Effects of oscillating electric fields on conotoxin peptide conformation: A molecular dynamic simulation study

Abstract

Molecular Dynamics (MD) simulation is a computational method frequently used in biological and material sciences to efficiently model atomic and molecular interactions occurring in biological systems and effects of external stimuli on molecules and cells.In this study, M − 1 conotoxin protein was simulated under the oscillating (time-varying) electric fields of strengths 2e−9, 6e−9 and 4.7e−8 V/nm at the frequency of 1800 MHz. Conformational changes in conotoxin were studied using Root Mean Square Deviation (RMSD), Root Mean Square Fluctuation (RMSF), secondary structure analysis and Radial Distribution Functions (RDF). We also performed cluster analysis for Conotoxin by running three simulations at the same parameters to analyse an overall conformation of the peptide.Our findings show that applied oscillating electric field of 4.7e−8 V/nm produced changes in the conformation of conotoxin, whereas, at 6e−9 V/nm, only minor changes were observed, which were then stabilised during the simulation. The results also reveal that the applied field at the lowest strength of 2e−9 did not induce any effects on conotoxin’s conformation.