This folder contains the PDBs for each PZAse structure obtained by homology modeling with SWISS-MODEL, the datasets generated by structural analysis and used to build log-linear models, and the set of log-linear models for each kinetic parameter.
This folder contains the scripts to perform normal mode analysis, molecular dynamics and to calculate geometrical descriptors for each PZAse structure.
This folder contains the scripts needed for building log-linear models to predict kinetic parameters.
The file position_analysis.Rmd takes four inputs:
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kinetic_parameters.csv: A CSV file containing the relative experimental means of the kinetic parameters.
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electrostatic_potentials.csv: A CSV file containing a dataset with the physicochemical descriptors.
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fluctuations.csv: A CSV file containing a dataset with the stability descriptors derived by normal mode analysis.
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rmsf_backbone.csv: A CSV file containing a dataset with the stability descriptors derived by molecular dynamics.
The outputs are the following figures:
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Comparison of fluctuations, RMSFs, and electrostatic potentials profiles for all the structures under study, highlighting the WT profiles in red.
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Three boxplots of fluctuations, RMSFs, and electrostatic potentials per position along PZAse for structures with a relative kcat greater or equal than 50, and other three similar boxplots for structures with a relative kcat less than 50.
And CSV files:
- Three CSVs files with the outputs of non-parametric tests per position for the mean value of fluctuations, RMSFs, and electrostatic potentials.
The file distance_analysis.Rmd takes twelve inputs:
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Activity_models.RData: A set of R objects for the log-linear models for activity
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Efficiency_models.RData: A set of R objects for the log-linear models for efficiency
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Km_models.RData: A set of R objects for the log-linear models for KM
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Kcat_models.RData: A set of R objects for the log-linear models for kcat
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distance_to_aa_8.csv: A CSV file with the distances between alpha-carbons of each amino-acid of each structure and Asp8
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distance_to_aa_49.csv: A CSV file with the distances between alpha-carbons of each amino-acid of each structure and Asp49
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distance_to_aa_51.csv: A CSV file with the distances between alpha-carbons of each amino-acid of each structure and His51
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distance_to_aa_57.csv: A CSV file with the distances between alpha-carbons of each amino-acid of each structure and His57
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distance_to_aa_71.csv: A CSV file with the distances between alpha-carbons of each amino-acid of each structure and His71
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distance_to_aa_96.csv: A CSV file with the distances between alpha-carbons of each amino-acid of each structure and Lys96
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distance_to_aa_138.csv: A CSV file with the distances between alpha-carbons of each amino-acid of each structure and Cys138
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residues.txt: A text file containing the identity of all the residues in PZAse
The output are three figures, one for each kind of descriptors, displaying the 20 nearest residues to each amino-acid of the active site and metal coordination site of wild-type PZAse. Residues associated with selected descriptors are highlighted in red.