogen bonds were assigned using the geometry criteria with separation distance of <3.5 Å and A-D-H angle of >90°. The maximum distance allowed for a potential van der Waals interaction was 4.0 Å. Protein surface electrostatic potentials were calculated in PyMOL v2.3 (Schrödinger LLC). Briefly, hydrogens were added to proteins using PDB2PQR64 (link), and an electrostatic potential map was calculated using APBS65 (link). Epitopes for antibodies in Fig. 3 were identified as gp120 residues containing an atom within 4 Å of an antibody as calculated in PyMOL v2.3 (Schrödinger, LLC).
Yang Z., Dam K.M., Bridges M.D., Hoffmann M.A., DeLaitsch A.T., Gristick H.B., Escolano A., Gautam R., Martin M.A., Nussenzweig M.C., Hubbell W.L, & Bjorkman P.J. (2022). Neutralizing antibodies induced in immunized macaques recognize the CD4-binding site on an occluded-open HIV-1 envelope trimer. Nature Communications, 13, 732.
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2

Structural Modeling of Protein Complexes

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Sequences were obtained from Uniprot and the LIR-central database (Chatzichristofi et al., 2023 (link)). AF2-multimer was used with MMseqs2 through Google Colab (https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/AlphaFold2.ipynb#scrollTo=UGUBLzB3C6WN). The top ranked structure was relaxed using AMBER and examined using Pymol V2.4.1 (Pymol V2.4.1, Schrödinger, LLC). Predicted LDDT (pLDDT) per residue was estimated by pLDDT metric output by AF2 as a metric of model confidence. pLDDT scores were colored in pymol using the Pymol extension Color AlphaFold (https://github.com/cbalbin-bio/pymol-color-alphafold).
North B.J., Ohnstad A.E., Ragusa M.J, & Shoemaker C.J. (2024). The LC3-interacting region of NBR1 is a protein interaction hub enabling optimal flux. bioRxiv.
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3

Structural Analysis of CG10 Fab-B41-sCD4 Complex

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Structural figures were made using PyMOL v2.5.1 (Schrödinger, LLC) or ChimeraX v1.2.5 (80 (link)). Interacting residues between CG10 Fab and B41-sCD4 were analyzed in PDBePISA (81 (link)) using the following definitions: potential hydrogen bonds were assigned using geometric criteria of an interatomic distance of <3.5 Å between the donor and acceptor residues and an A-D-H angle of >90°. Hydrogen atoms were added to proteins using PDB2PQR (82 (link)). The maximum distance allowed for van der Waals interaction was 4.0 Å. RMSDs were calculated for Cα atoms after superimposition in PyMOL v2.5.1 (Schrödinger, LLC) of the CG10 Fab from the CG10-B41-sCD4 complex and the unbound CG10 Fab X-ray structure.
Yang Z., Dam K.M., Gershoni J.M., Zolla-Pazner S, & Bjorkman P.J. (2022). Antibody Recognition of CD4-Induced Open HIV-1 Env Trimers. Journal of Virology, 96(24), e01082-22.
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4

Structural Determination of crPTEN Variants

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n-crPTEN-13sp-T1, 4p-crPTEN-13sp-T2 and 4p-crPTEN-20sp-T3 data were collected at National Synchrotron Light Source-II at beamlines 17-ID-1(AMX) on a DECTRIS Eiger X 9M detector and 17-ID-2 (FMX) on a DECTRIS Eiger X 16M detector. n-crPTEN-13sp-T1, 4p-crPTEN-13sp-T2 were collected using a vector over the length of the crystal. 4p-crPTEN-20sp-T3 data were collected using crystals ranging in sizes from 10-13 μm using multiple crystals mounted in a single loop55 . Three data sets were scaled using XSCALE with a resolution cut-off criterion was 〈I/σ(I)〉 of 2.9 Å. Datasets were indexed, integrated and scaled using fastdp56 (link), XDS57 (link), and aimless58 (Table S1). The structure for the n-crPTEN-13sp-T1, 4p-crPTEN-13sp-T2 and 4p-crPTEN-20sp-T3 were determined by direct refinement using PDB ID 1D5R 59 as the starting model. The data were refined using iterative rounds of refinement with REFMAC560 ,61 (link) and manual rebuilding in Coot62 (link). Structures were validated using Coot62 (link) and PDB Deposition tools with more than 95 % of residues in preferred and allowed regions according to Ramachandran statistics (Table S1). Figures were rendered in PyMOL (v2.2.3, Schrödinger, LLC, New York, NY). Buried areas were calculated with PDBePISA63 (link).
Dempsey D.R., Viennet T., Park E., Henriquez S., Chen Z., Jeliazkov J.R., Phan K.L., Coote P., Gray J.J., Eck M.J., Gabelli S.B., Arthanari H, & Cole P.A. (2021). The Structural Basis of PTEN Regulation by Multi-Site Phosphorylation. Nature structural & molecular biology, 28(10), 858-868.
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5

Structural Modeling of PU.1 Variants

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To three-dimensionally model patient PU.1 variants, the crystal structure of murine PU.1 bound to duplex DNA was used. This structure has been assigned Protein Data Bank accession no. 1PUE (Kodandapani et al., 1996 (link)). Ribbon representation of the interaction was generated with PyMOL v2.2.3 (Schrödinger, LLC).
Le Coz C., Nguyen D.N., Su C., Nolan B.E., Albrecht A.V., Xhani S., Sun D., Demaree B., Pillarisetti P., Khanna C., Wright F., Chen P.A., Yoon S., Stiegler A.L., Maurer K., Garifallou J.P., Rymaszewski A., Kroft S.H., Olson T.S., Seif A.E., Wertheim G., Grant S.F., Vo L.T., Puck J.M., Sullivan K.E., Routes J.M., Zakharova V., Shcherbina A., Mukhina A., Rudy N.L., Hurst A.C., Atkinson T.P., Boggon T.J., Hakonarson H., Abate A.R., Hajjar J., Nicholas S.K., Lupski J.R., Verbsky J., Chinn I.K., Gonzalez M.V., Wells A.D., Marson A., Poon G.M, & Romberg N. (2021). Constrained chromatin accessibility in PU.1-mutated agammaglobulinemia patients. The Journal of Experimental Medicine, 218(7), e20201750.
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6

Bioinformatic analysis of xylanase XynRA2 from Roseithermus sacchariphilus

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The gene sequence of putative xylanase (GenBank: ARA92359.1) was extracted from the complete genome of R. sacchariphilus RA (GenBank: CP020382.1) [20 (link),21 (link)]. The mature xylanase gene was designated as xynRA2. The protein sequence similarity was assessed using NCBI BLASTp program (https://blast.ncbi.nlm.nih.gov/Blast.cgi). Multiple sequence alignments were performed using Clustal Omega (https://www.ebi.ac.uk/Tools/msa/clustalo/). A phylogenetic tree of XynRA2 with its closest homologs was constructed with the neighbor-joining algorithm using MEGA v7.0 software [59 (link)] with a bootstrap value of 1000. The signal peptide sequence was predicted using SignalP v4.1 (http://www.cbs.dtu.dk/services/SignalP/). Conservative domains were identified using InterPro. The homology model of XynRA2 was performed using SWISS-MODEL (https://swissmodel.expasy.org/) with an evolved CBM of Xyn10A from R. marinus (PDB: 3JXS) [60 (link)] and GH10 xylanase (XynB) from Xanthomonas axonopodis pv citri (PDB: 4PN2) complexed with xylotriose as a template [61 (link)]. The predicted model and its surface electrostatic potential were assessed using APBS plugin in PyMOL (v2.2.3, Schrödinger Inc., New York, NY, USA).
Teo S.C., Liew K.J., Shamsir M.S., Chong C.S., Bruce N.C., Chan K.G, & Goh K.M. (2019). Characterizing a Halo-Tolerant GH10 Xylanase from Roseithermus sacchariphilus Strain RA and Its CBM-Truncated Variant. International Journal of Molecular Sciences, 20(9), 2284.
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7

Structural Characterization of p53R175H-HLA-A*02:01 Complex

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Crystals of the ternary complex H2-Fab–p53R175H/HLA-A*02:01 were grown by vapor diffusion in hanging drops set up with a TTP mosquito robot with a reservoir solution of 0.2 M ammonium chloride and 20% (w/v) PEG 3350 MME. Crystals were flash-cooled in mother liquor. Data were collected at National Synchrotron Light Source-II at beamlines 17-ID-1(AMX) on a Dectris EIGER X 16M detector. The dataset was indexed, integrated, and scaled using fastdp (67 (link)), XDS (68 (link)), and aimless (69 (link)). Monoclinic crystals of H2-Fab–p53R175H/HLA-A*02:01 diffracted to 3.5 Å. The structure for the H2-Fab-p53R175H/HLA-A*02:01 complex was determined by molecular replacement with PHASER (70 (link)) using PDB ID 6O4Y (71 (link)) and 6UJ9 as the search models. The data were refined to a final resolution of 3.5 Å using iterative rounds of refinement with REFMAC5 (72 (link), 73 (link)) and manual rebuilding in Coot (74 (link)). Structures were validated using Coot and PDB Deposition tools. The model has 95.2% of the residues in preferred and 3.8% in allowed regions according to Ramachandran statistics (table S4). Figures were rendered in PyMOL (v2.2.3, Schrödinger, LLC). Buried areas were calculated with PDBePISA (37 (link)). The docking angle that determines the relative orientation between the pHLA and the Fab/TCR was calculated by the web server TCR3d (75 (link), 76 (link)).
Hsiue E.H., Wright K.M., Douglass J., Hwang M.S., Mog B.J., Pearlman A.H., Paul S., DiNapoli S.R., Konig M.F., Wang Q., Schaefer A., Miller M.S., Skora A.D., Azurmendi P.A., Murphy M.B., Liu Q., Watson E., Li Y., Pardoll D.M., Bettegowda C., Papadopoulos N., Kinzler K.W., Vogelstein B., Gabelli S.B, & Zhou S. (2021). Targeting a neoantigen derived from a common TP53 mutation. Science (New York, N.Y.), 371(6533), eabc8697.
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8

Structural Characterization of Tha-1 Homodimer

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To identify the HEPN domain within Tha, the HHpred web-server was used (https://toolkit.tuebingen.mpg.de/tools/hhpred, version 57c8707149031cc9f8edceba362c71a3762bdbf8). To analyse the structure of Tha-1, AlphaFold226 (link) and ColabFold v1.5.227 (link) were used to generate a model for the structure of the Tha-1-Tha-1 homodimer. The structure was analysed, and images were generated by PyMOL v2.5.4 (Schrödinger). The DALI web server (accessed 27 March 2023)28 (link) searches against PDB90 (a collection of representative structures with less than 90% sequence identity from the PDB database) were performed for the truncated dimer (164–301).
Rostøl J.T., Quiles-Puchalt N., Iturbe-Sanz P., Lasa Í, & Penadés J.R. (2024). Bacteriophages avoid autoimmunity from cognate immune systems as an intrinsic part of their life cycles. Nature Microbiology, 9(5), 1312-1324.
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9

Homology Modeling of Peptide Transporters

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Homology models for PepT1 and PepT2 were made as previously described (Morellet et al., 2022 (link)). Briefly, the crystalized protein structures of PepT from Bacillus cereus (PDB ID: 3gb0), PepT from Salmonella enterica ser. Typhimurium (PDB ID: 1fno), and PepT2 from S. aureus (PDB ID: 3rza) were obtained from the RCSB Protein Data Bank (https://www.rcsb.org/). The predicted structure of PepT1 (UniProt ID: Q2FIP8) was obtained from Alphafold v2 (https://alphafold.ebi.ac.uk/). Structural alignments were generated using PyMOL v2.5.4 (Schrödinger).
Torres N.J., Rizzo D.N., Reinberg M.A., Jobson M.E., Totzke B.C., Jackson J.K., Yu W, & Shaw L.N. (2023). The identification of two M20B family peptidases required for full virulence in Staphylococcus aureus. Frontiers in Cellular and Infection Microbiology, 13, 1176769.
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10

Structural Homology Modeling of β-III-spectrin ABD

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The β-III-spectrin ABD structural homology model was generated through the i-Tasser server [26 (link)]. The top template structure was the plectin ABD (PDB ID: 1MB8). The crystal structure of β-II-spectrin calponin homology domain 2 (PDB ID: 1BKR) was used for alignment with the generated β-III-spectrin ABD homology model. Analyses of the structures, including identification of predicted contacts for different mutated residues, and alignment, was performed with PyMOL v2.5.4 (Schrödinger, New York, NY, USA).
Atang A.E., Keller A.R., Denha S.A, & Avery A.W. (2023). Increased Actin Binding Is a Shared Molecular Consequence of Numerous SCA5 Mutations in β-III-Spectrin. Cells, 12(16), 2100.
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