Some PbMLS-interacting proteins from metabolic pathways such as the glycolytic
pathway, the tricarboxylic acid cycle, the methyl citrate cycle and the glyoxylate cycle were selected for analysis. Because PbMLS participates in the glyoxylate cycle, interaction between proteins from different metabolic pathways would be expected. Because no crystal structure of PbMLS-interacting proteins described here was reported, a three-dimensional homology Selonsertib model for each protein was constructed based on the structure template listed in Additional file 6: Table S5. All of the 3D-structure templates used to build models of the proteins have a resolution of < 2.0 Å and an identity of > 49%, with a coverage of > 91%. Homology
models of the PbMLS-interacting proteins have very little conformational change when compared to their templates (Additional file 6: Table S5). The largest deviations were observed for enolase and fructose 1,6 bisphosphate aldolase, with 2.65 Å and 1.44 Å of root mean square derivation (RMSD) when superposed on the template when considering the non-hydrogen atoms. For enolase, there is a significant conformational Tucidinostat molecular weight change only in the C-terminal regions and between PRO143 and ASN155 (data not shown). Alpha-helix-like secondary-structure patterns were observed in a greater proportion in the homology models PbMLS-interacting proteins. For almost all of the structures, the alpha-helix-like pattern corresponded to more than 40% of the whole structure, while the beta-sheet-like pattern accounted for less than 20%, except for the protein ubiquitin, whose quantity of beta-sheet-like pattern was greater (Additional file 6: Table S5). Ramachandran plots of homology models were assessed stereo-chemically through the RAMPAGE web server  (data not shown). For all of the proteins, the Φ and Ψ distributions of
the Ramachandran plots were always above 94% in the favored regions and less than 3.5% in the allowed regions. The quality factors of the structures were estimated by the ERRAT web server and are summarized in Additional file 6: Table S5. Molecular dynamics All of the proteins were subjected to at least 20 ns simulation using GROMACS software . For Cyclin-dependent kinase 3 the proteins gamma actin, 2-methylcitrate synthase, triosephosphate isomerase and ubiquitin, that time was insufficient to achieve RMSD stability of non-hydrogen atoms with respect to the structure homology models. In those cases, more simulation time was provided until this condition was achieved. The times required are listed for each protein. For almost all of the proteins, the deviations from their homology models were low (approximately 3.0 Å). Specifically, TEW-7197 ubiquitin and 2-methylcitrate synthase had the highest RMSDs. The increase was 7.65 Å and 6.34 Å after 60 ns and 40 ns, respectively.