Automatically fixing errors in glycoprotein structures with Rosetta

By Brandon Frenz, S. Rämisch, A. J. Borst, A. Walls, Jared Adolf-Bryfogle, William R. Schief, D. Veesler, Frank DiMaio. 2018

110 citations recorded by the source corpus.

Summary Recent advances in single-particle cryo-electron microscopy (cryoEM) have resulted in determination of an increasing number of protein structures with resolved glycans. However, existing protocols for the refinement of glycoproteins at low resolution have failed to keep up with these advances. As a result, numerous deposited structures contain glycan stereochemical errors. Here, we describe a Rosetta-based approach for both cryoEM and X-ray crystallography refinement of glycoproteins which is capable of correcting conformational and configurational errors in carbohydrates. Building upon a previous Rosetta framework, we introduced additional features and score terms enabling automatic detection, setup and refinement of glycan-containing structures. We benchmarked this approach using twelve crystal structures and showed that glycan geometries can be automatically improved while maintaining good fit to the crystallographic data. Finally, we used this method to refine carbohydrates of the human coronavirus NL63 spike glycoprotein and of an HIV envelope glycoprotein, demonstrating its usefulness for cryoEM refinement.

Subfields: Molecular Biology, Structural Biology

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Molecular Biology

1. Jeffrey J. Gray
2. Jared Adolf-Bryfogle
3. William R. Schief
4. Frank DiMaio
5. D. Veesler
6. A. Walls
7. Maxim V. Shapovalov
8. Neil P. King

In Structural Biology

1. D. Veesler
2. A. Walls
3. M. A. Tortorici
4. Frank DiMaio
5. Andrew T. McGuire
6. A. Wall
7. Young-Jun Park

Citations in the corpus

• Mapping Neutralizing and Immunodominant Sites on the SARS-CoV-2 Spike Receptor-Binding Domain by Structure-Guided High-Resolution Serology (2020, unknown): “…of the SARS-CoV neutralizing mAb S230-and ACE2-mediated transition of SARS-CoV S from the prefusion to the postfusion states (Song et al., 2018; Walls et al., 2019), the cryo-EM observation of S 1 subunit trimers released from the MERS-CoV S ectodomain upon cleavage at S 1 /S 2 (Yuan et al.,…”
• Unexpected Receptor Functional Mimicry Elucidates Activation of Coronavirus Fusion (2020, unknown): “…Adams et al., 2010 http://www.phenix-online.org/ PISA Krissinel and Henrick, 2007 http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html Rosetta Frenz et al., 2019 https://www.rosettacommons.org/software Leginon Suloway et al., 2005…”
• Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein (2020, methodology): “Glycan refinement relied on a dedicated Rosetta protocol, which uses physically realistic geometries based on prior knowledge of saccharide chemical properties (Frenz et al., 2019), and was aided by using both sharpened and unsharpened maps.”
• Growing Glycans in Rosetta: Accurate de novo glycan modeling, density fitting, and rational sequon design (2021, methodology): “We build on earlier work that enabled representing and evaluating carbohydrate structures within Rosetta [40] and in loading, representing, and refining glycans from the Protein Data Bank [41].”