Data files

Output of the 3D-structures modeled by comparative modeling tool for LDH enzymes from four LABs (in the PDB format, tarred). Four LABs include Enterococcus faecalis, Lactococcus lactis, Streptococcus pyogenes and Lactobacillus plantarum. Output of the SEEK Model https://seek.sysmo-db.org/models/118.

The modeling was performed against a x-ray structure of LDH from B. stearothermophilis (template, PDH ID: 1LDN).

Output files of phosphate probe binding on the surface of LDH from lactococcus lactis type 1. File with extension XPLOR can be visualized with a program VMD to identify the most favorable position for the phosphate binding. This relates to the Model "Part 4".

The Table represents the simulation results of how the presence of phosphate ions (Pi) in the solution might affect the activity of four LDH enzymes. This includes the algorithmic analysis of the binding energies values computed by the GRID program (see Part 4, model) for each enzyme in presence and absence of FBP molecule at pH 6 and 7. The analysis was performed by using the algorithm proposed in Part 5, model.

For each modeled 3D structure of LHD (see Part 1: 3D structure modeling for LDH enzymes) was computed electrostatic potential by using the UHBD program. The files are in GRD format (binary) and can be visualized with the graphical programs as CHIMERA or VMD.

The output includes the similarity matrix of LDH enzymes based on comparison of the electrostatic potentials at allosteric and catalytic binding sites, separately. The similarity indices were generated by the PIPSA program (http://projects.villa-bosch.de/mcmsoft/pipsa/3.0/).

Heterologous Expression of LDHs from different lactic acid bacteria in Escherichia coli DH5α. Assessment of kinetic parameters of LDH to include in a catabolic model .

Heterologous Expression of LDHs from different lactic acid bacteria in Escherichia coli DH5α.

Assessment of kinetic parameters of LDH to include in a catabolic model.