Computational protocol: Cell foundry with high product specificity and catalytic activity for 21-deoxycortisol biotransformation

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Protocol publication

[…] The amino acid sequences of CYP11B1 from diversity species were aligned by ClustalW with default settings []. In the meanwhile, in order to analyze and design the complex structure of CYP11B1_Hs mutant1 (G25R/G46R/L52M) with the substrate, three-dimensional structure models were developed by Swiss-Model (http://swissmodel.expasy.org/) with the high sequence homology (>90% identify) and high-resolution crystal structure of CYP11B2 (the aldosterone synthase from Homo sapiens with ligand, PDB accession 4dvq-F) as the template. The structure models were subjected to energy minimization by Swiss-Pdb Viewer (http://spdbv.vital-it.ch/). Afterwards enzyme-ligand docking was performed by AutoDockVina program []. And the docking studies were run with 17-OHP as the ligand for above-mentioned structure model. The 17-OHP structure files (ligand) were retrieved from ZINC site []. Docking cluster analysis was performed in the AutoDockVina program environment, and clusters were characterized by binding energy (in kilocalories per mole). Establishment of docking models was also followed by energy minimization. The built complex structural analysis was done with Pymol software []. The mutation at specific amino acid site was also introduced by this software, which allowed exploration of the spatial and molecular interactions among amino acids. […]

Pipeline specifications

Software tools Clustal W, SWISS-MODEL, Swiss-PdbViewer, PyMOL
Databases ExPASy
Application Protein structure analysis
Organisms Escherichia coli str. K-12 substr. MG1655, Bos taurus, Homo sapiens, Escherichia coli
Chemicals Heme, Steroids, 17-alpha-Hydroxyprogesterone