Article
Biochemistry & Molecular Biology
Luis Guevara, Melissa Gouge, Amanda Ohler, S. Gage Hill, Soham Patel, Adam R. Offenbacher
Summary: Hydrogen tunneling in enzyme reactions plays an important role in connecting protein thermal motions to catalysis. This study investigated the effect of solvent viscosity on protein thermal motions in lipoxygenases (LOXs) and found that viscosity does not affect the catalytic reaction of soybean lipoxygenase (SLO), but inhibits the activity of 15LOX-2. These findings provide insights into the role of water hydration layers in hydrogen tunneling in LOX.
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS
(2023)
Article
Materials Science, Biomaterials
Lina Koschinski, Bohdan Lenyk, Marie Jung, Irene Lenzi, Bjoern Kampa, Dirk Mayer, Andreas Offenhaeusser, Simon Musall, Viviana Rincon Montes
Summary: The combination of electrophysiology and neuroimaging methods allows simultaneous measurement of electrical activity signals with calcium dynamics in vivo. Transparent neural implants have been proposed to overcome limitations of traditional techniques, but their effectiveness remains unclear. This study compared two types of transparent surface micro-electrocorticography (mu ECoG) implants and found that the combination of solid gold interconnects and PEDOT:PSS-based electrodes offered the best overall properties for long-term chronic multimodal recordings. These implants showed functional stability for four months and allowed simultaneous mapping of electrical and calcium neural signals during imaging.
JOURNAL OF MATERIALS CHEMISTRY B
(2023)
Article
Chemistry, Multidisciplinary
Emily R. Ruskowitz, Brizzia G. Munoz-Robles, Alder C. Strange, Carson H. Butcher, Sebastian Kurniawan, Jeremy R. Filteau, Cole A. DeForest
Summary: Proteins play a crucial role in regulating various biological processes, and new techniques are needed to effectively control protein activity in living systems and biomaterials to study cell signaling and guide biological fate. This study presents a generalizable strategy for activating protein function with precise spatiotemporal control. By using a genetically encoded and light-activated SpyLigation (LASL), bioactive proteins can be reassembled from non-functional fragments with the help of cytocompatible light. The researchers demonstrate protein activation and subcellular localization control in solution, biomaterials, and living mammalian cells. These photoclick-based optogenetic approaches are expected to greatly contribute to understanding and directing complex cellular fates in both time and three-dimensional space.
Article
Biochemistry & Molecular Biology
Michael Paulsmeyer, John Juvik
Summary: The study delves into the characterization of the anthocyanin acyltransferase Aat1 in maize, revealing its specific acyltransferase activity and ability to utilize various substrates for reaction. This provides new insights into the structure-function relationships of dimalonyltransferases and the activity of monocot anthocyanin acyltransferases.
Article
Mechanics
Ashik Ullah Mohammad Masuk, Ashwanth K. R. Salibindla, Rui Ni
Summary: The experimental study focuses on investigating the breakup mechanisms and probability of Hinze-scale bubbles in turbulence. By tracking both bubbles and surrounding tracer particles, the researchers quantified the breakup probability of bubbles close to the Hinze scale and analyzed different breakup mechanisms. The study also provides models linking turbulence characteristics, bubble deformation, and Weber numbers, ultimately offering a unique way to extract the breakup probability of bubbles near the critical Hinze scale.
JOURNAL OF FLUID MECHANICS
(2021)
Article
Biotechnology & Applied Microbiology
Purna Bahadur Poudel, Dipesh Dhakal, Jong Cheol Lee, Jae Kyung Sohng
Summary: Methylation plays important roles in various biological processes, and this study characterized the function of ThnM3 in regioselective modifications of 1,8-dihydroxynaphthalene.
ENZYME AND MICROBIAL TECHNOLOGY
(2024)
Article
Biochemical Research Methods
Diego Vidaurre
Summary: The study highlights potential biases and loss of sensitivity when using PCA for estimating time-varying functional connectivity in high-dimensional fMRI data. The proposed method of combining dimensionality reduction and connectivity estimation in one step overcomes these limitations. This approach facilitates the understanding of dynamic neuronal communication in the brain based on variations in functional connectivity patterns.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Food Science & Technology
Chunyun Ma, Yan Zhang, Chuankai Yang, Yuhang Zhang, Miaorong Zhang, Jianguo Tang
Summary: Cetyl trimethyl ammonium bromide (CTAB)-activated lipase-mineral hybrid microflowers (CTAB-Lip-MHFs) showed good substrate affinity and stability for fatty acid production through hydrolysis of olive oil.
LWT-FOOD SCIENCE AND TECHNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Olivia Teixeira, Ingrid Bernardes Santana Martins, Thamires Quadros Froes, Alexandre Suman de Araujo, Maria Cristina Nonato
Summary: Tuberculosis (TB) is a major cause of global mortality, characterized by high transmission and co-infection rates with HIV. The search for a new TB treatment is urgent. The enzyme DHODH has been identified as a potential target against TB, and inhibitors against DHODH could be developed as a new generation of TB drugs.
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS
(2023)
Article
Optics
Peng Chen, Zhi-Xiong Shen, Chun-Ting Xu, Yi-Heng Zhang, Shi-Jun Ge, Ling-Ling Ma, Wei Hu, Yan-Qing Lu
Summary: Holography, as a recognized technology for optical data encoding and extracting, has attracted increasing attention in miniaturization, multifunctionality, and tunability. However, the simultaneous realization of dynamic tunability and high-dimensional multiplexing remains a critical challenge. In this study, an innovative solution is proposed by utilizing the limited penetration depth of light in chiral liquid crystals and their intrinsic stimuli-responsive characteristics. Through the integration of a photoactive chiral dopant and photopatterning, light-activated spectrally tunable, polarization- and direction-dependent holograms are created simultaneously. An encrypted signal light is demonstrated as an example, where the wavelength, propagation direction, helicity of light, and reaction duration serve as customized keys for information decryption.
LASER & PHOTONICS REVIEWS
(2022)
Article
Plant Sciences
Manman Chang, Jingyu Ma, Ying Sun, Liying Tian, Linlin Liu, Qi Chen, Zhaoliang Zhang, Xiaochun Wan, Jun Sun
Summary: This study reveals that Theanine, an important secondary metabolite in tea, is regulated by light. It was found that light up-regulates the expression of CsGGT2 gene, which affects the accumulation of Theanine. CsGGT2 encodes an enzyme that has both synthesis and degradation functions of Theanine. Therefore, light regulates the degradation of Theanine in tea plants by regulating the expression of CsGGT2 gene.
PLANT CELL AND ENVIRONMENT
(2023)
Review
Environmental Sciences
Hongliang Dai, Yang Sun, Dong Wan, Haq Nawaz Abbasi, Zechong Guo, Hongya Geng, Xingang Wang, Yong Chen
Summary: Eutrophication is a significant environmental issue, and the study of microorganisms that can remove nitrogen and phosphorus simultaneously is crucial for mitigating eutrophication. Various genera, including Bacillus, Pseudomonas, Paracoccus, and Arthrobacter, have been found to accomplish simultaneous N and P removal. The mechanism of N and P removal by denitrifying P accumulating organisms (DPAOs) differs from traditional biological removal processes. The denitrifying P removal (DPR) technology based on DPAOs' metabolic function has the potential to overcome challenges in traditional N and P removal processes and can be applied to low C/N ratio urban sewage treatment.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Chemistry, Multidisciplinary
Chathuri J. Kombala, Sanjaya D. Lokugama, Aikaterini Kotrotsou, Tianzhe Li, Alyssa C. Pollard, Mark D. Pagel
Summary: A newly developed CEST agent can simultaneously measure pH and evaluate protease activity, with the ability to determine pH values through selective saturation signals and ratio analysis.
Article
Biochemistry & Molecular Biology
Andrew E. Huckleby, Jhawn G. Saul, Hyunshun Shin, Staci Desmarais, Apparao Bokka, Junha Jeon, Sung-Kun Kim
Summary: This study demonstrated the inhibitory effect of two compounds with two hydroxamate functional groups on MBL from Bacillus anthracis. The inhibition was found to be competitive and the compounds showed potential as inhibitors to overcome bacterial resistance.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Physical
Qun Wan, Brad C. Bennett, Troy Wymore, Zhihong Li, Mark A. Wilson, Charles L. Brooks, Paul Langan, Andrey Kovalevsky, Chris G. Dealwis
Summary: Acid-base catalysis is a common chemical mechanism employed by enzymes, but a complete mechanistic description for most enzymes remains lacking. Using DHFR as an example, direct observation of the catalytic proton was achieved through a neutron structure. Combining structures and calculations, a mechanism involving dynamics for solvent entry and substrate protonation was proposed.
Review
Biochemistry & Molecular Biology
Harshwardhan Poddar, Derren J. Heyes, Giorgio Schiro, Martin Weik, David Leys, Nigel S. Scrutton
Summary: Dynamic changes in protein structures are crucial for protein function and can be investigated with unprecedented temporal and spatial resolution using X-ray free electron lasers. Light-activated proteins are attractive targets for time-resolved structural studies, as they allow for visualization of early chemical changes and global structural changes.
Article
Biochemistry & Molecular Biology
Celine Lafaye, Sylvain Aumonier, Joaquim Torra, Luca Signor, David von Stetten, Marjolaine Noirclerc-Savoye, Xiaokun Shu, Ruben Ruiz-Gonzalez, Guillaume Gotthard, Antoine Royant, Santi Nonell
Summary: The study shows that modifying the chromophore structure of miniSOG can significantly improve its photosensitizing properties. Replacing flavin mononucleotide (FMN) with riboflavin (RF) without the bulky phosphate group increases the yield of singlet oxygen. Mutagenizing residues stabilizing the phosphate group allows for the modification of miniSOG's photophysical properties.
PHOTOCHEMICAL & PHOTOBIOLOGICAL SCIENCES
(2022)
Article
Chemistry, Multidisciplinary
Lea Albert, Jatin Nagpal, Wieland Steinchen, Lei Zhang, Laura Werel, Nemanja Djokovic, Dusan Ruzic, Malte Hoffarth, Jing Xu, Johanna Kaspareit, Frank Abendroth, Antoine Royant, Gert Bange, Katarina Nikolic, Soojin Ryu, Yali Dou, Lars-Oliver Essen, Olalla Vazquez
Summary: A genuine on-off optochemical probe has been developed for hematopoietic control in zebrafish with unprecedented stability. This interdisciplinary study uncovers the mechanism of action of the probe, providing a new method for future investigations.
ACS CENTRAL SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Matthew J. Rodrigues, Nitai Giri, Antoine Royant, Yang Zhang, Rachel Bolton, Gwyndaf Evans, Steve E. Ealick, Tadhg Begley, Ivo Tews
Summary: The Pdx1 enzyme catalyzes the formation of pyridoxal 5-phosphate (PLP) through an imine relay mechanism, involving stereoselective deprotonation and substrate-assisted phosphate elimination. The I-333 intermediate, characterized by structural, UV-vis absorption spectroscopy and mass spectrometry analyses, plays a central role in PLP biosynthesis.
RSC CHEMICAL BIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Manuel Maestre-Reyna, Cheng-Han Yang, Eriko Nango, Wei-Cheng Huang, Eka Putra Gusti Ngurah Putu, Wen-Jin Wu, Po-Hsun Wang, Sophie Franz-Badur, Martin Saft, Hans-Joachim Emmerich, Hsiang-Yi Wu, Cheng-Chung Lee, Kai-Fa Huang, Yao-Kai Chang, Jiahn-Haur Liao, Jui-Hung Weng, Wael Gad, Chiung-Wen Chang, Allan H. Pang, Michihiro Sugahara, Shigeki Owada, Yuhei Hosokawa, Yasumasa Joti, Ayumi Yamashita, Rie Tanaka, Tomoyuki Tanaka, Fangjia Luo, Kensuke Tono, Kai-Cheng Hsu, Stephan Kiontke, Igor Schapiro, Roberta Spadaccini, Antoine Royant, Junpei Yamamoto, So Iwata, Lars-Oliver Essen, Yoshitaka Bessho, Ming-Daw Tsai
Summary: In this study, time-resolved serial femtosecond X-ray crystallography was used to analyze the entanglement between FAD and its redox sensor triad. It was found that this process regulates FAD re-hybridization and protonation.
Article
Chemistry, Physical
Tobias M. Hedison, Andreea I. Iorgu, Donato Calabrese, Derren J. Heyes, Muralidharan Shanmugam, Nigel S. Scrutton
Summary: This study investigates the structural, dynamical, and functional relationship of copper nitrite reductases (CuNiRs) through combining crystallographic techniques and solution-state approaches. The findings shed light on the catalytic mechanisms of these enzymes and suggest the involvement of protein dynamics. The importance of integrating high-resolution crystallographic techniques and low-resolution solution-state approaches in studying metalloenzymes is emphasized.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Multidisciplinary Sciences
Jonathan S. Trimble, Rebecca Crawshaw, Florence J. Hardy, Colin W. Levy, Murray J. B. Brown, Douglas E. Fuerst, Derren J. Heyes, Richard Obexer, Anthony P. Green
Summary: The ability to program new modes of catalysis into proteins using genetic code expansion methodology has led to the development of photoenzymes that operate through triplet energy transfer catalysis. This allows for versatile reactivity in organic synthesis that is not possible with current biocatalysis methods. The study demonstrates the successful installation of a genetically encoded photosensitizer into a protein scaffold, resulting in a photoenzyme that can perform cycloadditions with high efficiency and selectivity. The photoenzyme outperforms small-molecule catalysts by being able to operate under aerobic conditions and at ambient temperatures. This research opens up new possibilities for excited-state chemistry in protein active sites and provides a foundation for the development of enantioselective photocatalysts.
Article
Multidisciplinary Sciences
R. Astashkin, K. Kovalev, S. Bukhdruker, S. Vaganova, A. Kuzmin, A. Alekseev, T. Balandin, D. Zabelskii, I Gushchin, A. Royant, D. Volkov, G. Bourenkov, E. Koonin, M. Engelhard, E. Bamberg, V Gordeliy
Summary: This study presents the high-resolution structures of the SyHR protein from the cyanobacterial anion pumps family, providing insights into the molecular mechanisms of SyHR and cyanobacterial anion pumps in general.
NATURE COMMUNICATIONS
(2022)
Article
Biochemical Research Methods
Kyprianos Hadjidemetriou, Nicolas Coquelle, Thomas R. M. Barends, Elke De Zitter, Ilme Schlichting, Jacques-Philippe Colletier, Martin Weik
Summary: By combining various techniques, researchers have elucidated the catalytic mechanism of fatty-acid photodecarboxylase, which converts free fatty acids into hydrocarbon compounds. The study faced challenges and further experiments are needed to identify the photoproducts and their movements during the catalytic cycle.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Martin Weik, Tatiana Domratcheva
Summary: This review highlights recent advances in studying structural changes of light-sensitive proteins using time-resolved crystallography at X-ray free electron lasers and quantum chemical calculations.
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2022)
Article
Biochemical Research Methods
Theodorus W. J. Gadella, Laura van Weeren, Jente Stouthamer, Mark A. Hink, Anouk H. G. Wolters, Ben N. G. Giepmans, Sylvain Aumonier, Jerome Dupuy, Antoine Royant
Summary: We have evolved mScarlet3, a cysteine-free monomeric red fluorescent protein, with fast and complete maturation, high brightness, quantum yield (75%) and fluorescence lifetime (4.0 ns). The crystal structure of mScarlet3 reveals a barrel rigidified at one of its heads by a large hydrophobic patch of internal residues. mScarlet3 performs well as a fusion tag, shows no apparent cytotoxicity, and outperforms existing red fluorescent proteins as a Forster resonance energy transfer acceptor and as a reporter in transient expression systems.
Article
Biochemistry & Molecular Biology
Kirill Kovalev, Fedor Tsybrov, Alexey Alekseev, Vitaly Shevchenko, Dmytro Soloviov, Sergey Siletsky, Gleb Bourenkov, Michael Agthe, Marina Nikolova, David von Stetten, Roman Astashkin, Sergey Bukhdruker, Igor Chizhov, Antoine Royant, Alexander Kuzmin, Ivan Gushchin, Riccardo Rosselli, Francisco Rodriguez-Valera, Nikolay Ilyinskiy, Andrey Rogachev, Valentin Borshchevskiy, Thomas R. Schneider, Ernst Bamberg, Valentin Gordeliy
Summary: By studying a bacterial inward proton-pumping rhodopsin, researchers have uncovered its molecular mechanism and revealed how proton wires mediate ion selectivity and proton transport through cell membrane. Proton transport is essential for cell life and understanding the mechanisms behind it is a challenge. The study presents a comprehensive function-structure analysis of a light-driven bacterial inward proton pump, providing insights into proton translocation and the use of synchrotron source for rhodopsin studies. The results also have implications for optogenetics.
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Harshwardhan Poddar, Ronald Rios-Santacruz, Derren J. J. Heyes, Muralidharan Shanmugam, Adam Brookfield, Linus O. O. Johannissen, Colin W. W. Levy, Laura N. N. Jeffreys, Shaowei Zhang, Michiyo Sakuma, Jacques-Philippe Colletier, Sam Hay, Giorgio Schiro, Martin Weik, Nigel S. S. Scrutton, David Leys
Summary: This study provides insights into the mechanism of CarH, a photoreceptor involved in transcriptional regulation. The authors show that the response of CarH to light integrates both B-12 photochemistry and redox changes to drive large-scale conformational changes.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Landon Zarowny, Damien Clavel, Ryan Johannson, Kevin Duarte, Hadrien Depernet, Jerome Dupuy, Heather Baker, Alex Brown, Antoine Royant, Robert E. Campbell
Summary: In this study, we successfully created a new fluorescent protein, NeonCyan1, and two additional mutants with distinct spectral hues through modification of mNeonGreen. Structural, computational, and photophysical characterization of these proteins provided insight into the factors that control the fluorescence emission color. Although not recommended as replacements for contemporary fluorescent proteins, these new variants demonstrate potential suitability for live cell imaging applications.
PROTEIN ENGINEERING DESIGN & SELECTION
(2022)