Allison Heath, From coarse-grain to all-atom: Toward multiscale analysis of protein landscapes

Computer simulations have become an important tool in studying protein motion because they provide atomic detail that is currently unattainable by experimental processes. Unfortunately, traditional protein simulation techniques are too computationally intensive to study large scale motions because they explicitly model all of the atoms in the system.

Coarse grain models have emerged as way to reduce the computational complexity by representing many atoms as a single particle, but as a trade off they omit important details found in all-atom simulations. This has led to great interest in multiscale techniques to combine the efficiency of coarse grain models with the all-atom details. Many of these techniques require adding all-atom detail to coarse grain structures, yet the feasibility of doing this consistently is unknown. It is unclear how to properly add all-atom details to coarse grain structures to produce low energy all-atom structures. Furthermore, there have been no previous studies on whether moving from coarse grain to all-atom structures changes properties of the resulting ensemble of structures.

I will present a method that efficiently generates realistic all-atom protein structures starting from the C-alpha atom positions. This algorithm is then applied to an ensemble of structures obtained during coarse grain protein folding simulations. The results show that the algorithm consistently produces all-atom, low energy structures which agree well with experimental data and structures obtained from traditional all-atom methods.