Article
Biochemistry & Molecular Biology
Tyler B. Alt, Matthew R. Hoag, Graham R. Moran
Summary: This article presents the first comprehensive kinetic investigation of a bacterial form of DPD, revealing its similarity to the mammalian form in terms of mechanism but with distinct aspects in substrate roles.
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS
(2023)
Article
Chemistry, Multidisciplinary
Ryan A. Herold, Christopher J. Schofield, Fraser A. Armstrong
Summary: The study utilizes a nanoporous electrode material, the e-Leaf, to control enzyme cascades and gain detailed kinetic insight into an anti-cancer drug mechanism. The e-Leaf allows for the quantification of IDH1 R132H inhibition kinetics and reveals factors underlying inhibitor residence time. The study highlights the importance of this method in obtaining detailed kinetic and mechanistic information that is difficult to obtain using conventional techniques.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Mathematics, Applied
Ming Fang
Summary: This article presents the application of the renormalization group (RG) method in singular perturbation problems and extends it to competitive systems. By analyzing the enzyme-substrate-inhibitor kinetics model, it is found that the RG method can provide new predictions for the concentrations of substrate, inhibitor, and complexes.
MATHEMATICAL METHODS IN THE APPLIED SCIENCES
(2022)
Article
Chemistry, Multidisciplinary
Olivia M. Manley, Haoyu Tang, Shan Xue, Yisong Guo, Wei-chen Chang, Thomas M. Makris
Summary: BesC is a member of an emerging family of diiron enzymes that catalyze an unusual type of carbon-carbon cleavage reaction. It activates O-2 in a substrate-gated manner to generate a diferric-peroxo intermediate, initiating a unique reaction trajectory by cleaving the C4-H bond as the rate-limiting step in a single turnover reaction.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Chemistry, Physical
Emilie F. Gerard, Thirakorn Mokkawes, Linus O. Johannissen, Jim Warwicker, Reynard R. Spiess, Christopher F. Blanford, Sam P. Hay, Derren J. Heyes, Sam P. de Visser
Summary: This study elucidates the role of vanadium haloperoxidase protein in substrate halogenation through a combination of experimental and computational approaches. Activity studies demonstrate the essentiality of substrate binding for the reaction of hypohalide with substrate. Stopped-flow measurements reveal that the rate-determining step is partially dependent on hypohalide formation. Molecular mechanics and molecular dynamics simulations identify the substrate binding area and highlight the stable binding of selected substrates in a binding tunnel.
Article
Agriculture, Multidisciplinary
Yixiong Tian, Haocun Kong, Xiaofeng Ban, Caiming Li, Zhengbiao Gu, Zhaofeng Li
Summary: This study investigated the molecular mechanism of substrate specificity through studying the glycogen-debranching enzyme from Saccharolobus solfataricus (SsGDE) and two isoamylases from Pseudomonas amyloderamosa (PaISO) and Chlamydomonas reinhardtii (CrISO). The results showed that the aromatic residues in the substrate-binding region play an important role in substrate binding. By modifying the substrate-binding region of SsGDE, variants Y323F and V375F with significantly enhanced activities were obtained.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2023)
Article
Pharmacology & Pharmacy
Songya Zhang, Lin Zhang, Anja Greule, Julien Tailhades, Edward Marschall, Panward Prasongpholchai, Daniel J. Leng, Jingfan Zhang, Jing Zhu, Joe A. Kaczmarski, Ralf B. Schittenhelm, Oliver Einsle, Colin J. Jackson, Fabrizio Alberti, Andreas Bechthold, Youming Zhang, Manuela Tosin, Tong Si, Max J. Cryle
Summary: WS9326A is a peptide antibiotic synthesized by a non-ribosomal peptide synthetase (NRPS). The cytochrome P450 encoded by sas16 (P450Sas) is critical for the formation of an unusual amino acid residue in WS9326A. In this study, the researchers identified the substrate of P450Sas and elucidated its role in the biosynthetic pathway of WS9326A. The results suggest that P450Sas catalyzes the direct dehydrogenation of a dipeptide intermediate, expanding the range of P450 enzymes that can be used for the production of biologically active peptides.
ACTA PHARMACEUTICA SINICA B
(2023)
Article
Plant Sciences
Merve Seven, U. Cem Derman, Andrew J. Harvey
Summary: Xyloglucan endotransglycosylase/hydrolase (XTH) enzymes have been found to exhibit broad substrate specificities, including cellulose analogues and mixed-link beta-glucans, in addition to the standard xyloglucan. This discovery opens up a wide range of potential roles for these enzymes, both within plants and in various industries. Furthermore, genome screening and expression analyses suggest that the XTH genes in the "ancestral" clades are unique to angiosperms, predominantly expressed in reproductive tissues, leading to the proposal of renaming this phylogenetic group as the group-IV clade.
Article
Biochemistry & Molecular Biology
Karen Rodriguez-Nunez, Alejandra Cortes-Monroy, Marcela Serey, Yunus Ensari, Mehdi D. Davari, Claudia Bernal, Ronny Martinez
Summary: This article investigates the effect of site saturation mutagenesis on Rhizobium sp. Histamine Dehydrogenase (Rsp HDH) and proposes a tradeoff between substrate affinity and substrate inhibition in the catalytic mechanism of HDHs, which provides new insights for enzyme engineering.
Article
Biochemistry & Molecular Biology
Natasha D. Vetter, David R. J. Palmer
Summary: Kanosamine is an antibiotic and antifungal compound synthesized in Bacillus subtilis. Through the synthesis of phosphonate analogues of G6P, it was demonstrated that the phosphoryloxymethylene moiety of the substrate is critical for effective catalysis, with energetic contributions from the bridging oxygen, bridging C6 methylene, and phosphodianion being crucial. Additionally, phosphite was shown to rescue the low reactivity of xylose and generate enzymatically truncated and nonhydrolyzable analogues of kanosamine 6-phosphate.
Article
Multidisciplinary Sciences
Christina Papini, Zechen Wang, Shalley N. Kudalkar, Travis Parke Schrank, Su Tang, Tomoaki Sasaki, Cory Wu, Brandon Tejada, Samantha J. Ziegler, Yong Xiong, Natalia Issaeva, Wendell G. Yarbrough, Karen S. Anderson
Summary: APOBEC3 family members are cytidine deaminases that play a role in cancer development and progression. Our study explored the kinetic features of A3A and A3B and found that they have different substrate preferences and purine sequence preferences. In HPV+ HNSCC, the catalytic activity of A3B and its preference for purine sequences were found to be more important than A3A. This study provides insights into APOBEC3-related carcinogenesis and facilitates drug discovery.
Article
Biochemistry & Molecular Biology
Gabriel Vallejos-Baccelliere, Sergio B. Kaufman, Rodolfo M. Gonzalez-Lebrero, Victor Castro-Fernandez, Victoria Guixe
Summary: Methanogenic archaea have potential applications in biotechnology, and this study sheds light on the regulatory mechanisms of their sugar metabolism. The activation of enzymatic activities by adenosine monophosphate (AMP) and the inhibition caused by sugar binding were elucidated, providing important insights into the metabolism of these microorganisms.
Article
Chemistry, Applied
Hongxing Zhu, Muhan Zhang, Peng Wang, Chong Sun, Weimin Xu, Jingjing Ma, Yongzhi Zhu, Daoying Wang
Summary: Moderate oxidation of the myoglobin hemin prosthetic group can improve the solubility and gel properties of myosin, but excessive oxidation reduces its physical and chemical properties and water retention. Hemin prosthetic group shows high affinity for myosin.
Article
Biochemistry & Molecular Biology
D. Eric Dollins, Jian-Ping Xiong, Stuart Endo-Streeter, David E. Anderson, Vinay S. Bansal, Jay W. Ponder, Yi Ren, John D. York
Summary: The study on INPP1 reveals the impact of substrate and lithium on the metal binding sites within the catalytic center, as well as the effect of a mutation on the inhibitory action. The results provide insights into the structural basis for lithium inhibition and substrate recognition, as well as defining a sequence motif for metal binding within this family of enzymes.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
Article
Chemistry, Multidisciplinary
Anna J. Kiss-Szeman, Pal Straner, Imre Jakli, Naoki Hosogi, Veronika Harmat, Dora K. Menyhard, Andras Perczel
Summary: This article presents the structure and function of mammalian acylaminoacyl peptidase, an enzyme that regulates the proteasome activity. The enzyme forms a unique toroid-shaped structure and exhibits flexibility in the active site, allowing for substrate selection through a double-gated channel system. These findings are significant for drug design and the study of the ubiquitin-proteasome system.
Article
Biochemistry & Molecular Biology
Soojung Hahn, Gyuri Kim, Sang-Man Jin, Jae Hyeon Kim
Summary: This study utilized three-dimensional intestinal organoids to investigate the effects of metformin on inflammatory bowel disease (IBD) and found that metformin can enhance intestinal barrier function and reduce levels of inflammatory cytokines.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
V. V. Sudarev, M. S. Gette, S. V. Bazhenov, O. M. Tilinova, E. V. Zinovev, I. V. Manukhov, A. I. Kuklin, Yu. L. Ryzhykau, A. V. Vlasov
Summary: This study investigated the self-assembly processes of ferritin-based protein complexes and obtained structurally characterized oligomeric states. These results provide new potential and opportunities for the application of ferritin in various fields.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Yalda Sabaghi, Farnaz Pourfarzad, Leila Zolghadr, Azita Bahrami, Tahereh Shojazadeh, Alireza Farasat, Nematollah Gheibi
Summary: p-Coumaric acid (p-CA) is a plant compound with anti-cancer activities. This study designed a nano-liposomal carrier containing p-CA to enhance its effectiveness against melanoma cells. The findings showed that the liposomal form of p-CA had a greater impact on the cells. Kinetic modeling indicated that the best fitting model was zero-order.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
M. D. Nazmul Hasan, Md Mahfuzur Rahman, Al Asmaul Husna, Nobuhiro Nozaki, Osamu Yamato, Naoki Miura
Summary: This study investigated the expression of ncRNAs other than miRNAs in different histologic subtypes of canine mammary gland tumors (MGT). Three aberrantly expressed ncRNAs were identified as potential biomarkers for differentiating MGT subtypes. YRNA and tRFs expression levels were found to be decreased in metastatic compared to primary MGT cell lines.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Seine A. Shintani
Summary: In this study, the researchers used signal analysis to study the instantaneous amplitude and phase of sarcomeric oscillations in skeletal muscle. They identified two types of oscillations, sarcomeric oscillations and sarcosynced oscillations, and visualized their behavior during propagating waves. The researchers discovered the presence of sarcomeric defect holes and sarcomeric collision holes, which are important indicators for understanding the oscillation properties of sarcomeres. This finding has important implications for improving our understanding of muscle function and its regulatory mechanisms.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Shuanglin Zhang, Yuzhong Jia, Guolan Ma, Yanyan Yang, Zhenzhen Cao, Antao Luo, Zefu Zhang, Shihan Li, Jie Wen, Hanfeng Liu, Jihua Ma
Summary: Bupleurum is an antiarrhythmic agent that may exert its effects by inhibiting L-type calcium channels.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Tomotaka Ohkubo, Yasuhiko Matsumoto, Hiroaki Sasaki, Kaoru Kinoshita, Yuki Ogasawara, Takashi Sugita
Summary: This study found that Citrobacter koseri inhibits the growth of Staphylococcus epidermidis, disrupting the balance between S. epidermidis and Staphylococcus aureus, and exacerbating inflammation in atopic dermatitis.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Toshifumi Asano, Philipp Sasse, Takao Nakata
Summary: A Cre recombination-based fluorescent reporter system was developed to monitor cell-cell fusion. The system successfully detected the formation of multinuclear myotubes and placental syncytiotrophoblast. This tool could facilitate the study of cell-to-cell fusion.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Ke Shi, Yunlong Shan, Xiao Sun, Kuida Chen, Qiong Luo, Qiang Xu
Summary: This study found that low expression of TP53INP2 is associated with poor survival in colorectal cancer (CRC) patients. As the malignancy of CRC progresses, TP53INP2 expression gradually decreases. Knockdown of TP53INP2 promotes CRC cell proliferation and tumor growth. Mechanistically, TP53INP2 deficiency decreases phosphorylation of beta-catenin, leading to increased accumulation and enhanced nuclear translocation and transcriptional activity. Additionally, TP53INP2 sequesters TIM50, inhibiting its activation of beta-catenin. In conclusion, downregulation of TP53INP2 promotes CRC progression by activating beta-catenin.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Martina Rossi, Fabio Tomaselli, Alejandro Hochkoeppler
Summary: Oligomeric enzymes are known for their higher catalytic rates compared to monomeric enzymes, but the extent of additivity in their activity is still not well understood. This study used tetrameric rabbit lactate dehydrogenase as a model to examine the kinetics of its catalytic action. Surprisingly, when the concentration of the limiting reactant exceeded that of a single subunit, there was a significant slowdown in the enzyme's conformational rearrangements.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Amin Sahraei, Mohammad Javad Shamsoddini, Fakhrossadat Mohammadi, Leila Hassani
Summary: This study explored the inhibitory effects of gallium curcumin, indium curcumin, and vanadyl curcumin on the amyloid fibrillation of hen egg white lysozyme, as well as the binding interactions of these metal complexes with the enzyme. The results showed that indium curcumin and vanadyl curcumin exhibited higher binding affinities and stronger inhibitory effects on amyloid fibrillation compared to gallium curcumin.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Takahiro Sasaki, Yoshiki Kuse, Shinsuke Nakamura, Masamitsu Shimazawa
Summary: PGRN deficiency plays a significant role in cardiac remodeling and arrhythmias post-myocardial infarction (MI), potentially by promoting metabolic abnormalities in macrophages.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Hongwei Zhao, Yiqiang Li, Yibo Zhang, Chi Zhang
Summary: Electrical brain stimulation technology is commonly used to treat brain neurological disorders, but it can cause side effects. This study investigated the impact of electric fields on nerve fibers and revealed the possible origin of side effects. The findings provide guidance for selecting electrical parameters in clinical stimulation therapy.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Julia S. Scott, Lake-Ee Quek, Andrew J. Hoy, Johannes V. Swinnen, Zeyad D. Nassar, Lisa M. Butler
Summary: The fatty acid elongation enzyme ELOVL5 plays a critical role in promoting metastasis in prostate cancer. Knocking down ELOVL5 leads to the accumulation of malonyl-CoA, which inhibits fatty acid oxidation in mitochondria. This study highlights the importance of fatty acid elongation in regulating cell viability and provides a potential target for prostate cancer treatment.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Zan Zhou, Wen-jun Jiang, Li Li, Jun-qiang Si
Summary: This study investigates the effect of noise exposure on cognitive function in mice and explores the underlying molecular mechanisms. The findings suggest that noise exposure leads to increased inflammation, increased phosphorylation of Tau protein, and decreased levels of postsynaptic density protein, resulting in cognitive impairment.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)