Project C01.2

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C1.2

Project Summary

Structural investigation of UL3 from herpes simplex virus type 1: A structural homolog of a conserved DNA-binding protein domain in herpesviral proteins?

The herpes simplex virus 1 (HSV-1) belongs to the family of Orthoherpesviridae, being a widespread member of the subfamily of Alphaherpesvirinae, with a prevalence of 64 % in people under age 50 [1]. HSV-1 infection typically manifests as cold sores and genital herpes, while particularly in immunocompromised individuals and neonates it can also include severe complications such as herpes stromal keratitis, meningitis and herpes simplex encephalitis. After primary infection, HSV-1 can establish a lifelong latency in ganglionic neurons with the potential to reactivate [2, 3]. 

Recent AI-based homology studies within the Orthoherpesviridae family using the HerpesFolds algorithm have discovered structural homology in the viral DNA binding domain of important key players in the latency establishment, maintenance and regulation [4-9]. These homolog structures include the Ebstein-Barr nuclear antigen 1 (EBNA1) of the Ebstein-Barr virus (EBV), the latency associated nuclear antigen (LANA-1) of the Kaposi’s sarcoma associated herpesvirus (KSHV), and the unique long protein 3 (UL3) of HSV-1. This makes UL3 an interesting target when discussing a potential structure-function relationship.The aim of this project is to investigate the structure of UL3 with a focus on the DNA binding domain in comparison with predicted homolog structures in other herpesviruses. We plan to elucidate the structure by employing conventional X-ray crystallography, in cellulo crystallization approaches [10], microcrystal electron diffraction (mED), as well as cryo-electron microscopy. A crystallographically determined structure and a functional characterization of UL3 could be used for future structure-based identification and development of small molecule inhibitors.

C1.2

References

1. Harfouche M, AlMukdad S, Alareeki A, et al. Estimated global and regional incidence and prevalence of herpes simplex virus infections and genital ulcer disease in 2020: mathematical modelling analyses. Sex Transm Infect. 2025 May 19;101(4):214-223. doi: 10.1136/sextrans-2024-056307.
2. Whitley R, Baines J. Clinical management of herpes simplex virus infections: past, present, and future. F1000Res. 2018 Oct 31;7:F1000 Faculty Rev-1726. doi: 10.12688/f1000research.16157.1.
3. Zhu S, Viejo-Borbolla A. Pathogenesis and virulence of herpes simplex virus. Virulence. 2021 Dec;12(1):2670-2702. doi: 10.1080/21505594.2021.1982373. 
4. Soh TK, Ognibene S, Sanders S, Schäper R, Kaufer BB, Bosse JB. A proteome-wide structural systems approach reveals insights into protein families of all human herpesviruses. Nat Commun. 2024 Nov 26;15(1):10230. doi: 10.1038/s41467-024-54668-2.
5. Bochkarev A, Barwell JA, Pfuetzner RA, et al. Crystal structure of the DNA-binding domain of the Epstein-Barr virus origin-binding protein EBNA 1. Cell. 1995 Oct 6;83(1):39-46. doi: 10.1016/0092-8674(95)90232-5.
6. Hellert J, Weidner-Glunde M, Krausze J, et al. A structural basis for BRD2/4-mediated host chromatin interaction and oligomer assembly of Kaposi sarcoma-associated herpesvirus and murine gammaherpesvirus LANA proteins. PLoS Pathog. 2013;9(10):e1003640. doi: 10.1371/journal.ppat.1003640. 
7. Jumper J, Evans R, Pritzel A, et al. Highly accurate protein structure prediction with AlphaFold. Nature. 2021 Aug;596(7873):583-589. doi: 10.1038/s41586-021-03819-2.
8. Evans R, O’Neill M, Pritzel A, et al. Protein complex prediction with AlphaFold-Multimer. bioRxiv 2021.10.04.463034; doi: 10.1101/2021.10.04.463034.
9. Mirdita M, Schütze K, Moriwaki Y, Heo L, Ovchinnikov S, Steinegger M. ColabFold: making protein folding accessible to all. Nat Methods. 2022 Jun;19(6):679-682. doi: 10.1038/s41592-022-01488-1.
10. Schönherr R, Boger J, Lahey-Rudolph JM, et al. A streamlined approach to structure elucidation using in cellulo crystallized recombinant proteins, InCellCryst. Nat Commun. 2024 Feb 24;15(1):1709. doi: 10.1038/s41467-024-45985-7.