Article
Biochemistry & Molecular Biology
Waraporn Auiewiriyanukul, Wataru Saburi, Tomoya Ota, Jian Yu, Koji Kato, Min Yao, Haruhide Mori
Summary: The study found that the Asn258 mutants of BspAG13_31A have significant impacts on the structure and function of the enzyme. N258G/P mutations enhance trisaccharide specificity, the N258P mutation also enhances activity towards sucrose and produces erlose through transglucosylation. N258G shows a higher specificity for transglucosylation with p-nitrophenyl alpha-D-glucopyranoside and maltose.
Article
Biochemistry & Molecular Biology
Marina Ikegaya, Enoch Y. Park, Takatsugu Miyazaki
Summary: Glycoside hydrolase family 31 (GH31) contains a-glycoside hydrolases with different substrate specificities involved in various physiological functions. This study characterized two a-galactosidases, BsGH31_19 and FpGH31_19, and found that they showed high substrate specificity against a-(1?4)-linkages in a-(1?4)-galactobiose and globotriose, unlike other reported GH31 a-galactosidases PsGal31A and MYORG. Structural analyses revealed differences in amino acid residues and dimer interfaces between BsGH31_19 and FpGH31_19 compared to PsGal31A and MYORG, providing insights into the molecular diversity and evolutionary relationships of GH31 a-galactosidases and other a-galactosidase families.
Article
Biochemistry & Molecular Biology
Komal Ghauri, Tjaard Pijning, Nayla Munawar, Hazrat Ali, Muhammad A. Ghauri, Munir A. Anwar, Russell Wallis
Summary: The crystal structure of an inulin-type fructan producing enzyme from the archaeon Halalkalicoccus jeotgali was resolved in this study, revealing unique features compared to previously reported FTFs. The high negative electrostatic surface potential of InuHj likely contributes to its halophilicity. The findings provide targets for future structure-function studies of FTF enzymes, especially those from archaea.
Article
Biotechnology & Applied Microbiology
Guangqi Li, Xuan Zhou, Zhihong Li, Yunpeng Liu, Dongyang Liu, Youzhi Miao, Qun Wan, Ruifu Zhang
Summary: This study characterized and engineered a thermophilic GH10 family xylanase XynAF1 to improve its thermostability, resulting in a 6-fold increase in stability through rational design and saturation mutagenesis. The high-resolution X-ray crystallographic structure of XynAF1 revealed a rigid skeleton contributing to its hyperthermophilic characteristics. The study provides a promising biocatalyst for high-temperature biotechnological applications.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2021)
Article
Polymer Science
Mohammad Asad, Muhammad Nadeem Arshad, Abdullah M. Asiri, Mohammed M. Rahman, Snigdha Kumaran, Mohammed Musthafa Thorakkattil Neerankuzhiyil
Summary: Chitosan-bounded copper (chitosan-Cu) was utilized for the green synthesis of novel ferrocenated spiropyrrolidine hybrids. A one-pot three-component 1,3-dipolar cycloaddition reaction using tyrosine, glycine, and isatin derivatives was employed to form spiropyrrolidines from 1-(4-bromophenyl)-ferrocene-prop-2-en-1-one and azomethine ylides. The synthesized spiropyrrolidines showed good antibacterial activity against Gram-positive and Gram-negative bacterial strains.
Article
Biochemistry & Molecular Biology
Andrea Dali, Thomas Gabler, Federico Sebastiani, Alina Destinger, Paul Georg Furtmueller, Vera Pfanzagl, Maurizio Becucci, Giulietta Smulevich, Stefan Hofbauer
Summary: Coproporphyrin ferrochelatases (CpfCs) are enzymes that catalyze the penultimate step in the coproporphyrin-dependent heme biosynthesis pathway. The discovery of the correct substrate for these ferrochelatases and the characterization of their binding mode provide valuable insights into the iron insertion process. This knowledge is essential for understanding the preconditions and mechanisms of iron insertion in CpfCs.
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
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
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
Salila Pengthaisong, Yanling Hua, James R. Ketudat Cairns
Summary: This study reports mutants of GH116 family glycosynthases, demonstrating their activity and specificity in transferring glucose from alpha-fluoroglucoside to cellobiose acceptor. Structural analysis reveals the complex structures of glycosynthases, providing a foundation for the synthesis of oligosaccharides and glycosides of interest.
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS
(2021)
Article
Biochemistry & Molecular Biology
Shane M. Carey, Sean P. Kearns, Matthew E. Millington, Gregory S. Buechner, Beda E. Alvarez Jr, Leily Daneshian, Brendan Abiskaroon, Maksymilian Chruszcz, Edward L. D'Antonio
Summary: The importance of F337 in TcGlcK was investigated using the hole mutagenesis approach, revealing its key interactions with aromatic tail groups in inhibitor molecules. Mutants retaining activity and structural similarity were obtained, suggesting the possibility of TcHxK existing as a monomer lacking the F337 residue. Similar D-glucosamine inhibitors may bind less strongly to TcHxK due to the absence of van der Waals contacts from residue side chains.
Article
Chemistry, Physical
Meng Huang, Salila Pengthaisong, Ratana Charoenwattanasatien, Natechanok Thinkumrob, Jitrayut Jitonnom, James R. Ketudat Cairns
Summary: This study investigated the importance of glucose-binding residues in GH116 beta-glucosidases through mutagenesis, kinetic characterization, X-ray crystallography, and ONIOM calculations. The mutations significantly affected the enzyme's catalytic properties, and the amino acid residues involved in glucose binding showed strong electrostatic interactions with the substrate. These findings have important implications for the design of inhibitors and the improvement of GH116 enzymes for various applications.
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
Biology
Virginia Kroef, Sabine Ruegenberg, Moritz Horn, Kira Allmeroth, Lena Ebert, Seyma Bozkus, Stephan Miethe, Ulrich Elling, Bernhard Schermer, Ulrich Baumann, Martin Sebastian Denzel
Summary: The hexosamine biosynthetic pathway (HBP) is crucial in metabolism, health, and aging as it produces UDP-GlcNAc. In addition to the known regulation by GFPT, a new regulator, AMDHD2, has been identified that modulates the HBP by its loss leading to increased UDP-GlcNAc levels and HBP activation.
Article
Oceanography
Jiting Jin, Wandong Fu, Miaofei Liao, Baoqin Han, Jing Chang, Yan Yang
JOURNAL OF OCEAN UNIVERSITY OF CHINA
(2017)
Article
Biochemistry & Molecular Biology
Qianqian Lyu, Keke Zhang, Qiaoyun Zhu, Zhijian Li, Yujie Liu, Elisabeth Fitzek, Tanner Yohe, Liming Zhao, Weihua Li, Tao Liu, Yanbin Yin, Weizhi Liu
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS
(2018)
Article
Chemistry, Applied
Jing Qiao, Yuying Liu, Zhiwen Jiang, Yan Yang, Wanshun Liu, Baoqin Han
CARBOHYDRATE POLYMERS
(2018)
Article
Biochemistry & Molecular Biology
Zhiwen Jiang, Zhe Li, Wei Zhang, Yan Yang, Baoqin Han, Wanshun Liu, Yanfei Peng
Article
Biochemistry & Molecular Biology
Pei Zhang, Shirui Zhao, Yaoyao Yu, Huan Wang, Yan Yang, Chenguang Liu
Article
Biochemistry & Molecular Biology
Zhiwen Jiang, Yanan Song, Jing Qiao, Yan Yang, Wei Zhang, Wanshun Liu, Baoqin Han
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2019)
Article
Biochemistry & Molecular Biology
Qianqian Lyu, Keke Zhang, Yanhong Shi, Weihua Li, Xiaotong Diao, Weizhi Liu
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS
(2019)
Article
Food Science & Technology
Xia Pan, Pengyu Liang, Luyao Teng, Yuhao Ren, Jixian Peng, Weizhi Liu, Yan Yang
FOOD SCIENCE & NUTRITION
(2019)
Article
Engineering, Chemical
Lulu Wang, Luyao Teng, Xiaokang Zhang, Xiaohua Liu, Qianqian Lyu, Yan Yang, Weizhi Liu
JOURNAL OF ADHESION SCIENCE AND TECHNOLOGY
(2020)
Article
Biochemical Research Methods
Keke Zhang, Tao Liu, Weizhi Liu, Qianqian Lyu
Summary: The study found that AlyF protein interacts with a long-chain alginate oligosaccharide G6, revealing that its substrate-binding cleft is fully occupied by six sugars. Three specific loops mainly function in binding long substrates (degree of polymerization >4), stabilizing and orienting the substrate in the cleft. These results provide the first possible alginate lyase-substrate binding profile for the rational design of new enzymes for industrial purposes.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2021)
Article
Agriculture, Multidisciplinary
Keke Zhang, Yan Yang, Weidong Wang, Weizhi Liu, Qianqian Lyu
Summary: The study demonstrated that protein engineering of alginate lyase AlyF can alter product distribution, and redesigning sugar-binding affinity can achieve this goal.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2021)
Article
Biology
Keke Zhang, Zhijian Li, Qiaoyun Zhu, Huansheng Cao, Xinxin He, Xiao-Hua Zhang, Weizhi Liu, Qianqian Lyu
Summary: Characterization of PL7 alginate lyase structure and products enables a bioinformatics approach to predict product distribution from the amino acid sequence.
COMMUNICATIONS BIOLOGY
(2022)
Article
Chemistry, Applied
Jing Qiao, Zhiwen Jiang, Yan Yang, Jinhua Chi, Xuesong Qiao, Baoqin Han, Wanshun Liu
CARBOHYDRATE POLYMERS
(2017)
Article
Chemistry, Applied
Ming He, Baoqin Han, Zhiwen Jiang, Yan Yang, Yanfei Peng, Wanshun Liu
CARBOHYDRATE POLYMERS
(2017)
Article
Biochemistry & Molecular Biology
A. Prabakaran, Amit Alexander
Summary: The molecular interactions and mucoadhesive nature of chitosan-coated liposomes with mucin are crucial for the development of an effective drug delivery system. The positively charged SA-CH-LPs showed stronger interaction and better mucoadhesive properties compared to negatively charged SALPs, thereby improving drug retention in the nasal cavity and enhancing therapeutic efficacy.
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS
(2024)
Article
Biochemistry & Molecular Biology
Maryam Noei-Khesht Masjedi, Esmaeil Sadroddiny, Jafar Ai, Saeed Balalaie, Yazdan Asgari
Summary: This study discovered an effective strategy for cargo sorting within exosomes by incorporating an appropriate cleavage site, providing further insight into the potential of exosomes as nano-shuttles bearing therapeutic biomolecules.
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS
(2024)
Article
Biochemistry & Molecular Biology
Pei -Gee Yap, Chee-Yuen Gan
Summary: This study collected the sequences of 128 tyrosinase inhibitory peptides and analyzed their hydrophobicity/hydrophilicity properties and amino acid profiles. Molecular docking analysis was used to investigate the binding interactions between peptides and tyrosinase. The study found that hydrophobic and/or polar neutral properties facilitate or stabilize peptide binding with tyrosinase, and short peptides with cysteine and tyrosine tend to bind to the active site of tyrosinase. These findings provide detailed explanations for the relationship between peptide/amino acid structures and tyrosinase inhibition, as well as potential anti-melanogenesis mechanisms for peptide-based treatments against skin hyperpigmentation.
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS
(2024)
Article
Biochemistry & Molecular Biology
Ye Yang, Hai-Lian Chen, Su Fang Wu, Wei Bao
Summary: The study found that CHMP4B and VPS4A play an important role in reversing GSDMD-mediated pyroptosis by facilitating cell membrane remodeling in endometrial carcinoma.
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS
(2024)
Article
Biochemistry & Molecular Biology
Aya Al Othman, Dmitry Bagrov, Julian M. Rozenberg, Olga Glazova, Gleb Skryabin, Elena Tchevkina, Alexandre Mezentsev, Mikhail Durymanov
Summary: Arc protein is found in glutamatergic neurons of vertebrates and can be transferred between neurons in extracellular vesicles (EVs). In glioma cells, Arc protein is also present in EVs and can facilitate the transfer of mRNA, potentially contributing to tumor progression and affecting synaptic plasticity in cancer patients.
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS
(2024)
Article
Biochemistry & Molecular Biology
Nan Zhang, Meng-yu Shen, Qing-li Meng, Hao-ping Sun, Fang-yi Fan, Hai Yi, Yong-jian Yang
Summary: In this study, it was demonstrated for the first time that FAT1 inhibited AML proliferation by reducing autophagy level. FAT1 achieved this by decreasing the expression of ATG4B, which is related to autophagy. Mechanistically, FAT1 decreased the levels of phosphorylated and intranuclear smad2/3, thus decreasing the activity of the ATG4B gene promoter. It was also found that FAT1 competitively bound to TGF-beta R II, leading to reduced phosphorylation of TGF-beta R I and smad2/3. Knockdown of FAT1 promoted AML autophagy and proliferation in vivo.
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS
(2024)
Article
Biochemistry & Molecular Biology
Oleh Demianchuk, Myroslava Vatashchuk, Dmytro Gospodaryov, Viktoria Hurza, Marian Ivanochko, Vitalii Derkachov, Vladyslav Berezovskyi, Oleh Lushchak, Kenneth B. Storey, Maria Bayliak, Volodymyr I. Lushchak
Summary: This study investigated the effects of a high-fat high-fructose diet (HFFD) on the behavior, energy metabolism, and oxidative stress markers in the cerebral cortex of mice. The results showed that HFFD stimulated locomotion and defecation, while an AKG-supplemented diet had a tendency to promote anxiety-like behavior. Additionally, there were significant differences in glutathione-dependent detoxification and processes related to autophagy between the two diets.
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS
(2024)
Article
Biochemistry & Molecular Biology
Yusaku Chukai, Ginga Ito, Yasuo Miki, Koichi Wakabayashi, Ken Itoh, Eriko Sugano, Hiroshi Tomita, Tomokazu Fukuda, Taku Ozaki
Summary: The study found that mitochondrial calpain-5 plays an important role in the occurrence and development of ischemia-reperfusion injury and is expressed in the human and mouse brains. Targeting the expression or activity of mitochondrial calpain-5 may have significant implications for suppressing inflammation during I/R injuries such as cerebrovascular diseases.
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS
(2024)
Article
Biochemistry & Molecular Biology
Aline Dias da Purificaca, Victor Debbas, Leonardo Yuji Tanaka, Gabriele Veronica de Mello Gabriel, Joao Wosniak Junior, Tiphany Coralie De Bessa, Sheila Garcia-Rosa, Francisco Rafael Martins Laurindo, Percillia Victoria Santos Oliveira
Summary: The ER transmembrane chaperones DNAJB12 and DNAJB14 play important roles in protein folding and ER stress response. They are regulated by thiol redox processes and are involved in ER protein reflux.
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS
(2024)
Article
Biochemistry & Molecular Biology
Ekaterina O. Bryanskaya, Andrey Y. Vinokurov, Angelina I. Dolgikh, Andrey Dunaev, Plamena R. Angelova, Andrey Y. Abramov
Summary: FAD autofluorescence in cells can assess enzymatic activity, and its intensity variations may be related to different cell types and tissues. High levels of FAD autofluorescence can indicate cell pathology and potentially predict the occurrence of apoptosis and necrosis.
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS
(2024)
Article
Biochemistry & Molecular Biology
Rumei Luan, Manyu Luo, Dongyan Ding, Xin Su, Junling Yang
Summary: Zinc deficiency can worsen obesity-related lung damage, and Nrf2 activation is one of the important mechanisms of this protective effect. Regulating zinc homeostasis can contribute to the prevention and treatment of obesity-related lung injury.
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS
(2024)