Article
Biochemical Research Methods
Min Fang, Yufeng He, Zhihua Du, Vladimir N. Uversky
Summary: This paper proposes a novel algorithm, DeepCLD, for predicting intrinsically disordered proteins. The algorithm utilizes specific scoring matrix, ResNet, and bidirectional CudnnLSTM to improve prediction accuracy and efficiency.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2022)
Article
Virology
Maria Fernanda de Castro-Amarante, Samuel Santos Pereira, Lennon Ramos Pereira, Lucas Souza Santos, Alexia Adrianne Venceslau-Carvalho, Eduardo Gimenes Martins, Andrea Balan, Luis Carlos de Souza Ferreira
Summary: This study evaluated the cross-inhibition effect of the DV2 peptide against Zika virus (ZIKV) and found that it efficiently inhibited ZIKV infectivity and reduced mortality in mice. These findings suggest that synthetic stem-based peptides have therapeutic potential against ZIKV infections.
Article
Biochemistry & Molecular Biology
Katharina Laass, Felipe Garcia Quiroz, Johannes Hunold, Stefan Roberts, Ashutosh Chilkoti, Dariush Hinderberger
Summary: The study reveals the hydration dynamics in phase-separating IDPs, showing that side-chain rehydration forms a dynamic water shield that affects solubility. This water shell strength is a sequence feature of IDPs, encoding for the stability of their phase-separated assemblies. The complexity of nanoscopic water-IDP interactions dictates their rich phase separation behavior.
Article
Biochemistry & Molecular Biology
Salome Araujo-Abad, Maria Fuentes-Baile, Bruno Rizzuti, J. Fernando Bazan, Adrian Villamarin-Ortiz, Miguel Saceda, Eduardo Fernandez, Miguel Vidal, Olga Abian, Adrian Velazquez-Campoye, Camino de Juan Romero, Jose L. Neira
Summary: RYBP is a multifunctional IDP involved in transcriptional regulation, while PADI4 is a well-folded protein implicated in arginine conversion. Both proteins were found to associate in the nucleus and cytosol of cancer cells, suggesting a potential role in cancer development and progression.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Multidisciplinary Sciences
Maurice Dekker, Erik Van der Giessen, Patrick R. Onck
Summary: The intrinsically disordered FG-Nups in the central channel of the nuclear pore complex (NPC) form a selective permeability barrier and undergo phase separation, with GLFG-Nups acting as hydrophobic stickers essential for the formation of FG-Nup condensates. The different FG-Nups can be divided into two classes based on their observed phase separation behavior: the central FG-Nups form a dynamic percolated network, while the peripheral FG-Nups likely form an entropic brush.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Oncology
Qian Zhang, Zhiqiang Zhang, Guodi Liu, Dehua Li, Zhangjie Gu, Linsong Zhang, Yingjiao Pan, Xingbing Cui, Lu Wang, Guoping Liu, Xiaoli Tian, Ziming Zhang
Summary: This study demonstrates that B7-H3 targeted CAR-T cells have high anti-tumor efficacy against osteosarcoma.
Article
Biochemistry & Molecular Biology
Aditya Mittal, Anandkumar Madhavjibhai Changani, Sakshi Taparia
Summary: This study identified unique signatures of intrinsic disorder by systematically synthesizing different peptide libraries, expanding the known intrinsically disordered proteins and providing a major advancement in exploring the functional manifestations of such proteins.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2021)
Article
Multidisciplinary Sciences
Kristina Boyko, Erin A. Rosenkranz, Derrick M. Smith, Heather L. Miears, Melissa Oueld Es Cheikh, Micah Z. Lund, Jeffery C. Young, Patrick N. Reardon, Mark Okon, Serge L. Smirnov, John M. Antos
Summary: This study demonstrates the use of SML for segmental isotopic labeling of IDR-containing samples, reducing complexity of NMR spectra. Through segmental assignment, different segments within the IDR can be identified and studied for their characteristics and responses. This method shows promise in selectively labeling and probing target segments within larger IDR contexts.
Article
Chemistry, Multidisciplinary
Siyao Wang, Qingqing Zhou, Yunxue Li, Bingcheng Wei, Xinliang Liu, Jie Zhao, Farong Ye, Zhongneng Zhou, Bei Ding, Ping Wang
Summary: Native chemical ligation (NCL) and expressed protein ligation (EPL) techniques provide efficient ways to assemble proteins with precise chemical features. This study introduces a quinoline-based photolabile protecting group (PPZQ) for cysteine, enabling various ligation strategies including NCL and EPL-desulfurization methods. The PPZQ group is compatible with radical desulfurization and shows great potential in protein caging/uncaging investigations.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Chemistry, Physical
Wenning Wang
Summary: Recent progress in atomic MD simulation studies of intrinsically disordered proteins (IDPs) includes the development of force fields and sampling methods, as well as applications in IDP-involved protein-protein interactions. Large-scale simulations and advanced sampling techniques allow for a more accurate estimation of the thermodynamics and kinetics of IDP-mediated protein interactions. The holistic landscape of the binding process of IDPs is emerging through these simulations.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2021)
Article
Chemistry, Multidisciplinary
Hang Zhao, Emmanuel Ibarboure, Vusala Ibrahimova, Ye Xiao, Elisabeth Garanger, Sebastien Lecommandoux
Summary: This research focuses on the rational design and synthesis of thermoresponsive hybrid polypeptide-polymer conjugates, which are used in combination with an artificial cytoplasm system to study the spatial organization and temperature-responsive dynamic assembly of artificial organelle structures within cell-mimicking entities.
Article
Biochemical Research Methods
Yumeng Liu, Xiaolong Wang, Bin Liu
Summary: Intrinsically disordered proteins/regions (IDPs/IDRs) are important for biological functions, and accurate prediction is crucial for protein structure and function predictions. However, most existing methods tend to predict fully ordered proteins as disordered, ignoring the fact that most newly sequenced proteins are fully ordered. The proposed RFPR-IDP method, trained on both ordered and disordered proteins, outperforms existing predictors in predicting both ordered and disordered proteins.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Biochemistry & Molecular Biology
Fangmei Tan, Nan Sun, Linsong Zhang, Jiahui Wu, Shifeng Xiao, Qiulong Tan, Vladimir N. Uversky, Yun Liu
Summary: The soybean LOC protein is a heat-stable protein with unknown function, conserved in Fabaceae. It is predicted to contain high levels of intrinsic disorder, but also has disorder-based protein-protein binding sites and short a-helical segments. The protein can prevent lactate dehydrogenase inactivation and increase survival under osmotic stress, suggesting a potential chaperone or cell protector role.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2021)
Article
Biochemistry & Molecular Biology
Christopher J. Brown, Chandra S. Verma, David P. Lane, Dilraj Lama
Summary: A study was conducted to develop peptide derivatives from intrinsically disordered eIF4G scaffold through molecular dynamics simulations and biophysical assays for regulating eIF4E protein interactions. Insights into the differential binding affinities of these peptides and the rate-limiting Y4: P38 hydrogen-bond interaction between the peptide and eIF4E were key findings. These insights were used to design features into the peptide to generate a potent eIF4E binder for potential therapeutic interventions in oncology.
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS
(2021)
Article
Biochemistry & Molecular Biology
Jung Min Kim, Baik Lin Seong, Jinho Jung
Summary: This study developed a method to label intrinsically disordered native proteins (IDNPs) in mammalian cells while preserving their active structures. By using pure fluorescent methionine and ATTO 565-biotin, IDNPs were labeled at the N- or C-terminus and their concentrations were detected using Ni-NTA beads. The study also demonstrated double labeling of genetically encoded fluorescent-Tat expression using a single fluorescent dye pair and FRET ratio and two-color correlation analysis. This research aims to address native protein processing and achieve ultrasensitive protein folding for nanoscale biological and ecological applications.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Polymer Science
Xiaojin Yan, Bo Hou, Yu Shao, Yu-Chun Xu, Wei-Yi Li, Qing-Yun Guo, Jinlin He, Peihong Ni, Wen-Bin Zhang
Summary: The self-assembly of giant molecules has attracted attention due to their fast phase separation kinetics and small feature size. However, there is not much study on multicomponent giant surfactants. In this work, a series of triblock bola-form giant surfactants with diverse functionalities were built through a modular synthetic strategy. These molecules were thoroughly characterized and it was revealed that they exhibit different phase separation scenarios.
MACROMOLECULAR RAPID COMMUNICATIONS
(2023)
Article
Materials Science, Composites
Jingjing Wei, Xiaohui Zhang, Fang Wang, Yu Shao, Wen-Bin Zhang, Hui Wu
Summary: In recent years, conductive hydrogels have made remarkable progress in simulating human skin. However, developing a hydrogel with high mechanical strength, satisfactory ionic conductivity, and extensive adhesion remains a challenge. In this study, a double network composite hydrogel was reported, which exhibited high mechanical strength, good ionic conductivity, antibacterial effects, and extensive adhesion. Natural cellulose nanofibers synergistically enhanced the mechanical strength of the hydrogel.
COMPOSITES SCIENCE AND TECHNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Jianxiang Liang, Yunying Fang, Chang An, Yuanbin Yao, Xiaomei Wang, Wenbin Zhang, Ruoyu Liu, Lulu Wang, Mohammad Aslam, Yan Cheng, Yuan Qin, Ping Zheng
Summary: Passion fruit is a tropical fruit with significant agricultural, economic, and ornamental values. The study identified and classified 138 passion fruit bHLH genes, revealing their structural conservation and functional diversity. The expansion of the PebHLH gene family mainly occurred through segmental duplication, and their diverse regulatory roles might be related to the presence of different cis-regulatory elements in their promoter regions. This study provides insights for further functional investigation of PebHLHs and improvement of passion fruit breeding.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Chemistry, Physical
Yu-Chun Xu, Li Ding, Ze-Fan Yao, Yu Shao, Jie-Yu Wang, Wen-Bin Zhang, Jian Pei
Summary: Excellent progress has been made in the optoelectronic properties of conjugated polymers by controlling solution-state aggregation. However, it is still challenging to fully understand the complex aggregation process and microstructures of conjugated polymers due to their wide variety and complex structures. This Perspective focuses on discussing the chain conformations, aggregation, and factors influencing solution-state aggregation and microstructures. Strategies to regulate solid-state microstructures and obtain high-performance polymer-based devices from solution-state aggregation are also summarized.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Polymer Science
Tingting Yang, Ling Wang, Wen-Hao Wu, Shicheng Wei, Wen-Bin Zhang
Summary: We report an entirely protein-based hydrogel as an artificial ECM that can regulate the growth of embryonic stem cells. A synergy between chemical and physical cross-linking was achieved by SpyTag/SpyCatcher reaction and P zipper association. The stress relaxation behaviors of the hydrogels can be tuned by single-point mutation on a P zipper. Faster relaxation promotes the growth of HeLa tumor spheroids and embryonic stem cells, while mechanical regulation of embryonic stem cells occurs via retention of the cells at the G1 phase. Genetically encoded protein materials show promise as a platform for understanding and controlling complex cell-matrix interactions in 3D cell culture.
Article
Chemistry, Multidisciplinary
Tianzuo Li, Fan Zhang, Jing Fang, Yajie Liu, Wen-Bin Zhang
Summary: Chemical topology refers to the arrangement of atoms and bonds in a molecule. The linear configuration of proteins is determined by the molecular mechanism for translation. Our research group has developed methods for the cellular synthesis of topological proteins, such as lasso proteins, protein rotaxanes, and protein catenanes, opening up new protein classes and paving the way for exploring their practical applications.
CHINESE JOURNAL OF CHEMISTRY
(2023)
Article
Polymer Science
Yu Shao, Bo Hou, Weiyi Li, Xiaojin Yan, Xiaoge Wang, Yuchun Xu, Qingshu Dong, Weihua Li, Jinlin He, Wen -Bin Zhang
Summary: In this work, we designed and synthesized three-component bolaform giant surfactants that can form three-phase-four-layer lamellar (LAM3) structures with sub-5 nm feature sizes. By utilizing phase separation among three mutually incompatible components, we obtained LAM3 structures with sharp interfaces and d-spacings of 12-19 nm. Moreover, the morphology of the LAM3 structures can be transformed into a hierarchical lamellar structure with extremely small Si-rich layers (approximately 2 nm in thickness) through oxygen plasma treatment. This study demonstrates the versatility of these bolaform giant surfactants in producing unconventional nanostructures with small feature sizes.
Article
Multidisciplinary Sciences
Zhiyu Qu, Jing Fang, Yu-Xiang Wang, Yibin Sun, Yajie Liu, Wen-Hao Wu, Wen-Bin Zhang
Summary: A single-domain green fluorescent protein catenane was designed and synthesized by rewiring the connectivity of GFP's secondary motifs, showcasing the rich structural diversity of proteins. This design and synthesis strategy can be applied to other proteins with similar folds, expanding the family of single-domain fluorescent proteins.
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Multidisciplinary
Yu Shao, Di Han, Yangdan Tao, Fengfeng Feng, Ge Han, Bo Hou, Hao Liu, Shuguang Yang, Qiang Fu, Wen-Bin Zhang
Summary: In this study, the synthesis, assembly, and phase behaviors of regioisomeric Janus nanograins with distinct core symmetry were investigated. The nanograins, named B2DB2, exhibited different behaviors in solution and bulk due to the preference of BPOSS for crystallization and DPOSS for phase separation. The phase complexity observed was attributed to the competition between crystallization and phase separation, influenced by core symmetry.
ACS CENTRAL SCIENCE
(2023)
Article
Chemistry, Analytical
Jingjing Wei, Yu Shao, Shixin Qiao, Aaron Li, Shaogang Hou, Wen-Bin Zhang
Summary: This feature article focuses on the experimental use of quartz crystal microbalance with dissipation (QCM-D) as a powerful analytical technique to probe biological events ranging from biomacromolecular interactions and conformational changes of biomacromolecules to surface immobilization of biomacromolecules and cell morphological changes.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Yu Shao, Di Han, Yangdan Tao, Fengfeng Feng, Ge Han, Bo Hou, Hao Liu, Shuguang Yang, Qiang Fu, Wen-Bin Zhang
Summary: We report the synthesis, assembly, and phase behaviors of a series of precisely defined regioisomeric Janus nanograins with distinct core symmetry, which can generate unconventional phase structures and considerable phase complexity in soft matter. The results demonstrate that regioisomerism could indeed generate profound phase complexity.
ACS CENTRAL SCIENCE
(2023)
Article
Chemistry, Multidisciplinary
Jiyeon Lee, Dahye Im, Yajie Liu, Jing Fang, Xibao Tian, Minsu Kim, Wen-Bin Zhang, Jongcheol Seo
Summary: A technique combining ion mobility spectrometry-mass spectrometry (IMS-MS) and supercharging electrospray ionization (ESI) has been demonstrated to effectively differentiate protein chemical topology. By incorporating as many charges as possible into proteins via supercharging ESI, the protein chains can be largely unfolded and stretched, revealing their hidden chemical topology. Different chemical topologies result in different geometric sizes of the unfolded proteins due to constraints in torsional rotations. The introduction of new topological indices allows for successful differentiation of various protein chemical topologies. This technique provides an easy classification of the topological features of complex proteins, previously concealed by their inherent complexity, and establishes a visual standard for discerning protein topologies.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Biochemistry & Molecular Biology
Bo Yan, Zhangcheng Ding, Wenbin Zhang, Gaihong Cai, Hui Han, Yan Ma, Yang Cao, Jiawen Wang, She Chen, Youwei Ai
Summary: This study reveals the physical interaction between phosphodiesterase 3A (PDE3A) and Schlafen 12 (SLFN12), which plays a crucial role in SLFN12-mediated cell death induced by cytotoxic PDE3A modulators.
CELL CHEMICAL BIOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Wen-Hao Wu, Jianwen Guo, Longshuai Zhang, Wen-Bin Zhang, Weiping Gao
Summary: This article reviews recent progress in the application of cyclic or multicyclic peptides and proteins to the development of artificial peptides and proteins. In addition to simple cyclic forms, various macrocycle variants, such as knots and links, have been developed. The chemical tools and synthetic strategies for the biological synthesis of these macrocycles are summarized, demonstrating its potential as a powerful alternative to chemical synthesis. Furthermore, the application of these macrocycles to therapeutic peptides/proteins has led to significant improvements in pharmaceutical performances.
RSC CHEMICAL BIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Xilin Bai, Yajie Liu, Jiyeon Lee, Jing Fang, Wen-Hao Wu, Jongcheol Seo, Wen-Bin Zhang
Summary: This study presents the molecular design, synthesis, and characterization of protein pretzelanes with a chemical topology of a bridged Hopf link. By utilizing intramolecular chain entwining and genetically encoded side-chain coupling reactions, the model protein pretzelane was directly synthesized in Escherichia coli. Various proteins of interest were successfully inserted at the bridge region, resulting in diverse protein pretzelanes. The topological structure was verified using several techniques, and the results showed that the pretzelane topology not only retained the functional properties of the inserted proteins but also improved thermal resilience.