Fig 4 - uploaded by Ashfaq Ahmad
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Screenshot of the residues of the target protein: bovine kappa-casein (Swiss Prot AC: P02668). The diagram depicting low (blue) and high (red) energy values suggesting the stability of protein model.
Source publication
The stability of the milk casein is dependent on the presence of Kappa-casein on the surface of the micelle where it serves as an interface between the hydrophobic caseins andthe aqueous environment of milk. Crystal structure of Shewanella oneidensis FMN-binding oxidoreductase was chosen as a template for homology modeling of Bovine Kappa-casein (C...
Context in source publication
Context 1
... energy graph of target (CASK) calculated by PROSA [13] in terms of Z-score (-1.49) indicated the overall quality of protein structure whereas it was -6.18 for template (2GOU) molecule. It is evident from the result, the energy graphs corresponded to highly stable structures (Fig. 4) and the values of energy, for the target molecule, well below Zero point. The SUPERPOSE results indicated that the homology model superimpose well on the corresponding units of the template (Fig. 5). The RMSD value between template and the predicted model using all main-chain atoms was found to be 0.1224A 0 and 0.1060A 0 . This value ...
Citations
... The KFP-1 structure was predicted according to the homology model of bovine -CN, which was created using Shewanella oneidensis FMN-binding oxidoreductase (PDB ID: 2GOU) as the template. [28] Residues were mutated, atomic distances were measured, and structural images were exported using PyMOL viewer software (https://pymol.org/academic). The hydropathy index was calculated using the GRAVY calculator (http://www. ...
... As shown in Figure 5C, the predicted tertiary structure of KFP-1 consists of an -helix (residues 2-9), a loop (residues 10-12), and a -strand (residues 13-17). This structure was predicted according to the homology model of bovine -CN using FMN-binding oxidoreductase as a template [28] (Figure 5A), in which the aligned sequences correspond to the fragment of amino acids 283-296 in FMN-binding oxidoreductase and the fragment of amino acids 138-154 in bovine -CN (Swiss-Prot accession: P02668) (Figure 5B). The sequence of KFP-1 is highly homologous to residues 138-154 of bovine -CN with 88% similarity and nearly 71% identity. ...
... A) The tertiary structure of Shewanella oneidensis FMN-binding oxidoreductase (PDB ID: 2GOU), which was used as a structural template of bovine -casein ( -CN). [28] The structure of bovine -casein (residues 138-154) (B) was predicted according to the framed region (magenta) of (A). The structure of KFP-1 (C) was predicted from bovine -CN 138-154 with residue modifications. ...
Scope
Kefir is an acidic and alcoholic fermented milk product with multiple health-promoting benefits. Our previous study demonstrated that kefir enhanced calcium absorption in intestinal Caco-2 cells. In this study, kefir-fermented peptide-1 (KFP-1) was isolated from the kefir peptide fraction, and its function as a calcium-binding peptide was characterized.
Methods and results
KFP-1 was identified as a 17-residue peptide with a sequence identical to that of κ-casein (residues 138–154) in milk protein. KFP-1 was demonstrated to promote calcium influx in Caco-2 and IEC-6 small intestinal cells in a concentration-dependent manner. TRPV6, but not L-type voltage-gated calcium channels, was associated with the calcium influx induced by KFP-1. An in vitro calcium binding assay indicated that the full-length KFP-1 peptide has a higher calcium-binding capacity than the two truncated KFP-1 peptides, KFP-1∆C5 and KFP-1C5. Alexa Fluor 594 labeling showed that KFP-1 is taken up by Caco-2 cells and interacts with calcium ions and TRPV6 protein. Moreover, KFP-1 was found moderately resistant to pepsin and pancreatin digestions and enhanced calcium uptake by intestinal enterocytes in vivo.
Conclusion
These data suggest that KFP-1, a novel calcium-binding peptide, binds extracellular calcium ions and enters Caco-2 and IEC-6 cells, and promotes calcium uptake through TRPV6 calcium channels. The present study is of great importance for developing kefir-derived metal ion-binding peptides as functional nutraceutical additives.
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The enzymes of shikimate pathway are essential for fungi, algae, bacteria and plants and their absence in mammals have made these enzymes strong candidates for drug designing. The 5- enolpyruvylshikimate 3-phosphate synthase (EPSP synthase) is the sixth enzyme of shikimate biosynthetic pathway. This agriculturally important enzyme is the prime target for the non-selective herbicide Glyphosate. We have constructed tertiary structure of V. cholerae EPSP synthase in open and closed conformations. Protein structure prediction using homology modeling provided valuable information regarding structure function relationships of this enzyme. There are significant differences in the relative orientation of the two domains in open and closed conformations. The open conformation of EPSP is prominent in the absence of substrate/inhibitor while it turns to closed conformation after binding to substrate/inhibitor which rotates the C-terminal domain at about 25 degrees.
