Computational protocol: Characterization of Kbot21 Reveals Novel Side Chain Interactions of Scorpion Toxins Inhibiting Voltage-Gated Potassium Channels

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Protocol publication

[…] The homology model of Kbot21 was built using the NMR structures of the BmBKTx1 peptide [] (PDB code: 1Q2K). In order to partially account for the flexibility of the scorpion peptides, all the 21 NMR solutions presented in the PDB file were used as templates to build 21 models of Kbot21. The structural models were generated by simply mutating the 13th (Val to Arg) and 24th (Asn to Asp) amino acids using SCWRL4 program [] followed by 50 and 500 steps of energy minimization using steepest-descent and adopted basis Newton-Raphson methods respectively.The Kv1.2 is a potassium channel belonging to the Shaker-like subfamily. Its full length crystallography structure was solved for the first time by Long et al. []. However, in our study we used the crystal structure of Kv1.2-Kv2.1 paddle chimera channel due to its better quality []. In our study we were restricted only to the pore domain.The homology models of Kv2.1 and Kv1.4 were build with MODELLER 9v8 [] using only the pore domain of the channel crystal structure (PDB code: 2R9R) []. Sequences of human Kv2.1 and Kv1.4 were retrieved from Uniprot database (http://www.uniprot.org/) under Q14721 and P22459 codes, respectively. Twenty structures were generated for each subtype and their respective DOPE [] scores were calculated. The models of Kv1.4 and Kv2.1 with the lowest DOPE values were selected and retained. […]

Pipeline specifications

Software tools SCWRL, MODELLER
Application Protein structure analysis
Organisms Buthus occitanus, Mesobuthus martensii
Chemicals Potassium