Pseudoknots are a fundamental RNA tertiary structure with important roles in regulation of mRNA translation. Molecular force spectroscopic approaches such as optical tweezers can track the pseudoknot's unfolding intermediate states by pulling the RNA chain from both ends, but the kinetic unfolding pathway induced by this method may be different from that in vivo, which occurs during translation and proceeds from the 5' to 3' end. Here we developed a ribosome-mimicking, nanopore pulling assay for dissecting the vectorial unfolding mechanism of pseudoknots. The pseudoknot unfolding pathway in the nanopore, either from the 5' to 3' end or in the reverse direction, can be controlled by a DNA leader that is attached to the pseudoknot at the 5' or 3' ends. The different nanopore conductance between DNA and RNA translocation serves as a marker for the position and structure of the unfolding RNA in the pore. With this design, we provided evidence that the pseudoknot unfolding is a two-step, multistate, metal ion-regulated process depending on the pulling direction. Most notably, unfolding in both directions is rate-limited by the unzipping of the first helix domain (first step), which is Helix-1 in the 5' → 3' direction and Helix-2 in the 3' → 5' direction, suggesting that the initial unfolding step in either pulling direction needs to overcome an energy barrier contributed by the noncanonical triplex base-pairs and coaxial stacking interactions for the tertiary structure stabilization. These findings provide new insights into RNA vectorial unfolding mechanisms, which play an important role in biological functions including frameshifting.
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http://dx.doi.org/10.1021/jacs.5b07910 | DOI Listing |
Sci Rep
January 2025
School of Sports and Health, Nanjing Sport Institute, Nanjing, China.
A high-calorie diet and lack of exercise are the most important risk factors contributing to metabolic dysfunction-associated steatotic liver disease (MASLD) initiation and progression. The precise molecular mechanisms of mitochondrial function alteration during MASLD development remain to be fully elucidated. In this study, a total of 60 male C57BL/6J mice were maintained on a normal or amylin liver NASH (AMLN) diet for 6 or 10 weeks.
View Article and Find Full Text PDFSpectrochim Acta A Mol Biomol Spectrosc
January 2025
School of Food Science and Technology, Jiangnan University, Wuxi, PR China.
This study investigates camel milk protein structural dynamics during digestion using Fourier Transform Infrared (FTIR) spectroscopy and Two-Dimensional Infrared (2D-IR) homo-correlation and hetero-correlation analysis. The synchronous 2DIR homo-correlation map reveals that NH bending and C-N stretching vibrations (amide II) are sensitive to digestion, indicating significant impacts on secondary structures. The asynchronous 2DIR homo-correlation indicates a stepwise process, where initial disruptions in NH interactions precede changes in CO stretching vibrations (amide I), highlighting the sequence of structural alterations during protein unfolding and degradation.
View Article and Find Full Text PDFBMC Palliat Care
January 2025
DEFACTUM, Central Region Denmark, Aarhus, Denmark.
Background: Despite growing research on the daily life of people with advanced cancer, more specific knowledge is needed about the specific strategies these people use to manage everyday activities.
Purpose: This study explores how people with advanced cancer manage their everyday activities and describe their specific strategies.
Methods: The qualitative study was designed with an explorative approach.
Nature
January 2025
Institute of Molecular Health Sciences, Department of Biology, Swiss Federal Institute of Technology (ETH) Zurich, Zurich, Switzerland.
During normal cellular homeostasis, unfolded and mislocalized proteins are recognized and removed, preventing the build-up of toxic byproducts. When protein homeostasis is perturbed during ageing, neurodegeneration or cellular stress, proteins can accumulate several forms of chemical damage through reactive metabolites. Such modifications have been proposed to trigger the selective removal of chemically marked proteins; however, identifying modifications that are sufficient to induce protein degradation has remained challenging.
View Article and Find Full Text PDFNat Commun
January 2025
ZJU-UIUC Institute, Interdisciplinary Center for Quantum Information, State Key Laboratory of Extreme Photonics and Instrumentation, Zhejiang University, Hangzhou, China.
The bidirectional interactions between metamaterials and artificial intelligence have recently attracted immense interest to motivate scientists to revisit respective communities, giving rise to the proliferation of intelligent metamaterials and metamaterials intelligence. Owning to the strong nonlinear fitting and generalization ability, artificial intelligence is poised to serve as a materials-savvy surrogate electromagnetic simulator and a high-speed computing nucleus that drives numerous self-driving metamaterial applications, such as invisibility cloak, imaging, detection, and wireless communication. In turn, metamaterials create a versatile electromagnetic manipulator for wave-based analogue computing to be complementary with conventional electronic computing.
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