Article .

Article.

A short summary of the research article entitled “Insight into RIPK4 mutations I121N and T184I involved in popliteal pterygium syndrome lethal type using computational methods”. #research

Summary.

?Introduction.

?The popliteal pterygium syndrome is a genetic disorder that affects the face, limbs, and genitals. Many birth defects have been reported in this syndrome. Almost The total number of cases of popliteal pterygium syndrome worldwide is 25,100. The affected people with the disease may have abnormal genital characteristics and no growth delay. Their intelligence is also normal. The tradition remains an autosomal leading. it is produced by genetic change in IRF6 gene. popliteal pterygium syndrome is a part of IRF6 related disorder. receptor interacting serine threonine protein kinase 4 (RIPK4) is that involve in causing popliteal syndrome. lethal type RIPK4 receptor in provocative responses. the most important mutation of RIPK4 causing popliteal syndrome located at position of 121 and 184 both cause in the loss of functionality RIPK45-10. Among the proteins, the serine/threonine kinase domain contains a mutation at amino acid position 121 (p.I1e121Asn) caused by an exchange of conserved isoleucine with asparagine.

Methodology:

It has been retrieved from OMIM database (Online Mendelian Inheritance in Man) MIM# 263650, an online database containing human genes and diseases. An online tool PSIPRED was used to predict secondary structures of wild type RIPK4 and mutants I121A and T184I. While the crystal structure of murine receptor-interacting protein kinase 4 (RIPK4) has been reported by X-ray diffraction method, it does not cover the entire sequence. In light of the lack of a complete structure of human RIKP4 protein, we used MODELLER to predict the structures of all three sequences of this protein (Wild type, I121A, and T184I mutants). For the four templates (5WNI-L, 6ES0, 4C8B, and 4WNI-L), the murine receptor-interacting protein kinase 4 (RIPK4) crystal structure was taken as a template. For 3D protein structure visualization and to identify the effects of mutations on structure and behavior, superimposition of the wild and mutant structures of RIPK4 was performed using PyMol. We compared the binding sites of wild-type RIPK4 to those of its mutants to determine the effect of mutations on these sites. 3Drefine was used to minimize predicted structures of RIPK4 and its mutants (I121N, and T184I) during docking analysis. In full STRING network type, all 50 closely related proteins of RIPK4 were retrieved from the STRING database with a medium confidence score of 0.4. To determine whether the mutation had a significant effect on residual interactions, we docked a common protein in the network with RIPK4 native and mutant models. RIPK4 and its mutants (I121N and T184I) were docked with neighboring proteins using the Hex Protein Docking method in protein-protein docking. RIPK4 and its mutants (I121A and T184I) were docked with ligands (4GD, 4GF, 6GE, 6QY, 6R0, 8BY, 8YB, 9LI, 9YS, 9YY, 33Y, 064) with PyRx software to see interactions. LigPlus was used to analyze interactions between wild and mutant structures with neighbor proteins and ligands.?Which more studied by means of LigPlus.the resulting 2D pictures were associated to classify any possible changes in interacting residues caused by the mutation at position |120N and T181|.For MSA an online tool T coffee was used providing sequence of orthologs in text format along with the sequence of PIRK4 wild type. the resultant phylogenetic tree formed using bootstrap values were then interrupted to identify the evolution among orthologous of pirk4 gene

?Results.

The secondary structure predicted using PSIPRED showed variation in the number of residues of coils, helix, and sheets among the wild and mutant sequences of RIPK4, which confirms the

effect of the mutation on the structure.?Tertiary?structure prediction. the tertiary structure prediction is the three dimensional and globular structure formed by the packing together of folding of secondary structure of polypeptide chain structure evaluation is the predicted structure was evaluated by Ramachandran plot approach of PAMAGE software to detect the percentage of residue laying in the favored region to identify the predicted structure. structure?refinement?all three structure of RIPK4 wild and both mutant types predicted by using MODELLER while refine using 3rd?tool to minimize the energy of system.?Pocket generation.?than these identified pouches of wildtype RIPK4?and its mutation was compared to distinguish the effect of mutation on necessary places of the protein before docking analysis the active sites of RIPK4 protein and its mutants were identified using CSTP the online tool for the identification of active sites.?in the protein protein docking. the protein protein docking is the prediction of the structure of the complex. given?the structure of individual protein in the heart of docking methodology is the notion of steric and physicochemical coplanarity at the protein protein interface.?docking analysis molecular docking analysis is the bioinformatic based approach to analysis the fit binding and interaction between protein and ligand based on their binding energy. All these ligands were docked with both wildtype and mutant type protein structure because they give both mutant docked compounds. evolutionary analysis?fifteen orthologs of RIPK4 were selected and retrieved from the ensemble database pairwise alignment of homo sapiens with selected orthologs were performed using THR position using 184 between all orthologs phylogenetic analysis?The resultant phylogenetic tree formed using bootstrap values were then interrupted to identify the evolution among orthologs of the PIRK4 gene.?

?Discussion

?RIPK4 protein plays a dynamic role in the progress of epithelial membrane then can be accountable for for Popliteal Pterygium Syndrome. To identify its role and functionality, in silico education of protein RIPK4 wild kind and it’s both sports I121A and T184I were directed Secondary and tertiary construction prediction and Calculation, cutting interface, Pocket identification, and Phylogenetic analysis were over. PSIPRED results indicated the change in the number of residues in helices, elements, and coils of the secondary structures of RIPK4 and both I121A and T184I mutants. Homology model of RIPK4 protein and both variations spotted major differences among their secondary and tertiary formations; flat slight modification was verified through superimposition by positioning the RIPK4 protein with its mutations separately. CASTp results showed that the total number of active sites identified in RIPK4 and both I121A and T184I mutants. The docking result shows verity not only in the linking ruins of RIPK4 (wild type & mutants) with ligands and protein but also depicted is the changes changes in in the hydrogen bonding, hydrophilic and hydrophobic talks. T-Coffee results bare 100% amino acid protection in all 15 orthologs class that shows its conserved the importance in protein conserved region and protein functionality. These results revealed the importance of these mutated amino acids and it also revealed that it does not affect the structure of protein only but also its active sites thus leading to an adjustment in the protein role resulting in the illness state.

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