Protocol detail

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).

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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.

Publication 2023

PyMOL v2.5.4

Bacillus cereus Pept Protein Salmonella enterica

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Variable analysis

independent variables

Predicted structure of PepT1 (UniProt ID: Q2FIP8) obtained from Alphafold v2
Crystallized 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) obtained from the RCSB Protein Data Bank

dependent variables

Structural alignments generated using PyMOL v2.5.4 (Schrödinger)

control variables

Not explicitly mentioned

controls

No positive or negative controls were explicitly mentioned in the provided information.

Annotations

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