Protocol for Biochemical Analysis and Structure Determination of the ZZ Domain of the E3 Ubiquitin Ligase HERC2

Characterization of multiple interactions between the envelope E protein of SARS-CoV-2 and human BRD4

The SARS-CoV-2 envelope (E) protein hijacks human BRD4 (bromodomain and extra-terminal domain protein 4). Here, we describe a protocol to characterize the interaction of the acetylated E protein with BRD4 in vivo. We detail steps to use NMR spectroscopy to map the binding interface and include steps to monitor the effect of BRD4 inhibitors in SARS-CoV-2-infected human lung bronchial epithelial cells. This approach could be applied to study interactions involving other viral and human proteins. For complete details on the use and execution of this protocol, please refer to Vann et al. (2022).¹.

Protein purification, crystallization, and structure determination of human DEAD-box RNA helicase DDX21 in different unwinding states

RNA helicase DDX21 plays vital roles in ribosomal RNA processing and the regulation of host innate immunity during virus infection. Here, we describe the optimized protocols for nucleic acid-free protein purification and crystallization of DDX21 in its different unwinding states. Rational design of the flexible region within the helicase core, and biophysical approach to characterize interactions between DDX21 and RNA, leads to successful crystallization of DDX21. This protocol can be applied to the crystallography of other DExD/H-box RNA helicases.

For complete details on the use and execution of this protocol, please refer to Chen et al. (2020).

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Optimized protocols for nucleic acid-free DDX21 protein purification

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Rational design of the flexible region within DDX21 helicase core

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Biophysical approach to characterize interactions between DDX21 and RNA

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Crystallization of ligand-free DDX21 or in complex with ATP analogs or RNA of interest

Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.

The ZZ domain of HERC2 is a receptor of arginylated substrates

The E3 ubiquitin ligase HERC2 has been linked to neurological diseases and cancer, however it remains a poorly characterized human protein. Here, we show that the ZZ domain of HERC2 (HERC2ZZ) recognizes a mimetic of the Nt-R cargo degradation signal. NMR titration experiments and mutagenesis results reveal that the Nt-R mimetic peptide occupies a well-defined binding site of HERC2ZZ comprising of the negatively charged aspartic acids. We report the crystal structure of the DOC domain of HERC2 (HERC2DOC) that is adjacent to HERC2ZZ and show that a conformational rearrangement in the protein may occur when the two domains are linked. Immunofluorescence microscopy data suggest that the stimulation of autophagy promotes targeting of HERC2 to the proteasome. Our findings suggest a role of cytosolic HERC2 in the ubiquitin-dependent degradation pathways.

Structural and biophysical characterization of the nucleosome-binding PZP domain

The core subunit of the MORF acetyltransferase complex BRPF1 contains a unique combination of zinc fingers, including a plant homeodomain (PHD) finger followed by a zinc knuckle and another PHD finger, which together form a PZP domain (BRPF1PZP). BRPF1PZP has been shown to bind to the nucleosome and make contacts with both histone H3 tail and DNA. Here, we describe biophysical and structural methods for characterization of the interactions between BRPF1PZP, H3 tail, DNA, and the intact nucleosome. For complete details on the use and execution of this protocol, please refer to Klein et al. (2020).