Article
Chemistry, Applied
Kyeonghye Guk, Soyeon Yi, Hyeran Kim, Suhyeon Kim, Eun-Kyung Lim, Taejoon Kang, Juyeon Jung
Summary: The PoreGlow system based on split green fluorescent protein (GFP) was developed and assessed for the rapid and accurate detection of L. monocytogenes. It showed high sensitivity and specificity, with no cross-reactivity with other bacteria. This system is promising for the early detection of L. monocytogenes in food products, which is crucial for preventing outbreaks and protecting public health.
Article
Chemistry, Analytical
Ping-Heng Lin, Ssu-Tzu Tsai, Yu-Chia Chang, Yi-Ju Chou, Yi-Chun Yeh
Summary: In this study, the performance of whole-cell biosensors is enhanced by incorporating logic AND gates. Comparison between the HrpR/S system and self-associating split fluorescent proteins using the Spy Tag/Spy Catcher system demonstrates the utility of the latter in developing high-performance whole-cell biosensors. This approach offers advantages such as engineering simplicity, reduced basal activity, and improved selectivity.
ANALYTICA CHIMICA ACTA
(2023)
Article
Biotechnology & Applied Microbiology
Guo-Teng Liang, Cuixin Lai, Zejun Yue, Hanbin Zhang, Danyang Li, Zhong Chen, Xingyu Lu, Liang Tao, Fedor V. Subach, Kiryl D. Piatkevich
Summary: In this study, a pair of engineered flavin-binding fluorescent proteins, miniGFP1 and miniGFP2, were developed. These miniGFPs showed improved photochemical properties and high sensitivity to transition metal ions, making them potential fluorescent biosensors for live cell imaging and metal ion detection.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Abigail R. Orun, Ethan T. Shields, Sara Dmytriw, Ananya Vajapayajula, Caroline K. Slaughter, Christopher D. Snow
Summary: Researchers have designed isoreticular cocrystals as scaffolds for DNA-binding molecules. These cocrystals have tunable DNA-DNA junctions and can accommodate different guest molecules during crystallization. The design principles can be applied to existing cocrystals to develop programmable scaffolds for DNA-binding molecules.
Article
Chemistry, Multidisciplinary
Weicheng Peng, Caden C. Maydew, Hiu Kam, Jacob K. Lynd, Jasmine N. Tutol, Shelby M. Phelps, Sameera Abeyrathna, Gabriele Meloni, Sheel C. Dodani
Summary: Chloride is crucial for all forms of life and recent research has demonstrated the potential of chloride-sensitive fluorescent proteins for cellular applications. This study presents a bioinformatics strategy to efficiently identify and design new chloride-sensitive fluorescent proteins, using GFPxm163 as an example.
Article
Multidisciplinary Sciences
Chuanfeng Wang, Liang Lu, Wei Li, Dingyun Shao, Chaoliang Zhang, Jun Lu, Weiqing Yang
Summary: This article proposes the construction of green self-powered devices based on biodegradable materials, using green materials to create transient biotriboelectric nanogenerator. By adding cellulose nanocrystals (CNC), the voltage and current output are significantly improved, and admirable signal stability is demonstrated. A soft arch sensor is also successfully assembled, which can monitor human motions in real time.
Article
Biochemical Research Methods
Anna Yudenko, Anastasia Smolentseva, Ivan Maslov, Oleg Semenov, Ivan M. Goncharov, Vera V. Nazarenko, Nina L. Maliar, Valentin Borshchevskiy, Valentin Gordeliy, Alina Remeeva, Ivan Gushchin
Summary: Protein-fragment complementation assays are commonly used to study protein-protein interactions. The development of CagFbFP, a small thermostable FbFP based on a LOV domain-containing protein, provides a split fluorescent reporter that can be used to investigate protein-protein interactions in anaerobic conditions without the need for exogenous fluorophores. This advancement in fluorescent protein technology may lead to further development of LOV and PAS domain-based fluorescent reporters and optogenetic tools.
ACS SYNTHETIC BIOLOGY
(2021)
Article
Chemistry, Multidisciplinary
Ryan E. Johnson, Makay T. Murray, Lucas J. Bycraft, Stacey D. Wetmore, Richard A. Manderville
Summary: A simple and efficient method for the synthesis of fluorescent molecular rotors (FMRs) is reported, which involves on-strand aldehyde capture using 6-hydroxy-indanone as a handle. The resulting internal FMR chalcones demonstrate high quantum yields, large Stokes shifts, and bright emissions in the visible region, making them suitable for various biotechnological applications.
Article
Multidisciplinary Sciences
Hau B. Nguyen, Thomas C. Terwilliger, Geoffrey S. Waldo
Summary: Research has shown the utility of split fluorescent proteins for large scale protein labeling in cells, but efficient split fluorescent proteins that do not cross-react are needed for multiplexing experiments. The newly proposed split ccGFP from C. californica complements up to threefold faster compared to the original A. victoria split GFP, enabling multiplexed labeling with existing A. victoria split YFP and CFP.
SCIENTIFIC REPORTS
(2021)
Article
Multidisciplinary Sciences
Cassandra M. Stawicki, Torri E. Rinker, Markus Burns, Sonal S. Tonapi, Rachel P. Galimidi, Deepthi Anumala, Julia K. Robinson, Joshua S. Klein, Parag Mallick
Summary: This study presents a straightforward method for preparing fluorescent nanoparticle probes using commercially available reagents and common laboratory equipment, enhancing their performance for biological research. The functionalized nanoparticles with DNA aptamers showed high affinity and stability, making them suitable for various biological experiments.
SCIENTIFIC REPORTS
(2021)
Article
Chemistry, Analytical
Honglin Yang, Jinxia Xue, Jizhou Li, Guangxu Hu, Hongtao Li, Shuguang Lu, Zhifeng Fu
Summary: In this study, a bifunctional protein was successfully expressed, which can bind to MRSA and emit fluorescence, making it a potential tool for rapid diagnosis and antibiotic susceptibility testing.
ANALYTICA CHIMICA ACTA
(2022)
Article
Biology
Ryo Tamura, Fangchao Jiang, Jin Xie, Daichi Kamiyama
Summary: The article describes a method to expand the number of orthogonal split FP systems with spectrally distinct colors, utilizing rational design and cycles of directed evolution to broaden the spectral color palette of FP1-10/11. They demonstrate a multiplexing approach using the new orthogonal split FP systems, allowing simultaneous imaging of four distinct proteins in single cells.
COMMUNICATIONS BIOLOGY
(2021)
Article
Biophysics
Hyeran Kim, Seul Gee Hwang, Kyeonghye Guk, Yoonji Bae, Hwangseo Park, Eun-Kyung Lim, Taejoon Kang, Juyeon Jung
Summary: RSV infections can cause severe diseases, and the emergence of drug-resistant RSV strains is concerning. We studied an antibody that can specifically detect palivizumab-resistant RSV strains and developed a rapid detection method for the S275F RSV antigen.
BIOSENSORS & BIOELECTRONICS
(2021)
Article
Biochemistry & Molecular Biology
Igor E. Kasheverov, Alexey I. Kuzmenkov, Denis S. Kudryavtsev, Ivan S. Chudetskiy, Irina V. Shelukhina, Evgeny P. Barykin, Igor A. Ivanov, Andrei E. Siniavin, Rustam H. Ziganshin, Mikhail S. Baranov, Victor I. Tsetlin, Alexander A. Vassilevski, Yuri N. Utkin
Summary: The study found that the introduction of a synthetic GFP chromophore induced a considerably lower decrease in affinity between protein and peptide neurotoxins and receptors compared to full-length GFP attachment. This new method can be used for visualizing nAChR in tissue slices and cell cultures.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Multidisciplinary Sciences
Luca Zinzula, Angela Maria Mereu, Massimiliano Orsini, Christine Seeleitner, Andreas Bracher, Istvan Nagy, Wolfgang Baumeister
Summary: This study established a split-green fluorescent protein method to probe the assembly of Ebola virus and Marburg virus VP35 coiled-coil. Screening of a small compound library led to the identification of two inhibitors, validating the importance of VP35 coiled-coil as an antiviral target.
Review
Biochemistry & Molecular Biology
Todd O. Yeates, Matthew P. Agdanowski, Yuxi Liu
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2020)
Article
Biochemistry & Molecular Biology
Kevin A. Cannon, Rachel U. Park, Scott E. Boyken, Una Nattermann, Sue Yi, David Baker, Neil P. King, Todd O. Yeates
Editorial Material
Biochemistry & Molecular Biology
Jan Steyaert, Todd O. Yeates
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2020)
Article
Biochemistry & Molecular Biology
Vikram Khipple Mulligan, Christine S. Kang, Michael R. Sawaya, Stephen Rettie, Xinting Li, Inna Antselovich, Timothy W. Craven, Andrew M. Watkins, Jason W. Labonte, Frank DiMaio, Todd O. Yeates, David Baker
Article
Biochemistry & Molecular Biology
Jessica M. Ochoa, Vy N. Nguyen, Mengxiao Nie, Michael R. Sawaya, Thomas A. Bobik, Todd O. Yeates
Article
Multidisciplinary Sciences
Joshua Laniado, Todd O. Yeates
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2020)
Review
Biochemistry & Molecular Biology
Andrew M. Stewart, Katie L. Stewart, Todd O. Yeates, Thomas A. Bobik
Summary: Bacterial microcompartments (MCPs) are large and diverse proteinaceous organelles that compartmentalize metabolic pathways and sequester toxic or volatile intermediates. Recent studies have expanded our understanding of MCP diversity, structure, function, and potential applications, revealing new types of MCPs and their associations with human disease. Structural studies have provided new insights into MCP assembly and mechanisms, while biotechnology applications are utilizing MCP principles for nanobioreactors, nanocontainers, and molecular scaffolds.
TRENDS IN BIOCHEMICAL SCIENCES
(2021)
Article
Chemistry, Multidisciplinary
Joshua Laniado, Kevin A. Cannon, Justin E. Miller, Michael R. Sawaya, Dan E. McNamara, Todd O. Yeates
Summary: Protein molecules add rich functionality to nanoscale architectures, particularly in high-symmetry protein cages. This study introduces a method for designing protein assemblies, successfully creating cubically symmetric cages through a combination of two simpler symmetries. Experimental testing revealed the formation of the intended octahedral cage, while another design resulted in a collapsed structure of lower stoichiometry and symmetry, providing insights for improved creation of nanoscale protein architectures.
Article
Surgery
Eric O. Yeates, Catherine Juillard, Areg Grigorian, Morgan Schellenberg, Natthida Owattanapanich, Galinos Barmparas, Daniel Margulies, Kent Garber, Henry Cryer, Areti Tillou, Sigrid Burruss, Liz Penaloza-Villalobos, Ann Lin, Ryan Arthur Figueras, Megan Brenner, Christopher Firek, Todd Costantini, Jarrett Santorelli, Terry Curry, Diane Wintz, Walter L. Biffl, Kathryn B. Schaffer, Thomas K. Duncan, Casey Barbaro, Graal Diaz, Arianne Johnson, Justine Chinn, Ariana Naaseh, Amanda Leung, Christina Grabar, Todd O. Yeates, Jeffry Nahmias
Summary: This study found that during the stay-at-home orders in California, patients with Medicaid experienced a significant increase in trauma volume, suggesting that the most impoverished groups in society continue to be disproportionately exposed to trauma during a pandemic.
Article
Multidisciplinary Sciences
Jessica M. Ochoa, Kaylie Bair, Thomas Holton, Thomas A. Bobik, Todd O. Yeates
Summary: Bacterial microcompartments are organelle-like structures made of proteins, carrying out specialized metabolic functions in various bacteria. The MCPdb database categorizes and organizes known microcompartment protein structures and their larger assemblies, serving as a growing resource for scientists interested in understanding these protein-based metabolic organelles in bacteria.
Review
Microbiology
Jessica M. Ochoa, Todd O. Yeates
Summary: Bacterial microcompartments are organelle-like structures composed entirely of proteins that enhance metabolic functions. Recent studies have highlighted nuanced variations in microcompartment shell proteins, showing how variation and specialization enable complex molecular machine construction. Engineering synthetic miniaturized microcompartment shells provides additional frameworks for dissecting principles of microcompartment structure and assembly.
CURRENT OPINION IN MICROBIOLOGY
(2021)
Article
Multidisciplinary Sciences
Hau B. Nguyen, Thomas C. Terwilliger, Geoffrey S. Waldo
Summary: Research has shown the utility of split fluorescent proteins for large scale protein labeling in cells, but efficient split fluorescent proteins that do not cross-react are needed for multiplexing experiments. The newly proposed split ccGFP from C. californica complements up to threefold faster compared to the original A. victoria split GFP, enabling multiplexed labeling with existing A. victoria split YFP and CFP.
SCIENTIFIC REPORTS
(2021)
Article
Biochemical Research Methods
Jessica M. Ochoa, Oscar Mijares, Andrea A. Acosta, Xavier Escoto, Nancy Leon-Rivera, Joanna D. Marshall, Michael R. Sawaya, Todd O. Yeates
Summary: This study reports the structures of six hexameric shell proteins from type I and type II choline-utilization microcompartments, revealing shared electrostatic surface properties among the four types of shell proteins described.
ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS
(2021)
Article
Food Science & Technology
Lyman K. Monroe, Duc P. Truong, Jacob C. Miner, Samantha H. Adikari, Zachary J. Sasiene, Paul W. Fenimore, Boian Alexandrov, Robert F. Williams, Hau B. Nguyen
Summary: Conotoxins are toxic peptides with rich disulfide bonds found in cone snail venom, which have a wide range of pathophysiological effects and potential therapeutic applications. However, the identification and characterization of conotoxin toxicities are difficult, costly, and time-consuming. Recent machine learning methods have improved the prediction of conotoxins, but they still face limitations due to the conformational flexibility and various disulfide bond patterns present in these peptides.
Article
Biochemistry & Molecular Biology
Joshua Laniado, Kyle Meador, Todd O. Yeates
Summary: Advances in protein engineering have led to the creation of novel protein assemblies with great size and complexity, with diverse applications. Researchers have developed a computer program, nanohedra, to rapidly identify favorable docking/interface arrangements based on construction rules and algorithms, improving the success rate in this challenging area of protein engineering.
PROTEIN ENGINEERING DESIGN & SELECTION
(2021)
