Cold-Induced Changes in the Protein Ubiquitin

Conformational changes are essential for protein-protein and protein-ligand recognition. Here we probed changes in the structure of the protein ubiquitin at low temperatures in supercooled water using NMR spectroscopy. We demonstrate that ubiquitin is well folded down to 263 K, although slight rearrangements in the hydrophobic core occur. However, amide proton chemical shifts show non-linear temperature dependence in supercooled solution and backbone hydrogen bonds become weaker in the region that is most prone to cold-denaturation. Our data suggest that the weakening of the hydrogen bonds in the β-sheet of ubiquitin might be one of the first events that occur during cold-denaturation of ubiquitin. Interestingly, the same region is strongly involved in ubiquitin-protein complexes suggesting that this part of ubiquitin more easily adjusts to conformational changes required for complex formation

Arrhythmia Classification and Diagnosis Based on ECG Signal: A Multi-Domain Collaborative Analysis and Decision Approach

Electrocardiogram (ECG) signal plays a key role in the diagnosis of arrhythmia, which will pose a great threat to human health. As an effective feature extraction method, deep learning has shown excellent results in processing ECG signals. However, most of these methods neglect the cooperation between the multi-lead ECG series correlation and intra-series temporal patterns. In this work, a multi-domain collaborative analysis and decision approach is proposed, which makes the classification and diagnosis of arrhythmia more accurate. With this decision, we can realize the transition from the spatial domain to the spectral domain, and from the time domain to the frequency domain, and make it possible that ECG signals can be more clearly detected by convolution and sequential learning modules. Moreover, instead of the prior method, the self-attention mechanism is used to learn the relation matrix between the sequences automatically in this paper. We conduct extensive experiments on eight advanced models in the same field to demonstrate the effectiveness of our method

Structural Plasticity in Human Heterochromatin Protein 1β

<div><p>As essential components of the molecular machine assembling heterochromatin in eukaryotes, HP1 (Heterochromatin Protein 1) proteins are key regulators of genome function. While several high-resolution structures of the two globular regions of HP1, chromo and chromoshadow domains, in their free form or in complex with recognition-motif peptides are available, less is known about the conformational behavior of the full-length protein. Here, we used NMR spectroscopy in combination with small angle X-ray scattering and dynamic light scattering to characterize the dynamic and structural properties of full-length human HP1β (hHP1β) in solution. We show that the hinge region is highly flexible and enables a largely unrestricted spatial search by the two globular domains for their binding partners. In addition, the binding pockets within the chromo and chromoshadow domains experience internal dynamics that can be useful for the versatile recognition of different binding partners. In particular, we provide evidence for the presence of a distinct structural propensity in free hHP1β that prepares a binding-competent interface for the formation of the intermolecular β-sheet with methylated histone H3. The structural plasticity of hHP1β supports its ability to bind and connect a wide variety of binding partners in epigenetic processes.</p> </div

Plant secondary succession and soil degradation in humid red beds areas, South China

In South China, large amounts of strongly eroded badlands that are difficult for natural recovery formed in red beds soft rock, posing serious environmental hazards. This process is thought to be related to a unique nutrient cycle and plant-soil feedback in alkaline soil. In this study, we investigated 44 plant communities and some soil samples to explore the reasons for this erosion from the perspective of secondary succession and its driving factors. The results showed that the natural secondary succession (NSS) in red beds soft rock is the sequence of primary forest to scrub grass, xerophytes, and badlands. Masson pine and Masson pine/Schima superba communities have formed under the efforts of artificial intervention restoration. The community ecological gradient (CEG) and deciduosity rate substantially increased along the NSS, whereas the biomass, and diversity index rapidly decreased. The plantation community showed the opposite trend with increasing recovery years. Limitations in terms of soil water content, pH value, and available nitrogen (AN) for the community markedly increased, and we confirmed these were the largest contributors to redundancy analysis at the community scale. Compared with acidic soil, alkaline soil with a rough texture and high pH could not maintain enough water for plants during dry seasons, which inhibited the absorption of AN by plants. Therefore, in primary forests, the CEG and deciduosity rates need to be increased so that the plant community can adapt to harsh environments. plantation forests achieved soil acidification through litter accumulation. In the scrub grass and xerophyte, continuous reduction in litter and the intensification of soil erosion destroyed the balance between red argillaceous rock bed erosion and species invasion, leading to community degradation. Therefore, much attention should be given to primary forest protection and limiting factors mitigation in degraded communities

Proton-detected solid-state NMR detects the inter-nucleotide correlations and architecture of dimeric RNA in microcrystals

We report a novel proton-detected MAS solid-state NMR strategy based on 15N–15N proton assisted recoupling to detect the inter-nucleotide NH⋯N hydrogen bonds within the Watson–Crick base pairs of micro-crystallized dimeric RNA and to confirm the kissing-loop structure. This would contribute to advances in the structural determination of RNA using solid-state NMR

Backbone dynamics probed by ¹⁵N- relaxation rates.

<p><b>A, B, C. </b>¹⁵N spin-relaxation rates for ¹⁵N-perdeuterated hHP1β measured at a proton Larmor frequency of 600 MHz at 298 K. Residues with severe peak overlap or insufficient signal-to-noise ratio were excluded. R₁ (A), R₂ (B) and steady-state ¹H-¹⁵N heteronuclear NOE (C) are shown along the protein sequence. The R₂ rates were derived from R_1ρ measurements upon correction for the off-resonance tilted field as described in the Methods. <b>D.</b> Graphical analysis of reduced spectral density mapping. The solid line represents the theoretical function of J(ω_N) versus J(0) assuming a rigid single Lorentzian motion. Experimental values are plotted as points with labels specific for each hHP1β domain. <b>E.</b> The rotational correlation time τ_c, determined for each residue from the R₂/R₁ ratio, is shown as a function of residue number. <b>F.</b> Illustration of the diffusion tensor of CD (left, axially symmetric) and CSD (right, fully anisotropic) in full-length hHP1β. The x- and y-axes are shown as half-axes only for the fully anisotropic tensor. Pictures were prepared using MolMol <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0060887#pone.0060887-Koradi1" target="_blank">[57]</a>.</p

Internal dynamics.

<p><b>A. </b>¹⁵N linewidths of perdeuterated hHP1β as a function of residue number, measured from a TROSY-HSQC recorded at 700 MHz and 303 K. <b>B.</b> R_ex values of CD in full-length hHP1β as a function of residue number. <b>C.</b> Comparison of steady-state ¹H-¹⁵N heteronuclear NOE values of CD in full-length hHP1β in the free state (black circles) with those of CD in full-length hHP1β in complex with the H3K_C9me3 peptide (1–15) at a molar ratio of 1∶4 (white circles). Both measurements were performed at 298 K, 600 MHz proton Larmor frequency, 5 s recycle delay, on a 0.3 mM ¹⁵N-perdeuterated hHP1β sample.</p

Effects of Mn average oxidation state on the oxidation behaviors of As(III) and Cr(III) by vernadite

Vernadite is a poorly crystalline phyllomanganate that widely distributed in natural environments, and plays a pivotal role in the geochemical transformations of heavy metal and other pollutants. Though many works have done about the reaction mechanisms between vernadite-like minerals and As(III)/Cr(III), the effects of some basic structure characteristics of the mineral, such as Mn average oxidation state (AOS), on the oxidation of As (III)/Cr(III) are not fully understood. In this study, vernadite samples with different Mn AOSs but almost the same particle sizes (Ver and Ver20) were synthesized, characterized, and their reactivities towards As(III)/Cr(III) oxidation and As(V)/Cr(VI) adsorption were compared. It is found that Ver and Ver20 have almost the same point of zero charge (PZC), but ver20 has increased contents of layer Mn(III) at particle edges and interlayer Mn (III) and Mn(II), thus greatly reduced Mn AOS. Decrease in Mn AOS greatly reduces the oxidation capacity and initial reaction rate (K-obs) of this mineral towards As(III) on mineral-water interfaces. The apparent As(III) oxidation amount and K-obs by Ver are 202 +/- 8mmolkg(-1) and 0.3515 min(-1) while that by Ver20 are 162 +/- 7mmolkg(-1) and 0.0139 min(-1). The oxidation capacity and K-obs for Cr(III) by these vernadie samples are also decreased but in a less extent compared to that in As(III) oxidation, e.g. Cr(III) oxidized by Ver and Ver20 are 2895 +/- 47 and 1974 +/- 109 mmol kg(-1) and the K-obs are 0.0439 and 0.0169 min(-1) respectively. Adsorption density of As(V) or Cr(VI) on Ver20 is similar to 15-18% higher than that on Ver. These results suggest the more important role Mn AOS plays in As(III) oxidation than Cr(III) oxidation, and helps understand the geochemical behaviors of these toxic metals in natural environments mediated by Mn oxide minerals

Rotational diffusion tensor of CD and CSD within full-length hHP1β.

<p>Diffusion tensor parameters for the different tumbling models, obtained from experimental ¹⁵N spin-relaxation data through ROTDIF, are listed: the overall rotational correlation time τ_c; D_xx, D_yy and D_zz are the principal values of the diffusion tensor; Q is the quality factor defined as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0060887#pone.0060887-Walker1" target="_blank">[27]</a>; P defines the probability that an improvement in the fit when a more complex model is applied has occurred by chance. The best model for CD and CSD is marked in bold. The little improvement in the fit with the more complex fully-anisotropic model was not statistically significant for CD.</p