A research group led by Prof. PIAO Hailong from the Dalian Institute of Chemical Physics (DICP) of the Chinese Academy of Sciences (CAS), in collaboration with Prof. LIU Hongxu's group from the department of Thoracic Surgery of the Liaoning Cancer Hospital & Institute, have characterized the cellular composition and spatial architecture of tumor microenvironment in human multiple primary lung cancers (MPLCs) by integrating single cell RNA-seq and spatial transcriptomics.
　　This study was published in Cell Death & Disease on July 25.
　　Illustration of cellular composition and spatial architecture of MPLCs based on single cell and spatial transcriptomics (Image by CHEN Di)
　　MPLCs refer to several primary tumors growing synchronously in the lung. With the widespread of high-resolution computed tomography, MPLCs are being diagnosed more frequently. However, it is still difficult to distinguish MPLC and intrapulmonary metastasis (IPM) in clinic, especially in cases of similar histologies.
　　In this study, the researchers conducted integrative analysis of both single-cell transcriptome and spatial transcriptome data based on bioinformatics and machine learning methods.
　　They identified a previously undescribed sub-population of epithelial cells termed as CLDN2+ alveolar type II (AT2), specifically enriched in MPLCs. Possessing a relatively stationary state, this subtype played an important role in cellular communication, aggregating spatially in tumor tissues and dominating the malignant histopathological patterns.
　　They verified that the CLDN2 protein expression could help distinguish MPLCs from intrapulmonary metastasis and solitary lung cancer. Moreover, they found that a cell surface receptor TNFRSF18/GITR was highly expressed in T cells of MPLCs, suggesting TNFRSF18 as one potential immunotherapeutic target in MPLCs. Meanwhile, high inter-lesion heterogeneity was observed in MPLCs.
　　"Our findings might provide insights into diagnostic biomarkers and therapeutic targets and advance our understanding of the cellular and spatial architecture of MPLCs," said Prof. PIAO.
　　This work was supported by the National Natural Science Foundation of China, the Dalian Science and Technology Innovation Funding, the Liaoning Revitalization Talents Program and etc.

　　The in-cell dynamic structures of proteins are crucial for unraveling their biological functions. With the advancement of deep learning algorithms aiding protein structure prediction, AlphaFold2 has achieved comprehensive protein structure prediction.
　　However, predicting the structures of flexible regions remains unclear.
　　Recently, a group led Prof. ZHANG Lihua from the Dalian Institute of Chemical Physics (DICP) of the Chinese Academy of Sciences (CAS), in collaboration with Associate Prof. GONG Zhou from the Precision Measurement Science and Technology Innovation Research Institute of CAS, have proposed a strategy using in vivo chemical cross-linking and mass spectrometry (in vivo XL-MS) to decode the dynamic structure of proteins in cells.
　　This study was published in Angewandte Chemie International Edition on July 05.
　　In vivo XL-MS is potential for analyzing the in-cell dynamic structures of proteins due to its high throughput, high sensitivity, and low requirements for protein purity.
　　In this study, the researchers utilized AlphaFold2's structures as prior information, combining in vivo XL-MS data with various structural calculation methods to assess the compatibility between structures and cross-linking information. They have achieved the reconstruction of the in-cell dynamic structures of various proteins, especially multi-domain proteins and intrinsically disordered proteins (IDPs).
　　Schematic illustration of a hierarchical strategy to decode protein dynamics in vivo with XL-MS (Image by ZHANG Beirong)
　　They focused on multi-domain proteins and proposed a strategy to treat the domains as a whole, utilizing XL-MS data between the domains to model the dynamic structures of proteins inside cells. They characterized the dynamic structures of three multi-domain proteins, namely calmodulin, hnRNP A1, and hnRNP D0, within cells.
　　Additionally, for IDPs, they introduced two complementary structural characterization strategies: one involved directly converting XL-MS data into distance constraints for IDP structure calculation, while the other strategy employed unbiased sampling using all-atom molecular dynamics simulations, followed by evaluation and selection of the sampled structures based on XL-MS data. By employing these two strategies, they decoded the ensemble conformations of two highly mobile high-mobility group proteins, HMG-I/Y and HMG-17, inside cells.
　　"Our study provides crucial technical support for a deeper understanding of the molecular mechanisms underlying protein functionality in the cellular microenvironment," said Prof. ZHANG.
　　This work was supported by the National Natural Science Foundation of China, the National Key R&D Program, the Youth Innovation Promotion Association of CAS.

　　Glycans perform varied and crucial functions in numerous cellular activities. The diverse roles of glycans are matched by their highly complex structures, which derive from differences in composition, branching, regio- and stereochemistry, and modification. This incomparable structural diversity is challenging to the structural analysis of glycans.
　　Recently, a joint research group led by Prof. QING Guangyan and Prof. LIANG Xinmiao from the Dalian Institute of Chemical Physics (DICP) of the Chinese Academy of Sciences (CAS) has developed a glycan identification method based on nanopore single-molecule sensing through a glycan derivatization strategy.
　　The study was published in Nature Communications on March 28.
　　Clear discrimination among four glycan isomers by single nanopore analysis, the glycans are labelled with a benzene tag (Image by Minmin Li)
　　Identifying and sequencing glycans using nanopore single-molecule techniques has sparked potential interests. However, it has achieved little progress over the past dozen years. Only a handful of cases that focused on either high molecular weight polysaccharides or some monosaccharides were reported.
　　For smaller but structurally more diverse glycans with greater biological significance, single molecule detection with nanopore has not yet been achieved, largely because fast passage of glycan through nanopore cannot be sensed because of the small size and weak affinity of glycan with nanopore.
　　To address the challenge, the researchers introduced a derivatization strategy by linking an aromatic-type tag group to small glycans via a high-efficiency and facile reductive amination reaction. The resulting tagged glycan was sensed with a wild-type aerolysin nanopore by presenting strong nanopore blockage signals.
　　The researchers obtained scatter plot based on blockage current and dwell time as the fingerprint map by processing the nanopore single-molecule blockage events. They identified different glycan isomers, glycans with varying lengths, and branched simple glycans.
　　Moreover, they revealed that multiple cation-π interactions between the aromatic tag of glycan with K238 residues of nanopore interface retarded the translocation of tagged glycan and contributed to the sensing.
　　"This study pushes the boundary of nanopore sensing beyond its traditional focus on nucleic acid and protein, and activates its power in the glycomics and glycoscience field, which might pave the way towards nanopore glycan sequencing", said Prof. QING.
　　This work was supported by the National Natural Science Foundation of China and the Innovation Grant of DICP.

　　Cellulose nanocrystal (CNC), an emerging bio-based material, has been widely applied in fields like electronics, bioplastics and energy.
　　However, functional failure of such materials in wet or liquid environments inevitably impairs their development in biomedicine, membrane separation, environmental monitoring, and wearable devices.
　　Now, a research group led by Prof. QING Guangyan from the Dalian Institute of Chemical Physics (DICP) of the Chinese Academy of Sciences reported a sustainable, insoluble, and chiral photonic cellulose nanocrystal patch for calcium ion (Ca2+) sensing in sweat.
　　The study, published in Small on Apr 13, provides a new idea for the functionalization of CNC.
　　Highly elastic hydrogels constructed by heat-induced hydrogen bond remodeling can switch between wet and dry states (Image by ZHANG Fusheng and LI Qiongya)
　　The researchers developed a simple and efficient method to fabricate insoluble CNC-based hydrogels. They found that by utilizing intermolecular hydrogen bond reconstruction, thermal dehydration enabled the optimized CNC composite photonic film to form a stable hydrogel network in an aqueous solution. Moreover, they indicated that hydrogel could be reversibly switched between dry and wet states, which was convenient for specific functionalization.
　　The introduction of functionalized molecules by adsorption swelling in a liquid environment resulted in a hydrogel with freeze resistance (–20°C), strong adhesion, good biocompatibility, and high sensitivity to Ca2+.
　　"This work is expected to facilitate the application of sustainable cellulose sensors to monitor other metabolites (i.e., glucose, urea, and vitamins, etc.)," said Prof. QING. "It also lays foundation for digitally controlled hydrogel systems operating in environmental monitoring, membrane separations, and wearable devices."

　　As the executor of life activities, proteins exert their specific biological functions through interactions such as forming protein complexes. The localization effects, crowding effects, and organelle microenvironments within cells are crucial for maintaining the structure and function of protein complexes. Therefore, it's important to analyze protein complexes accurately.
　　Recently, a research team led by Prof. ZHANG Lihua from the Dalian Institute of Chemical Physics (DICP) of the Chinese Academy of Sciences (CAS) has developed a glycosidic-bond-based mass-spectrometry-cleavable cross-linker, which improves the data analysis throughput and identification accuracy of cross-linking information with good amphiphilicity and biocompatibility. It enables in-vivo cross-linking of protein complexes in live cells and achieves large-scale and precise analysis.
　　This study was published in Angewandte Chemie International Edition on March 30.
　　Chemical cross-linking mass spectrometry (CXMS), especially in-vivo CXMS, is a large-scale analysis of in-situ conformation and interaction interface of protein complexes in living cells. However, in-vivo CXMS in living cells faces challenges such as high cell disturbance and complex spectra retrieval of cross-linked peptides.
　　In this study, the researchers incorporated glycosidic bonds into the design of functional cross-linkers based on the high biocompatibility of glucose molecules and the mass spectrometry cleavable feature of glycosidic bonds. They screened and obtained trehalose, a highly biocompatible molecule, as the skeleton molecule and developed a mass spectrometry cleavable cross-linker, trehalose disuccinimidyl succinate (TDS).
　　This cross-linker showed superior cell viability maintenance compared to currently reported membrane-permeable chemical cross-linkers and enabled efficient cross-linking of protein complexes in cells under low disturbance conditions.
　　The researchers found that low-energy glycosidic bond-high-energy peptide bond mass spectrometry selective fragmentation mode reduced the analysis complexity of the cross-linked peptide fragment spectra, significantly improving the efficiency and accuracy of cross-linked peptide identification.
　　They identified conformation of 1453 proteins corresponding to over 3,500 cross-linked peptide pairs, and 843 protein-protein interaction information from Hela cells.
　　"We have accurately realized in-vivo cross-linking and global analysis of protein complexes in live cells," said Prof. ZHANG. "And we provided an important toolkit for exploring the interaction sites of protein function regulation in live cell microenvironment."
　　This work was supported by the National Natural Science Foundation of China, the National Key R&D Program, and the Youth Innovation Promotion Association of CAS.

　　Water oxidation reaction involves a four-electron and four-proton transfer process, which requires an uphill energy transformation and limits the efficiency of the overall photocatalytic water splitting reaction.
　　Although loading appropriate water oxidation cocatalysts can enhance the performance of water oxidation reactions, the interfacial barrier between the semiconductor and the water oxidation cocatalyst can impede the transfer and utilization of photogenerated charges.
　　Recently, a research team led by Profs. LI Can and LI Rengui from the Dalian Institute of Chemical Physics (DICP) of the Chinese Academy of Sciences (CAS) has developed a strategy to controllably assemble a charge-transfer mediator in photocatalysis, which could increase surface charge-transfer efficiency and photocatalytic water oxidation activity.
　　This study was published in Angew. Chem. Int. Ed. on March 23.
　　Inspired by natural photosynthesis, the researchers employed partially oxidized graphene (pGO) as a charge-transferring mediator on the hole-accumulating facets of lead chromate (PbCrO4) photocatalyst. The pGO could be selectively assembled on the hole-accumulating facets of PbCrO4 by an ultrasonic deposition process, and cobalt-complex Co4O4 molecules could be anchored on the pGO as water oxidation cocatalyst.
　　Partially oxidized graphene operates as a charge-transfer mediator between the water oxidation cocatalyst (Co4O4) and the hole-accumulating {-101} facets of PbCrO4 (Image by JIANG Wenchao)
　　Based on techniques such as surface photovoltage spectroscopy, they confirmed that introducing the pGO charge transfer mediator between the hole-accumulation facets of PbCrO4 and Co4O4 molecules could effectively suppress charge recombination at the interface, thus prolonging the lifetime of photogenerated charges and enhancing the photocatalytic water oxidation performance.
　　"This strategy of rationally assembling charge transfer mediator provides a feasible way for accelerating charge transfer and charge utilization in semiconductor photocatalysis," said Prof. LI Rengui.
　　This study was supported by the Fundamental Research Center of Artificial Photosynthesis (FReCAP) of the National Natural Science Foundation of China, and the National Key Research and Development Program of China.