Molecular modeling of the photoprotein mnemopsin chimeric (PMC): with a structural and functional recovery approach of the EF-hand II loop

Ramezani, Hanieh; Karimi Takaromi, Zahra; Mohammadi, Amir Reza; Khatami, Fatemeh; Jafarian, Vahab

doi:10.48311/biot.2025.103432.0

Molecular modeling of the photoprotein mnemopsin chimeric (PMC): with a structural and functional recovery approach of the EF-hand II loop

Document Type : Original Research

Authors

hanieh Ramezani ¹

Zahra Karimi Takaromi ¹

Amir reza Mohammadi ¹

Fatemeh Khatami ²

vahab jafarian ³

¹ M.Sc. Student of biochemistry, Department of biology, Faculty of science, University of Guilan, Rasht, I.R. Iran.

² Ph.D. Student of biochemistry, Department of biology, Faculty of science, University of Guilan, Rasht, I.R. Iran.

³ Professor of biochemistry, Department of biology, Faculty of science, University of Guilan, Rasht, I.R. Iran.

https://doi.org/10.48311/biot.2025.103432.0

Abstract

Mnemiopsin 2 is a Ca2+ regulated photo protein with 207 residues and a molecular weight of 24722 Daltons. In the structure of this photoprotein, the EF-hand I-III-IV motifs have retained their function in binding to Ca2+, while the EF-hand II has lost its activity during evolution. Each EF-hand has a helix-loop-helix (HLH) structure. Loops with length of 12 residues are responsible for Ca2+ binding. In this study, in order to recovery the structural and functional of the EF-hand loop II, a Photoprotein Mnemiopsin Chimeric (PMC) was designed using direct evolution and rational design. The mutant structure were modeled by Modeller v2.10 software. Then the best model was evaluated using the Chimera x.8.1 software and Modeval and SAVES and ModEval server for RMSD, RRDistance, Z-Dope, Errat and Verify 3D parameters were investigated. Also, the secondary structure, free energy of folding and accessible surface of the models were investigated by the VADAR server. The hydrophobicity and instability index were evaluated by Protscale and ProtParam servers. The Prosite results indicate the formation of EF-hand II loop in PMC. It is worth mentioning that Changes in the surface hydrophobicity of the recovered EF-hand II motif may affect the interaction with Ca2+. That means, due to the increase the Ca2+ binding sites, sensitivity to Ca2+ and activity were predicted to change.

Keywords

Bioinformatics

Bioluminescence

Mutation

Photoprotein

Structural recovery

Subjects