Biology subjects

Henen, M. A.

Publications and source records attributed to Henen, M. A..

7 recordsLinked to original sources

bioRxiv2026

Imipramine binds to Amyloid-beta(1-42) monomers in vitro, as shown by NMR spectroscopy.

Imipramine is known as an older generation tricyclic antidepressant drug. It has been identified in prior studies that imipramine blocks Apolipoprotein E4 (ApoE4)-induced amyloid-{beta}(A{beta}) aggregation and is associated with an improved AD diagnosis [Johnson et al. Alzheimers Research Therapy, 2022, 14, 88]. Using NMR methods such as 1H-1H NOESY and Saturation Transfer Difference Spectroscopy, we demonstrate the binding of A{beta} monomers to imipramine when the full-length A{beta} (1-42) sequence is considered. The more abundant but less toxic form, A{beta} (1-40) does not show interaction with imipramine.

biophysics↗

bioRxiv2026

ZBP1's Inability to Convert Unmodified RNAs to the Z-form Underlies a Balanced Mechanism of RNA Recognition with ADAR1

Z-DNA Binding Protein 1 (ZBP1) is a critical pattern recognition receptor within the innate immune response to viral infection. ZBP1 senses foreign nucleic acids in the unusual, left-handed Z-conformation via binding through its N-terminal Z1 and Z2 domains and activates downstream pro-pyroptotic, -apoptotic, and -necroptotic pathways to initiate cell death and allow for viral clearance. Both dsDNA and dsRNA can adopt the Z-conformation, however, the conformational change is energetically expensive, especially for dsRNA, and typically requires chemical modifications or protein binding to induce a right-to-left-handed conversion and stabilization. ZBP1 has been previously shown to bind and convert B-DNA to the Z-conformation and was assumed to be able to convert A-RNA as well, despite the lack of experimental validation. Here, we use a variety of Nuclear Magnetic Resonance (NMR) and other biophysical and biochemical experiments to characterize the Z-DNA and Z-RNA binding properties of ZBP1s Z1 and Z2 domains. While ZBP1s Z domains are able to convert and stabilize unmodified dsDNA in the Z-conformation, both domains are incapable of flipping unmodified A-conformation dsRNA. We show that ZBP1s Z domains require dsRNAs with Z-promoting chemical modification in order for them to bind and stabilize the Z-conformation. These results contrast with the Z domain from Adenosine Deaminase Acting on RNA 1 (ADAR1), which can bind and flip both dsDNA and dsRNA into the Z-conformation, potentially indicating finely tuned competition between ADAR1 and ZBP1 for pro-survival and pro-death outcomes, respectively. This work highlights the functional variability of Z domains and narrows down the potential physiological substrates of ZBP1 in infection and disease. Graphical O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=81 SRC="FIGDIR/small/719927v1_ufig1.gif" ALT="Figure 1"> View larger version (18K): org.highwire.dtl.DTLVardef@11a03caorg.highwire.dtl.DTLVardef@eec771org.highwire.dtl.DTLVardef@67d152org.highwire.dtl.DTLVardef@1df808d_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2025

Zα and Zβ domains of ADAR1 and ZBP1 bind to G-quadruplexes with low micromolar affinity

1While it is well established that the Z domains of ADAR1 and ZBP1 proteins bind Z-form-prone nucleic acids (Z-NAs), it has also been shown that the Z domain of ADAR1 binds DNA G-Quadruplexes (GQ). However, no binding partner of the structurally homologous Z{beta} domain of ADAR1 has been identified to date. Based on AlphaFold and molecular dynamics simulations, it has recently been suggested that the Z{beta} domain of ADAR1 targets its substrate by recognizing GQs. Here, we provide the first experimental evidence for Z{beta} domain binding to select G-quadruplex RNA and DNA in vitro, with structural specificity and low micromolar affinity. We also demonstrate that the Z domains of ZBP1 bind to both DNA and RNA GQs with similar affinity. These findings extend the range of potential functional roles for these proteins and open new hypotheses for testing in cells.

biophysics↗

bioRxiv2025

Z-Form Stabilization By The Zα Domain Of Adar1p150 Has Subtle Effects On A-To-I Editing

The role of Adenosine Deaminase Acting on RNA 1 (ADAR1)s Z-conformation stabilizing Z domain in A-to-I editing is unclear. Previous studies on Z mutations faced limitations, including variable ADAR1p150 expression, differential editing analysis challenges, and unaccounted changes in ADAR1p150 localization. To address these issues, we developed a Cre-lox system in ADAR1p150 KO cells to generate stable cell lines expressing Z mutant ADAR1p150 constructs. Using total RNA sequencing analyzing editing clusters as a proxy for dsRNAs, we found that Z mutations slightly decreased overall A-to-I editing, consistent with recent findings. These decreases correlated with mislocalization of ADAR1p150 rather than reduced editing specificity, and practically no statistically significant differentially edited sites were identified between wild-type and Z mutant ADAR1p150 constructs. These results suggest that Zs impact on editing is minor and that phenotypes in Z mutant mouse models and human patients may arise from editing-independent inhibition of Z-DNA-Binding Protein 1 (ZBP1), rather than changes in RNA editing.

cell biology↗

bioRxiv2023

SASH1 interacts with TNKS2 and promotes human melanocyte stem cell maintenance

Both aging spots (hyperpigmentation) and hair graying (lack of pigmentation) are associated with aging, two seemingly opposite pigmentation phenotypes. It is not clear how they are mechanistically connected. This study investigated the underlying mechanism in a family with an inherited pigmentation disorder. Clinical examinations identified accelerated hair graying and skin dyspigmentation (intermixed hyper and hypopigmentation) in the family members carrying the SASH1S519N variant. Cell assays indicated that SASH1 promoted stem-like characteristics in human melanocytes, and SASH1S519N was defective in this function. Multiple assays showed that SASH1 binds to tankyrase 2 (TNKS2), which is required for SASH1s promotion of stem-like function. Further, the SASH1S519N variant is in a bona fide Tankyrase-binding motif, and SASH1S519N alters the binding kinetics and affinity. Results here indicate SASH1 as a novel protein regulating the appropriate balance between melanocyte stem cells (McSC) and mature melanocytes (MCs), with S519N variant causing defects. We propose that dysfunction of McSC maintenance connects multiple aging-associated pigmentation phenotypes in the general population.

cell biology↗

bioRxiv2023

An evolutionarily conserved strategy for ribosome binding and inhibition by β-coronavirus non-structural protein 1

An important pathogenicity factor of SARS-CoV-2 and related coronaviruses is Nsp1, which suppresses host gene expression and stunts antiviral signaling. SARS-CoV-2 Nsp1 binds the ribosome to inhibit translation through mRNA displacement and induces degradation of host mRNAs through an unknown mechanism. Here we show that Nsp1-dependent host shutoff is conserved in diverse coronaviruses, but only Nsp1 from {beta}-CoV inhibits translation through ribosome binding. The C-terminal domain of all {beta}-CoV Nsp1s confers high-affinity ribosome-binding despite low sequence conservation. Modeling of interactions of four Nsp1s to the ribosome identified few absolutely conserved amino acids that, together with an overall conservation in surface charge, form the {beta}-CoV Nsp1 ribosome-binding domain. Contrary to previous models, the Nsp1 ribosome-binding domain is an inefficient translation inhibitor. Instead, the Nsp1-CTD likely functions by recruiting Nsp1s N-terminal "effector" domain. Finally, we show that a viral cis-acting RNA element has co-evolved to fine-tune SARS-CoV-2 Nsp1 function, but does not provide similar protection against Nsp1 from related viruses. Together, our work provides new insight into the diversity and conservation of ribosome-dependent host-shutoff functions of Nsp1, knowledge that could aide future efforts in pharmacological targeting of Nsp1 from SARS-CoV-2, but also related human-pathogenic {beta}-coronaviruses. Our study also exemplifies how comparing highly divergent Nsp1 variants can help to dissect the different modalities of this multi-functional viral protein.

biochemistry↗

bioRxiv2022

PBRM1 BD2 and BD4 associate with RNA to facilitate chromatin association

PBRM1 is a subunit of the PBAF chromatin remodeling complex, which is mutated in 40-50% of clear cell renal cell carcinoma patients. It is thought to largely function as a chromatin binding subunit of the PBAF complex, but the molecular mechanism underlying this activity is not fully known. PBRM1 contains six tandem bromodomains which are known to cooperate in binding of nucleosomes acetylated at histone H3 lysine 14 (H3K14ac). Here we demonstrate that the second and fourth bromodomains from PBRM1 also bind nucleic acids, selectively associating with double stranded RNA elements. Disruption of the RNA binding pocket is found to compromise PBRM1 chromatin binding and inhibit PBRM1-mediated cellular growth effects.

biochemistry↗