Conformational dynamics in specialized C₂H₂ zinc finger domains enable zinc‐responsive gene repression in S. pombe

Protein Science, Год журнала: 2025, Номер 34(2)

Опубликована: Янв. 25, 2025

Abstract Loz1 is a zinc‐responsive transcription factor in fission yeast that maintains cellular zinc homeostasis by repressing the expression of genes required for uptake high conditions. Previous deletion analysis found region containing two tandem C 2 H zinc‐fingers and an upstream “accessory domain” rich histidine, lysine, arginine residues to be sufficient zinc‐dependent DNA binding gene repression. Here we report unexpected biophysical properties this pair seemingly classical fingers. Isothermal titration calorimetry NMR spectroscopy reveal distinct events localized spectra complex dynamic behavior spanning time scales from fast 10 −12 –10 −10 slow >10 0 s. Slow exchange due cis‐trans isomerization TGERP linker results doubling many signals protein. Conformational on −3 s timescale throughout first finger distinguishes it second linked weaker affinity zinc. These findings mechanism sensing illuminate how protein's rough free‐energy landscape enables sensing, regulated expression.

Язык: Английский

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Zn(II) Affinity and Structural Conformations of 2His‐2Cys Zinc Finger‐Like Motif Peptide Determined by Ion Mobility–Mass Spectrometry and PM6 Molecular Modeling

Journal of Mass Spectrometry, Год журнала: 2025, Номер 60(3)

Опубликована: Фев. 14, 2025

ABSTRACT This study focuses on investigating the conformational structure and zinc(II) affinity of a zinc finger‐like motif (ZFM) peptide with sequence acetyl‐ His 1 ‐Cys 2 ‐Gly 3 ‐Pro 4 5 ‐ 6 7 , where bold highlights potential binding sites. Zinc fingers are crucial protein motifs known for their high specificity ions. The ZFM peptide's contains 2His‐2Cys zinc‐binding sites similar to those in natural finger proteins but without hydrophobic core, making it valuable model studying zinc(II)–peptide interactions. Previous research related peptides showed that collision cross sections B3LYP modeling predicted His‐2Cys‐carboxyl terminus coordination was more stable than 2His‐2Cys. Employing comprehensive approach integrating ion mobility–mass spectrometry theoretical techniques, various modes have been thoroughly compared ascertain influence competitive threshold collision‐induced dissociation method measuring relative gas‐phase Zn(II) peptide. measured is greater recently two primary structures, Cys Asp indicating preference ‐His side groups coordinating over or Asp‐His‐Cys‐carboxyl these heptapeptides.

Язык: Английский

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Structural insights into a highly flexible zinc finger module unravel INSM1 function in transcription regulation

Nature Communications, Год журнала: 2025, Номер 16(1)

Опубликована: Март 4, 2025

Orderly development of neuroendocrine and nervous system mammals requires INSM1, a key regulator for cell differentiation. Ectopic expression INSM1 is closely correlated with human tumorigenesis, which makes reliable diagnostic biomarker potential therapeutic target. To date, known as transcription repressor binding to GGGG-contained DNA element TEAD1 using its five zinc fingers (ZFs), while the mechanism remains unknown. Here, we reveal highly variable conformations whole structure ZFs, among ZF1 adopts an unusual CCHC-fold. binds TEAD domain through hydrophobic interactions, forms ternary complex TEAD1-targeted DNA. Based on this, cooperates repress genes. ZF2 ZF3 can bind but have no specificity due long flexible interdomain linker. Instead, collaborates CTCF target genome loci having regulate adjacent This study defines functional mode by cooperating diverse DNA-binding proteins targeting specific in regulation, provides structural information designing INSM1-related drugs probes.

Язык: Английский

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Novel Compound Heterozygous Variants in ZNF526 Causing Dentici‐Novelli Neurodevelopmental Syndrome: A Case Report and Literature Review

Molecular Genetics & Genomic Medicine, Год журнала: 2025, Номер 13(4)

Опубликована: Апрель 1, 2025

ABSTRACT Background The ZNF526 gene encodes a ubiquitously expressed Kruppel‐type zinc finger protein crucial in transcriptional regulation. Recent studies suggest that biallelic pathogenic variants may lead to Dentici‐Novelli neurodevelopmental syndrome, characterized by microcephaly, developmental delay, epilepsy, and ocular anomalies. To date, phenotypic details have been reported for only six patients with variants. Methods This study gathered clinical information genetic data from child disorders. A three‐dimensional model was employed predict variant effects on structure. literature review conducted compare this case previously cases, analyzing features findings. Results proband, 7‐month‐old girl, exhibited limb hypotonia, abnormal brain imaging, seizures. Chromosomal karyotype analysis copy number variation analyses were normal. Whole exome sequencing revealed two heterozygous the (NM_133444.3): c.1426del (p.Val476Phefs*9), de novo frameshift variant, c.1513T;> C (p.Cys505Arg), inherited her mother. These unreported are separate alleles, forming compound state correlated presentation. Ocular anomalies absent, while café‐au‐lait spots represent novel feature. Among 12 cases of 11 unique identified, loss‐of‐function possibly linked Conclusion describes youngest patient broadening mutation spectrum detailing associated profile. findings valuable diagnosis family counseling syndrome.

Язык: Английский

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“Disguise strategy” to bacteria: A multifunctional hydrogel with bacteria-targeting and photothermal conversion properties for the repair of infectious bone defects

Bioactive Materials, Год журнала: 2025, Номер 47, С. 343 - 360

Опубликована: Фев. 12, 2025

Язык: Английский

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Keep Fingers on the CpG Islands

Epigenomes, Год журнала: 2024, Номер 8(2), С. 23 - 23

Опубликована: Июнь 19, 2024

The post-genomic era has ushered in the extensive application of epigenetic editing tools, allowing for precise alterations gene expression. use reprogrammable editors that carry transcriptional corepressors significant potential long-term silencing treatment human diseases. ideal scenario involves targeting a specific genomic location by DNA-binding domain, ensuring there are no off-target effects and process yields genetic remnants aside from modifications (i.e., DNA methylation). A notable example is recent study on mouse Pcsk9 gene, crucial cholesterol regulation expressed hepatocytes, which identified synthetic zinc-finger (ZF) proteins as most effective efficiently, specifically, persistently. This discussion focuses enhancing specificity ZF-array binding optimizing interactions between amino acids bases across three promoters containing CpG islands.

Язык: Английский

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C(P)XCG Proteins of Haloferax volcanii with Predicted Zinc Finger Domains: The Majority Bind Zinc, but Several Do Not

International Journal of Molecular Sciences, Год журнала: 2024, Номер 25(13), С. 7166 - 7166

Опубликована: Июнь 28, 2024

In recent years, interest in very small proteins (µ-proteins) has increased significantly, and they were found to fulfill important functions all prokaryotic eukaryotic species. The halophilic archaeon Haloferax volcanii encodes about 400 µ-proteins of less than 70 amino acids, 49 which contain at least two C(P)XCG motifs are, thus, predicted zinc finger proteins. determination the NMR solution structure HVO_2753 revealed that only one fingers actually bound zinc, while a second was metal-free. Therefore, aim current study homologous production additional quantification their content. Attempts produce 31 failed, underscoring particular difficulties working with µ-proteins. total, 14 could be produced purified, content determined. Only nine complexed five zinc-free. Three latter analyzed using ESI-MS another metal, most likely cobalt or nickel. haloarchaea, variability is higher anticipated, can metal-free, bind metal. Notably, AlphaFold2 cannot correctly predict whether not four cysteines have tetrahedral configuration prerequisite for metal binding.

Язык: Английский

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Conformational dynamics in specialized C₂H₂zinc finger domains enable zinc-responsive gene repression inS. pombe

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Сен. 21, 2024

Abstract Loz1 is a zinc-responsive transcription factor in fission yeast that maintains cellular zinc homeostasis by repressing the expression of genes required for uptake high conditions. Previous deletion analysis found region containing two tandem C 2 H zinc-fingers and an upstream “accessory domain” rich histidine, lysine, arginine residues to be sufficient zinc-dependent DNA binding gene repression. Here we report unexpected biophysical properties this pair seemingly classical fingers. Isothermal titration calorimetry NMR spectroscopy reveal distinct events localized spectra complex dynamic behavior responsive spanning time scales from fast 10 −12 -10 −10 slow > 0 sec. Slow exchange due cis-trans isomerization TGERP linker results doubling many signals protein. Conformational on −3 s timescale throughout first finger distinguishes it second linked weaker affinity zinc. These findings mechanism sensing illuminate how protein’s rough free-energy landscape enable sensing, regulated expression.

Язык: Английский

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DNA-binding proteins from MBD through ZF to BEN: recognition of cytosine methylation status by one arginine with two conformations

Nucleic Acids Research, Год журнала: 2024, Номер unknown

Опубликована: Сен. 26, 2024

Abstract Maintenance methylation, of palindromic CpG dinucleotides at DNA replication forks, is crucial for the faithful mitotic inheritance genomic 5-methylcytosine (5mC) methylation patterns. MBD proteins use two arginine residues to recognize symmetrically-positioned methyl groups in fully-methylated 5mCpG/5mCpG and 5mCpA/TpG dinucleotides. In contrast, C2H2 zinc finger (ZF) CpA, whether methylated or not, within longer specific sequences a site- strand-specific manner. Unmethylated sites, often island (CGI) promoters, need protection by protein factors maintain their hypomethylated status. Members BEN domain bind CGCG CACG elements CGIs regulate gene expression. Despite overall structural diversity, MBD, ZF all guanine, adopting either ‘straight-on’ ‘oblique’ conformation. The straight-on conformation accommodates group (5mC/T)pG dinucleotide, while oblique can clash with 5mC, leading preferential binding unmethylated sequences.

Язык: Английский

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The N-terminus of YY1 regulates DNA and RNA binding affinity for both the zinc-fingers and an unexpected nucleic acid binding domain

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Окт. 5, 2024

ABSTRACT Transcription factors (TFs) play central roles in dictating cellular identity and function by regulating gene expression programs. Beyond their well-folded DNA binding domains (DBDs) which recognize cognate elements the genome, TFs are enriched for intrinsically disordered regions (IDRs), have a host of proposed functions including facilitating protein-protein interactions, aiding site search, RNA. Defining intrinsic regulatory properties requires further mechanistic investigation. We chose to investigate RNA Yin Yang 1 (YY1), ubiquitously expressed TF directly involved transcriptional activation, repression genome architecture. Through systematic vitro nucleic acid experiments we resolve conflicting literature defining interface YY1, demonstrating that there two within YY1: its canonical 4 zinc finger DBD previously unannotated domain, term REPO-NAB. Furthermore, discover surprising autoinhibitory N-terminus protein imparts on each these domains. Our results provide new example IDR-mediated regulation enables future mechanistically precise functional investigations.

Язык: Английский

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