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Increasing sequence diversity in protein design by combining Rosetta with molecular dynamics

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Citation

Ludwiczak, J., Jarmula, A., & Dunin-Horkawicz, S. (2017). Increasing sequence diversity in protein design by combining Rosetta with molecular dynamics. In 7th Alpbach Workshop: Coiled Coil, Fibrous and Repeat Proteins (pp. 40).


Cite as: https://hdl.handle.net/21.11116/0000-000B-6F0C-D
Abstract
Protein design is a procedure for computing natural-like sequences that will fold into a specifiedstructure. It has already been demonstrated that considering the backbone flexibility during thedesign process positively influences the diversity of the resulting sequences [1]. Rosetta Design, acommonly used software for protein design, allows for the effective exploration of the sequencespace, while the molecular dynamics (MD) simulations can thoroughly sample the protein nativestate conformational space. By combining these two approaches, we developed an iterative designprocedure, in which backbone conformational ensembles obtained by clustering of MD trajectoriesare used as templates for the design. We show that such a combined approach can generatesignificantly more diverse sequences than currently used procedures. The observed increase in thediversity is achieved without a loss in the quality of sequences, measured as overall resemblance ofthe designed sequences to natural sequences. In addition, we implemented a MD-based protocol [2]that can be used for assessing the stability of designed models and selecting the best candidates forexperimental validation or generating the structural ensembles that can be used as an input forfurther design simulations. In sum, our results demonstrate that the MD ensemble-based flexiblebackbone design significantly outperforms the current state-of-the-art methods and thus should be amethod of choice for the design of virtually all protein classes, including coiled coils. Finally, tomake the procedure accessible for the community we provide a set of easy-to-use scripts forperforming the simulations and visualizing the results.