Analysing replica exchange simulations of conotoxin peptides Charlie Holdship, Prof. Jonathan Essex, Prof. Jeremy Frey University of Southampton, UK Conotoxin peptides are a class of neurotoxin derived from marine cone snail venom and target human nicotinic acetylcholine receptors (nAChR’s). To elucidate their mechanism of action, the solution conformations of the peptides must be determined before their interaction to nAChR’s can be modelled. Although some of these peptides have experimentally determined structures, some structures are still unknown due to their variety. To that end, molecular dynamics simulations of 5 conotoxins (4 with experimental structures and 1 unknown) have been run using Hamiltonian replica exchange (REST2) to enhance the sampling and more extensively explore the conformational space of the peptides. The results of these simulations were analyzed using dimension reduction algorithms such as principal component analysis (PCA) to obtain potentially stable backbone conformations of the peptides. The accompanying side chain conformations are determined using a method known as local PCA. 1 This method reduces the dataset by defining cut-off distance from a desirable property (in this case a stable backbone conformation) and then performs a second PCA on this subset to find the most common sidechain positions for the defined backbone conformation. Finally, a clustering algorithm, MDASH (molecular dynamics analysis by Salt and Hudson), 2 was used to establish the number of different conformations seen throughout the simulation and their relative populations based on the amount of simulation time spent in each conformation. The results from both analysis methods will be presented together with the different possible conformations of the conotoxin peptides. References 1. Kambhatla, N., & Leen, T. K. (1997). Neural Computation, 9(7), 1493-1516. https://doi.org/10.1162/neco.1997.9.7.1493 2. Salt, D. W., Hudson, B. D., Banting, L., Ellis, M. J., & Ford, M. G. (2005). Journal of Medicinal Chemistry, 48(9), 3214-3220. https://doi.org/10.1021/jm049216s
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