Latest in Research

The push-to-open mechanism of the tethered mechanosensitive ion channel NompC

2021-06-16

The push-to-open mechanism of the tethered mechanosensitive ion channel NompC

NompC is a mechanosensitive ion channel responsible for the sensation of touch and balance in Drosophila melanogaster. Based on a resolved cryo-EM structure, we performed all-atom molecular dynamics simulations and electrophysiological experiments to study the atomistic details of NompC gating. Our results showed that NompC could be opened by compression of the intracellular ankyrin repeat domain but not by a stretch, and a number of hydrogen bonds along the force convey pathway are important for the mechanosensitivity. Under intracellular compression, the bundled ankyrin repeat region acts like a spring with a spring constant of ~13 pN nm−1 by transferring forces at a rate of ~1.8 nm ps−1. The linker helix region acts as a bridge between the ankyrin repeats and the transient receptor potential (TRP) domain, which passes on the pushing force to the TRP domain to undergo a clockwise rotation, resulting in the opening of the channel. This could be the universal gating mechanism of similar tethered mechanosensitive TRP channels, which enable cells to feel compression and shrinkage.

RNA Backbone Torsion and Pseudotorsion Angle Prediction Using Dilated Convolutional Neural Networks

2021-05-31

RNA Backbone Torsion and Pseudotorsion Angle Prediction Using Dilated Convolutional Neural Networks

RNA three-dimensional structure prediction has been relied on using a predicted or experimentally determined secondary structure as a restraint to reduce the conformational sampling space. However, the secondary-structure restraints are limited to paired bases, and the conformational space of the ribose-phosphate backbone is still too large to be sampled efficiently. Here, we employed the dilated convolutional neural network to predict backbone torsion and pseudotorsion angles using a single RNA sequence as input. The method called SPOT-RNA-1D was trained on a high-resolution training data set and tested on three independent, nonredundant, and high-resolution test sets. The proposed method yields substantially smaller mean absolute errors than the baseline predictors based on random predictions and based on helix conformations according to actual angle distributions.

Pairing a high-resolution statistical potential with a nucleobase-centric sampling algorithm for improving RNA model refinement

2021-05-18

Pairing a high-resolution statistical potential with a nucleobase-centric sampling algorithm for improving RNA model refinement

Refining modelled structures to approach experimental accuracy is one of the most challenging problems in molecular biology. Despite many years’ efforts, the progress in protein or RNA structure refinement has been slow because the global minimum given by the energy scores is not at the experimentally determined “native” structure. Here, we propose a fully knowledge-based energy function that captures the full orientation dependence of base–base, base–oxygen and oxygen–oxygen interactions with the RNA backbone modelled by rotameric states and internal energies. A total of 4000 quantum-mechanical calculations were performed to reweight base–base statistical potentials for minimizing possible effects of indirect interactions. The resulting BRiQ knowledge-based potential, equipped with a nucleobase-centric sampling algorithm, provides a robust improvement in refining near-native RNA models generated by a wide variety of modelling techniques.

A Bifunctional N-Heterocyclic Carbene as a Noncovalent Organocatalyst for Enantioselective Aza-Michael Addition Reactions

2021-05-17

A Bifunctional N-Heterocyclic Carbene as a Noncovalent Organocatalyst for Enantioselective Aza-Michael Addition Reactions

Chiral N-heterocyclic carbenes (NHCs) have been recently established as powerful catalysts for enantioselective bond-forming processes via noncovalent interactions. The underlying HOMO-raising activation of nucleophiles takes advantage of the strong Brønsted basicity of NHCs. However, the scope of compatible electrophiles has been quite limited. In this article, we report a bifunctional NHC with an embedded hydrogen-bonding motif that shows remarkable tolerance of various Michael acceptors in an asymmetric aza-conjugate addition reaction. The catalytic efficiency far exceeds that of the benchmark tertiary amine-thiourea scaffold.

Sarm1-mediated neurodegeneration within the enteric nervous system protects against local inflammation of the colon

2021-05-13

Sarm1-mediated neurodegeneration within the enteric nervous system protects against local inflammation of the colon

Axonal degeneration is one of the key features of neurodegenerative disorders. In the canonical view, axonal degeneration destructs neural connections and promotes detrimental disease defects. Here, we assessed the enteric nervous system (ENS) of the mouse, non-human primate, and human by advanced 3D imaging. We observed the profound neurodegeneration of catecholaminergic axons in human colons with ulcerative colitis, and similarly, in mouse colons during acute dextran sulfate sodium-induced colitis. However, we unexpectedly revealed that blockage of such axonal degeneration by the Sarm1 deletion in mice exacerbated the colitis condition. In contrast, pharmacologic ablation or chemogenetic inhibition of catecholaminergic axons suppressed the colon inflammation. We further showed that the catecholaminergic neurotransmitter norepinephrine exerted a pro-inflammatory function by enhancing the expression of IL-17 cytokines. Together, this study demonstrated that Sarm1-mediated neurodegeneration within the ENS mitigated local inflammation of the colon, uncovering a previously-unrecognized beneficial role of axonal degeneration in this disease context.

Insights Gained from Single-Cell Analysis of Immune Cells in the Tumor Microenvironment

2021-04-29

Insights Gained from Single-Cell Analysis of Immune Cells in the Tumor Microenvironment

Understanding tumor immune microenvironments is critical for identifying immune modifiers of cancer progression and developing cancer immunotherapies. Recent applications of single-cell RNA sequencing (scRNA-seq) in dissecting tumor microenvironments have brought important insights into the biology of tumor-infiltrating immune cells, including their heterogeneity, dynamics, and potential roles in both disease progression and response to immune checkpoint inhibitors and other immunotherapies. This review focuses on the advances in knowledge of tumor immune microenvironments acquired from scRNA-seq studies across multiple types of human tumors, with a particular emphasis on the study of phenotypic plasticity and lineage dynamics of immune cells in the tumor environment. We also discuss several imminent questions emerging from scRNA-seq observations and their potential solutions on the horizon.

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