Computational protocol: Dynamic Interplay between the Periplasmic and Transmembrane Domains of GspL and GspM in the Type II Secretion System

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Protocol publication

[…] C-terminal regions of OutL (residues 311 to 400) and OutM (residues 83 to 162) were modeled with the homology molecular modeling program MODELLER 9v11 []. For OutL, the software identified the following crystal structure as template allowing a very confident modeling of the studied region: PDB entry 2W7V (periplasmic domain of EpsL from the type 2 secretion system of V. parahaemolyticus). For OutM, a unique structure was used as template as well (PDB entry 1UV7: periplasmic domain of EpsM from V. cholerae). For both modeling studies, 30 distinct models have been generated, and their geometry was assessed by a Ramachandran plot calculated with the program PROCHECK []. Consequently, the most satisfying model was retained. For OutL, it has 96.3% of non-proline and non-glycine residues in the most favored regions, 3.7% in additionally allowed regions and none in disallowed regions. For OutM, Ramachandran plot values were 97.2% residues in most favored regions, 2.8% in additionally allowed regions and none in disallowed regions. […]

Pipeline specifications

Software tools MODELLER, PROCHECK
Application Protein structure analysis
Organisms Dickeya dadantii