Xiangren Kong

As an important post-translational modification, ubiquitination mediates ∼80% of protein degradation in eukaryotes. The degree of protein ubiquitination is tightly determined by the delicate balance between specific ubiquitin ligase (E3)-mediated ubiquitination and deubiquitinase-mediated deubiquitination. In 2017, we developed UbiBrowser 1.0, which is an integrated database for predicted human proteome-wide E3-substrate interactions. Here, to meet the urgent requirement of proteome-wide E3/deubiquitinase-substrate interactions (ESIs/DSIs) in multiple organisms, we updated UbiBrowser to version 2.0 (http://ubibrowser.ncpsb.org.cn). Using an improved protocol, we collected 4068/967 known ESIs/DSIs by manual curation, and we predicted about 2.2 million highly confident ESIs/DSIs in 39 organisms, with >210-fold increase in total data volume. In addition, we made several new features in the updated version: (i) it allows exploring proteins' upstream E3 ligases and deubiquitinases simultaneously; (ii) it has significantly increased species coverage; (iii) it presents a uniform confidence scoring system to rank predicted ESIs/DSIs. To facilitate the usage of UbiBrowser 2.0, we also redesigned the web interface for exploring these known and predicted ESIs/DSIs, and added functions of 'Browse', 'Download' and 'Application Programming Interface'. We believe that UbiBrowser 2.0, as a discovery tool, will contribute to the study of protein ubiquitination and the development of drug targets for complex diseases.

Traditional Chinese medicine (TCM) is increasingly recognized and utilized worldwide. However, the complex ingredients of TCM and their interactions with the human body make elucidating molecular mechanisms challenging, which greatly hinders the modernization of TCM. In 2016, we developed BATMAN-TCM 1.0, which is an integrated database of TCM ingredient-target protein interaction (TTI) for pharmacology research. Here, to address the growing need for a higher coverage TTI dataset, and using omics data to screen active TCM ingredients or herbs for complex disease treatment, we updated BATMAN-TCM to version 2.0 (http://bionet.ncpsb.org.cn/batman-tcm/). Using the same protocol as version 1.0, we collected 17 068 known TTIs by manual curation (with a 62.3-fold increase), and predicted ∼2.3 million high-confidence TTIs. In addition, we incorporated three new features into the updated version: (i) it enables simultaneous exploration of the target of TCM ingredient for pharmacology research and TCM ingredients binding to target proteins for drug discovery; (ii) it has significantly expanded TTI coverage; and (iii) the website was redesigned for better user experience and higher speed. We believe that BATMAN-TCM 2.0, as a discovery repository, will contribute to the study of TCM molecular mechanisms and the development of new drugs for complex diseases.

Abstract Coordination bonds with a dynamic nature and wide‐spectrum bond energy have gained great popularity in use for fabricating tough soft materials. However, most existing coordination‐based elastomers are prepared through complicated procedures, usually involving elaborate synthesis of ligand‐containing monomers or polymers, ion diffusion to form coordination complexes, and removal of organic solvent during the synthesis, which are neither easy operation nor environmentally friendly. Here, a facile and effective strategy is demonstrated to fabricate tough metallosupramolecular elastomers by one‐pot polymerization of aqueous precursor solutions containing commercial agents, 2‐acrylamido‐2‐methyl‐1‐propanesulfonic acid, 2‐[2‐(2‐methoxyethoxy)ethoxy]ethyl acrylate, and Zr 4+ ions. After solvent (i.e. water) evaporation, the obtained elastomers are transparent and extremely tough owing to the presence of sulfonate‐Zr 4+ coordination complexes as physical crosslinks. Their mechanical properties are tunable over a wide spectrum by adjusting the composition of copolymers and the density of coordination bonds. This eco‐friendly strategy is further extended to various commercial monomers, manifesting good universality to toughen elastomers. Furthermore, the abundant functional groups of copolymers make the elastomers adhesive to various substrates including themselves, favoring applications such as interfacial adhesion and encapsulations. The easy fabrication, tunable mechanical properties, and adhesion ability endow the elastomers with great potential as the substrate of wearable soft electronics.

With inspiration from natural systems, various soft actuators and robots have been explored in recent years with versatile applications in biomedical and engineering fields. Soft active materials with rich stimulus-responsive characteristics have been an ideal candidate to devise these soft machines by using different manufacturing technologies. Among these technologies, three-dimensional (3D) printing shows advantages in fabricating constructs with multiple materials and sophisticated architectures. In this Review, we aim to provide an overview of recent progress on 3D printing of soft materials, robotics performances, and representative applications. Typical 3D printing techniques are briefly introduced, followed by state-of-the-art advances in 3D printing of hydrogels, shape memory polymers, liquid crystalline elastomers, and their hybrids as soft actuators and robots. From the perspective of material properties, the commonly used printing techniques and action-generation principles for typical printed constructs are discussed. Actuation performances, locomotive behaviors, and representative applications of printed soft materials are summarized. The relationship between printing structures and action performances of soft actuators and robots is also briefly discussed. Finally, the advantages and limitations of each soft material are compared, and the remaining challenges and future directions in this field are prospected.