Article
Biochemical Research Methods
Ulrich Kratzer, Cornelia Sommersdorf, Sandra Maier, Teresa R. Wagner, Markus Templin, Thomas O. Joos, Ulrich Rothbauer, Anne Zeck, Oliver Poetz
Summary: N-Hydroxysuccinimide esters are commonly used to modify biomolecules like antibodies or proteins. Primary amine groups react with the ester to form covalent amide bonds, and TRIS does not interfere with biotinylation using NHS chemistry.
BIOCONJUGATE CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Kuei-Hsiang Chen, You-Ren Lai, Nguyen The Duc Hanh, Steven S. -S. Wang, Yu-Kaung Chang
Summary: In this study, a polyacrylonitrile nanofiber membrane functionalized with tris(hydroxymethyl)aminomethane was used as an affinity membrane for lysozyme adsorption in membrane chromatography. The dynamic adsorption behavior of lysozyme was investigated under various operating parameters, and the results showed that the pseudo-second-order kinetic model fitted well with the experimental data. The breakthrough curve characteristics were analyzed using different dynamic adsorption models, and the Yoon-Nelson model was found to be the best fit for the experimental data.
Review
Anesthesiology
Misty A. Radosevich, Patrick M. Wieruszewski, Erica D. Wittwer
Summary: Tris-hydroxymethyl aminomethane (THAM) is an amino alcohol used clinically to buffer acid loads and raise pH in acidotic conditions. Available since 2020 in the United States, THAM may have clinical utility in managing acid-base derangements in conditions such as liver transplantation and acute respiratory distress syndrome (ARDS). However, clinical evidence supporting its use is limited, and high-quality evaluations are necessary.
ANESTHESIA AND ANALGESIA
(2023)
Article
Chemistry, Physical
Hana Sipova-Jungova, Ludmila Jurgova, Erika Hemmerova, Jiri Homola
Summary: Functional materials with organic coatings on inorganic substrates are considered potential platforms for various applications, leading to the investigation of their interactions with the micro-environment becoming a key research direction in surface science. This study focused on the interactions of Tris buffer with self-assembled monolayers (SAMs) of alkanethiols and short DNAs using a surface plasmon resonance (SPR) biosensor, showing that the interaction is a complex multiphasic process. The study also revealed how the interaction of Tris with immobilized DNA molecules can affect the determination of surface concentrations and hybridization efficiencies.
APPLIED SURFACE SCIENCE
(2021)
Article
Biochemical Research Methods
Lubna Ghani, Xiang Zhang, Chastine F. Munk, Parameswaran Hariharan, Baoliang Lan, Hong Sik Yun, Bernadette Byrne, Lan Guan, Claus J. Loland, Xiangyu Liu, Pil Seok Chae
Summary: High-resolution membrane protein structures are crucial for understanding cellular processes and drug discovery. Traditional detergents have limited stability, necessitating the development of novel agents for membrane protein structural study. The designed TTGs showed improved stability of membrane proteins compared to maltoside detergents, likely due to their high hydrophobicity, optimal hydrophilic-lipophilic balance, and absence of cis-trans isomerism.
BIOCONJUGATE CHEMISTRY
(2023)
Article
Chemistry, Inorganic & Nuclear
Y. A. Kondratenko, A. A. Nikonorova, A. A. Zolotarev, M. Y. Arsent'ev, G. G. Nyanikova, V. L. Ugolkov, E. I. Sysoev, T. A. Kochina
Summary: In this study, new coordination compounds analogues of hydrometallatranes were synthesized and characterized using FT-IR spectroscopy, mass spectrometry, and elemental analysis. The crystal structure of the TRIS complex with Cu(II) cinnamate was determined by X-ray diffraction, and the structural parameters and gap energy were calculated using the DFT method. The effect of some TRIS hydrometallatranes on the growth of corrosion aggressive thionic bacteria was also studied.
INORGANICA CHIMICA ACTA
(2022)
Article
Chemistry, Analytical
Vasiliy S. Chernyshev, Mikhail Skliar
Summary: This article introduces a method for quantifying extracellular vesicles (EVs) using a quartz crystal microbalance (QCM) as a biosensor. This method has the advantages of high sensitivity, small sample volume, and low cost, and is of great importance for research in cell-to-cell signaling, disease modeling, and drug development.
Article
Engineering, Chemical
Ding Ling Gao, Yan Xue Xue, Fei Fei Dai, Yu Xiang Liu, Na Qin, Ya Yuan Zhang, Jian Hua Chen, Qian Yang
Summary: In this study, a polyaniline-p-phenylenediamine composite membrane with a nanoparticle-like surface morphology was fabricated, and its surface was hydroxylated by interfacial polymerization of Tris(hydroxymethyl)aminomethane (THAM). The introduction of THAM enhanced the membrane's hydrophilicity, electro-negativity, and antifouling performance. The TPAPD/PES composite membrane showed improved flux and phosphate rejection, indicating its potential for practical applications in wastewater treatment.
SEPARATION AND PURIFICATION TECHNOLOGY
(2024)
Article
Chemistry, Multidisciplinary
Kavita B. B. Hiremath, Murugesh Shivashankar, Natarajan Chandrasekaran
Summary: A series of new Tris hydroxymethyl aminomethane Schiff base derivatives were synthesized and characterized using various spectroscopic techniques. The binding interaction of these synthesized molecules with human serum albumin (HSA) was studied under pH=7.40 conditions. The results showed that the ligands had a high affinity for HSA and induced conformational changes in HSA. The antimicrobial activity of the synthesized compounds was also tested against Escherichia coli, Stap. aureus, Aspergillus niger, and Aspergillus flavus.
Article
Chemistry, Analytical
Jin Zhu, Yushan Xie
Summary: This study designs an electrodeless biosensing detection chip for RNA virus medical detection using quartz crystal microbalance technology and local surface plasmon resonance technology. The arrangement structure and spacing of gold nanorod dimers greatly affect the local surface plasmon resonance and biomolecule detection results. The electrodeless biosensor chip shows better sensing performance under the same simulation conditions.
Article
Green & Sustainable Science & Technology
Meng Chen, Hu Yang, Zhen-liang Xu, Chong Cheng
Summary: This study demonstrated the separation of anionic dyes in saline solutions using uncharged PAN-Tris UF membranes. The membrane pore size and zeta potential significantly influenced the rejection behavior of dyes, with membrane performance depending on the molecular size, valence, and membrane properties. Furthermore, investigation of the separation mechanism revealed insights that could guide the rational design of UF membranes for highly effective treatments of dye-containing wastewater.
JOURNAL OF CLEANER PRODUCTION
(2022)
Article
Chemistry, Physical
Minghao Wang, Ben Ma, Junwen Chen
Summary: In order to overcome the practical stability and efficiency problems of tin-based perovskite solar cells (PSCs), researchers added a passivation material THAM into the formamidinium tin iodide (FASnI(3))perovskite, which improved light absorption ability and film crystallinity while inhibiting the oxidation of Sn2+. PSCs with THAM-doped FASnI(3) perovskite films achieved a high power conversion efficiency of 9.18%. Furthermore, the storage stabilities of PSCs were significantly prolonged, with 85% of initial efficiency maintained for 550 hours in an N-2 environment.
JOURNAL OF PHYSICAL CHEMISTRY C
(2023)
Article
Chemistry, Analytical
Lidija S. Vrhovac, Sonja A. Selemetjev, Sasa Vatic, Aleksandar Mitrovic, Jelica R. Milosevic, Aleksandar D. Lolic, Andelo D. Beletic, Natalija D. Polovic
Summary: A method for measuring TgAb in human serum based on QCM technology was developed, showing good accuracy and reliability compared to traditional RIA methods. The developed method has advantages in terms of better linearity upper limit and precision.
Article
Engineering, Chemical
Xiaochen Zhao, Xudong Wang, Yonghao Dong, Hongmin Zhang, Wei Zhao, Jin Wang, Lei Wang
Summary: By intercalating and introducing adhesive molecules, the interlayer spacing of graphitic carbon nitride nanosheets is expanded, resulting in larger interlayer channels and improved separation performance and water flux of the composite membrane.
JOURNAL OF MEMBRANE SCIENCE
(2022)
Article
Multidisciplinary Sciences
Samira Mohammadi, S. Morteza Mousavi-Khoshdel
Summary: In this research, tris(hydroxymethyl)aminomethane-functionalized graphene oxide (GO@T) with high specific capacitance and cyclic stability was synthesized and investigated. Density functional theory calculations were used to study the properties of GO and GO@T.
SCIENTIFIC REPORTS
(2023)
Article
Biochemistry & Molecular Biology
Qiaojing Huang, Yanyan Wang, Zhirong Liu, Luhua Lai
Summary: This study investigated the interaction mechanism between a plant transcriptional repressor VRN1 and DNA under stress conditions. By using simulations and calculations, the study revealed the important role of the linker in regulating the phase separation between VRN1 and DNA, providing important insights into the understanding of phase separation processes in living cells.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Chemistry, Medicinal
Weixin Xie, Fanhao Wang, Yibo Li, Luhua Lai, Jianfeng Pei
Summary: This article highlights the latest developments in using deep learning techniques combined with 3D molecular generative models for de novo drug design, and discusses future research directions.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2022)
Article
Chemistry, Medicinal
Qiaojing Huang, Luhua Lai, Zhirong Liu
Summary: Dynamic allosteric regulation refers to a type of regulation that does not involve noticeable conformational changes. By developing a unified anisotropic elastic network model, the contribution of pure dynamic allosteric regulation was quantitatively estimated. The study found that pure dynamic allosteric regulation has a generally small contribution, which decays exponentially with the distance between the substrate and the allosteric ligand. Toy models were also used to analyze the factors determining dynamic allosteric regulation in proteins.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2022)
Article
Medicine, General & Internal
Shuaishi Gao, Ziwei Dai, Hanyu Xu, Luhua Lai
Summary: In this study, we analyzed the metabolic tasks of different cancer types and established cancer type-specific metabolic models, providing new insights into the development of specific anti-cancer drugs and treatment plans for specific cancer subtypes.
FRONTIERS IN MEDICINE
(2022)
Article
Biochemistry & Molecular Biology
Shiwei Wang, Haoyu Lin, Zhixian Huang, Yufeng He, Xiaobing Deng, Youjun Xu, Jianfeng Pei, Luhua Lai
Summary: This study constructed the CavitySpace database, the first pocket library for all proteins in the human proteome. By analyzing known ligand binding sites, it was found that these sites can be well recovered. The predicted binding sites were grouped according to their similarity, which can be used in protein function prediction and drug repurposing studies. Novel binding sites in highly reliable predicted structure regions provide new opportunities for drug discovery.
Article
Chemistry, Medicinal
Youjun Xu, Jinchuan Xiao, Chia-Han Chou, Jianhang Zhang, Jintao Zhu, Qiwan Hu, Hemin Li, Ningsheng Han, Bingyu Liu, Shuaipeng Zhang, Jinyu Han, Zhen Zhang, Shuhao Zhang, Weilin Zhang, Luhua Lai, Jianfeng Pei
Summary: In this study, a practical software called MolMiner was developed using deep neural networks to recognize atom and bond elements from documents. The recognized elements can be easily connected as a molecular graph with a distance-based construction algorithm. MolMiner achieved state-of-the-art performance on benchmark data sets and a self-collected external data set from scientific papers.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2022)
Article
Biochemistry & Molecular Biology
Jiale Liu, Changsheng Zhang, Luhua Lai
Summary: The study focuses on protein side-chain modeling using GeoPacker, a method that combines geometric deep learning with ResNet to accurately predict side-chains in protein structures. GeoPacker outperforms other methods in both speed and accuracy, making it a valuable tool for protein structure simulation and design.
Article
Chemistry, Medicinal
Liying Wang, Zhongtian Yu, Shiwei Wang, Zheng Guo, Qi Sun, Luhua Lai
Summary: A deep learning-based stepwise strategy was developed to selectively screen for highly active covalent inhibitors of SARS-CoV-2 3CL protease, providing new possibilities for drug development against COVID-19.
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Chenjing Cai, Haoyu Lin, Hongyi Wang, Youjun Xu, Qi Ouyang, Luhua Lai, Jianfeng Pei
Summary: The drug development pipeline consists of in vitro assays, in vivo assays, and clinical trials. We developed three subdivisional models using graph neural networks to predict the compound's capacity to pass through the in vivo testing, clinical trials, and market approval stages. By combining active learning and ensemble learning, we improved the quality of the models and achieved satisfactory performance in internal and external test datasets. Our model system, miDruglikeness, also showed a powerful ability in virtual screening tasks, providing a comprehensive drug-likeness prediction tool for drug discovery and development.
Article
Chemistry, Physical
Juan Xie, Gaoxiang Pan, Yibo Li, Luhua Lai
Summary: This study demonstrates the importance of protein topology in allosteric regulation, showing that allosteric proteins mainly have multiple domains or subunits, and allosteric sites are often located between domains of the same fold type. A novel method, called TopoAlloSite, was developed to predict the location of allosteric sites on protein topology, successfully identifying cryptic allosteric sites in several proteins. This research provides insights for finding new druggable targets and designing allosteric drugs.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Virology
Zhao-Xi Wang, Bing Liu, Tian Yang, Daqi Yu, Chu Zhang, Liming Zheng, Jin Xie, Bin Liu, Mengxi Liu, Hailin Peng, Luhua Lai, Qi Ouyang, Songying Ouyang, Yong-An Zhang
Summary: Aquaculture accounts for 70% of global aquatic products, but viral diseases are a major problem. SVCV causes a highly contagious disease in common carp, but there are no vaccines or effective treatments. This study resolved the structure of SVCV ribonucleoprotein complex (RNP) and screened antiviral drugs based on this structure, finding that suramin has good antiviral effects.
JOURNAL OF VIROLOGY
(2023)
Article
Chemistry, Multidisciplinary
Shuai Liu, Xiangyu Sun, Huan Lu, Daiqin Chen, Xue Li, Lei Li, Shenge Su, Zhongpu Zhao, Xinran Cao, Libing Liu, Luhua Lai, Xueguang Lu, Chunying Shu, Chunru Wang, Chunli Bai
Summary: A fullerene-based nanocomplex was designed for the inhalation delivery of siRNA, which protects siRNA against degradation, improves cellular uptake and gene knockdown efficiency, and prolongs pulmonary retention. By packaging PD-L1 siRNA, this nanocomplex significantly inhibits the progression of metastatic lung cancer in a mouse model without obvious adverse events and toxicity. This fullerene-based nanocomplex opens up the possibility of siRNA for treating a diverse range of pulmonary diseases.
Article
Biology
Juan Xie, Weilin Zhang, Xiaolei Zhu, Minghua Deng, Luhua Lai, Shozeb Haider
Summary: Allostery plays a fundamental role in biological processes, but predicting the impact of allosteric mutations, modifications, and effector binding on protein function is challenging. We developed a novel computational method, KeyAlloSite, to predict allosteric sites and identify key allosteric residues based on the evolutionary coupling model. Our predictions are consistent with previous experimental studies and key cancer mutations. KeyAlloSite can be applied in studying the evolution of protein allosteric regulation, designing and optimizing allosteric drugs, and performing functional protein design and enzyme engineering.
Editorial Material
Chemistry, Multidisciplinary
Jintao Zhu, Luhua Lai, Jianfeng Pei
ACS CENTRAL SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Xiaoyu Qing, Qian Wang, Hanyu Xu, Pei Liu, Luhua Lai
Summary: Loop epitopes at protein-protein binding interfaces are underexplored as drug targets due to their high flexibility, relatively few hot spots, and solvent accessibility. However, this study demonstrates that cyclic peptides derived from loop epitopes can inhibit protein activity by directly binding to the dimer interface and disrupting the oligomer formation. These findings suggest that rationally designed cyclic peptides can modulate protein oligomers and be used to design inhibitors for other seemingly intractable oligomeric proteins.
Article
Biochemical Research Methods
Saranya Krishnan, Shina Sasi, Preshobha Kodakkattumannil, Salima Al Senaani, Geetha Lekshmi, Martin Kottackal, Khaled M. A. Amiri
Summary: This study aimed to develop an efficient DNA extraction protocol suitable for diverse plant species and tissues. A reliable and consistent protocol was described for the extraction of high-quality DNA from difficult-to-extract plant species. The optimized protocol was successful in extracting high-quality DNA from various plant species and tissues, making it useful for genomic studies of recalcitrant plants.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Eisaku Hokazono, Saori Fukumoto, Takeshi Uchiumi, Susumu Osawa
Summary: This study proposes a method for detecting nucleic acid amplification using pyrophosphate, which requires only two reagents and an automated analyzer. The technique has high sensitivity and reproducibility, and can detect pyrophosphate within 10 minutes. Therefore, this method has the potential to be a new, rapid, and simple detection technique for amplified nucleic acids.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Drew S. Sowersby, L. Kevin Lewis
Summary: SURE electrophoresis is a new method for concentrating samples in gels, which allows efficient detection of highly dilute DNA samples. This approach generates single bands with enhanced signal intensities and minimal band broadening.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Hongyi Liang, Guoliang Yin, Guangxi Shi, Zhiyong Liu, Xiaofei Liu, Jingwei Li
Summary: The mechanism of Echinacoside (ECH) in treating breast cancer (BC) was explored through network pharmacology and experimental validation. It was found that ECH plays an important role in anti-BC by regulating the PI3K/AKT/HIF-1 alpha/VEGF signaling pathway, and it exhibits multi-target and multi-pathway effects.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Daniel S. Kantner, Emily Megill, Anna Bostwick, Vicky Yang, Carmen Bekeova, Alexandria Van Scoyk, Erin L. Seifert, Michael W. Deininger, Nathaniel W. Snyder
Summary: This study compared the results of different methods for measuring the amount of acetyl-Coenzyme A. The colorimetric ELISA kit did not produce interpretable results, while the fluorometric enzymatic kit showed comparable results to the LC-MS-based methods depending on the matrix and extraction conditions. LC-MS/MS and LC-HRMS methods produced well-aligned results, especially when using stable isotope-labeled internal standards.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Jingyan Xu, Hanying Tan, Xionghui Ma, Linjing Su, Zhi Zhang, Yuhao Xiong
Summary: This study investigates the co-catalytic capabilities of MoO3 nanosheets in enhancing the enzyme-like catalytic activity of a two-dimensional ultrathin Fe(III)-modified covalent triazine framework (Fe-CTF) under neutral pH conditions. The Fe-CTF/MoO3 co-catalytic system exhibits enzyme-mimicking activity and enables the development of a colorimetric method for glucose detection. Furthermore, a straightforward one-pot colorimetric method is established for screening XOD inhibitors.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Lichao Zhang, Kang Xiao, Xueting Wang, Liang Kong
Summary: A novel fusion technology was designed to identify FAD-binding sites, achieving the best results on two independent test datasets and outperforming existing methods significantly. The high performance and certainty of the method were demonstrated through statistical tests and cross-entropy loss analysis.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Abdulkadir Kilic, Mehmet Aslan, Abdulkadir Levent
Summary: This study developed a simple, rapid, sensitive, and selective voltammetric technique for the electrochemical characterization and detection of the highly risky drug Edoxaban. The optimized voltammetric method showed good analytical working range and was successfully applied to urine and tablet samples.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Su Hyun Kim, Nara Shin, Jong-Min Jeon, Jeong-Jun Yoon, Jeong Chan Joo, Hee Taek Kim, Shashi Kant Bhatia, Yung-Hun Yang
Summary: To address environmental issues caused by traditional plastics, bioplastics have gained attention as alternatives. Although bioplastics have better degradability, their degradation still takes longer than anticipated. This study proposes a novel screening method to identify bioplastic degraders faster, saving time and providing more quantitative data.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Irem Okman Kocoglu, Pinar Esra Erden, Esma Kilic
Summary: In this study, an electrochemical biosensor based on carbon nanofibers and ionic liquid modification was constructed for tyramine detection. The biosensor showed linear response, low detection limit, high sensitivity, and exhibited good reproducibility, stability, and anti-interference ability.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Liana U. Akhmetzianova, Timur M. Davletkulov, Assol R. Sakhabutdinova, Alexey Chemeris, Irek M. Gubaydullin, Ravil R. Garafutdinov
Summary: A new program called LAMPrimers iQ has been developed for high-quality LAMP primer design, and its advantages in providing higher specificity and reliable detection of viral RNA were validated using SARS-CoV-2 coronavirus RNA as a model target.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Tommaso Pileri, Alberto Sinibaldi, Agostino Occhicone, Norbert Danz, Elena Giordani, Matteo Allegretti, Frank Sonntag, Peter Munzert, Patrizio Giacomini, Francesco Michelotti
Summary: This study developed a biosensing device based on one-dimensional photonic crystal to detect HER2 in breast cancer. The device combines label-free and fluorescence operation modes, allowing for real-time and accurate detection in less than 20 minutes. It offers a promising technique for combined label-free and fluorescence detection in disease diagnosis and therapeutic monitoring.
ANALYTICAL BIOCHEMISTRY
(2024)
