Coarse-grained simulations of intrinsically disordered peptides

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Abstract

Intrinsically disordered proteins (IDPs) are functional proteins which lack a unique and stable tertiary structure. IDPs such as n16N are involved in biomineralisation, the process by which organisms produce mineral materials, such as shells. Here, the role that accelerated simulation can play in the study of IDPs is examined and furthered. The coarse-grained models PLUM and PRIME20 are implemented and refined based on existing single-chain n16N simulations. In conjunction with the replica exchange molecular dynamics technique, the models are used to simulate systems of 1, 2, 3 and 6 chains of n16N, and a mutant form n16NN. The modified PLUM model is in striking agreement with existing hypotheses regarding the structure of n16N, when simulations are run in multiplicity. The PRIME20 model has difficulty producing plausible backbone structure in every system size, though it does fulfil some expectations regarding residue interaction specificity. New hypotheses are offered on bulk n16N and n16NN aggregation based on the presented data. Future directions for development of accelerated simulation techniques for IDPs are suggested.

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