Modeling the Structure of Helical Assemblies with Experimental Constraints in Rosetta

Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1764)

Abstract

Determining high-resolution structures of proteins with helical symmetry can be challenging due to limitations in experimental data. In such instances, structure-based protein simulations driven by experimental data can provide a valuable approach for building models of helical assemblies. This chapter describes how the Rosetta macromolecular package can be used to model homomeric protein assemblies with helical symmetry in a range of modeling scenarios including energy refinement, symmetrical docking, comparative modeling, and de novo structure prediction. Data-guided structure modeling of helical assemblies with experimental information from electron density, X-ray fiber diffraction, solid-state NMR, and chemical cross-linking mass spectrometry is also described.

Key words

Structure prediction Structure determination Helical symmetry Helical assemblies Fibrils Fibers Rosetta 

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Department of Biochemistry and Structural Biology, Center for Molecular Protein ScienceLund UniversityLundSweden

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