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Auditory transduction is mediated by chordotonal (Cho) neurons in Drosophila larvae, but the molecular identity of the mechanotransduction (MET) channel is elusive. Here, we established a whole-cell recording system of Cho neurons and showed that two transient receptor potential vanilloid (TRPV) channels, Nanchung (NAN) and Inactive (IAV), are essential for MET currents in Cho neurons. NAN and IAV form active ion channels when expressed simultaneously in S2 cells. Point mutations in the pore region of NAN-IAV change the reversal potential of the MET currents. Particularly, residues 857 through 990 in the IAV carboxyl terminus regulate the kinetics of MET currents in Cho neurons. In addition, TRPN channel NompC contributes to the adaptation of auditory transduction currents independent of its ion-conduction function. These results indicate that NAN-IAV, rather than NompC, functions as essential pore-forming subunits of the native auditory transduction channel in Drosophila and provide insights into the gating mechanism of MET currents in Cho neurons.

The COVID-19 (coronavirus disease 2019) pandemic is caused by SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2). SARS-CoV-2 produces a small hydrophobic envelope (E) protein which shares high homology with SARS-CoV E protein. By patch-clamp recording, the E protein is demonstrated to be a cation-selective ion channel. Furthermore, the SARS-CoV-2 E protein can be blocked by a SARS-CoV E protein inhibitor hexamethylene amiloride. Using structural model and virtual screening, another E protein inhibitor AZD5153 is discovered. AZD5153 is a bromodomain protein 4 inhibitor against hematologic malignancies in clinical trial. The E protein amino acids Phe23 and Val29 are key determinants for AZD5153 sensitivity. This study provides two promising lead compounds and a functional assay of SARS-CoV-2 E protein for the future drug candidate discovery.

The SARS-CoV-2 S protein is a major point of interaction between the virus and the human immune system. As a consequence, the S protein is not a static target but undergoes rapid molecular evolution. In order to more fully understand the selection pressure during evolution, we examined residue positions in the S protein that vary greatly across closely related viruses but are conserved in the subset of viruses that infect humans. These "evolutionarily important" residues were not distributed evenly across the S protein but were concentrated in two domains: the N-terminal domain and the receptor-binding domain, both of which play a role in host cell binding in a number of related viruses. In addition to being localized in these two domains, evolutionary importance correlated with structural flexibility and inversely correlated with distance from known or predicted host receptor-binding residues. Finally, we observed a bias in the composition of the amino acids that make up such residues toward more human-like, rather than virus-like, sequence motifs.

The lipopolysaccharide (LPS)-induced endocytosis of Toll-like receptor 4 (TLR4) is an essential step in the production of interferon-β (IFN-β), which activates the transcription of antiviral response genes by STAT1 phosphorylated at Tyr701 Here, we showed that STAT1 regulated proinflammatory cytokine production downstream of TLR4 endocytosis independently of IFN-β signaling and the key proinflammatory regulator NF-κB. In human macrophages, TLR4 endocytosis activated a noncanonical phosphorylation of STAT1 at Thr749, which subsequently promoted the production of interleukin-6 (IL-6) and IL-12p40 through distinct mechanisms. STAT1 phosphorylated at Thr749 activated the expression of the gene encoding ARID5A, which stabilizes IL6 mRNA. Moreover, STAT1 phosphorylated at Thr749 directly enhanced transcription of the gene encoding IL-12p40 (IL12B). Instead of affecting STAT1 nuclear translocation, phosphorylation of Thr749 facilitated the binding of STAT1 to a noncanonical DNA motif (5'-TTTGANNC-3') in the promoter regions of ARID5A and IL12B The endocytosis of TLR4 induced the formation of a complex between the kinases TBK1 and IKKβ, which mediated the phosphorylation of STAT1 at Thr749 Our data suggest that noncanonical phosphorylation in response to LPS confers STAT1 with distinct DNA binding and gene-regulatory properties that promote both IL12B expression and IL6 mRNA stabilization. Thus, our study provides a potential mechanism for how TLR4 endocytosis might regulate proinflammatory cytokine production.

The leakage failure of the austenitic stainless steel tubes in the hydrogenation unit of a petrochemical company was analyzed. The causes of the failure were investigated by visual examination, chemical compositions analysis of the tube, microscopic examination, metallographic examination and scale layer analysis. The results showed that the directly reason of the failure is pitting corrosion and stress corrosion cracking. We concluded that the improper heat treatment of the austenitic stainless tubes and existence of the corrosive substances including wet hydrogen sulfide and hydrogen chloride in the working medium, result in the occurrence of the corrosion, and the complex flowing conditions accelerate the corrosion process. Proposals were put forward in this paper.

APOBEC3G (A3G) is a cellular protein that inhibits HIV-1 infection through virion incorporation. The interaction of the A3G N-terminal domain (NTD) with RNA is essential for A3G incorporation in the HIV-1 virion. The interaction between A3G-NTD and RNA is not completely understood. The A3G-NTD is also recognized by HIV-1 Viral infectivity factor (Vif) and A3G-Vif binding leads to A3G degradation. Therefore, the A3G-Vif interaction is a target for the development of antiviral therapies that block HIV-1 replication. However, targeting the A3G-Vif interactions could disrupt the A3G-RNA interactions that are required for A3G's antiviral activity. To better understand A3G-RNA binding, we generated in silico docking models to simulate the RNA-binding propensity of A3G-NTD. We simulated the A3G-NTD residues with high RNA-binding propensity, experimentally validated our prediction by testing A3G-NTD mutations, and identified structural determinants of A3G-RNA binding. In addition, we found a novel amino acid residue, I26 responsible for RNA interaction. The new structural insights provided here will facilitate the design of pharmaceuticals that inhibit A3G-Vif interactions without negatively impacting A3G-RNA interactions.

The oxidized amyloses with different carboxyl content were prepared to include linalool for antimicrobial activity in aqueous environment. The results show that linalool can be effectively reserved from volatilization through encapsulation into amylose and oxidized amyloses. The inclusion ability of oxidized amyloses towards linalool is decreasing with the increase of oxidation level due to the depolymerization of amylose. However, the solubilization effect of oxidized amyloses to linalool is enhanced efficiently owning to the high water solubility of oxidized amyloses. It is interesting that the inclusion complexes have good antimicrobial activity in aqueous environment. Linalool solubilized by oxidized amyloses presents better antimicrobial performance than that solubilized by amylose, mainly resulting from that amylose-linalool inclusion complex would aggregate and retrograde fast in aqueous solution, which is disadvantageous for the release of linalool. The study suggests that oxidized amylose is a promising solubilizer and carrier of linalool for antimicrobial activity in aqueous environment.

An ultrasensitive electrochemical DNA biosensor has been developed based on the assembly of highly conductive gold nanoparticles (AuNPs) on the free terminal of hairpin-structured probe DNA. The hairpin probe DNA was first immobilized on a gold electrode surface through Au S bond. Then the thioglycolic acid (TGA) was grafted on the 3′-end of hairpin DNA via the carboxylic-amino condensation reaction. Followed by, the AuNPs were further attached through reaction with the thiol-group of TGA. Thus, a highly conductive biointerface with ultralow charge-transfer resistance was obtained. Quantitative analysis exhibited that the target DNA could be detected over the range from 1.0 × 10−17 to 1.0 × 10−11 M. The detection limit was estimated to be 1.7 × 10−18 M. Also the biosensor showed good hybridization selectivity, stability and regeneration ability.

The mechanistic target of rapamycin complex 1 (mTORC1) plays a central role in regulating cell growth and metabolism by responding to cellular nutrient conditions. The activity of mTORC1 is controlled by Rag GTPases, which are anchored to lysosomes via Ragulator, a pentameric protein complex consisting of membrane-anchored p18/LAMTOR1 and two roadblock heterodimers. Here we report the crystal structure of Ragulator in complex with the roadblock domains of RagA-C, which helps to elucidate the molecular basis for the regulation of Rag GTPases. In the structure, p18 wraps around the three pairs of roadblock heterodimers to tandemly assemble them onto lysosomes. Cellular and in vitro analyses further demonstrate that p18 is required for Ragulator-Rag GTPase assembly and amino acid-dependent activation of mTORC1. These results establish p18 as a critical organizing scaffold for the Ragulator-Rag GTPase complex, which may provide a platform for nutrient sensing on lysosomes., mTORC1 activity is controlled through Rag GTPases, which are anchored to the lysosome through the Ragulator. Here, the authors give molecular insights into Ragulator-Rag GTPase assembly and present the crystal structures of the Ragulator alone and in complex with the RagA-C roadblock domains.

What physical mechanism leads to organization of a highly condensed and confined circular chromosome? Computational modeling shows that confinement-induced organization is able to overcome the chromosome's propensity to mix by the formation of topological domains. The experimentally observed high precision of separate subcellular positioning of loci (located on different chromosomal domains) in Escherichia coli naturally emerges as a result of entropic demixing of such chromosomal loops. We propose one possible mechanism for organizing these domains: regulatory control defined by the underlying E. coli gene regulatory network requires the colocalization of transcription factor genes and target genes. Investigating this assumption, we find the DNA chain to self-organize into several topologically distinguishable domains where the interplay between the entropic repulsion of chromosomal loops and their compression due to the confining geometry induces an effective nucleoid filament-type of structure. Thus, we propose that the physical structure of the chromosome is a direct result of regulatory interactions. To reproduce the observed precise ordering of the chromosome, we estimate that the domain sizes are distributed between 10 and 700 kb, in agreement with the size of topological domains identified in the context of DNA supercoiling.

Reversible acetylation on lysine residues, a crucial post-translational modification (PTM) for both histone and non-histone proteins, governs many central cellular processes. Due to limited data and lack of a clear acetylation consensus sequence, little research has focused on prediction of lysine acetylation sites. Incorporating almost all currently available lysine acetylation information, and using the support vector machine (SVM) method along with coding schema for protein sequence coupling patterns, we propose here a novel lysine acetylation prediction algorithm: LysAcet. When compared with other methods or existing tools, LysAcet is the best predictor of lysine acetylation, with K-fold (5- and 10-) and jackknife cross-validation accuracies of 75.89%, 76.73%, and 77.16%, respectively. LysAcet's superior predictive accuracy is attributed primarily to the use of sequence coupling patterns, which describe the relative position of two amino acids. LysAcet contributes to the limited PTM prediction research on lysine epsilon-acetylation, and may serve as a complementary in-silicon approach for exploring acetylation on proteomes. An online web server is freely available at http://www.biosino.org/LysAcet/.

RNA–LIM is a procedure that can analyze various pseudo-potentials describing the affinity between single-stranded RNA (ssRNA) ribonucleotides and surface amino acids to produce a coarse-grained estimate of the structure of the ssRNA at the protein interface. The search algorithm works by evolving an ssRNA chain, of known sequence, as a series of walks between fixed sites on a protein surface. Optimal routes are found by application of a set of minimal “limiting” restraints derived jointly from (i) selective sampling of the ribonucleotide amino acid affinity pseudo-potential data, (ii) limited surface path exploration by prior determination of surface arc lengths, and (iii) RNA structural specification obtained from a statistical potential gathered from a library of experimentally determined ssRNA structures. We describe the general approach using a NAST (Nucleic Acid Simulation Tool)-like approximation of the ssRNA chain and a generalized pseudo-potential reflecting the location of nucleic acid binding residues. Minimum and maximum performance indicators of the methodology are established using both synthetic data, for which the pseudo-potential defining nucleic acid binding affinity is systematically degraded, and a representative real case, where the RNA binding sites are predicted by the amplified antisense RNA (aaRNA) method. Some potential uses and extensions of the routine are discussed. RNA–LIM analysis programs along with detailed instructions for their use are available on request from the authors.

The reaction of [Ag(dppm)(NO 3 ] 2 with sodium phenylacetate and dppm in THF at room temperature gave rise to the silver complexes [Ag(dppm)(O 2 CCH 2 Ph)] 2 ( 1 ) and [Ag 2 (dppm) 3 ](NO 3 ) 2 ( 2 ), respectively. Their crystal structures have been determined by single crystal X-ray diffraction analysis. Complex 1 is binuclear with a silver-silver separation of 3.080 A and bridged by two dppm ligands. The cation in complex 2 possesses a Ag 2 P 6 core with AgAg distance of 2.987 A and the silver atoms are each coordinated by three phosphorus atoms in an ideal trigonal-planar environment. Their IR, Raman, 1 H and 31 P NMR spectroscopic properties are also reported.

We present a novel protein distance matrix based on the minimum line of arc between two points on the surface of a protein. Two methods for calculating this distance matrix are developed and contrasted. The first method, which we have called TOPOL, is an approximate rule based algorithm consisting of successive rounds of vector addition. The second method is adapted from the graph theoretic approach of Dijkstra. Both procedures are demonstrated using cytochrome c, a 12,500 Da protein, as a test case. In respect to computational speed and accuracy the TOPOL procedure compares favorably against the more complex method based on shortest path enumeration over a surface manifold grid. Some potential uses of the algorithmic approaches and calculated surface protein distance measurement are discussed.

Catalytic performance of palladium supported on activated carbons and mesoporous aluminosilicate Al-SBA-15 were investigated at 300 °C under 8 MPa H2 for hydrotreating of bio-oil model compounds, including phenol, anisole, and furfural. With Pd/C catalysts, phenol, anisole, and furfural have been mainly hydrogenated into cyclohexanol, 1-methoxycyclohexane and (tetrahydro-furan-2-yl)-methanol, respectively. Pd/C shows high hydrogenation activity, but poor deoxygenation ability. Differently, in the presence of Pd/Al-SBA-15, the main hydrotreating products of phenol, anisole, and furfural are cyclohexane, cyclohexane, and tetrahydropyran. The high hydrodeoxygenation activity of Pd/Al-SBA-15 is due to the synergistic effect of the noble metal, which has high hydrogenation ability and the support, which has acidic property, high surface area, and large pore size.