Article
Biochemistry & Molecular Biology
Hyun-Jong Eun, Jooyeon Lee, Su-Jin Kang, Bong-Jin Lee
Summary: Toxin and Antitoxin systems are crucial for bacterial survival against harsh environments like antibiotic treatments, with the VapBC system being the most abundant among them in Mycobacterium tuberculosis. The VapBC43 system, related to vancomycin treatment response, features a structure where a single VapB43 molecule binds to a VapC43 dimer. Despite lacking conserved acidic residues, VapC43 exhibits ribonuclease activity, and its structural information may aid in developing inhibitors for use as adjuvants in vancomycin therapy against M. tuberculosis.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Christoph Grininger, Mario Leypold, Philipp Aschauer, Tea Pavkov-Keller, Lina Riegler-Berket, Rolf Breinbauer, Monika Oberer
Summary: The study uncovered new insights into the structural changes of the monoacylglycerol lipase of Mycobacterium tuberculosis, highlighting its importance as a potential therapeutic target.
Article
Biochemistry & Molecular Biology
Ki-Hwa Kim, Chang Woo Lee, Bashu Dev Pardhe, Jisub Hwang, Hackwon Do, Yung Mi Lee, Jun Hyuck Lee, Tae-Jin Oh
Summary: 7 alpha-Hydroxysteroid dehydrogenase (7 alpha-HSDH) plays a role in catalyzing the dehydrogenation of steroid substrates at the 7 alpha position. Structural studies reveal significant conformational changes in the apo form of 7 alpha-HSDH, with only the ternary complex structure showing a fully closed conformation. The transition from open to closed conformation is essential for catalytic activity, positioning important residues for catalysis.
JOURNAL OF STEROID BIOCHEMISTRY AND MOLECULAR BIOLOGY
(2021)
Article
Chemistry, Multidisciplinary
Ji Sung Koo, Sung-Min Kang, Won-Min Jung, Do-Hee Kim, Bong-Jin Lee
Summary: This study investigates a novel three-component regulatory system, HipBA, and reveals that the toxic fragment HipA(C) is inactivated by HipA(N) instead of HipB. It provides important insights into the detailed regulatory mechanism of the HipBA(N+C) system and the rationale behind its construction as a three-component system.
Article
Chemistry, Physical
Qi Han, Kate M. Smith, Connie Darmanin, Timothy M. Ryan, Calum J. Drummond, Tamar L. Greaves
Summary: This study investigates the conformational changes of lysozyme in the presence of ionic liquids using a combination of spectroscopic techniques, small angle X-ray scattering, and X-ray crystallography. The results show that the secondary structure of lysozyme remains stable while the tertiary structure, particularly the loop regions, are sensitive to the concentration and type of ionic liquids.
JOURNAL OF COLLOID AND INTERFACE SCIENCE
(2021)
Article
Microbiology
Kemin Tan, Jennifer K. Teschler, Ruiying Wu, Robert P. Jedrzejczak, Min Zhou, Ludmilla A. Shuvalova, Michael J. Endres, Lucas F. Welk, Keehwan Kwon, Wayne F. Anderson, Karla J. F. Satchell, Fitnat H. Yildiz, Andrzej Joachimiak
Summary: VxrA and VxrB form a cognate histidine kinase-response regulator pair in Vibrio cholerae, positively regulating virulence, the type VI secretion system, biofilm formation, and cell wall homeostasis. VxrA has a unique periplasmic sensor domain and lacks a cytoplasmic linker domain, suggesting a potentially unique signal sensing and transmission mechanism. Crystal structures of VxrA-SD reveal a novel structural fold and proposed scissor-like closing regulation mechanism for VxrA HK.
JOURNAL OF BACTERIOLOGY
(2021)
Article
Physics, Applied
Jong Woo Kim, Mathew J. Cherukara, Ashish Tripathi, Zhang Jiang, Jin Wang
Summary: Coherent surface scattering imaging requires a mathematical conversion to visualize specimen structures, which can now be predicted using a deep learning neural network model to instantly obtain results from scattering patterns. This is highly beneficial for both experimental effectiveness and data analysis.
APPLIED PHYSICS LETTERS
(2021)
Article
Biochemistry & Molecular Biology
Yunseok Heo, Inhwan Lee, Sunjin Moon, Ji-Hye Yun, Eun Yu Kim, Sam-Yong Park, Jae-Hyun Park, Woo Taek Kim, Weontae Lee
Summary: Phospholipase is an important enzyme involved in membrane remodeling, digestion, and cellular mechanism regulation. This study focuses on PLA1, a less studied group of phospholipases, and reports the molecular structures of plant PLA1s derived from Arabidopsis thaliana and Capsicum annuum. These novel PLA1s form homodimers, which is different from the monomeric form of PLAs. The study also reveals a new domain essential for homodimerization in plant PLA1s.
Article
Chemistry, Multidisciplinary
Cen Chen, Ziyuan Fang, Zhen Huang
Summary: Crystallization phasing and obtaining high-quality crystals are major challenges for X-ray crystallographic analysis of nucleic acids. In this study, the authors addressed these challenges by incorporating selenium atoms into DNA duplexes, which resulted in larger and higher quality crystals compared to standard DNA crystals. These findings provide a simple strategy to overcome crystallization challenges in nucleic acid crystallography.
CRYSTAL GROWTH & DESIGN
(2022)
Article
Biochemistry & Molecular Biology
Camila Campos-Escamilla, Dritan Siliqi, Luis A. Gonzalez-Ramirez, Carmen Lopez-Sanchez, Jose Antonio Gavira, Abel Moreno
Summary: The conformational changes of iron-free and iron-loaded transferrin at different pH values were studied using Macromolecular X-ray Crystallography and Small Angle X-ray Scattering techniques. While apo-Tf remained mostly globular in solution, holo-Tf showed a more elongated and flexible shape with co-existing closed, partially open, and open conformations.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Olivier Nicolas Lemaire, Marie-Caroline Mueller, Joerg Kahnt, Tristan Wagner
Summary: Ketol-acid reductoisomerase (KARI) plays a crucial role in the biosynthesis of branched-chain amino acids and has been studied for its specificity and potential in antibiotic development. A recent structural study on a KARI from a methanogenic archaea revealed the conformational movements necessary for substrate and coenzyme binding, as well as the conservation of active site environment. The dodecameric structure of this KARI provides insights into the evolution and cellular role of KARIs.
Article
Multidisciplinary Sciences
Akimitsu Higuchi, Wataru Shihoya, Masae Konno, Tatsuya Ikuta, Hideki Kandori, Keiichi Inoue, Osamu Nureki
Summary: SzRs, a newly identified rhodopsin family in Asgard archaea, exhibit unique kinetic behaviors in inward H+ release compared to other H+ pumps. The crystal structure of SzR AM_5_00977 revealed that key residues and structural features are different from other microbial rhodopsins, suggesting a distinct mechanism for inward H+ release.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biology
Hai Li, Chia-Ying Huang, Elena G. Govorunova, Oleg A. Sineshchekov, Adrian Yi, Kenneth J. Rothschild, Meitian Wang, Lei Zheng, John L. Spudich
Summary: The crystal structure of bromide-bound GtACR1 reveals structural changes that relax the constrictions of the channel and involve a novel salt-bridge switch mechanism. These findings suggest that substrate binding induces a transition from an inactivated state to a pre-activated state in the dark, facilitating channel opening.
Article
Biochemistry & Molecular Biology
Blake T. Riley, Stephanie A. Wankowicz, Saulo H. P. de Oliveira, Gydo C. P. van Zundert, Daniel W. Hogan, James S. Fraser, Daniel A. Keedy, Henry van den Bedem
Summary: The new qFit 3 software automates the analysis of dynamic protein structure data by generating a multi-conformer model, providing important insights for biological research. The software has been improved to run efficiently on small servers, desktops, or laptops. qFit 3 is open-source and available at the specified URL.
Article
Biochemistry & Molecular Biology
Sunbin Deng, Jiaxi Cai, Stephen C. Harrison, Huilin Zhou, Stephen M. Hinshaw
Summary: Successful mitosis relies on the correct attachment of chromosomes to microtubules. The kinetochore plays a crucial role in this process by recognizing specific chromatin and ensuring the formation of only one kinetochore per chromatid at the correct location. The crystal structure of the Cse4 peptide bound to the inner kinetochore Okp1-Ame1 complex provides insights into centromere recognition and the organization of the inner kinetochore.
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
Biochemistry & Molecular Biology
Shuangyue Wang, Zhi Geng, Heng Zhang, Zhun She, Yuhui Dong
Summary: The T6SS is a secretion system that secretes toxic effectors for inter-bacterial competition and host infection. The cognate immunity proteins protect bacteria from their own effectors. PAAR proteins play a crucial role in this process.
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
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
Biochemistry & Molecular Biology
Yan-Hua Li, Hai-Feng Hou, Zhi Geng, Heng Zhang, Zhun She, Yu-Hui Dong
Summary: This study presents the crystal structure of the multi-functional enzyme PBCV1dCD in complex with different nucleotide substrates. The results reveal that PBCV1dCD can deaminate not only dCMP and dCTP, but also dCDP, making it unique among other dCD family proteins. The analysis of the structural basis identifies a key residue, Trp121, which is essential for the deamination and substrate binding ability of PBCV1dCD.
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS
(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)