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Corrigendum to “Exploring and understanding the functional role, and biochemical and structural characteristics of an acidic phospholipase A2, AplTx-I, purified from Agkistrodon piscivorus leucostoma snake venom” [Toxicon 127 (2017) 22–36] (S004101011730003X) (10.1016/j.toxicon.2017.01.002)

Abstract:

2.5.2. Homology modeling and molecular dynamic studies The homology model of AplTx-I were built (using the crystal structure 1M8R as a template) and optimized using the Prime software from Schrödinger suite (Schrödinger Release, 2011). Then, the model was neutralized by adding Na + counter ions to balance the net charge of the systems and NaCl at a concentration of 0.01 M was added to simulate physiological conditions. The constructed model was subjected to molecular dynamics simulations (MDs) to reduce any close contacts resulting from the inclusion of new residues. MDs was performed using the OPLS-AA force field (Kaminski et al., 2001) within the Desmond package v2.0 contained in Maestro 9.2 suite. The simulation was set in 20 ns and an isothermal-isobaric ensemble, with temperature (300 K), pressure (1 atm) and number of atoms constant using the Nosé-Hoover method with a relaxation time of 1 ps applying the MTK algorithm. The SHAKE algorithm (Kräutler et al., 2001) was employed for every hydrogen atom and the cutoff for van der Waals forces was set at 9 Å and the long-range electrostatic forces were modeled using the particle mesh Ewald method. A restriction was applied on the backbone atoms with a constant force of 0.5 kcal × mol -1 × Å -2 . Data were collected every 4ps during the MDs. The stability of the models during the MDs was validated by calculating the Root Mean Squared Deviation (RMSD). To test the quality of the models (after MDs), they were validated using PROCHECK (Laskowski et al., 1993). The authors would like to apologize for any inconvenience caused.