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TitleA general computational design strategy for stabilizing viral class I fusion proteins.
Journal, issue, pagesNat Commun, Vol. 15, Issue 1, Page 1335, Year 2024
Publish dateFeb 13, 2024
AuthorsKaren J Gonzalez / Jiachen Huang / Miria F Criado / Avik Banerjee / Stephen M Tompkins / Jarrod J Mousa / Eva-Maria Strauch /
PubMed AbstractMany pathogenic viruses rely on class I fusion proteins to fuse their viral membrane with the host cell membrane. To drive the fusion process, class I fusion proteins undergo an irreversible ...Many pathogenic viruses rely on class I fusion proteins to fuse their viral membrane with the host cell membrane. To drive the fusion process, class I fusion proteins undergo an irreversible conformational change from a metastable prefusion state to an energetically more stable postfusion state. Mounting evidence underscores that antibodies targeting the prefusion conformation are the most potent, making it a compelling vaccine candidate. Here, we establish a computational design protocol that stabilizes the prefusion state while destabilizing the postfusion conformation. With this protocol, we stabilize the fusion proteins of the RSV, hMPV, and SARS-CoV-2 viruses, testing fewer than a handful of designs. The solved structures of these designed proteins from all three viruses evidence the atomic accuracy of our approach. Furthermore, the humoral response of the redesigned RSV F protein compares to that of the recently approved vaccine in a mouse model. While the parallel design of two conformations allows the identification of energetically sub-optimal positions for one conformation, our protocol also reveals diverse molecular strategies for stabilization. Given the clinical significance of viruses using class I fusion proteins, our algorithm can substantially contribute to vaccine development by reducing the time and resources needed to optimize these immunogens.
External linksNat Commun / PubMed:38351001 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution2.41 - 3.72 Å
Structure data

29035

8fez

EMDB-29035, PDB-8fez:
Prefusion-stabilized SARS-CoV-2 spike protein
Method: EM (single particle) / Resolution: 3.72 Å

PDB-7tn1:
Multistate design to stabilize viral class I fusion proteins
Method: X-RAY DIFFRACTION / Resolution: 3.1 Å

PDB-8e15:
A computationally stabilized hMPV F protein
Method: X-RAY DIFFRACTION / Resolution: 2.41 Å

Chemicals

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

ChemComp-HOH:
WATER

Source
  • severe acute respiratory syndrome coronavirus 2
  • respiratory syncytial virus
  • human metapneumovirus
  • enterobacteria phage t2 (virus)
KeywordsVIRAL PROTEIN / Respiratory syncytial virus / Fusion protein / Human metapneumovirus / computational stabilization / prefusion state

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