Biological insights from hydrogen exchange mass spectrometry

Over the past two decades, hydrogen exchange mass spectrometry (HXMS) has achieved the status of a widespread and routine approach in the structural biology toolbox. The ability of hydrogen exchange to detect a range of protein dynamics coupled with the accessibility of mass spectrometry to mixtures and large complexes at low concentrations result in an unmatched tool for investigating proteins challenging to many other structural techniques. Recent advances in methodology and data analysis are helping HXMS deliver on its potential to uncover the connection between conformation, dynamics and the biological function of proteins and complexes. This review provides a brief overview of the HXMS method and focuses on four recent reports to highlight applications that monitor structure and dynamics of proteins and complexes, track protein folding, and map the thermodynamics and kinetics of protein unfolding at equilibrium. These case studies illustrate typical data, analysis and results for each application and demonstrate a range of biological systems for which the interpretation of HXMS in terms of structure and conformational parameters provides unique insights into function. This article is part of a Special Issue entitled: Mass spectrometry in structural biology.     

Tunable Nanoporous Network Polymer Nanocomposites having Size‐Selective Ion Transfer for Dye‐Sensitized Solar Cells

Nanoporous network polymer nanocomposites with tunable pore size for size‐dependent selective ion transport are successfully prepared via the surface‐induced cross‐linking polymerization of methyl methacrylate (MMA) and 1,6‐hexanediol diacrylate (HDDA) on the surfaces of nanocrystalline TiO₂ particles. The morphologies of the porous network polymer layer and nanopores were investigated by transmission electron microscopy (TEM), field emission scanning electron microscopy (FE‐SEM), and Brunauer–Emmett–Teller (BET) experiments. The porous layer size‐selectively screened the ions that contacted the nanocrystalline TiO₂ particles, as demonstrated by ion conductivity measurements, electrochemical impedance spectroscopy (EIS), and transient absorption spectroscopy (TAS).     

STIM1 long and STIM1 gate differently TRPC1 during store-operated calcium entry

During myogenesis, a long splice variant of STIM1, called STIM1L is getting expressed, while the level of STIM1 remains constant. Previous work demonstrated that STIM1L is more efficient in eliciting store-operated Ca²⁺ entry (SOCE), but no current analysis of the channel(s) activated by this new STIM1L isoform was performed until now. In this study, we investigate the ionic channel(s) activated by STIM1L and whether differences exist between the two STIM1 isoforms, using HEK-293 T cells as a model system. Our data show that STIM1 and STIM1L activate Orai1 channel but also the endogenously expressed TRPC1. The channel activation occurs in two steps, with first Orai1 activation followed, in a subset of cells, by TRPC1 opening. Remarkably, STIM1L more frequently activates TRPC1 and preferentially interacts with TRPC1. In low intracellular Ca²⁺ buffering condition, the frequency of TRPC1 opening increases significantly, strongly suggesting a Ca²⁺-dependent channel activation. The ability of STIM1L to open Orai1 appears decreased compared to STIM1, which might be explained by its stronger propensity towards TRPC1. Indeed, increasing the amount of STIM1L results in an enhanced Orai1 current. The role of endogenous TRPC1 in STIM1- and STIM1L-induced SOCE was confirmed by Ca²⁺ imaging experiments. Overall, our findings provide a detailed analysis of the channels activated by both STIM1 isoforms, revealing that STIM1L is more prone to open TRPC1, which might explain the larger SOCE elicited by this isoform.     

Pareuchiloglanis (Teleostei: Sisoridae) from the Pearl River,China with description of three new species

We describe three new species of Pareuchiloglanis. Based on a comparison of 17 valid species of Pareuchiloglanis, the genus can be divided into two groups contingent on their gill opening size and the anus position. One group, which we call the large gill opening group, has a large gill opening extending to the base of the first pectoral-fin element; the anus is obviously closer to pelvic-fin insertion than the anal-fin origin; this group includes five species distributed in the Red and Pearl Rivers, China. The other group has a small gill opening extending only to the middle base of the pectoral-fin elements; the anus is usually located at the midpoint of the pelvic-fin insertion to the anal-fin origin or slightly behind. This group includes the other 12 species, which are distributed in the Mekong and Yangtze Rivers. The large-gill-opening group can be divided into two sub-groups based on the length of the caudal peduncle. One sub-group has a long caudal-peduncle and the distance from the anal-fin origin to caudal-fin base is greater than distance from the pelvic-fin insertion. This sub-group is only distributed in the Pearl River drainage. Another sub-group has a short caudal peduncle and the distance from the anal-fin origin to the caudal-fin base is typically smaller than the distance from the pelvic-fin insertion. This sub-group is only distributed in the Red River basin of China and Vietnam. The former will be called the large-gill-opening group with long caudal peduncle in the text and only includes one species P. longicauda. During our ongoing taxonomic work of specimens collected from Nanpan-jiang and Beipan-jiang (upper Pearl River drainage in Yunnan, China), some Pareuchiloglanis specimens that had the characters of the large-gill-opening group with long caudal peduncle represent three undescribed species.     

Retracted: Kinesin family member 2C aggravates the progression of hepatocellular carcinoma and interacts with competing endogenous RNA

Kinesin family member 2C (KIF2C), a substantial mitotic regulator, has been verified to exert a malignant function in several cancers. However, its function in hepatocellular carcinoma (HCC) remains unclear. In this study, the expression profile of KIF2C in HCC was characterized through the dataset from the TCGA and clinical tissue microarrays containing 220 pairs of resected HCC tissues and adjacent nontumor tissues in our hospital. The results indicated that KIF2C was substantially higher expression in tumor tissues than adjacent nontumor tissues. High expression of KIF2C significantly correlated with large tumor (>5.0 cm) (P = .001) and implied a dismal postoperative overall survival (OS) (hazard ratio [HR] = 1.729; P = .002) in our cohort of patients. Gain and loss of function assays displayed that KIF2C promoted HCC cell proliferation, accelerated cell cycle progression, and impeded apoptosis. By bioinformatic tools and mechanistic investigation, we found that KIF2C interacted with various cell-cycle-related proteins and was significantly involved in growth-promoting pathways. KIF2C upregulated PCNA and CDC20 expression. Subsequently, we investigated the regulation of KIF2C by competing endogenous RNA and elucidated that has-miR-6715a-3p was directly bond to the 3′-untranslated region of KIF2C through dual luciferase assays, thereby inhibiting KIF2C expression. Furthermore, the long noncoding RNA GS1-358P8.4 was found to be a candidate of KIF2C for has-miR-6715a-3p binding. HCC patients with high lncRNA-GS1-358P8.4 expression had shorter OS and relapse-free survival compared to those with low expression, which was accordance with the KIF2C. Taken together, KIC2C aggravated HCC progression, it could serve as a prognostic indicator and confer a novel target for clinical treatment.     

A prognostic five long–noncoding RNA signature for patients with rectal cancer

This study aimed to identify prognostic long noncoding RNAs (lncRNAs) signature for predicting the prognosis of patients with rectal cancer. LncRNA-sequencing data and clinicopathological data of patients with rectal cancer were retrieved from The Cancer Genome Atlas database. Univariate and multivariate Cox proportional hazards regression analysis, the least absolute shrinkage, and selection operator analysis and the Kaplan-Meier curve method were employed to identify prognostic lncRNAs and construct multi-lncRNA signature. Finally, five lncRNAs (AC079789.1, AC106900.2, AL121987.1, AP004609.1, and LINC02163) were identified to construct a five-lncRNA signature. According to the five-lncRNA signature, patients with rectal cancer were divided into a high-risk group and low-risk group. Patients with rectal cancer had significantly poorer overall survival in the high-risk group than in the low-risk group. We used a time-dependent receiver operating characteristic curve to assess the power of the five-lncRNA signature by calculating the area under the curve (AUC). The AUCs for predicting 3-year survival and 5-year survival were 0.742 and 0.935, respectively, which indicated a good performance of the five-lncRNA signature. The five-lncRNA signature was independently associated with the prognosis of patients with rectal cancer through using univariate and multivariate Cox regression analysis. The biological function of the five lncRNAs was enriched in some cancer-related biological processes and pathways by performing functional enrichment analysis of their correlated protein-coding genes. In conclusion, we developed a five-lncRNA signature as a potential indicator for rectal cancer.