Anna Feldman-Salit

Comparative Systems Biology: Lactic Acid Bacteria

Despite high similarity in sequence and catalytic properties, the L-lactate dehydrogenases (LDH) in lactic acid bacteria (LAB) display differences in their regulation which may arise from their adaptation to different habitats. We combined experimental and computational approaches to investigate the effects of fructose-1,6-bisphosphate (FBP), phosphate (Pi) and ionic strength (NaCl concentration) on 6 LDHs from 4 LABs studied at pH 6 and pH 7. We find: (1) The extent of activation by FBP (Kact) ...

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/).

3D structure prediction of LDH enzymes from four LAB by comparative modeling against x-ray structure of LDH from B. stearothermophilis (template, PDB ID: 1LDN). The computation was performed with a protocol that uses "automodel.very_fast" settings of Modeller program (http://salilab.org/modeller/).

Comparison of electrostatic potentials within the allosteric binding sites of LDH enzymes to estimate the binding affinity of the FBP molecule is performed with the PIPSA program. The program uses the structure of enzymes in the PDB format and computed electrostatic potentials in the GRD format.

Computation is performed for the modeled 3D structures of LDH enzymes (in PDB format) with the UHBD program, for pH 6 and pH 7.

Binding energies of phosphate ions to the allosteric and catalytic sites were estimated with a program GRID (http://www.moldiscovery.com/soft_grid.php). The calculations were performed for the modeled LDH structures from four LABs, at pH 6 and 7, in presence and absence of the FBP molecule. The phosphate ion was presented as a probe.

In order to estimate whether Pi has an activatory or an inhibitory effect on the enzymes, the computed probe binding energies (from GRID results, Part 4) were compared with those for the LDH from L. plantarum whose activity is known to be unaffected by Pi.

The binding energies of the Pi probe in the allosteric binding site (AS) and the COO probe in the catalytic binding site (CS) of LDH from L. plantarum were defined as E¬AS,threshold and ECS,threshold, respectively. For the other LDH enzymes, ...

Structural models of the LAB PYKs of L. lactis, L. plantarum, S. pyogenes and E. faecalis including the "best" docking solutions of potential allosteric ligands. The structures were derived by homology modeling based on the template of E. coli and B. stearothermophilus. PYK models and ligands are provided as .pdb files and can be displayed by using the program PyMOL, for instance.

Poster presented at the 12th International Conference on Systems Biology (ICSB), Heidelberg/Mannheim, August 28 - September 1, 2011.