Article
Biochemistry & Molecular Biology
Rui Xiang, Junchao Wang, Wenjuan Xu, Min Zhang, Mingzhu Wang
Summary: Akkermansia muciniphila is a beneficial microorganism in the human gut that is closely related to intestinal health, with membrane proteins encoding proteins related to pilus formation. The crystal structure of Amuc_1102 reveals an immunoglobulin (Ig)-like fold and trimeric assembly, providing insights into type IV pilus formation in A. muciniphila.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Tobias Irmscher, Yvette Roske, Igor Gayk, Valentin Dunsing, Salvatore Chiantia, Udo Heinemann, Stefanie Barbirz
Summary: Pathogenic microorganisms often reside in glycan-based biofilms, which are regulated by bacterial communities through small-molecule signaling. Extracellular glycosidases play a crucial role in the reorganization or degradation of the glycan matrix.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
Article
Multidisciplinary Sciences
Lucas Gewehr, Benedikt Junglas, Ruven Jilly, Johannes Franz, Wenyu Eva Zhu, Tobias Weidner, Mischa Bonn, Carsten Sachse, Dirk Schneider
Summary: The dynamin-like protein SynDLP in the cyanobacterium Synechocystis sp. PCC 6803 forms ordered oligomers and interacts with negatively charged thylakoid membrane lipids independently of nucleotides. The structural characteristics of SynDLP suggest it to be a bacterial ancestor of eukaryotic dynamin.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Nina M. van Sorge, Daniel A. Bonsor, Liwen Deng, Erik Lindahl, Verena Schmitt, Mykola Lyndin, Alexej Schmidt, Olof R. Nilsson, Jaime Brizuela, Elena Boero, Eric J. Sundberg, Jos A. G. van Strijp, Kelly S. Doran, Bernhard B. Singer, Gunnar Lindahl, Alex J. McCarthy
Summary: Streptococcus agalactiae, also known as group B Streptococcus (GBS), is a major cause of neonatal sepsis in humans. In a recent study, it was found that the surface-expressed beta protein of GBS binds to human CEACAM1 and CEACAM5 receptors, with the crystal structure revealing a novel IgI3 fold. This discovery suggests a potentially widely applicable mechanism for bacteria to target CEACAMs.
Article
Cell Biology
Gang Du, Linlin Zhao, Yumei Zheng, Anissa Belfetmi, Tiantian Cai, Boying Xu, Karen Heyninck, Kim Van Den Heede, Marie-Ange Buyse, Pietro Fontana, Michael Bowman, Lih-Ling Lin, Hao Wu, James Jeiwen Chou
Summary: Members of the TNFRSF can be activated to induce death of cancer cells or stimulate proliferation of immune cells. The self-association structure of the ectodomain of DR5-ECD, a representative member of TNFRSF, has been determined by NMR. The preligand association of DR5 serves an autoinhibitory role and disruption of the preligand cluster can enhance receptor signaling. This mechanism provides a new opportunity for developing agonistic molecules by targeting receptor preligand clustering.
Article
Biology
Amit K. Gandhi, Zhen-Yu J. Sun, Yu-Hwa Huang, Walter M. Kim, Chao Yang, Gregory A. Petsko, Nicole Beauchemin, Richard S. Blumberg
Summary: This study investigates the oligomer structure of human CEACAM1 protein and reveals that homodimerization mediated by the GFCC' face enables flexible interactions with the ABED face. Structural modeling and NMR studies suggest that carbohydrate side-chain modifications do not hinder oligomerization. Furthermore, the presence of a conserved metal ion binding site on the G strand of the FG loop enhances oligomerization. These findings provide biophysical insights into the mechanisms of CEACAM1 oligomerization beyond dimerization.
COMMUNICATIONS BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Biao Ruan, Yanan He, Yingwei Chen, Eun Jung Choi, Yihong Chen, Dana Motabar, Tsega Solomon, Richard Simmerman, Thomas Kauffman, D. Travis Gallagher, John Orban, Philip N. Bryan
Summary: In order to better understand how protein structure is encoded by amino acid sequence, we created mutational pathways connecting three common folds and analyzed the stability and function of the proteins at high sequence-identity intersections. By embedding the amino acid sequence encoding a smaller fold into a larger fold and designing a new sequence compatible with two sets of native interactions, we generated protein pairs with different folds. Furthermore, the substitution of a single amino acid in the larger folds can switch both their fold and function. These findings shed light on the ambiguity in the protein folding code and demonstrate the possibility of abrupt fold switching in the evolution of new protein structures.
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Multidisciplinary
Margaret M. Braasch-Turi, Jordan T. Koehn, Kateryna Kostenkova, Cameron Van Cleave, Jacob W. Ives, Heide A. Murakami, Dean C. Crick, Debbie C. Crans
Summary: Lipoquinones, such as ubiquinones and menaquinones, are essential lipid components involved in energy production. This study investigates the location, orientation, and conformation of UQ-2 and MK-2 in model membrane systems. The results suggest that the folding and location of lipoquinones are influenced by the headgroup structure and polarity.
FRONTIERS IN CHEMISTRY
(2022)
Article
Materials Science, Multidisciplinary
Xiaobo Zhao, Shanshan Li, Jingchun Jiang, Junyuan Bai, Hongbo Xie, Hucheng Pan, Yanzhong Tian, Yuping Ren, Changqing Teng, Lu Wu, Gaowu Qin
Summary: Understanding the atomistic details of phase transformations in high-entropy alloys is crucial for tailoring materials with desired properties. This study confirmed the occurrence of unusual omega and omega-like transformations in a refractory high-entropy alloy, leading to the formation of hierarchical microstructures. The atomic-level mechanisms of these transformations were revealed using advanced microscopy techniques and first-principles calculations. The insights gained from this study provide theoretical guidance for designing advanced high-entropy alloys with specific properties.
Article
Multidisciplinary Sciences
Zhaotong Cong, Li-Nan Chen, Honglei Ma, Qingtong Zhou, Xinyu Zou, Chenyu Ye, Antao Dai, Qing Liu, Wei Huang, Xianqiang Sun, Xi Wang, Peiyu Xu, Lihua Zhao, Tian Xia, Wenge Zhong, Dehua Yang, H. Eric Xu, Yan Zhang, Ming-Wei Wang
Summary: This study reports the cryo-EM structures of GLP-1R bound to an ago-allosteric modulator, revealing how the modulator executes positive allosteric modulation by enhancing both agonist binding and G protein coupling.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Yan Liu, Rui Wang, Zhigang Wang, Da Li, Tian Cui
Summary: In this study, the authors report the prediction of a nitrogen-rich iodine nitride compound (IN6) with an unusual twelve-fold coordination of the iodine atom under high pressure. They discovered the existence of a hypercoordinated IN6 compound composed of N-6 rings and an unusual iodine-nitrogen covalent bond network using particle swarm optimization method and first-principles calculations. The formation of twelve-fold iodine hypercoordination is facilitated by the presence of high pressure and N-6 rings. The findings also suggest that halogen elements with lower atomic numbers have weaker valence expansion propensity in halogen nitrides.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Zhaohui Jin, Bowen Yu, Ying Huang
Summary: Oxpecker, a homolog of Rhino/HP1D, is expressed exclusively in Drosophila ovaries and belongs to the Heterochromatin Protein 1 family, similar to Rhino. It recognizes piRNA clusters enriched with the heterochromatin marker H3K9me3 and recruits Deadlock and Moonshiner to promote transcription of piRNA precursors, thereby protecting the genome. The crystal structure of the Oxp chromodomain in complex with the histone H3K9me3 peptide has been solved, revealing its dimerization and stronger binding ability to H3K9me3 compared to Rhino. Furthermore, Oxp and Rhino can form a heterodimer, suggesting its involvement in transposon silencing in the absence of CSD.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Woo-Chan Ahn, Yan An, Kyung-Mo Song, Kwang-Hyun Park, Su-jin Lee, Byung-Ha Oh, Jong-Tae Park, Eui-Jeon Woo
Summary: Maltodextrin glucosidase (MalZ) is an important enzyme in the maltose utilization pathway in Escherichia coli. The crystal structure of MalZ reveals its substrate binding and hydrolysis mechanism, providing insights for protein engineering.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2022)
Article
Engineering, Environmental
Xueqin Mu, Xiangyao Gu, Ru Zhou, Lei Li, Guofei Lu, Changyun Chen, Suli Liu, Shichun Mu, Wei Chen
Summary: By precisely tuning the geometric and phase structure of noble metal-based heterostructure nanomaterials, an effective way has been found to induce fast hydrogen evolution reaction kinetics in alkaline media. The in-situ metastable interface of five-fold twinned Ru supported on vertically oriented Cu nanosheets shows unprecedented overpotentials and high stability, making it one of the best alkaline HER catalysts for Ru-based catalysts. This structure also possesses nearly 100% Faradaic yield and effectively promotes the formation of heterostructure nanosheet arrays with abundant active sites, enhancing the alkaline hydrogen evolution kinetics.
CHEMICAL ENGINEERING JOURNAL
(2022)
Article
Biochemistry & Molecular Biology
Mathias Percipalle, Yamanappa Hunashal, Jan Steyaert, Federico Fogolari, Gennaro Esposito
Summary: Two nanobodies, Nb23 and Nb24, have been shown to inhibit the self-aggregation of beta 2-microglobulin. The structure of Nb23 was modeled and validated using experimental data, showing differences in CDR3 loop orientation compared to Nb24, which may affect target antigen affinity or complex stability.
Article
Biochemistry & Molecular Biology
Do-Hee Kim, Sung-Min Kang, Sung-Min Baek, Hye-Jin Yoon, Dong Man Jang, Hyoun Sook Kim, Sang Jae Lee, Bong-Jin Lee
Summary: Staphylococcus aureus, a pathogenic bacterium with global distribution, has been the focus of recent research on developing novel antibiotics based on its toxin-antitoxin systems. This study investigates the structure and function of the PemIK system in S. aureus, providing valuable information for the discovery and development of antibiotics that inhibit the direct binding between PemI and PemK.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Dentistry, Oral Surgery & Medicine
Bongkun Choi, Ji-Eun Kim, Si-On Park, Eun-Young Kim, Soyoon Oh, Hyuksu Choi, Dohee Yoon, Hyo-Jin Min, Hyung-Ryong Kim, Eun-Ju Chang
Summary: Sphingosine-1-phosphate (S1P) regulates the osteogenic differentiation of dental pulp stem cells (DPSCs) through its expression and AKT activation. Inflammatory conditions lead to an elevation of S1P, which inhibits the osteogenic capacity of DPSCs.
INTERNATIONAL JOURNAL OF ORAL SCIENCE
(2022)
Article
Dentistry, Oral Surgery & Medicine
So Mi Jeon, Je Sun Lim, Su Hwan Park, Hyung Joon Kim, Hyung-Ryong Kim, Jong-Ho Lee
Summary: PD-L1 and PD-1 signaling negatively regulate the osteo-/odontogenic differentiation of hDPSCs. Blocking PD-1 signaling enhances osteo-/odontogenic differentiation of hDPSCs, suggesting it as a potential therapeutic strategy.
INTERNATIONAL JOURNAL OF ORAL SCIENCE
(2022)
Article
Biotechnology & Applied Microbiology
Dongyun Kim, Hyeongjin Lee, Geum-Hwa Lee, The-Hiep Hoang, Hyung-Ryong Kim, Geun Hyung Kim
Summary: The goal of this study was to fabricate bioactive cell-laden biocomposites supplemented with bone-derived decellularized extracellular matrix (dECM) with calcium phosphate ceramic and assess their effect on the osteogenic and odontogenic differentiation of human dental pulp stem cells (hDPSCs). The dECM-based biocomposites exhibited significantly higher osteogenic and odontogenic activities compared to collagen-based biocomposites, indicating their potential as promising biomaterials for dental tissue engineering.
BIOENGINEERING & TRANSLATIONAL MEDICINE
(2022)
Article
Nanoscience & Nanotechnology
Do Hoon Lee, Jun Chang Yang, Joo Yong Sim, Heemin Kang, Hyung-Ryong Kim, Steve Park
Summary: A soft bending sensor based on the inverse pyramid structure is able to suppress microcracks and open cracks gradually, which enables it to have a wide dynamic range of bending strain, high gauge factor, and high linearity. It can capture instantaneous changes in strain and vibrations and differentiate bending direction. This technology has the potential to advance wearable healthcare monitoring electronics and enable proprioceptive soft robotics.
ACS APPLIED MATERIALS & INTERFACES
(2022)
Article
Chemistry, Physical
Huijung Kim, Kubra Solak, Yoojoong Han, Yeon-Woo Cho, Kyeong-Mo Koo, Chang-Dae Kim, Zhengtang Luo, Hyungbin Son, Hyung-Ryong Kim, Ahmet Mavi, Tae-Hyung Kim
Summary: Electrically controlled mRNA delivery via a conductive hybrid film can guide osteogenic differentiation of human adipose-derived mesenchymal stem cells. This platform, capable of loading various types of RNAs, shows promise as a new nucleic acid delivery tool for stem cell-based therapeutics.
Article
Biochemical Research Methods
Sujung Hong, Jingu Lee, Jieun Moon, Eunji Kong, Jehwi Jeon, Yeon Soo Kim, Hyung-Ryong Kim, Pilhan Kim
Summary: In this study, non-invasive longitudinal cellular-level in vivo imaging of the oral mucosa was achieved using micro GRIN lens-based rotatory side-view confocal endomicroscopy. This technique allows for visualization of various immune cells, pericytes, nerve cells, and lymphatic and vascular endothelial cells, providing insights into the complex pathophysiology of oral mucosal diseases.
BIOMEDICAL OPTICS EXPRESS
(2022)
Article
Chemistry, Multidisciplinary
Keondo Lee, Donghyeon Lee, Sangwon Baek, Jihan Kim, Jaehyun Park, Sang Jae Lee, Sehan Park, Jangwoo Kim, Jong-Lam Lee, Wan Kyun Chung, Yunje Cho, Ki Hyun Nam
Summary: This study investigated the radiation damage caused by an XFEL to PDMS and PI materials, commonly used in sample delivery devices. The results showed different structural damages in PDMS and PI films, providing insights for developing applications of these materials in XFEL studies.
APPLIED SCIENCES-BASEL
(2022)
Review
Cell Biology
Rashedul Alam, Mohammad Fazlul Kabir, Hyung-Ryong Kim, Han-Jung Chae
Summary: Cancer cells adapt autophagy as a protective mechanism to counter stress, but the role of autophagy in tumorigenesis and drug resistance is complex and controversial. Accelerated autophagy poses a challenge for anticancer therapy, and addressing noncanonical ER stress or UPR components is an effective approach to suppress cytoprotective autophagy.
Article
Infectious Diseases
Ki-Young Lee, Bong-Jin Lee
Summary: Type II toxin-antitoxin (TA) modules are commonly found in prokaryotes and play roles in maintaining cell survival under adverse conditions. The antitoxins' intrinsically disordered regions (IDRs) have been shown to have helical conformations and function as central hubs in regulatory protein interaction networks. However, the biological and pathogenic functions of these IDRs are not well discussed compared to those in eukaryotic proteomes. This article focuses on the versatile roles of IDRs in type II antitoxins and provides insights into the discovery of new antibiotic candidates.
Meeting Abstract
Biophysics
Bong Jin Lee
BIOPHYSICAL JOURNAL
(2023)
Article
Biochemistry & Molecular Biology
Hoyoung Kim, Taehyun Lim, Go Eun Ha, Jee-Young Lee, Jun-Woo Kim, Nienping Chang, Si Hyun Kim, Ki Hun Kim, Jaeick Lee, Yongju Cho, Byeong Wook Kim, Alva Abrahamsson, Sung Hwan Kim, Hyo-Ji Kim, Sehan Park, Sang Jae Lee, Jaehyun Park, Eunji Cheong, B. Moon Kim, Hyun-Soo Cho
Summary: This study utilizes X-ray free electron laser technology to determine the structural characteristics of the corticotropin-releasing hormone receptor 1 protein complexes and develops potential antidepressant antagonist compounds.
EXPERIMENTAL AND MOLECULAR MEDICINE
(2023)
Article
Nanoscience & Nanotechnology
Su Yeong Kim, Jeong-Chan Lee, Giwan Seo, Jun Hee Woo, Minho Lee, Jaewook Nam, Joo Yong Sim, Hyung-Ryong Kim, Edmond Changkyun Park, Steve Park
Summary: The recent global spread of COVID-19 emphasizes the need for rapid and accessible diagnostic testing. Nanomaterial thin-film-based immunosensors show promise due to their mass manufacturability, on-site detection, and high sensitivity. However, understanding the relationship between thin-film properties and sensor performance is lacking. This study systematically analyzes the correlations between various thin-film properties and sensitivity, achieving optimal performance for diagnosing COVID-19 in early stages.
Article
Biochemistry & Molecular Biology
Hye-Ock Jang, Tea-Young Ahn, Ji-Min Ju, Soo-Kyung Bae, Hyung-Ryong Kim, Da-Sol Kim
Summary: This study found that Psoralea corylifolia extracts and bakuchiol can promote odontogenic differentiation in human dental pulp stem cells. These findings may contribute to future research on dentin regeneration.
CURRENT ISSUES IN MOLECULAR BIOLOGY
(2022)
