Project A04.2

Principal Investigators

Prof. Dr. Maya Topf & Prof. Dr. Charlotte Uetrecht


CSSB – Center for Structural Systems Biology
Leibniz Institute of Virology/University Medical Center Hamburg- Eppendorf
& Universität zu Lübeck

A4.2

PhD candidate

Shaina To

A4.2

Project Summary

Modeling interfaces and designing peptides and other molecules to disrupt capsid assembly, stability, and size

Human norovirus (hNoV) is the leading cause of acute viral gastroenteritis. The viral capsid of hNoV is particularly fascinating, able to persist on surfaces for long periods of time indicating high structural stability [1]. Additionally, variability of capsid size has been observed [2-4], dependent to an extent on the viral strain and the conditions in which assembly happens, which can be useful in biotechnological applications.

The capsid forms by a self-assembly process of the VP1 dimers. In nature, T=3 icosahedral capsids are the norm, with the T number indicating that each of the 60 asymmetrical units contains 3 subunits. However, the lack of robust cell culture systems hinders further investigations on the pathogen. Instead of the complete virion, virus-like particles (VLPs) are utilized, composed of only the major capsid protein VP1. For VLPs, 90 VP1 dimers form the natural T=3 capsid, but other icosahedral symmetries are possible, such as T=1 (only 1 protein unit per asymmetric unit) [2], potentially non-icosahedral [1], and T=4 (4 protein units per asymmetric unit) particles [3-4]. 

The VP1 protein consists of the shell (S) and the protruding (P) domain, which mediate the interdimer and intradimer interactions, respectively. However, the exact protein interactions within VP1 that govern the plasticity of size and stability of VLPs, which may be affected by strain sequence and/or buffer conditions, remain unknown [1]. Due to the dynamic nature of capsid assembly, structural prediction methods with static outputs are insufficient to model this process. Thus, we set out to develop an integrative modeling technique combining data from structure determination [3-4] and prediction methods and mass spectrometry-based structural proteomics [5], specifically, hydrogen deuterium exchange mass spectrometry (HDX-MS) [6-7]. Models determined by cryoEM and X-ray crystallography or predicted by AlphaFold [8] visualize the overall structure of the capsids, while HDX-MS provides insights on interface locations, solvent accessibility, secondary structures, and conformational changes. Integrating such information will allow us to model the different VP1 capsids in order to bring us closer to understanding hNoV capsid assembly.

References for Graphical abstract

  1. VP1 dimer in cryoEM model – Hu L, Salmen W, Chen R, Zhou Y, Neill F, Crowe JE Jr, Atmar RL, Estes MK, Prasad BVV. Atomic structure of the predominant GII.4 human norovirus capsid reveals novel stability and plasticity. Nat Commun. 2022 Mar 10;13(1):1241. doi: 10.1038/s41467-022-28757-z.
  2. HDX-MS – Stofella M, Grimaldi A, Smit JH, Claesen J, Paci E, Sobott F. Computational Tools for Hydrogen-Deuterium Exchange Mass Spectrometry Data Analysis. Chem Rev. 2024 Nov 13;124(21):12242-12263. doi: 10.1021/acs.chemrev.4c00438.
  3. T=3 (left capsid) PDB 6OTF
  4. T=1 (middle capsid) PDB 6OUC
  5. T=4 (right capsid) PDB 6OUU

References

  1. Pogan R, Dülfer J, Uetrecht C. Norovirus assembly and stability. Curr Opin Virol. 2018;31:59-65. doi: 10.1016/j.coviro.2018.05.003
  2. Pogan R, Weiss VU, Bond K, et al. N-terminal VP1 Truncations Favor T = 1 Norovirus-Like Particles. Vaccines (Basel). 2020 Dec 24;9(1):8. doi: 10.3390/vaccines9010008.
  3. Hu L, Salmen W, Chen R, et al. Atomic structure of the predominant GII.4 human norovirus capsid reveals novel stability and plasticity. Nat Commun. 2022 Mar 10;13(1):1241. doi: 10.1038/s41467-022-28757-z.
  4. Jung J, Grant T, Thomas DR, et al. High-resolution cryo-EM structures of outbreak strain human norovirus shells reveal size variations. Proc Natl Acad Sci U S A. 2019 Jun 25;116(26):12828-12832. doi: 10.1073/pnas.1903562116.
  5. Manalastas-Cantos K, Adoni KR, Pfeifer M, et al. Modeling Flexible Protein Structure With AlphaFold2 and Crosslinking Mass Spectrometry. Molecular & Cellular Proteomics. 2024;23(3):100724. doi:10.1016/j.mcpro.2024.100724
  6. Konermann L, Scrosati PM. Hydrogen/Deuterium Exchange Mass Spectrometry: Fundamentals, Limitations, and Opportunities. Molecular & Cellular Proteomics. 2024;23(11):100853. doi:10.1016/j.mcpro.2024.100853
  7. James EI, Murphree TA, Vorauer C, Engen JR, Guttman M. Advances in Hydrogen/Deuterium Exchange Mass Spectrometry and the Pursuit of Challenging Biological Systems. Chem Rev. 2022;122(8):7562-7623. doi:10.1021/acs.chemrev.1c00279
  8. Jumper J, Evans R, Pritzel A, et al. Highly accurate protein structure prediction with AlphaFold. Nature. 2021;596(7873):583-589. doi:10.1038/s41586-021-03819-2