Article
Biochemistry & Molecular Biology
Eiichiro Takamura, Shunsuke Taki, Hiroaki Sakamoto, Takenori Satomura, Haruhiko Sakuraba, Toshihisa Ohshima, Shin-ichiro Suye
Summary: Enzymes from hyperthermophilic archaea have potential industrial applications due to their superior thermal and long-term stability, but multicopper oxidases from these archaea have lower redox potential, impacting the cell voltage of biofuel cells. This study successfully increased the redox potential of the multicopper oxidase from a hyperthermophilic archaeon through mutations, enhancing catalytic activity and providing useful biocathode catalysts for high-voltage biofuel cells.
APPLIED BIOCHEMISTRY AND BIOTECHNOLOGY
(2021)
Article
Chemistry, Physical
Amit Kumar Simlandy, Warabhorn Rodphon, Turki M. Alturaifi, Binh Khanh Mai, Hui-Qi Ni, John A. Gurak Jr, Peng Liu, Keary M. Engle
Summary: A redox-neutral catalytic coupling of nitroalkanes and unactivated alkenes is reported in this study, which proceeds by a directed carbopalladation mechanism. The combination of PdI2 as the precatalyst and HFIP solvent enables the reaction uniquely. Structurally complex nitroalkane products, including nitro-containing carbo- and heterocycles, can be prepared under convenient conditions without the use of toxic or corrosive reagents. The reaction mechanism is examined through deuterium labeling experiments and isolation of a catalytically relevant intermediate. Different catalytic activation modes are utilized to demonstrate orthogonal methods for site-selective functionalization of a polyfunctional nitroalkyl ketone. Density functional theory (DFT) calculations reveal that the carbopalladation transition state is stabilized by a Na·I interaction and H·I hydrogen bond with HFIP.
Article
Chemistry, Physical
Amit Kumar Simlandy, Warabhorn Rodphon, Turki M. Alturaifi, Binh Khanh Mai, Hui-Qi Ni, John A. Gurak, Peng Liu, Keary M. Engle
Summary: We report a redox-neutral catalytic coupling of nitroalkanes and unactivated alkenes that proceeds by a directed carbopalladation mechanism. The reaction is enabled by the combination of PdI2 as the precatalyst and HFIP solvent. Complex nitroalkane products, including nitro-containing carbo- and heterocycles, can be prepared under convenient conditions without the need for toxic or corrosive reagents.
Article
Microbiology
Emily C. Hoedt, Francesca Bottacini, Nora Cash, Roger S. Bongers, Kees van Limpt, Kaouther Ben Amor, Jan Knol, John MacSharry, Douwe van Sinderen
Summary: Members of the genus Bifidobacterium are difficult to genetically manipulate due to their extensive and variable Restriction-Modification systems. A modified suicide vector, pFREM28, was developed to target specific genes in B. breve by removing known restriction sites, reducing the time, effort, and resources required for generating site-directed mutants. This approach could be applied to other (bifido)bacterial species as well.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Agriculture, Multidisciplinary
Su-Jin Jun, Jung-A Lee, Young-Wan Kim, Sang-Ho Yoo
Summary: Through site-directed mutagenesis, a robust mutant Bifidobacterium thermophilum (BtAS) strain BtAS(Y414F/P200R) with enhanced turanose productivity was successfully developed, showing an increase in turanose yield by two times compared to the wild type BtAS and completing the reaction in half the time.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Soroosh Pouyan, Milad Lagzian, Mohammad Hossein Sangtarash
Summary: This study characterized a new alpha-amylase from Bacillus cereus GL96 and used an in-silico approach to redesign the enzyme for improved thermal stability. The engineered enzyme showed higher stability and activity at elevated temperatures compared to the wild-type enzyme. Specifically, the D162K mutation resulted in the best performance, with increased optimum temperature and improved stability. This mutant enzyme holds promise for further investigation and industrial applications.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2022)
Article
Plant Sciences
Xia Li, Geng Chen, Qing-Qing Gao, Chun-Fan Xiang, Cheng-Xiao Yuan, Xiao-Ning Li, Yan-Yu Shu, Guang-Hui Zhang, Yan-Li Liang, Sheng-Chao Yang, Chen-Xi Zhai, Yan Zhao
Summary: This study explored the key enzymes involved in cucurbitacins biosynthesis in the Chinese traditional medicinal plant Hemsleya chinensis. Using AlphaFold2 and molecular docking, the researchers successfully predicted the 3D structure of HcOSC6 and its binding features to 2,3-oxidosqualene. Mutagenesis experiments identified three key amino acid residues, E246, M261, and D490, which significantly affected the activity of HcOSC6. This study not only characterized three potential key residues for producing cucurbitacins, but also provided insights into their significant role in metabolic engineering.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Lena Goshayeshi, Sara Yousefi Taemeh, Nima Dehdilani, Mohammadreza Nasiri, Mohammad M. Ghahramani Seno, Hesam Dehghani
Summary: The study demonstrates the use of an RNA-guided piggyBac transposase and dual sgRNAs for site-directed integrations in the human ROSA26 safe harbor region. This methodology shows promise for targeting specific genomic regions, such as in cancer cells for inserting sequences into target regions or activating tumor suppressor genes.
Article
Agriculture, Multidisciplinary
Cheng-Hua Wang, Wu-Ping Xiong, Cheng Huang, Xiao-Ming Li, Qing-Yan Wang, Ri-Bo Huang
Summary: This study successfully increased the catalytic activity and efficiency of an exoinulinase under acidic conditions through rational site-directed mutagenesis. The mutants showed improved substrate preference for inulin and may serve as promising candidates for industrial inulin hydrolysis. The study demonstrates the potential of mutating non-conserved substrate recognition residues for industrial enzyme improvements.
JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE
(2021)
Review
Plant Sciences
Olawale Samuel Adeyinka, Bushra Tabassum, Brice Landry Koloko, Ifedayo Victor Ogungbe
Summary: The improvement of CRISPR-Cas gene editing technology has facilitated genetic modification of desirable agronomic traits in crops, such as resistance to pathogens, drought tolerance, nutritional value, and yield-related traits. This presents a significant opportunity for precise genetic diversification in plants.
Article
Biochemistry & Molecular Biology
Satoru Watanabe, Masahiro Ito, Takanori Kigawa
Summary: DiRect is a novel PCR-based mutagenesis method that achieves high quality product (>99% substitution) without the use of recombinant DNA technology. It has been successfully applied in the study of an industrially relevant enzyme, showing simplicity, efficiency, and potential scalability in site-directed mutagenesis.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2021)
Review
Chemistry, Organic
Houchao Xu, Jeroen S. Dickschat
Summary: In the past three decades, numerous terpene synthases have been characterized from various life kingdoms. The mechanisms of terpene synthases have been investigated through site-directed mutagenesis, providing valuable insights into their catalysis and resulting in mutants with improved yields.
SYNTHESIS-STUTTGART
(2022)
Article
Computer Science, Software Engineering
Madhavi Latha Yadav Bangaru, Ravi Kumar Medabalimi, Sobhan Babu, Nidhanapati K. Raghavendra
Summary: Silent mutations allowing for restriction site modification can aid in screening successful mutants during site-directed mutagenesis. However, introducing a new restriction site requires the analysis of degenerate sequences within mutant primers, which becomes increasingly laborious, time-consuming, and prone to errors as the number of degenerate codons increases. A software named 'REMP' was developed to instantly generate degenerate sequences with restriction sites that are 6-8 base pairs in length, allowing users to edit the list of restriction sites without the need for writing computer code or knowing a program language.
Article
Biochemistry & Molecular Biology
Qiuya Gu, Yu Lu, Jianli Zhou, Wenhua Yang, Ke Wang, Xiaobo Liu, Xiaobin Yu
Summary: Combinational mutagenesis was used to improve the catalytic efficiency and adaptability of alginate lyase from Pseudoalteromonas sp. Alg6B, which showed significant potential for the production of AOS from marine alginate.
PROCESS BIOCHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Jonas Gregor Wiese, Sooruban Shanmugaratnam, Birte Hoecker
Summary: The successful extension of a robust TIM-barrel scaffold by adding a short de novo helix opens up opportunities for diversifying it towards more pocket-like arrangements, making it a potential building block for future design of binding or catalytic sites.
Article
Microbiology
Ying Liu, Zengqiang Gao, Guangfeng Liu, Zhi Geng, Yuhui Dong, Heng Zhang
FRONTIERS IN MICROBIOLOGY
(2020)
Article
Biochemical Research Methods
Haiying Wen, Zhi Geng, Zengqiang Gao, Zhun She, Yuhui Dong
ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS
(2020)
Article
Biochemical Research Methods
Juan Zhou, Zengqiang Gao, Heng Zhang, Yuhui Dong
ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS
(2020)
Article
Instruments & Instrumentation
Zhongzhu Zhu, Han Xu, Lingfei Hu, Ming Li, Peng Liu, Yuhui Dong, Liang Zhou
Summary: With the development of fourth-generation synchrotron sources, coherent diffractive imaging (CDI) is becoming a mainstream method for 3D structure determination at nanometer resolution. The study proposes a wave optics model to analyze the effect of partial coherence on CDI, simulating light field distribution, coherence between any two points on a plane, and CDI experiments. Ultimately, it is found that a visibility higher than 0.95 is needed for good image quality of complex samples in plane-wave CDI simulations.
JOURNAL OF SYNCHROTRON RADIATION
(2021)
Article
Cell Biology
Liang Li, Zishuo Yu, Dan Zhao, Yulei Ren, Haifeng Hou, Yanhui Xu
Summary: This study determined the structures of 17-subunit human Pol III alpha and revealed its role in transcriptional regulation and cancer-related mechanisms.
Article
Multidisciplinary Sciences
Xizi Chen, Yilun Qi, Zihan Wu, Xinxin Wang, Jiabei Li, Dan Zhao, Haifeng Hou, Yan Li, Zishuo Yu, Weida Liu, Mo Wang, Yulei Ren, Ze Li, Huirong Yang, Yanhui Xu
Summary: This study elucidates the assembly mechanism of human TFIID-based PIC, showing two tracks for modular reorganization and direct promoter deposition, converging at a holo PIC with around 50 subunits. TFIID stabilizes PIC organization and supports CAK-mediated phosphorylation of Pol II.
Article
Chemistry, Multidisciplinary
Qiang Zhou, Zeng-Qiang Gao, Zheng Dong, Yu-Meng Jiang, Zhun She, Zhi Geng, Yu-Hui Dong
Summary: A new multi-lattice indexing method based on whole-pattern matching principle has been proposed for accurately identifying multiple crystal lattices in macromolecular crystallography. The method features local correction and iterative refinement, which are critical for processing multi-crystal data sets. Careful exclusion of overlapping reflections before scaling is confirmed to guarantee accurate data reduction results.
ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES
(2021)
Article
Multidisciplinary Sciences
Haifeng Hou, Yan Li, Mo Wang, Aijun Liu, Zishuo Yu, Ke Chen, Dan Zhao, Yanhui Xu
Summary: Termination of RNA polymerase III-mediated transcription occurs when the polymerase encounters a stretch of four or more deoxythymidine nucleotides on the non-template strand. The 3.6 angstrom cryo-EM structure of a human Pol III pre-termination complex assembled on a 7 dT-containing DNA template sheds light on the mechanism of poly-dT-dependent transcription termination of Pol III.
NATURE COMMUNICATIONS
(2021)
Article
Instruments & Instrumentation
Zheng Dong, Sen Chen, Himadri S. Gupta, Xiaoyi Zhao, Yiming Yang, Guangcai Chang, Jian Xue, Yiyang Zhang, Shengnian Luo, Yuhui Dong, Yi Zhang
Summary: This study investigates the multiscale mechanical responses of stomatopod dactyl club under high-speed impact and reveals the influence of hydration states on toughening mechanisms. A previously unreported 3D interlocking structural design is discovered and found to play a crucial role in resisting structural damage and hindering crack propagation.
JOURNAL OF SYNCHROTRON RADIATION
(2022)
Article
Multidisciplinary Sciences
Xiaoyun Yang, Zongqiang Li, Liang Zhao, Zhun She, Zengqiang Gao, Sen-Fang Sui, Yuhui Dong, Yanhua Li
Summary: This study reports three intermediate structures of PldA by employing an integrated approach combining structural biology and biochemistry. Structural analysis reveals that the significant conformational changes in the lid region and the peripheral helical domain trigger the switch of the active pocket of PldA to regulate the enzymatic activity. The structure-based mutational experiments identified a series of key residues responsible for substrate hydrolysis activity and the interactions between PldA and PA3488.
NATURE COMMUNICATIONS
(2022)
Article
Biochemical Research Methods
Hai-Ying Wen, Li-Bin Pan, Shu-Rong Ma, Xin-Yu Yang, Jia-Chun Hu, Hai-Fan Zhao, Zeng-Qiang Gao, Yu-Hui Dong, Yan Wang, Heng Zhang
Summary: The bacterial nitroreductase NfsB from Escherichia coli plays a key role in converting berberine into dihydroberberine, with the crystal structure revealing the binding mechanism between berberine and NfsB. This study sheds light on the transformation process of berberine by gut microbiota.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2022)
Article
Biochemical Research Methods
Yu-Meng Jiang, Han Miao, Xin-Yu Pan, Qi Wang, Zheng Dong, Zhi Geng, Yu-Hui Dong
Summary: Iterative projection algorithms have been widely used in protein crystallography to overcome the 'phase problem'. However, prior knowledge constraints are usually required for successful phase retrieval. In this study, a novel approach that utilizes low-resolution diffraction data to eliminate the need for a reference density distribution is proposed. The approach involves random assignment of phases and density modification to refine the initial envelope. Information entropy is introduced as a metric to evaluate the success of the phase-retrieval procedure. The effectiveness and robustness of this approach are demonstrated through validation using ten protein structures with high solvent content.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2023)
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)
