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2025-07-10
17:32
[PUBDB-2025-02340] Journal Article
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Hierarchy in regulator interactions with distant transcriptional activation domains empowers rheostatic regulation
Protein science 34(6), e70142 () [10.1002/pro.70142]  GO
Transcription factors carry long intrinsically disordered regions often containing multiple activation domains. Despite numerous recent high-throughput identifications and characterizations of activation domains, the interplay between sequence motifs, activation domains, and regulator binding in intrinsically disordered transcription factor regions remains unresolved. [...]
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2025-07-10
17:25
DBCoverage [PUBDB-2025-02339] Journal Article
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Structural heterogeneity and dynamics in the apical stem loop of s2m from SARS-CoV-2 Delta by an integrative NMR spectroscopy and MD simulation approach
In structured RNAs, helical elements are often capped by apical loops that are integral structural elements, ranging from 3 to >20 nts of size on average, and display a highly heterogeneous energy landscape profile, rendering structural characterization particularly challenging. We here provide a characterization of the SARS-CoV-2 Delta s2m element containing a highly dynamic nonaloop using an integrative approach of nuclear magnetic resonance spectroscopy (NMR), small angle X-ray scattering (SAXS), and molecular dynamics simulations (MD). [...]
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2025-07-10
17:15
DBCoverage [PUBDB-2025-02338] Journal Article
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Structural basis of ubiquitin ligase Nedd4-2 autoinhibition and regulation by calcium and 14-3-3 proteins
Nedd4-2 E3 ligase regulates Na+ homeostasis by ubiquitinating various channels and membrane transporters, including the epithelial sodium channel ENaC. In turn, Nedd4-2 dysregulation leads to various conditions, including electrolytic imbalance, respiratory distress, hypertension, and kidney diseases. [...]
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2025-07-10
17:02
[PUBDB-2025-02337] Journal Article
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Programmable Protein‐DNA Composite Nanostructures: from Nanostructure Construction to Protein‐Induced Micro‐Scale Material Self‐Assembly and Functionalization
Small xx, 2502060 () [10.1002/smll.202502060]  GO
The integration of DNA and protein-designed nanostructures represents a transformative approach to the development of programmable biopolymers for nanoscale construction. While DNA nanostructures excel in the readily programmable precision and scalability of base pairing, protein assemblies exploit the chemical diversity of amino acids for greater functional versatility. [...]
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2025-07-10
16:53
[PUBDB-2025-02336] Journal Article
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Insights into the solution structure of the actin-binding tail domain of metavinculin by small angle X-ray scattering and molecular dynamics simulations
Vinculin is a ubiquitously expressed focal adhesion protein that plays an important role in cell-matrix and cell-to-cell junctions. Metavinculin, a muscle-specific splice variant of vinculin, contains a 68-amino acid disordered insert region in its actin binding tail domain (MVt). [...]
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2025-07-10
16:42
DBCoverage [PUBDB-2025-02334] Journal Article
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AF4-to-SAXS: expanded characterization of nanoparticles and proteins at the P12 BioSAXS beamline
Biological small-angle X-ray scattering (SAXS) is a versatile and powerful technique for investigating the structural and biophysical properties of biologically and pharmaceutically relevant macromolecules and nanoparticles. SAXS offers detailed insights into macromolecular composition, size, shape and internal structure, while addressing key aspects such as oligomeric state, stability, molecular interactions, and conformational flexibility. [...]
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2025-07-10
16:22
[PUBDB-2025-02333] Journal Article
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Direct structural investigation of pH responsiveness in mRNA lipid nanoparticles: Refining paradigms
Using small angle X-ray scattering measurements, structural coherencies in lipid nanoparticle (LNP) formulations comprising messenger RNA (mRNA) were elucidated in response to pH changes and as a function of RNA to lipid ratio. Formulations were assembled using selected ionizable lipids with well-known activity from previous experiments, with otherwise identical composition. [...]
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2025-07-10
15:51
DBCoverage [PUBDB-2025-02331] Journal Article
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The molecular basis for acetylhistidine synthesis by HisAT/NAT16
Acetylhistidine has been detected in human blood, but its origin and function are not known. It is formed when the acetyl group of acetyl-CoA is transferred to the α-amino group of histidine. [...]
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2025-07-10
15:24
[PUBDB-2025-02329] Journal Article
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Interfacing B‐DNA and DNA Mimic Foldamers
A linker unit was designed and synthesized that can serve both as a hairpin turn in a DNA duplex and anchor point for an aromatic helical foldamer mimicking the shape and surface properties of B-DNA. Methods were developed to synthesize natural/non-natural chimeric molecules combining foldamer and DNA segments. [...]
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2025-07-10
15:01
DBCoverage [PUBDB-2025-02328] Journal Article
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CryoRhodopsins: A comprehensive characterization of a group of microbial rhodopsins from cold environments
Science advances 11(27), eadv1015 () [10.1126/sciadv.adv1015]  GO
Microbial rhodopsins are omnipresent on Earth; however, the vast majority of them remain uncharacterized. Here, we describe a rhodopsin group found in microorganisms from cold environments, such as glaciers, denoted as CryoRhodopsins (CryoRs). [...]
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