همایش ملی بیوانفورماتیک ایران

صفحه اصلی / 4th international edition and 13th Iranian Conference on Bioinformatics

Computational Analysis of the D92V Mutation in the EF-hand II Loop of the Mnemiopsin 2 Photoprotein

نویسندگان :

Hanieh Ramezani¹ Vahab Jafarian² Akram Shirdel³ Khosrow Khalifeh⁴ Fatemeh Khatami⁵

1- University of Guilan 2- University of Guilan 3- University of Zanjan 4- University of Zanjan 5- University of Guilan

کلمات کلیدی :

Bioinformatics،Bioluminescence،EF-hand loop،Homology modeling،Mutation

چکیده :

Mnemiopsin 2 is a calcium-regulated photoprotein that has bioluminescent properties. This photoprotein has 207 amino acids with a molecular weight of 24 kDa (Hosseinnia and Khalifeh, 2020). The structure of Mnemiopsin 2 has 4 EF-hand motifs. It's worth noting that EF-hand motifs I-III-IV have calcium binding function, but EF-hand II has lost its activity during evolution (Ghanbarlou and Shirdel, 2018). Three functional motifs are located in positions (I: 45-56), (III: 137-148), (IV: 171-182), respectively. Each EF-hand has a helix-loop-helix structure. In the structure of the loops, the conserved residues in positions 1, 6, and 12 have the ability bind to calcium, and residues 3, 5, 7, and in some cases 9 also have the potential to bind to calcium (Jafarian and Sajedi, 2018). The conserved residues in all the photoproteins include aspartic acid (D) at position 1, glycine (G) at position 6 and glutamic acid (E) at position 12. (Toma and Chong, 2005). In this study, the amino acid aspartic acid (polar) at position 92 in the EF-hand II loop was replaced with valine (non-polar). It should be noted that this amino acid is the eighth residue of the EF-hand II loop. Based on homology modeling, three-dimensional structural models of protein variants were constructed with Modeller v.10.4 software. The PDB input files in this software include files Berovin (PDB code: 5bpj), Mnemiopsin 1 (PDB code: 5vP3) for the structural model, Berovin (PDB code: 4mn0) for the calcium binding model and Aecuorin (PDB code: 1ej3) for coelenterazine binding pattern. The sequence-based parameters, including hydrophobicity, instability index, and PI, were obtained by ProtScale and ProtParam servers. Then, the best model was selected based on RMSD, Zdope, ERRAT, and Verify3D parameters, using Chimera x.1.8 software and ModEval, SAVES servers, respectively. Also, the evaluation of models in this study was done based on the parameters of the second structure on a VADAR server. Our aim in this study is to investigate the effects of replacing hydrophobic residue with hydrophilic ones in the EF-hand II loop. The increase in the isoelectric point in the mutant compared to the wild-type model can cause changes in the function of the loop and its calcium binding affinity. Evaluation of the secondary structure of the mutant shows increases in the coil structure. The results of bioinformatics studies indicate a decrease in the free energy of folding, which indicates the stabilization of the structure of the D92V mutant.