Protein structural dynamics and thermodynamics from advanced simulation techniques

TL;DRAbstract

In this work we apply simulation techniques, namely Monte Carlo simulations and a path integral based
\nmethod called Dominant Reaction Pathways
\n(DRP) approach, in order to study aspects of dynamics and thermodynamics in three different families of peculiar proteins. These proteins are, for reasons such as the presence of an intermediate state in the folding path or topological constraints or large size, different from ideal systems, as may be considered small globular proteins that fold in a two state manner. 
\nThe first treated topic is represented by the colicin immunity proteins IM9 and IM7, very similar in structure but with an apparently different folding mechanism. Our simulations suggest that the two proteins should fold with a similar folding mechanism via a populated on-pathway intermediate state. 
\nThen, two classes of pheromones that live in temperate and arctic water respectively are investigated. The two types of pheromones, despite the high structural

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