An extensive molecular dynamics simulations study to investigate the conformational dynamics and unfolding pathway of the TAF15-RRM domain in 8 M urea revealed that unfolding proceeds through stable, denaturant/temperature-accelerated partially unfolded intermediate ensembles that, by analogy with aggregation-prone int...
Vishakha Chaudhary, Priyanka Kataria, Kusum Yadav et al.· Journal of Biomolecular Stru...· 0 citations
Molecular rotors are valuable probes for studying local microenvironments because their optical behavior is closely linked to conformational dynamics. In this study, a chromyl-naphthyl (HCNP) donor-π-acceptor molecular rotor was developed for viscosity-responsive fluorescence and selective interaction with human serum...
Anju Ranolia, L. Narayan, M. K. Katiyar et al.· Journal of materials chemist...· 0 citations
SPINET is introduced, which predicts sequences from molecular dynamics trajectories that uses cellular sheaves to represent residue interactions within each frame and recurrent units to integrate information across frames, then predicts all amino acids in a single pass.
Jens Lundsgaard, Colin Mikulski, Zhi-Xuan Yan et al.· 0 citations
Sequence-specific detection of double-stranded DNA (dsDNA) under physiological conditions remains challenging because the complementary strand is inaccessible to conventional oligonucleotide probes, often requiring thermal denaturation or protein-assisted strand separation. Here, we developed a binary DNAzyme (BiDz)...
M. Ateiah, Vladislav A. Reushev, Nairouz Deeb et al.· Analytical Chemistry· 0 citations
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Glyphosate resistance in weeds is often mediated by target-site changes in 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS), but non-target-site resistance (NTSR) mechanisms are increasingly recognized as important contributors to field-evolved resistance. Here, we characterized a glyphosate-resistant
Eleusine in...
Yun-Long Li, Yi-Kai Dong, Yueh-Chih Su et al.· Frontiers in Plant Science· 0 citations
A combined biomarker model integrating coagulation and immune parameters provides moderate-to-good predictive performance for RSA, which may facilitate early risk stratification and individualized management, although external validation is required before routine implementation.
Yu-Cu Xie, Ping-Ping Huang, Xiao-Fen Gao et al.· Pakistan Journal of Medical...· 0 citations
Low concentrations of MGO enhanced human CC viability, reduced apoptosis, and boosted antioxidant defenses and proliferation-related pathways suggest MGO’s biomedical potential in cell survival and anti-apoptotic effects on reproductive medicine research.
Fahimeh Kabiri, T. Foroutan, Roghiyeh Pashaei-Asl et al.· Advanced Pharmaceutical Bull...· 0 citations
FINDING: Icosahedral viral capsid geometry is governed by the Caspar-Klug T-number, which quantizes the surface lattice into pentamer/hexamer clusters, directly encoding the golden ratio in its pentagonal substructure. | MATH: T = h² + hk + k² (h,k ≥ 0 integers); capsid has 60T protein subunits; 12 pentamers + 10(T−1)...
Andrew Stewart Caldin· Zenodo (CERN European Organi...· 0 citations
Metamorphic proteins challenge the classical view of protein folding by reversibly interconverting between two distinct, stable native structures. XCL1 (lymphotactin) is a prototypical example, transitioning between a monomeric mixed- α / β chemokine fold and an alternate all- β fold that forms a stable dimer. Here we...
B. Seifi, Greg de Souza, Stefan Wallin· Proteins: Structure, Functio...· 0 citations
First public release. Deterministic φ-lattice protein folding engine for the Nexus Resonance Codex (NRC), built on the Trageser Tensor Theorem (TTT) and 2048D φ-spiral manifolds. Experimental research code; APIs may evolve — pin the version.
James Trageser (jtrag)· Zenodo (CERN European Organi...· 0 citations
Findings are consistent with impaired proteostasis following acute HSP70 depletion and demonstrate the potential utility of an inhibitor-independent workflow for evaluating cellular responses associated with targeted chaperone depletion.
Hatice Esenkaya· Frontiers in Genetics· 0 citations
Abstract: Predicting the three-dimensional structure of a protein directly from its amino-acid sequence has remained one of the most persistent open problems in computational biology, commonly referred to as the protein folding problem. For decades, structural information was obtainable only through slow, expensive, an...
Mridhula Muthukumar· Zenodo (CERN European Organi...· 0 citations
A new machine-learning framework aims to improve the success rate of computational protein design while moving away from results that reproduce sequences found in nature.
