Homology modeling and molecular dynamics simulation of odonthubuthus doriae (Od1) scorpion toxin in comparison to the BmK M1



Zahra Karimi1, Sajad Falsafi-Zadeh1, Hamid Galehdari2 & Amir Jalali3*



1Bioinformatics Unit, Department of Genetics, Shahid Chamran University, Ahvaz, Iran; 2Department of Genetics, Shahid Chamran University, Ahvaz, Iran; 3Department of Pharmacology and Toxicology, School of Pharmacy and Toxicology Research Center, Jundishapur University of Medical Sciences, Ahvaz, Iran


Email; *Corresponding author


Article Type




Received May 11, 2012; Accepted May 15, 2012; Published May 31, 2012



All of the α-subgroups share similarity in their sequence and structure but different in the toxicity to various voltage-gated sodium channels (VGSCs). We modeled the first 3D structural model of the Od1 based on BmK M1 using homology modeling. The reliability of model for more investigation and compare to BmK M1 has been examined and confirmed. Then the model structure is further refined by energy minimization and molecular dynamics methods. The purpose of this modeling and simulation is comparison toxicity of two mentioned toxins by investigation structural feature of functional regions including core domain, 5-turn and C-terminal which make NC domain. In the one hand, it is intriguing that Od1 in comparison to BmK M1 shows same solvent accessible surface area (SASA) in 5-turn region but a little more exposed and feasibility (more SASA) in C-terminal region and key functional residues of C-terminal such as positive residues Arg58, lys62 and Arg (His)64. These data suggested that Od1 has similarity with BmK M1 but has more toxicity to sodium channel. In the other hand 5-turn proximity of C-terminal to 5-turn in BmK M1with cis peptide bond is less than Od1 without cis peptide bond which is a confirmation with experimental data about BmK M1.A better understanding of the 3-D structure of Od1and comparison to BmK M1 will be helpful for more investigation of functional characters action of natural toxins with a specialized role for VGSCs.



Homology modeling, Od1, BmKM1, Molecular dynamics simulation, α-like toxin



Karimi et al. Bioinformation 8(10): 474-478 (2012)

Edited by

P Kangueane






Biomedical Informatics



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