Article
Multidisciplinary Sciences
Zhengrong Xu, Lingna Guo, Xiaoyun Qian, Chenjie Yu, Shengju Li, Chengwen Zhu, Xiaofeng Ma, Hui Li, Guangjie Zhu, Han Zhou, Wenxuan Dai, Qian Li, Xia Gao
Summary: In this study, we identified two entry tunnels in the olfactory receptor TAAR9 and described the residues that form these tunnels. We also confirmed the function of these tunnels through site-directed mutagenesis, challenging the existing views regarding the number of entry tunnels and demonstrating their possible role in odorant recognition.
SCIENTIFIC REPORTS
(2022)
Article
Biochemistry & Molecular Biology
Kazune Tamura, Guillaume Dejean, Filip Van Petegem, Harry Brumer
Summary: The study examined the significant role of complex glycans in feeding the human gut microbiota and the prevalence of Bacteroidetes in the gut microbiota worldwide. It also investigated the role of cell-surface glycan-binding proteins in the polysaccharide utilization loci and provided insights into the structural specificities of three bacterial species.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
Article
Biology
Kouhei Tachibana, Aoi Fukazawa, Ryo Nishide, Takenao Ohkawa
Summary: This study explores the importance of structural similarity in protein pockets for discovering new ligands and proposes a method to search for proteins with similar pockets and extract significant spots in binding ligands. The effectiveness of the method is confirmed by classifying ligands based on the extracted significant spots in the ligand binding to the protein.
COMPUTATIONAL BIOLOGY AND CHEMISTRY
(2021)
Article
Chemistry, Physical
Francesco Piazza
Summary: The use of absorbing boundary conditions for diffusion-based problems in physical chemistry and biochemistry is common, but the explicit consideration of degradation and the geometry of reaction boundaries is often overlooked. In this study, a simple and general idea is introduced to derive appropriate boundary conditions based on the chemical reaction scheme and physical reaction boundaries. The results show that this mathematical analysis provides unique physical insight not accessible through standard treatments.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Chemistry, Multidisciplinary
Maciej Zakrzewski, Piotr Piatek
Summary: This study presents a series of heteroditopic carboxylate salt receptors with varying ion binding domain distances, showing different affinities and efficiencies in binding potassium salts. NMR titrations highlight the importance of receptor conformation, with certain conformations better adapting to interphase conditions during the extraction process.
NEW JOURNAL OF CHEMISTRY
(2021)
Article
Food Science & Technology
Samira Feyzi, Mehdi Varidi, Mohammad Reza Housaindokht, Zarrin Es'haghi
Summary: The research found that adjusting pH and NaCl concentration can affect the binding properties between whey protein isolate (WPI) and safranal, with pH 9 and NaCl concentration of 0.5 M being most favorable for binding. WPI has a single class of binding site for safranal, but two binding sites at pH 5; additionally, the structure of WPI is looser under acidic and basic conditions, possibly leading to aggregation.
Article
Multidisciplinary Sciences
Thierry Izore, Y. T. Candace Ho, Joe A. Kaczmarski, Athina Gavriilidou, Ka Ho Chow, David L. Steer, Robert J. A. Goode, Ralf B. Schittenhelm, Julien Tailhades, Manuela Tosin, Gregory L. Challis, Elizabeth H. Krenske, Nadine Ziemert, Colin J. Jackson, Max J. Cryle
Summary: Non-ribosomal peptide synthetases (NRPSs) are essential for assembling complex natural products, with condensation domains playing a central role in chain assembly. Structural snapshots of a condensation domain bound to an aminoacyl-PCP substrate reveal a mechanism for controlling substrate access and tuning selectivity, without requiring a distinct pocket for side chain selection during peptide assembly.
NATURE COMMUNICATIONS
(2021)
Article
Chemistry, Medicinal
Illimar Hugo Rekand, Ruth Brenk
Summary: DrugPred_RNA is a structure-based druggability predictor developed to identify druggable RNA binding sites. The method performed well in discriminating druggable from less druggable protein binding sites and can contribute to direct drug discovery efforts for RNA targets. This predictor is robust against conformational and sequence changes in the binding sites, enhancing confidence in its performance.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2021)
Article
Biochemistry & Molecular Biology
Natalja Fjodorova, Marjana Novic, Katja Venko, Viktor Drgan, Bakhtiyor Rasulev, Melek Turker Sacan, Safiye Sag Erdem, Gulcin Tugcu, Alla P. Toropova, Andrey A. Toropov
Summary: This research focused on the inhibitory effect of fullerene derivatives (FDs) on therapeutic targets associated with diabetic disease, as well as the key binding characteristics of FDs through protein-ligand binding analysis. The study provides important information for the potential use of FDs with different functional groups as promising medical antidiabetic agents.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Multidisciplinary Sciences
Julia Hernandez Lluesa, Luis Carlos Lopez-Romero, Jose Jesus Broseta Monzo, Marta Roca Marugan, Iris Viejo Boyano, Diana Rodriguez-Espinosa, Aina Gomez-Bori, Amparo Soldevila Orient, Ramon Devesa Such, Pilar Sanchez Perez, Julio Hernandez Jaras
Summary: This study aims to analyze the changes in lipid profiles of PD patients within 6 months of starting peritoneal dialysis. The results showed that the lipidomic profile of PD patients changed during this period, but there were no significant differences in classical lipid markers.
SCIENTIFIC REPORTS
(2022)
Article
Biology
Yao Zhou, Danyang Li, Diyin Li, Aizhong Chen, Liuqing He, Jianhua Luo, Liang Tao
Summary: In addition to LDLR, Clostridium novyi alpha-toxin (Tcn alpha) can also use LRP1 and Megalin as cellular entry receptors. The expression levels of LDLR and LRP1 vary in different cells, suggesting that the dominant entry receptor for Tcn alpha may be cell-type dependent.
COMMUNICATIONS BIOLOGY
(2022)
Article
Chemistry, Inorganic & Nuclear
William D. J. Tremlett, Tilo Soehnel, James D. Crowley, L. James Wright, Christian G. Hartinger
Summary: Using ferrocene-based ligand systems, a series of heterobimetallic architectures were designed to release and bind guest molecules. The complexes were characterized using various techniques and the disassembly and reassembly process of metallosupramolecular structures were investigated using NMR spectroscopy. Guest binding studies revealed interactions with anionic guests and the release of guests was induced by Cl- ions.
INORGANIC CHEMISTRY
(2023)
Article
Multidisciplinary Sciences
He Tian, Kathryn M. Gunnison, Manija A. Kazmi, Thomas P. Sakmar, Thomas Huber
Summary: In this study, Rho mutants were engineered as FRET sensors to measure the kinetics and energetics of 11CR binding using genetic code expansion and bioorthogonal labeling. The study found that mutations in the channel between transmembrane helices 5 and 6 dramatically affected 11CR binding kinetics, but not agonist release kinetics. The findings provided direct experimental evidence for the entry of 11CR between TM5/6 in Rho, involving dynamic allosteric control of the ligand entry channel. These findings proposed a conceptual framework for understanding the function of G protein-coupled receptors with hydrophobic ligands that enter their binding pockets through transmembrane pores.
Article
Chemistry, Physical
Didar Baimanov, Liming Wang, Ke Liu, Mengmeng Pan, Rui Cai, Hao Yuan, Wanxia Huang, Qingxi Yuan, Yunlong Zhou, Chunying Chen, Yuliang Zhao
Summary: This study investigates how the mirrored surface of chiral gold nanoparticles affects their coronal composition and subsequent clearance and distribution in vivo. The researchers found that chiral gold nanoparticles exhibit specific recognition for different coronal components, resulting in distinct cellular uptake and tissue accumulation. This study provides insights into the interaction between chiral nanoparticles and biological systems, which can guide the efficient fabrication of target nanomedicines.
NANOSCALE HORIZONS
(2023)
Article
Chemistry, Multidisciplinary
Hannah Kurz, Konstantin Schoetz, Ilias Papadopoulos, Frank W. Heinemann, Harald Maid, Dirk M. Guldi, Anna Koehler, Gerald Hoerner, Birgit Weber
Summary: The study presents a family of planar nickel(II) complexes with sensitive CISSS tracked by fluorescence detection. These complexes fluoresce in noncoordinating solvents but are fluorescence-silent in the presence of axial ligands. FD-CISSS shows higher sensitivity compared to absorption-based CISSS.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)