Review
Biochemistry & Molecular Biology
Yuchuan Wang, Pengcheng Liu, Jiao Chang, Yunping Xu, Jiangyun Wang
Summary: Selenocysteine is a rare naturally proteinogenic amino acid in living organisms and plays a crucial role in cellular functions. Its incorporation in vivo is highly species-dependent and requires the reprogramming of translation. Many strategies have been developed to overcome the challenges in producing synthetic selenoproteins for understanding their functions.
Article
Multidisciplinary Sciences
Santanu Mondal, Shu Wang, Yunan Zheng, Sudeshna Sen, Abhishek Chatterjee, Paul R. Thompson
Summary: The study presents a technology for site-specific incorporation of citrulline into proteins in mammalian cells. Incorporating citrulline into proteins can significantly reduce enzyme activity.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Sasilada Sirirungruang, Omer Ad, Thomas M. Privalsky, Swetha Ramesh, Joel L. Sax, Hongjun Done, Edward E. K. Baidoo, Bashar Amer, Chaitan Khosla, Michelle C. Y. Chang
Summary: A method to selectively incorporate fluorine into complex structures has been developed, which allows for the production of regioselectively fluorinated full-length polyketides. This approach combines the attributes of synthetic and natural molecules, offering potential for the identification and development of bioactive fluorinated small molecules.
NATURE CHEMICAL BIOLOGY
(2022)
Article
Biochemical Research Methods
Wei Chen, Tristan R. Gunther, Hannah E. R. Baughman, Elizabeth A. Komives
Summary: The transcription factor NF-KB plays a central role in immune and inflammatory responses. Understanding the regulation of NF-KB requires studying the thermodynamics, kinetics, and conformational dynamics of its interaction network. In this study, the researchers incorporated non-canonical amino acids into NF-KB and used site-specific labeling to investigate its conformational dynamics. They also expanded the toolbox of non-canonical amino acids for studying NF-KB and demonstrated their use in crosslinking mass spectrometry.
Article
Chemistry, Multidisciplinary
Haocheng Qianzhu, Elwy H. Abdelkader, Iresha D. Herath, Gottfried Otting, Thomas Huber
Summary: A mutant aminoacyl-tRNA synthetase has been discovered through a library selection system that allows for the site-specific incorporation of 7-fluoro-L-tryptophan in response to an amber stop codon. This enzyme enables the production of proteins with a single hydrogen atom replaced by a fluorine atom, serving as a sensitive nuclear magnetic resonance (NMR) probe. The substitution of a single hydrogen atom with a similar-sized and hydrophobicity element minimizes potential disruptions to the protein's structure, stability, and solubility. The fluorine atom facilitates the site-selective monitoring of protein response to ligand binding using F-19 NMR spectroscopy, as demonstrated with the Zika virus NS2B-NS3 protease.
Review
Biochemistry & Molecular Biology
Michiko Kimoto, Ichiro Hirao
Summary: This review discusses the current methods for incorporating new amino acids into proteins by designing new codon-anticodon interactions, including unnatural base pairs systems for expanding the genetic alphabet.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Chemistry, Multidisciplinary
Shengxi Chen, Xun Ji, Larisa M. Dedkova, Sidney M. Hecht
Summary: The NF-kappa B family of transcriptional activators is responsible for the expression of key genes controlling cell development and survival. The study found that site-specific phosphorylation of the p50 subunit can significantly increase CD40 expression, providing a potential target for cancer or viral immunotherapy.
CHEMICAL COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Jason C. Klima, Lindsey A. Doyle, Justin Daho Lee, Michael Rappleye, Lauren A. Gagnon, Min Yen Lee, Emilia P. Barros, Anastassia A. Vorobieva, Jiayi Dou, Samantha Bremner, Jacob S. Quon, Cameron M. Chow, Lauren Carter, David L. Mack, Rommie E. Amaro, Joshua C. Vaughan, Andre Berndt, Barry L. Stoddard, David Baker
Summary: The new design of fluorescence-activating proteins mFAPs incorporates pH, Ca2+, and protein-protein interaction sensing modalities, with increased photostability and smaller size. It can adjust fluorescence intensity and specificity, enabling sensitivity to different chromophores.
NATURE COMMUNICATIONS
(2021)
Article
Chemistry, Multidisciplinary
Yue Wang, Li-Juan Feng, Xiao-Dong Sun, Meiyi Zhang, Jian-Lu Duan, Fu Xiao, Yue Lin, Fan-Ping Zhu, Xiang-Pei Kong, Zhaojun Ding, Xian-Zheng Yuan
Summary: Diets with selenium-deficient crops can lead to immune disorders and cardiomyopathy. Selenium nanoparticles have shown promise in selenium-biofortified agriculture, but their application has been limited due to a lack of understanding of their behavior. In this study, we investigated the transport, transformation, and bioavailability of selenium nanoparticles through experiments in plants. The results showed that selenium nanoparticles, when sprayed onto plant leaves, were biotransformed into different forms of selenium and incorporated into selenium-binding proteins. These proteins were linked to stress reduction and enhanced plant growth. Furthermore, the use of a common agrochemical surfactant allowed for better distribution of selenium throughout the entire plant. Overall, the foliar application of selenium nanoparticles promotes plant growth without causing nanomaterial accumulation, providing an efficient method for selenium-fortified agriculture.
Article
Chemistry, Multidisciplinary
Khoa Chung, Michael J. Booth
Summary: This study developed a method to incorporate photocages into plasmids, enabling the conditional regulation of gene expression. The light-activated plasmids demonstrated the ability to remotely control cellular activity and reduce off-target toxicity, showing potential for future medical use. The simple approach to plasmid modification presented in this study may also be used to introduce novel chemical moieties for advanced function.
Article
Chemistry, Organic
Chenlu Dong, Xufeng Zhao, Yuki Katsuragi, Hojin Kim, Masahiko Hayashi, Ryosuke Matsubara
Summary: A novel C-C bond forming method has been developed, allowing for the incorporation of a furoxan ring into various types of C-H bonds. This method not only provides a concise route to alkylated furoxan derivatives, but also offers an efficient strategy for inserting nitrogen-containing functional groups into C-H bonds via transformation of the resulting furoxan ring.
JOURNAL OF ORGANIC CHEMISTRY
(2021)
Article
Chemistry, Multidisciplinary
Ross J. Taylor, Mauricio Aguilar Rangel, Michael B. Geeson, Pietro Sormanni, Michele Vendruscolo, Goncalo J. L. Bernardes
Summary: Post-translational protein-protein conjugation allows for the production of bioconjugates that are not achievable through genetic fusion. This study describes a method using x-clamp-mediated cysteine arylation with pentafluorophenyl sulfonamide functional groups to prepare protein-protein conjugates. By computationally designing antibodies targeting the SARS-CoV-2 receptor binding domain and using the pi-clamp sequence, dimerization was achieved, resulting in a significant increase in binding. This strategy enables the construction of molecule-protein-protein conjugates with precise chemical control over the modification sites.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Multidisciplinary Sciences
Sabit Ahmed, Afrida Rahman, Md. Al Mehedi Hasan, Md Khaled Ben Islam, Julia Rahman, Shamim Ahmad
Summary: The study introduces a computational tool, predPhogly-Site, that predicts phosphoglycerylation sites in proteins with around 99% accuracy, outperforming existing prediction tools.
Article
Biology
Minyong Chen, Diego M. Assis, Matthieu Benet, Colleen M. McClung, Elizabeth A. Gordon, Shourjo Ghose, Steven J. Dupard, Matthew Willetts, Christopher H. Taron, James C. Samuelson
Summary: Comparative site-specific N-glycoproteome analysis of colon cancer cells and non-tumorigenic colon cancer cells reveals significant changes in N-glycosylation, providing a molecular basis for further research on the role of N-glycosylation in protein function.
COMMUNICATIONS BIOLOGY
(2023)
Article
Chemistry, Analytical
Jiarong Wang, Bo Wu, Youjia Zhang, Liang Ge, Junfeng Wang
Summary: In this study, a 1D F-19 NMR-based method was developed for rapid detection of GEF activity of sGTPases, by tracking the conformational changes of the Arf6 switch region. This strategy could potentially be applied to monitor the conformational change of Arf6 or other sGTPase and detect the activities of sGTPase regulatory proteins in physiology and pathology environments.
ANALYTICAL CHEMISTRY
(2022)
