Article
Biology
Li Shen, Hongsong Feng, Yuchi Qiu, Guo-Wei Wei
Summary: A sequence-based virtual screening method utilizes natural language processing algorithms and optimized deep K-embedding strategies to encode biomolecular interactions without relying on 3D structure-based docking. It outperforms current methods in multiple datasets and has significant potential in drug discovery and protein engineering.
COMMUNICATIONS BIOLOGY
(2023)
Article
Chemistry, Analytical
Mariacristina Gagliardi, Laura Colagiorgio, Marco Cecchini
Summary: This study proposes a QCM-D method to investigate the interactions between polymeric nanoparticles and three different human blood proteins. The results indicate that bare nanoparticles have a high affinity towards fibrinogen and γ-globulin, while PEGylation greatly reduces these interactions and surfactant coating appears to increase them. These findings suggest that the proposed approach is valid for studying the interactions between nanoparticles and blood proteins.
Review
Chemistry, Multidisciplinary
Dongyoon Kim, Nowras Rahhal, Christoph Rademacher
Summary: Carbohydrates play important roles in cellular interactions and immune system recognition. Nanoparticles coated with carbohydrate structures can be captured by cellular receptors, triggering cellular responses and aiding in the study of carbohydrate-protein interactions.
FRONTIERS IN CHEMISTRY
(2021)
Article
Chemistry, Analytical
Joanna Xiuzhu Xu, Md Siddik Alom, Nicholas C. Fitzkee
Summary: An effective intensity-based reference using N-15 tryptophan as an external reference for H-1-N-15 2D NMR experiments is presented in this study to quantify competitive protein adsorption onto nanoparticle surfaces. The referencing system validated the binding capacity of single protein onto gold NPs and accurately quantified signals from protein mixtures. The proposed Trp reference enables the monitoring of competitive adsorption of different proteins in situ and in real time, highlighting the importance of studying protein-NP interactions in protein mixtures using H-1-N-15 2D NMR techniques.
ANALYTICAL CHEMISTRY
(2021)
Article
Chemistry, Applied
Katarzyna Kaczynska, Arno G. B. Wouters, Jan A. Delcour
Summary: The behavior of wheat gliadin nanoparticles (GNPs) modified with microbial transglutaminase (TG) at the air-water interface was studied, and it was found that co-gliadins were more susceptible to TG action and y-gliadins were more important for interface stability.
FOOD HYDROCOLLOIDS
(2022)
Article
Chemistry, Analytical
Jiawen Lyu, Yan Wang, Chengfei Ruan, Xiaolei Zhang, Kejia Li, Mingliang Ye
Summary: This study introduces a method utilizing mechanical stress induced protein precipitation (MSIPP) for drug target deconvolution, with a streamlined workflow allowing in situ sample preparation on microparticle surfaces. The MSIPP method has been successfully applied to multiple drug compounds and revealed DHFR as a target of Raltitrexed.
ANALYTICA CHIMICA ACTA
(2021)
Article
Engineering, Electrical & Electronic
Heng Zhang, Xiao Jin, Hanwen Zhao, Yongping Lin, Xiaofeng Li, Lianping Hou, John Marsh, Lei Dong, Daming Shi, Weiping Liu, Bin Xu, Bin Ni, Juan Liu, Jichuan Xiong, Xuefeng Liu
Summary: The research shows that introducing antibody-conjugated gold nanoparticles on the surface of virus particles can amplify photon scattering signal, increasing the sensitivity of virus detection. This method achieves 5.4 times higher sensitivity in detecting virus-gold particle doublets compared to conventional microscope imaging.
IEEE PHOTONICS JOURNAL
(2021)
Article
Multidisciplinary Sciences
Jian Zhang, Dezhi Zhu, Jianfeng Yan, Chang-An Wang
Summary: A new ultrafast laser-induced SMSI strategy has been proposed for constructing SMSI on a CeO2-supported Pt system, leading to enhanced activity and stability of the catalyst through the formation of surface defects and thin overlayer. This strategy can be extended to other noble metal systems and non-reducible oxide supports, providing a universal approach for engineering high-performance supported noble metal catalysts.
NATURE COMMUNICATIONS
(2021)
Article
Chemistry, Multidisciplinary
Amandeep Kaur, Ravneet Kaur Sandhu, Poonam Khullar, Kultar Singh, Gurinder Kaur Ahluwalia, Mandeep Singh Bakshi
Summary: This study investigated the interactions between Au and Ag nanoparticles using sodium dilauraminocystine and Gemini surfactant-stabilized nanoparticles, showing how these interactions are affected by the spacer and polymeric nature of the surfactant head group. Additionally, the control of Au-Ag nanoparticle interactions in an aqueous phase was demonstrated by surface-active magnetic nanoparticles placed at the aqueous-air interface. Water-soluble zwitterionic magnetic nanoparticles proved to be effective extractants for both Au and Ag nanoparticles from the aqueous phase, depending on the strength of interactions between them.
Article
Chemistry, Physical
Mengyao Wen, Yixiao Li, Wencheng Zhong, Qingfang Li, Liping Cao, Li-li Tan, Li Shang
Summary: This study systematically investigates the interactions between cationic nanoparticles and different serum proteins at nano-bio interfaces. The experimental results show that proteins bind to AuNCs with micromolar affinities and quench their fluorescence; protein adsorption onto cationic AuNCs significantly influences their cellular responses.
JOURNAL OF COLLOID AND INTERFACE SCIENCE
(2022)
Article
Chemistry, Multidisciplinary
Bekir Asilcan Unlu, Serife Akkoyun, Ahmet Karatay, Aytunc Ates, Ayhan Elmali
Summary: This study investigated the effect of aluminum (Al) concentration on the surface plasmon resonance (SPR) band position of aluminum/polyvinylpyrrolidone (Al/PVP) composite nanofibers and found that increasing Al content can enhance nonlinear absorption (NLA) effects. Experimental and theoretical analysis showed that the first model provided more accurate results. It was observed that the NLA performance of Al/PVP nanofibers significantly improved with increasing Al content, accompanied by aggregation effects and broadening and red shifting of the SPR band, indicating a decreasing interparticle distance in Al particles.
Article
Chemistry, Multidisciplinary
Patricia Perez Schmidt, Katiuscia Pagano, Cristina Lenardi, Marta Penconi, Ruth Mateu Ferrando, Claudio Evangelisti, Luigi Lay, Laura Ragona, Marcello Marelli, Laura Polito
Summary: This study presents a simple photo-induced synthesis method for the production of Glyco-UAuNPs using a reliable microfluidic approach at room temperature. The method eliminates the need for chemical reductants, templating agents, or co-solvents and demonstrates good feasibility and stability. Using nuclear magnetic resonance spectroscopy, the study shows a linear correlation between the exposed thiol ligands on the UAuNPs and the ligand concentration in the initial mixture, providing a precise design method for engineered UAuNPs or smart hybrid nano-systems.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Metallurgy & Metallurgical Engineering
Joao V. Mattioni, Douglas S. Franciscato, Fernando M. Melo, Luca M. Sihn, Bruno B. N. S. Brandao, Ulisses Condomitti, Marcelo Nakamura, Henrique E. Toma
Summary: The reaction between the ranelate ion and gold(III) ions produces stable gold nanoparticles, which can be used as a new method for extracting gold. This method allows for the extraction of even trace amounts of gold from aqueous solution under green and mild conditions, without using harmful and toxic reagents.
Article
Chemistry, Multidisciplinary
Long Li, Zhen Li, Ziying Wang, Shuyu Chen, Rongying Liu, Xuyang Xu, Zhi Zhang, Linfei Ye, Yu Ding, Quan Luo, Sheng Cao, Lei Zhang, Anne Imberty, Guosong Chen
Summary: By controlling the symmetry and number of supramolecular interactions on protein surfaces, nonspecific interactions between proteins can be induced to form various nanoscale assemblies, including coiling nanowires, nanotubes, and nanosheets, without manipulating the protein's native surfaces. These nanoscale assemblies can spontaneously evolve into more ordered architectures, crystals. These findings reveal a transformation mechanism of protein self-assembly that has not been exploited before and may provide an approach to generate complex and transformable biomacromolecular self-assemblies.
Article
Biochemical Research Methods
Yang Tian, Qiuyu Bao, Nian Wang, Ning Wan, Langlang Lv, Haiping Hao, Chaoyong He, Hui Ye
Summary: The study introduces an acetaldehyde labeling approach to complement formaldehyde labeling for probing ligand-protein interactions. The use of acetaldehyde allows for cleaner and more moderate reaction profiles compared to formaldehyde, enabling the identification of lysines involved in ligand-protein binding. Time-dependent changes in lysine accessibility profiles were detected using acetaldehyde labeling, further quantified by multiple reaction monitoring to sensitively determine ligand-binding sites and differentiate binding affinities among various ligands, which was confirmed by native mass spectrometry and molecular docking. Monitoring the chemical accessibility of these responsive peptides in cell lysates demonstrates the potential of these methods in characterizing ligand-protein interactions in complex cellular environments.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2021)
Article
Chemistry, Multidisciplinary
Tingjie Song, Xiaojing Wang, Dongbao Yao, Haojun Liang, Yi Lu
Summary: This study successfully identified and differentiated G4 DNA molecules with different topologies and nucleotide residues using synthetic G4 DNA-encoded nanoparticle approach, and validated the effectiveness and sensitivity of this method through monitoring plasmonic properties.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Biochemistry & Molecular Biology
Aaron P. Ledray, Sudharsan Dwaraknath, Khetpakorn Chakarawet, Madeline R. Sponholtz, Claire Merchen, Casey Van Stappen, Guodong Rao, R. David Britt, Yi Lu
Summary: A biosynthetic model of oxidases was constructed by replacing tyrosine with tryptophan, and it was demonstrated that tryptophan can also promote the oxygen reduction reaction, although with lower activity. Structural analysis and experimental results indicate that the difference in activity is due to the higher reduction potential of tryptophan. This study provides the first evidence that tryptophan can promote the oxygen reduction reaction and offers a structural basis for the observation of varying activities.
Article
Chemistry, Multidisciplinary
Yu Zhou, Evan N. Mirts, Sangdo Yook, Matthew Waugh, Rachel Martini, Yong-Su Jin, Yi Lu
Summary: We report a biocatalytic system for direct generation of TAL derivatives under mild conditions by rationally engineering the 2PS active site and rewiring the biocatalytic pathway in the metabolic network of E. coli. The system can produce high-value products, such as kavalactone precursors, with yields up to 17 mg/L culture. Computer modeling suggests that sterics and hydrogen-bond interactions play key roles in tuning the selectivity, efficiency, and yield.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Multidisciplinary
Xiaojing Wang, Skye Shepherd, Nantao Li, Congnyu Che, Tingjie Song, Yanyu Xiong, Isabella Rose Palm, Bin Zhao, Manish Kohli, Utkan Demirci, Yi Lu, Brian T. T. Cunningham
Summary: In this study, an efficient target recycling amplification process (TRAP) using photonic resonator absorption microscopy was developed for the digital detection of exosomal microRNAs (miRNAs). The TRAP approach demonstrated high sensitivity, robust selectivity, and a broad dynamic range, making it ideal for quantifying miRNA biomarkers in low concentrations or sample volume. Compared to traditional qRT-PCR, TRAP showed similar accuracy in profiling exosomal miRNAs derived from cancer cells, but with significantly enhanced detection limits for miRNA-375 and miRNA-21.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Biophysics
Shanni Hong, Zhenglin Yang, Quanbing Mou, Yunxia Luan, Bingbo Zhang, Renjun Pei, Yi Lu
Summary: This study presents a fluorescence aptamer sensor that can monitor the rapid leaching kinetics of quantum dots and the concentration of ions in living cells in real time. The sensor shows high specificity and can be used to study the biosafety and cytotoxicity mechanisms of various cadmium-based quantum dots.
BIOSENSORS & BIOELECTRONICS
(2023)
Article
Chemistry, Analytical
Zheng Wei Wong, Siu Yee New
Summary: A fluorescence biosensor based on hybridisation chain reaction amplification coupled with silver nanoclusters has been developed for nucleic acid detection, providing a reliable and low risk method for detecting target DNA.
Article
Chemistry, Multidisciplinary
Yunling Deng, Sudharsan Dwaraknath, Wenhao O. Ouyang, Cory J. Matsumoto, Stephanie Ouchida, Yi Lu
Summary: Researchers have synthesized cobalt porphyrin substituted myoglobin (CoMb) as a homogeneous catalyst for photo-driven CO2 to CO conversion in water. By optimizing the activity and product selectivity through varying pH and concentrations of the enzyme and the photosensitizer, they achieved high efficiency of CO generation. They further enhanced the CO2-reducing performance by introducing positively charged residues near the active site of CoMb.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Multidisciplinary
Zhimei Huang, Xianbo Ma, Fengze Jiang, Rong Wang, Zhenkun Wu, Yi Lu
Summary: DNAwalkers have been widely used in biosynthesis, biocomputing, and biosensing due to their programmability, biocompatibility, and signal amplification capacity. A dual spatially localized DNA walker was designed to drive high-speed stochastic movement along three-dimensional tracks using bipedal catalysts. The colocalization of autocatalytic circuits and the use of bipedal catalysts significantly increased the reaction kinetics. An RNA-responsive PCHA walker was constructed for mRNA imaging in live cells, providing a novel and efficient tool for biomolecule detection and biological functions regulation.
Article
Biotechnology & Applied Microbiology
Yuan Ma, Weijie Guo, Quanbing Mou, Xiangli Shao, Mingkuan Lyu, Valeria Garcia, Linggen Kong, Whitney Lewis, Carson Ward, Zhenglin Yang, Xingxin Pan, S. Stephen Yi, Yi Lu
Summary: GlycoRNA imaging in cells is achieved through a proximity ligation assay called ARPLA. This assay allows visualization of glycoRNAs, a recently discovered class of glycosylated molecules, in single cells with high sensitivity and selectivity. ARPLA enables the detection of spatial distributions of glycoRNAs on the cell surface, their colocalization with lipid rafts, and the intracellular trafficking of glycoRNAs.
NATURE BIOTECHNOLOGY
(2023)
Article
Multidisciplinary Sciences
Yuting Wu, Seyed-Fakhreddin Torabi, Ryan J. Lake, Shanni Hong, Zhengxin Yu, Peiwen Wu, Zhenglin Yang, Kevin Nelson, Weijie Guo, Gregory T. Pawel, Jacqueline Van Stappen, Xiangli Shao, Liviu M. Mirica, Yi Lu
Summary: By developing DNAzyme-based fluorescent turn-on sensors, we can selectively visualize either Fe2+ or Fe3+, revealing a decreased Fe3+/Fe2+ ratio during ferroptosis and an increased Fe3+/Fe2+ ratio in Alzheimer's disease mouse brain. The elevated Fe3+/Fe2+ ratio was mainly observed in amyloid plaque regions, suggesting a correlation between amyloid plaques and the accumulation of Fe3+ and/or conversion of Fe2+ to Fe3+. Our sensors can provide deep insights into the biological roles of labile iron redox cycling.
Article
Chemistry, Multidisciplinary
Huanhuan Fan, Claire E. E. McGhee, Ryan J. J. Lake, Zhenglin Yang, Zijian Guo, Xiao-Bing Zhang, Yi Lu
Summary: Manganese is an essential element in the human body and its detection in living cells is important. However, specific fluorescent sensors for Mn2+ are rare due to its paramagnetism and poor selectivity against other metal ions. This study reports the development of an RNA-cleaving DNAzyme with high selectivity for Mn2+ and its conversion into a fluorescent sensor. The sensor has been successfully used to detect Mn2+ in immune cells and tumor cells, as well as monitor the degradation of manganese-based nanomaterials in tumor cells.
Article
Chemistry, Inorganic & Nuclear
Yiwei Liu, Nicholas M. Marshall, Sheng-Song Yu, Wantae Kim, Yi-Gui Gao, Howard Robinson, Mark J. Nilges, Yan Zhang, Siu Yee New, Yi Lu
Summary: A study was conducted to investigate the effects of M13F, M44F, and G116F mutations on E & DEG; in azurin. The introduction of Phe residues at different positions and in different combinations can modulate E & DEG; in various ways, with a maximum change of 64 mV. X-ray crystal structures revealed that the spatial orientations of the Phe residues and H-bonding networks around the T1Cu-coordinating His117 are responsible for these effects. Furthermore, the study demonstrated the differential influence of M13F, M44F, and G116F mutations on the E & DEG; of T1Cu, with M13F decreasing E & DEG;, M44F increasing E & DEG;, and G116F showing a negligible effect. Combining certain mutations also resulted in cooperative effects on E & DEG;. Crystal structures provided insight into the steric effects and fine-tuning of hydrogen bond networks that contribute to these changes. Overall, the findings of this study contribute to the understanding and development of redox-active proteins with tunable properties.
INORGANIC CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Jessica S. Y. Ooi, Cher Ryn Lim, Chai Xian Hua, Jeck Fei Ng, Siu Yee New
Summary: This study investigates the effect of DNA hairpins on the stabilization of gold nanoparticles against salt-induced aggregation in label-free colorimetric biosensors. Results showed that longer hairpin stems generally provide better stabilization, and hairpins with toeholds beyond a certain length did not improve stabilization. The stability trend of the hairpins with a homopolymeric toehold was similar to that of ssDNA. Variants with a high proportion of adenine as terminal bases showed stronger stabilization, and the introduction of cytosine or guanine as preceding bases also enhanced stabilization. However, variants with guanine or thymine showed less protection against salt-induced aggregation, especially guanine-rich hairpins that could form G-quadruplexes. These findings can guide researchers in designing suitable DNA hairpins for label-free AuNP-based biosensors.
Article
Chemistry, Multidisciplinary
Yuting Wu, Whitney Lewis, Jing Luen Wai, Mengyi Xiong, Jiao Zheng, Zhenglin Yang, Chloe Gordon, Ying Lu, Siu Yee New, Xiao-Bing Zhang, Yi Lu
Summary: In this study, DNAzyme-based ratiometric sensors for zinc ions were developed using BRET technology. These sensors demonstrated high selectivity and generalizability, and zinc ion detection was achieved using a smartphone camera.
CHEMISTRY-SWITZERLAND
(2023)
