Article
Biochemistry & Molecular Biology
Runsha Chen, Xuechun Gao, Ting Nie, Jinhong Wu, Lin Wang, Ali Osman, Yan Feng, Xianghong Li, Yong Zhang
Summary: The crystal structure of the GDSL family esterase EstL5 has been determined, revealing a unique channel connecting the active site pocket and a surface cavity, as well as the functional relevance of this channel to enzyme catalysis. The study provides valuable insights for designing more efficient and robust biocatalysts.
ACTA BIOCHIMICA ET BIOPHYSICA SINICA
(2023)
Article
Biochemistry & Molecular Biology
Yi Zhang, Hai-Tao Ding, Wen-Xin Jiang, Xia Zhang, Hai-Yan Cao, Jing-Ping Wang, Chun-Yang Li, Feng Huang, Xi-Ying Zhang, Xiu-Lan Chen, Yu-Zhong Zhang, Ping-Yi Li
Summary: In this study, a cold-adapted AcXEs, AlAXEase, from an Arctic marine bacterium was characterized, showing high activity and unusual thermostability. The crystal structure revealed a flexible catalytic loop that contributes to the cold adaptation of AlAXEase, shedding light on the cold adaptation mechanisms of AcXEs.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Alice Grieco, Miguel A. Ruiz-Fresneda, Atanasio Gomez-Mulas, Juan Luis Pacheco-Garcia, Isabel Quereda-Moraleda, Angel L. Pey, Jose M. Martin-Garcia
Summary: This study reports the crystal structure of human NQO1 enzyme in covalent complex with PMSF, which unexpectedly does not abolish the enzyme's catalytic activity, indicating that the flexibility of the key residue Tyr128 may not be reduced by the PMSF molecule.
Article
Food Science & Technology
Xi He, Peng Liu, Xiaojian Tang, Ting Wang, Zhenshang Xu, Dongdong Hou, Dan Wu, Ning Han
Summary: In this study, the lp_1002 gene from Lactiplantibacillus plantarum WCFS1 was successfully cloned and overexpressed in L. plantarum WCFS1 strain. The recombinant strain exhibited higher lipase and esterase activities, and significantly reduced ester content during wine fermentation, indicating its potential application in food fermentation.
LWT-FOOD SCIENCE AND TECHNOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Xinchun Ran, Yaoyukun Jiang, Qianzhen Shao, Zhongyue J. Yang
Summary: EnzyKR is a new approach based on a deep learning framework for predicting enantiomeric outcomes in hydrolase-catalyzed kinetic resolution reactions. It automates the selection of enzyme scaffolds for separating a racemic substrate mixture and achieves good prediction performance using a structure-based encoding strategy.
Review
Biochemistry & Molecular Biology
Adamu Idris Matinja, Nor Hafizah Ahmad Kamarudin, Adam Thean Chor Leow, Siti Nurbaya Oslan, Mohd Shukuri Mohamad Ali
Summary: Microorganisms in cold environments use cold-active enzymes to adapt to low temperatures and perform efficient metabolism, which is crucial for industrial processes. However, the lack of complete understanding of the structure and cold adaptation mechanisms of cold-active enzymes hinders their industrial usage.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Analytical
Lei Feng, Ying Deng, Shufan Song, Yanqiu Sun, Jingnan Cui, Xiaochi Ma, Lingling Jin, Yan Wang, Tony D. James, Chao Wang
Summary: This study developed a fluorescence visualization tool to investigate the functional role of gut microbiota associated with obesity and disorders of lipid metabolism.
ANALYTICAL CHEMISTRY
(2022)
Review
Biotechnology & Applied Microbiology
Francesco Degli-Innocenti, Tony Breton, Selene Chinaglia, Ermes Esposito, Marco Pecchiari, Andrea Pennacchio, Alessandro Pischedda, Maurizio Tosin
Summary: Biodegradability standards measure the ultimate biodegradation of polymers by exposing them to natural microbial inoculums. This review discusses the factors that determine whether each inoculum is microbially unique and its relevance in interpreting test results. Based on available evidence, it can be concluded that if a certain polyester shows ultimate biodegradation when exposed to a natural inoculum, it can be considered biodegradable and need not be retested using other inoculums. However, if the polymer does not show ultimate biodegradation, it should be considered recalcitrant until proven otherwise.
Review
Polymer Science
Amber N. Johnson, Daniel E. Barlow, Abigail L. Kelly, Vanessa A. Varaljay, Wendy J. Crookes-Goodson, Justin C. Biffinger
Summary: Natural and synthetic polymers degrade over time due to changes in bonding, with microorganisms using chemical processes to release carbon sources. Polyesters and polyurethanes, making up 35% of global polymer production, are susceptible to degradation by enzymes released by microorganisms. This review focuses on recent research on biodegradation of these polymers.
POLYMER INTERNATIONAL
(2021)
Article
Biochemistry & Molecular Biology
Andre Mong Jie Ng, Hongfang Zhang, Giang Kien Truc Nguyen
Summary: The study introduces a new method for detecting lipolytic enzyme activity which is 1000-fold more sensitive than previous methods, allowing for detection of as low as 5pg and 180pg of lipolytic activity. By adjusting buffering capacity, the detection sensitivity can be controlled, facilitating screening of both high and low abundance lipolytic enzymes. Coupled with liquid chromatography-mass spectrometry, this method provides a useful tool for sensitive detection and identification of lipolytic enzymes.
Article
Multidisciplinary Sciences
Kathryn H. Gunn, Saskia B. Neher
Summary: Lipoprotein lipase (LPL) hydrolyzes triglycerides from circulating lipoproteins, and the structure of an active LPL dimer reveals a hydrophobic pore adjacent to the active site. The dimerization interface and pore may play a role in substrate specificity and acyl chain release from LPL.
NATURE COMMUNICATIONS
(2023)
Article
Microbiology
Dennis Sander, Yanfei Yu, Premankur Sukul, Sina Schaekermann, Julia E. Bandow, Trinetra Mukherjee, Subhra Kanti Mukhopadhyay, Lars Leichert
Summary: Lipolytic enzymes are important biocatalysts produced by various organisms and widely used in industrial applications. A new metaproteomics approach was used to identify a novel thermo- and solvent-stable lipolytic enzyme, DS-007, which exhibited high hydrolytic activity with substrates of shorter chain length.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Chemistry, Multidisciplinary
Jing Wang, Zhongliao Wang, Jinfeng Zhang, Siang-Piao Chai, Kai Dai, Jingxiang Low
Summary: This study explores the modulation of surface-active sites in CdCNS/CdS photocatalyst by employing a non-noble metal cocatalyst NiS, leading to enhanced photocatalytic performance and improved hydrogen production rate.
Article
Biochemistry & Molecular Biology
Leslie Lam, Marc A. Ilies
Summary: Esterases and lipases can process esters used as drugs and prodrugs, affecting their pharmacokinetics and biodistribution. The activity of these enzymes is highly dependent on the lipophilicity of the substrate, with classic esterases showing decreased activity and lipases generally displaying increased activity as lipophilicity increases.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biotechnology & Applied Microbiology
Taresh P. Khobragade, Seongseon Yu, Hyunsang Jung, Mahesh D. Patil, Sharad Sarak, Amol D. Pagar, Hyunwoo Jeon, Somin Lee, Pritam Giri, Geon-Hee Kim, Sung-Su Cho, Seong-Hwa Park, Hye-Jung Park, Heung M. Kang, Sung R. Lee, Myeong S. Lee, Jeong H. Kim, In S. Choi, Hyungdon Yun
Summary: A bienzymatic cascade was developed for the synthesis of beta-amino acids as an intermediate for sitagliptin production. Recombinant Escherichia coli were used for whole-cell biotransformation to achieve high conversion rates. The desired product was obtained with excellent conversions in small-scale reactions, and sitagliptin phosphate was synthesized with high yield and purity.
BIOTECHNOLOGY AND BIOENGINEERING
(2021)
Article
Biochemical Research Methods
Lulu Wang, Tingting Bu, Xue Bai, Shanru He, Jie Zhang, Liming Jin, Baoquan Liu, Yuesheng Dong, Nam Chul Ha, Chunshan Quan, Ki Hyun Nam, Yongbin Xu
Summary: The crystal structure of a domain-swapped dimeric MalE from Salmonella enterica (named SeMalE) in complex with maltopentaose is reported for the first time, showing a distinct structure from typical monomeric MalE family members. These findings provide new insights into maltodextrin-binding MalE proteins.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2022)
Article
Biochemical Research Methods
Ki Hyun Nam, Sehan Park, Jaehyun Park
Summary: This study reports the purification, crystallization, and preliminary XFEL diffraction analysis of endo-1,4-beta-xylanase from the fungus Hypocrea virens. The enzyme was overexpressed in Escherichia coli and spontaneously crystallized after purification. Preliminary XFEL diffraction data were collected and solved the phasing problem to obtain the initial model structure of the enzyme.
ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS
(2022)
Article
Chemistry, Multidisciplinary
Ki Hyun Nam
Summary: This study determined the crystal structures of human lysozyme in its native and N-acetyl-alpha-D-glucosamine (alpha-D-NAG)-bound forms. The results revealed the interactions between human lysozyme and alpha-D-NAG, providing insights into the sugar recognition mechanism of human lysozyme during the immune response.
APPLIED SCIENCES-BASEL
(2022)
Article
Biochemistry & Molecular Biology
Ki Hyun Nam
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Xue Bai, Jing Lan, Shanru He, Tingting Bu, Jie Zhang, Lulu Wang, Xiaoling Jin, Yuanchao Mao, Wanting Guan, Liying Zhang, Ming Lu, Hailong Piao, Inseong Jo, Chunshan Quan, Ki Hyun Nam, Yongbin Xu
Summary: In this study, a new enzyme named YqdH was discovered to convert aldehydes to alcohols using NAD(P)H, with different structural conformation and preferred metal ion compared to the known TmBDH. The crystal structures and key residues of YqdH were investigated, providing better understanding of the molecular function of BDH.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Tingting Bu, Jing Lan, Inseong Jo, Jie Zhang, Xue Bai, Shanru He, Xiaoling Jin, Lulu Wang, Yu Jin, Xiaoyu Jin, Liying Zhang, Hailong Piao, Nam-Chul Ha, Chunshan Quan, Ki Hyun Nam, Yongbin Xu
Summary: This study discovered that the pathogen Fusobacterium nucleatum, which is associated with destructive periodontal disease and colorectal cancer, has four genes that produce hydrogen sulfide, which helps protect against oxidative stress. By examining the structure and conducting inhibitor screening, two natural compounds were found to selectively inhibit the production of hydrogen sulfide by Fn1419. This research revealed the molecular mechanism of Fn1419 and identified a new potential inhibitor.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Chemistry, Multidisciplinary
Jangwoo Kim, Ki Hyun Nam
Summary: When X-rays pass through a material, heat is generated and transferred, which can affect the temperature of the sample and the experimental environment in serial crystallography experiments. This study investigated radiation damage and measured the level of heating near the X-ray interaction point. The findings provide valuable information for obtaining more accurate experimental parameters.
APPLIED SCIENCES-BASEL
(2023)
Article
Chemistry, Multidisciplinary
Ki Hyun Nam
Summary: Microfocusing X-rays are used to enhance the diffraction limit and quality of data collected from crystal samples, but they can also cause radiation damage. This study investigated radiation damage in single-point data collection using microfocusing X-rays and a thaumatin crystal. The results showed that diffraction intensity decreased significantly after the crystal rotation exceeded 180 degrees. Radiation damage led to increased temperature factors in certain amino acids of thaumatin, but it was minimal when the X-ray exposure time was 100 ms. Minimal radiation damage was observed in electron density maps when using minimal data that met specific parameters. These findings contribute to our understanding of radiation damage in macromolecules and have practical applications in data collection.
APPLIED SCIENCES-BASEL
(2023)
Editorial Material
Crystallography
Ki Hyun Nam
Article
Biotechnology & Applied Microbiology
Stefan Brott, Ki Hyun Nam, Francois Thomas, Theresa Dutschei, Lukas Reisky, Maike Behrens, Hanna C. C. Grimm, Gurvan Michel, Thomas Schweder, Uwe T. T. Bornscheuer
Summary: Marine algae produce complex polysaccharides that can be degraded by marine heterotrophic bacteria using carbohydrate-active enzymes. The degradation of the red algal polysaccharide porphyran involves oxidative demethylation, catalyzed by cytochrome P450 monooxygenase and its redox partners. Genes encoding zinc-dependent alcohol dehydrogenases (ADHs) were found near the genes for key enzymes in this process. The physiological role of these marine ADHs was investigated and it was found that they are required for the utilization of a specific substrate, G6Me.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2023)
Review
Chemistry, Analytical
Ki Hyun Nam
Summary: Fluorescent proteins (FPs) are optical probes that track the functions of genetically encoded target molecules. The fluorescence intensity of FPs can be changed by external factors such as pH or metal ions. FPs can also be used as probes to measure metal ion levels through metal-induced fluorescence quenching.
Article
Crystallography
Ki Hyun Nam
Summary: Serial crystallography (SX) has been used to visualize the molecular dynamics of macromolecules at room temperature with minimal radiation damage. However, the simultaneous growth of multiple crystals in large-scale batch crystallization has not been well-studied. In this study, the real-time monitoring of large-scale crystal growth during batch crystallization was reported using lysozyme as a model protein. The findings contribute to a better understanding of the phenomenon of multiple crystal growths in large-scale batch crystallization.
JOURNAL OF CRYSTAL GROWTH
(2023)
Article
Multidisciplinary Sciences
In Jung Kim, Soo Rin Kim, Kyoung Heon Kim, Uwe T. Bornscheuer, Ki Hyun Nam
Summary: This study presents functional and structural analysis of TsaGH11, an endo-1,4-beta-xylanase from Thermoanaerobacterium saccharolyticum. TsaGH11 is a thermophilic enzyme that exhibits high catalytic performance and flexibility in substrate binding. The findings expand our understanding of GH11 structural flexibility and have potential applications in industrial biomass degradation.
SCIENTIFIC REPORTS
(2023)
Review
Chemistry, Physical
In Jung Kim, Soo Rin Kim, Uwe T. Bornscheuer, Ki Hyun Nam
Summary: This review provides an overview of the importance of GH11 xylanases in bioprocessing and the key factors influencing their application. The engineering methods for achieving optimal pH shifting of GH11 xylanases in industrial applications are discussed, providing guidance for future research.
Article
Biochemistry & Molecular Biology
Ki Hyun Nam
Summary: This study investigates the structural dynamics of four loops above the substrate-binding pocket of beta-glucosidase (Bgl) enzyme. The flexibility of the loops and their role in substrate recognition were examined in Thermoanaerobacterium saccharolyticum. The findings demonstrate that the diversity in the conformation and structure of the loops contributes to the functional diversity of Bgl enzymes.
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)
