Review
Biochemical Research Methods
Zainab Noor, Seong Beom Ahn, Mark S. Baker, Shoba Ranganathan, Abidali Mohamedali
Summary: Accurate protein identification is crucial in proteomics, with mass spectrometry being the primary technique used. Understanding data generation and parameters used in computational tools is essential for proper protein identification. Bioinformatics and computational methodologies are also important for validating protein identification in proteomics.
BRIEFINGS IN BIOINFORMATICS
(2021)
Review
Chemistry, Medicinal
Luis A. R. Carvalho, Goncalo J. L. Bernardes
Summary: Activity-based protein profiling (ABPP) is a widely used method in malaria research that utilizes small molecular probes to study enzymatic activity, achieving significant advancements in the study of Plasmodium proteases, metabolic pathways, and target identification for antimalarials.
Article
Ophthalmology
Maite Lopez-Lopez, Uxia Regueiro, Susana Belen Bravo, Maria del Pilar Chantada-Vazquez, Carmen Pena, Elio Diez-Feijoo, Pablo Hervella, Isabel Lema
Summary: This study utilized a qualitative approach to explore the tear proteome of patients with keratoconus (KC), finding that the expression of certain proteins in tears of KC patients differed from the control group. These differences were linked to processes such as cell death, oxidative damage, and inflammation.
INVESTIGATIVE OPHTHALMOLOGY & VISUAL SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Wendell Albuquerque, Parviz Ghezellou, Leif Seidel, Johannes Burkert, Frank Will, Ralf Schweiggert, Bernhard Spengler, Holger Zorn, Martin Gand
Summary: This study presents the first comprehensive identification of proteome content from a white wine (cv. Silvaner). By using mass spectrometry-based proteomics, the wine protein composition was identified through in-solution and in-gel digestion methods after size exclusion chromatographic fractionation. A total of 154 characterized or uncharacterized proteins mainly from Vitis vinifera L. and Saccharomyces cerevisiae were identified, providing valuable information for wine authentication and understanding of organoleptic properties and stability.
Review
Chemistry, Multidisciplinary
Zak Vilen, Abigail E. Reeves, Mia L. Huang
Summary: The presence of glycan modifications on cell surface and other locations is important for cell recognition and function. But due to the complexity of glycosylation, the annotation of which proteins have glycan modifications, which glycan patterns are present, and which proteins can bind glycans is incomplete. The development of glycan-binding and glycan-based probes, along with high resolution mass spectrometry-based technologies, has greatly advanced the understanding of these problems and glycoscience as a whole.
ISRAEL JOURNAL OF CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Jacky M. K. Kwong, Joseph Caprioli, Ying H. Sze, Feng J. Yu, King K. Li, Chi H. To, Thomas C. Lam
Summary: Retinal proteins associated with primary and secondary RGC degeneration were investigated using SWATH label-free and target-based mass spectrometry. Different proteomic profiles were found in response to localized optic nerve injury, indicating potential roles in RGC loss and cell death.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemical Research Methods
Agnese Petrera, Christine von Toerne, Jennifer Behler, Cornelia Huth, Barbara Thorand, Anne Hilgendorff, Stefanie M. Hauck
Summary: The plasma proteome is a valuable resource for biomarker discovery, and can be analyzed using tools like LC-MS/MS and PEA. By combining different platforms, researchers can gain deeper insights into the complexity of the plasma proteome and discover changes in pathophysiological status. This approach shows promise for future biomarker and mechanistic studies.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Multidisciplinary Sciences
Florian Leonardus Rudolfus Lucas, Roderick Corstiaan Abraham Versloot, Liubov Yakovlieva, Marthe T. C. Walvoort, Giovanni Maglia
Summary: Nanopores can be used for protein identification by measuring peptide spectra produced from hydrolyzed proteins. The spectra from nanopore experiments and mass spectrometry share similar profiles, enabling protein fingerprinting. This approach is quantitative, showing the potential of a low-cost, portable nanopore-based analyzer for protein identification.
NATURE COMMUNICATIONS
(2021)
Review
Chemistry, Analytical
Ketki Bagwe, Noah Gould, Kendall R. Johnson, Alexander R. Ivanov
Summary: Tissues and cell populations exhibit high levels of heterogeneity at the cellular level, making it important to analyze smaller sample sizes to capture subtle differences between cells. Capillary electrophoresis coupled with mass spectrometry (CE-MS) is a powerful technique for proteomics and metabolomics analysis at the single-cell level, and this review focuses on its applications and recent advances in sample preparation, separation, MS acquisition, and data analysis.
TRAC-TRENDS IN ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Lin Bai, Guojian Yang, Zhaoyu Qin, Jiacheng Lyu, Yunzhi Wang, Jinwen Feng, Mingwei Liu, Tongqing Gong, Xianju Li, Zhengyang Li, Jixi Li, Jun Qin, Wenjun Yang, Chen Ding
Summary: This study used a novel method to analyze the binding activity of transcription factors under DNA modifications and identified potential readers for 5fC-modified DNA. By quantifying the modified DNA-binding activity of 1039 TFs, it revealed the hierarchical networks between the transcriptional protein machinery and modified DNA.
Article
Biochemistry & Molecular Biology
Hannah B. L. Jones, Raphael Heilig, Simon Davis, Roman Fischer, Benedikt M. Kessler, Adan Pinto-Fernandez
Summary: Activity-based protein profiling (ABPP) is an important method for characterizing specific enzymes, and has proven invaluable in drug discovery and pharmacodynamic studies. In this study, an improved ABPP-HT method was developed, combining state-of-the-art MS analysis tools to achieve high throughput and improved data accuracy.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Food Science & Technology
Huiyan Zhang, Shizhe Qi, Wenhao Yu, Shan Zhao, Yan Jin, Qiancheng Zhao, Yanxia Qi
Summary: In this study, anchovy antimicrobial peptides (AAMPs) were prepared and optimised from anchovy extracts. Proteomics analysis identified 4 unique peptides with inhibitory activity against E. coli and S. aureus. This work established a useful workflow for discovering novel AMPs from fish proteins, which could contribute to the development of effective antibiotics.
INTERNATIONAL JOURNAL OF FOOD SCIENCE AND TECHNOLOGY
(2023)
Article
Chemistry, Analytical
Yunming Liu, Minghui Qu, Mengting Pan, Xiaofang Zheng, Yuwei Sheng, Yongqin Ji, Changjun You, Xiaoxia Dai
Summary: A chemical proteomic strategy was developed to identify over 70 potential UTP-binding proteins in the human proteome, revealing their involvement in multiple cellular processes. This high-throughput analysis provides a new method for the identification and quantification of UTP-binding proteins.
ANALYTICA CHIMICA ACTA
(2021)
Review
Cell Biology
Alfredo Cabrera-Orefice, Alisa Potter, Felix Evers, Johannes F. Hevler, Sergio Guerrero-Castillo
Summary: Complexome profiling is an advanced method for studying the composition and abundance of protein complexes in biological samples, as well as their dynamics and the impact of mutations. It has been used to discover novel protein interactors and investigate pathophysiological mechanisms.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Immunology
Lia Martina, Caroline Asselman, Fabien Thery, Katie Boucher, Louis Delhaye, Teresa M. Maia, Bart Dermaut, Sven Eyckerman, Francis Impens
Summary: The study shows that RNF213 regulates transcription of multiple proteins to control bacterial infection and nitric oxide production, potentially providing a mechanism for its antimicrobial activity and its role in MMD development.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2021)
Article
Chemistry, Organic
Raphael Simonet-Davin, Jerome Waser
Summary: In this short review, applications of hypervalent iodine reagents for the azidation of organic compounds were described, with a focus on stable cyclic reagents. Important advances in the azidation of C-H bonds, alkenes, and other transformations were highlighted through selected key reports.
SYNTHESIS-STUTTGART
(2023)
Review
Chemistry, Multidisciplinary
Eliott Le Du, Jerome Waser
Summary: Although small, alkynes are highly versatile building blocks in organic chemistry, with applications ranging from biochemistry to material sciences. Traditional alkynylation reactions rely on the use of acetylenes as nucleophiles. However, the discovery and development of ethynyl hypervalent iodine reagents have greatly expanded the transfer of alkynes as electrophilic synthons. This feature article presents the progress in the field since 2018, including synthesis of alkynyl hypervalent iodine reagents, their use in base-mediated and transition-metal catalyzed alkynylations, and progress in radical-based alkynylations and atom-economical transformations.
CHEMICAL COMMUNICATIONS
(2023)
Article
Geology
Fabricio A. Caxito, Robert Frei, Alcides N. Sial, Gabriel J. Uhlein, William Alexandre Lima de Moura, Egberto Pereira, Rene Rodrigues
Summary: The Chapada Diamantina region in Brazil is a valuable natural laboratory for studying the fluctuations of Earth's biogeochemical cycles during its mid-age. The sedimentary successions in this region contain both Mesoproterozoic and Neoproterozoic carbonate levels. Analysis of the stromatolites from the Caboclo Formation and the cap carbonates and phosphatic stromatolites from the Salitre Formation reveals distinct redox conditions and suggests a gradual oxygenation of Earth's atmosphere and hydrosphere during the Ediacaran-Cambrian transition.
Article
Chemistry, Multidisciplinary
Stephanie G. E. Amos, Franck Le Vaillant, Jerome Waser
Summary: Alkynes and nitriles are important building blocks in organic synthesis, chemical biology, and materials science. This study investigates the conversion of alcohols into alkynes and nitriles using cesium oxalates and Ethynyl BenziodoXolones (EBXs), and explores the effects of backbone modification of EBXs on the deoxyalkynylation of cesium oxalates. Preliminary data on the development of new deoxycyanation and dethioalkynylation processes are also presented, along with the serendipitous discovery of C-H alkynylation of 1,2-dichloroethane.
HELVETICA CHIMICA ACTA
(2023)
Article
Geosciences, Multidisciplinary
Majken D. Poulsen, Nynke Keulen, Vincent J. van Hinsberg, Jochen Kolb, Robert Frei, Tonny B. Thomsen
Summary: Plumasite-type corundum occurrences in the Nattivit area in South-East Greenland provide a unique opportunity to study corundum formation in-situ. New field observations and analysis of elemental and isotopic geochemistry shed light on the history of crustal convergence, exhumation, and corundum formation.
PRECAMBRIAN RESEARCH
(2023)
Article
Chemistry, Multidisciplinary
Emma G. L. Robert, Vincent Pirenne, Matthew D. Wodrich, Jerome Waser
Summary: A convenient method for the one-step synthesis of beta-aminocyclobutane monoesters using commercially available reagents is reported. The obtained strained rings undergo dearomative annulation with indole partners using silylium catalysis, providing tricyclic indolines with four new stereocenters. The reaction can proceed both intra- and intermolecularly and the outcome can be selectively controlled based on reaction temperature, resulting in the formation of either akuamma or malagasy alkaloid-like tetracyclic structures.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Multidisciplinary
Xing-Yu Liu, Xinjian Ji, Christian Heinis, Jerome Waser
Summary: We present a new method for modifying peptides using highly reactive hypervalent iodine reagents called ethynylbenziodoxolones (EBXs). These peptide-EBXs can be easily synthesized through solution- and solid-phase peptide synthesis (SPPS). They can be used to couple peptides to other peptides or proteins via reaction with Cys, resulting in thioalkynes in organic solvents or hypervalent iodine adducts in water buffer. Additionally, a photocatalytic decarboxylative coupling to the C-terminus of peptides was developed, leading to macrocyclic peptides with unprecedented crosslinking.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Multidisciplinary
Nieves P. P. Ramirez, Jerome Waser
Summary: An asymmetric 3-component reaction catalyzed by a Cu-I-BOX catalyst was developed for the synthesis of chiral trifluoromethylated propargyl ethers and anilines. The reaction showed high enantioselectivity and yield with various nucleophiles and different electrophiles. The method also exhibited good diastereoselectivity with chiral substrates.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Review
Chemistry, Multidisciplinary
Eliott Le Du, Nieves P. Ramirez, Stefano Nicolai, Rosario Scopelliti, Farzaneh Fadaei-Tirani, Matthew D. Wodrich, Durga Prasad Hari, Jerome Waser
Summary: First synthesized in 1991, EthynylBenziodoXolones (EBXs) are now among the most versatile electrophilic alkynylation reagents. Due to their cyclic structure, these reagents exhibit enhanced stability compared to previously used alkynyl iodonium salts. The collected structural data of EBXs and their analogues, along with the calculated molecular electrostatic potentials (MEP), is expected to be highly useful for further developments in the field, considering the tight relationship between structure and reactivity in hypervalent iodine reagents.
HELVETICA CHIMICA ACTA
(2023)
Article
Engineering, Environmental
Elina Ceballos, Jordi Cama, Josep M. Soler, Robert Frei
Summary: Our study focused on the leaching processes of hexavalent chromium (Cr(VI)) in contaminated soil, resulting in groundwater contamination. Characterization of the soil using various techniques revealed that the main source of Cr was solid waste in the upper meter of the soil. Flow-through and column experiments were conducted to understand the release and mobility of Cr(VI), and numerical simulations helped interpret these processes. The accurate characterization of these processes is crucial for effectively mitigating Cr(VI) mobility in contaminated soils.
JOURNAL OF HAZARDOUS MATERIALS
(2023)
Article
Chemistry, Multidisciplinary
Oleksandr S. Liashuk, Oleksandr O. Grygorenko, Yulian M. Volovenko, Jerome Waser
Summary: A photochemical [2+2] cycloaddition reaction between alkynyl boronates and maleimides is reported. The reaction exhibited wide compatibility with different functional groups and provided 35-70% yield of maleimide-derived cyclobutenyl boronates. The prepared building blocks showed synthetic utility in various transformations, including cross-coupling, reduction, oxidation, and cycloaddition reactions.
CHEMISTRY-A EUROPEAN JOURNAL
(2023)
Article
Chemistry, Organic
Vladyslav Smyrnov, Jerome Waser
Summary: An electrophile-induced semipinacol rearrangement of cyclopropenylcarbinols is described, enabling the synthesis of polyfunctionalized cyclopropanes under mild metal-free conditions. The reaction demonstrates broad scope, accommodating various electrophiles, migrating groups, and substitution patterns on the cyclopropene. It is particularly useful for the synthesis of small ring-containing spirocycles, which are important building blocks in medicinal chemistry.
Article
Chemistry, Organic
Pierre Palamini, Julien Borrel, Mael Djaid, Morgane Delattre, Jerome Waser
Summary: We report the synthesis of ketene dithioarylacetals in 40-97% yield using thiophenols and acyl-EBXs generated in situ from a common hypervalent iodine precursor and alkynyl trifluoroborate salts. The products could be further modified to afford functionalized ketene dithioacetals and various S-substituted heterocycles.
Article
Chemistry, Multidisciplinary
Julien Borrel, Jerome Waser
Summary: We present a method for azidoalkynylation of alkenes, which provides a straightforward route to homopropargylic azides by using hypervalent iodine reagents and alkynyltrifluoroborate salts. The development of a photocatalytic redox-neutral radical polar crossover process was crucial for this transformation. A range of homopropargylic azides with electron-rich and -poor aryls, heterocycles, or ether substituents could be obtained in yields of 34-84%. These products serve as valuable building blocks that can be easily converted into pyrroles or bioactive amines.
