Article
Chemistry, Multidisciplinary
Sang A. Mun, Jongseo Park, Jung Youn Kang, Taein Park, Minwoo Jin, Jihyeong Yang, Soo Hyun Eom
Summary: EF-hand proteins containing a Ca2+-binding motif are involved in cellular regulation. In addition to Ca2+, these proteins can also interact with other metals such as Mg2+, Pb2+, and Zn2+. EFhd1 and EFhd2 are actin-binding proteins that modulate actin rearrangement through Ca2+-dependent and Ca2+-independent mechanisms. This study shows that the actin-related activities of EFhd1 and EFhd2 may also be regulated by Zn2+ through coordination within their EF-hands.
Article
Biochemistry & Molecular Biology
Alisa A. Vologzhannikova, Marina P. Shevelyova, Alexey S. Kazakov, Andrey S. Sokolov, Nadezhda Borisova, Eugene A. Permyakov, Nikoleta Kircheva, Valya Nikolova, Todor Dudev, Sergei E. Permyakov
Summary: The study investigated the interaction of Sr2+ with Ca2+ binding sites of a canonical EF-hand protein, alpha-parvalbumin, suggesting that Sr2+ and Ca2+ bind to CD/EF sites of alpha-PA with sequential binding processes. Despite lower affinity to Sr2+, alpha-PA competes with Ca2+ for the same EF-hands, inducing similar structural rearrangements. The presence of a secondary Sr2+ binding site(s) may contribute to Sr2+ impact on the functional activity of proteins.
Article
Cell Biology
Noopur Dave, Kaice LaFavers, Gustavo Arrizabalaga
Summary: Calcium signaling plays a crucial role in the regulation of the obligate intracellular parasite Toxoplasma gondii, and a novel EF-hand domain-containing protein, TgEFP1, has been identified in this calcium homeostasis network, localizing to the PLV/ELC and PV. Knockout of TgEFP1 results in faster parasite propagation, hypersensitivity to calcium ionophore-induced egress, and premature natural egress.
Article
Biochemistry & Molecular Biology
Kenji Okumura, Yukie Maruyama, Ryuichi Takase, Bunzo Mikami, Kousaku Murata, Wataru Hashimoto
Summary: The calcium binding EF-hand-like motif in AlgQ2 of Gram-negative Sphingomonas sp. A1 stabilizes the substrate-unbound AlgQ2, but is not required for the complexation of substrate-bound AlgQ2 and AlgM1M2SS.
BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY
(2021)
Article
Biology
Eider Nunez, Frederick Jones, Arantza Muguruza-Montero, Janire Urrutia, Alejandra Aguado, Covadonga Malo, Ganeko Bernardo-Seisdedos, Carmen Domene, Oscar Millet, Nikita Gamper, Alvaro Villarroel, Henry M. Colecraft
Summary: Neuronal K(V)7 channels are highly sensitive to reactive oxygen species, and the S2S3 linker of the voltage sensor plays a crucial role in redox modulation of the channels. Recent structural studies have revealed interactions between this linker and the Ca2+-binding loop of calmodulin, specifically the EF3 hand, which is essential for the signaling. Disrupting Ca2+ binding to EF3 abolishes the oxidation-induced enhancement of K(V)7.4 currents. Furthermore, the loading of EF3 with Ca2+ is critical for the reorientation of the AB fork, which translates the Ca2+ signals.
Article
Biochemistry & Molecular Biology
Emma L. Arevalo-Salina, Joel Osuna, Humberto Flores, Gloria Saab-Rincon
Summary: In this study, researchers investigated the behavior of Calbindin D-9k, a high-affinity modulator protein for Ca2+, and demonstrated that loop and helix II were necessary elements for the conformational change promoted by calcium. The fusion of chimeric motifs to an activity reporter gene indicated that the loop was the minimal element needed to induce a conformational change. The discrepancy between these results was discussed in terms of inter-motif interactions and the involvement of helix I in modulating Ca2+ affinity and restricting motif conformation.
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS
(2021)
Article
Biochemistry & Molecular Biology
Harley King, Sowmya Ajay Castro, Amol Arunrao Pohane, Cynthia M. Scholte, Vincent A. Fischetti, Natalia Korotkova, Daniel C. Nelson, Helge C. Dorfmueller
Summary: Endolysins are phage proteins that interact with bacterial cell walls through enzymatically active domains and cell wall binding domains, with the ability to lyse Gram-positive bacterial cells. They offer a potential alternative to traditional antibiotics, but research on the nature of CBDs and binding epitopes is still limited.
BIOCHEMICAL JOURNAL
(2021)
Article
Nanoscience & Nanotechnology
Jiai Yan, Xiaomei Lyu, Yiming Jiang, Kuan Rei Ng, Ruijin Yang, Feng Zhang, Wei Zhao
Summary: The increasing spread of antibiotic resistance in bacterial pathogens poses a huge threat to global human health. Precise targeting of bacterial pathogens while avoiding collateral damage to healthy tissues has become the overriding goal for bacterial infection treatment. Inspired by the host specificity of bacteriophages, a biomimetic intelligent platform was designed for highly precise photothermal treatment herein.
ACS APPLIED MATERIALS & INTERFACES
(2023)
Article
Parasitology
Muhammad Ehsan, Rui-Si Hu, Jun-Ling Hou, Hany M. Elsheikha, Xiao-Dong Li, Pan-Hong Liang, Xing-Quan Zhu
Summary: The study demonstrates the immunomodulatory effects of a recombinant tegumental calcium-binding EF-hand protein 4 of F. gigantica (rFg-CaBP4) on goat monocytes through various experiments, showing an increase in cytokine transcription levels and major histocompatibility complex (MHC) class-II molecule expression. This sheds light on the roles of calcium-binding EF-hand proteins in host-parasite interaction and the strategies used by F. gigantica to evade host immune responses.
PARASITES & VECTORS
(2021)
Review
Biochemistry & Molecular Biology
Marco Pedretti, Luca Bombardi, Carolina Conter, Filippo Favretto, Paola Dominici, Alessandra Astegno
Summary: Centrins are a family of small proteins containing EF hands found in all eukaryotes and often complexed with centrosome-related structures, displaying diverse cellular functions and large variance in Ca2+ sensing abilities compared to calmodulin (CaM). Current knowledge on centrins from biophysical and structural perspectives emphasizes centrin-target interactions, providing insight into their different functions and contribution to the complexity of Ca2+ signaling cascade. This understanding can help clarify the functional redundancy of centrins and centrin-binding proteins.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Virology
Robert J. Dorosky, Stephanie L. Lola, Haleigh A. Brown, Jeremy E. Schreier, Sheila M. Dreher-Lesnick, Scott Stibitz
Summary: The specific binding characteristics and killing activity of phage endolysin support their potential use in biotechnological applications. The cell wall binding domains (CBD) of lactobacilli phage lysins were characterized and found to exhibit different bindings to LAB strains. The CBD binding assay and the lytic activity assay suggest that these proteins may be useful for potency and purity testing of live biotherapeutic products.
Article
Immunology
Kanhu Charan Das, Ruchishree Konhar, Devendra Kumar Biswal
Summary: Continuous efforts have been made to develop candidate vaccines for tropical fascioliasis in livestock. The study aimed to create a multi-epitope subunit vaccine using calcium-binding proteins from F. gigantica. The vaccine construct was tested for its antigenicity, allergenicity, and physiochemical properties, and docked with toll-like receptor 2 for stability and interaction analysis. The research has implications for F. hepatica as well.
Article
Plant Sciences
Marcelo Daniel Sciorra, Elisa Fantino, Cecilia Eugenia Maria Grossi, Rita Maria Ulloa
Summary: Four members of the potato calcium-dependent protein kinase (CDPK) family exhibit structural and functional differences, with distinct expressions patterns regulated by various biotic stresses.
PLANT PHYSIOLOGY AND BIOCHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Regur Phanindranath, Digumarthi V. S. Sudhakar, Kumarasamy Thangaraj, Yogendra Sharma
Summary: Centrin-1, a Ca2+ sensor protein, plays a crucial role in cell division and microtubule organizing center in eukaryotes. Through an in-depth analysis of individual EF-hand motifs, it is found that all four EF-hand motifs of centrin-1 bind both Ca2+ and Mg2+. The lack of intermotif communication and independent filling mode of Ca2+ explain the moderate affinity binding characteristic of centrin-1.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Zhen Zhang, Francois P. Douillard, Hannu Korkeala, Miia Lindstrom
Summary: This study developed a method to specifically isolate Clostridium botulinum Group I strains by assessing the host specificity of the cell wall binding domains (CBD) of phage lysins. This method has potential applications in laboratory diagnostics of botulism and food safety risk assessment.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Physical
Xuan Zhang, Yiping Jiang, Qianqian Chen, Sheng Dong, Yingang Feng, Zhiqi Cong, Sason Shaik, Binju Wang
Summary: Understanding the molecular basis of controlled H2O2 activation is crucial for peroxide-driven catalysis by metalloenzymes. This study demonstrates the significant influence of substrates and dual-functional small molecules (DFSM) on H2O2 activation, with hydrogen bonding networks playing key roles in dictating the process.
Correction
Biophysics
Weibin Gong, Xingzhe Yao, Qihui Liang, Yufeng Tong, Sarah Perrett, Yingang Feng
BIOMOLECULAR NMR ASSIGNMENTS
(2022)
Article
Biochemistry & Molecular Biology
Yong Liu, Lingxuan Li, Cong Yu, Fuxing Zeng, Fengfeng Niu, Zhiyi Wei
Summary: The study predicts the complex structures of Myo2-GTD and its cargo adaptors using ColabFold and summarizes the versatile cargo-recognition mechanisms of Myo2 by comparing the interaction details of multiple complexes. The research provides an efficient solution for studying protein-protein interactions.
Article
Chemistry, Medicinal
Meixi He, Yingang Feng, Yi Wang, Mengchun Cheng, Xiaozhe Zhang, Lihua Zhang
Summary: In this study, a cysteine-rich glycation peptide, termed glycation-bidentatide (Gly-BTP), was discovered in the Chinese herb Achyranthes bidentata Blume. Cell bioactivity assay results suggested that Gly-BTP might have potential therapeutic effects and provide neuroprotection in NMDA-induced HT22 murine hippocampal neuronal cells. The discovery of Gly-BTP contributes to the understanding of the role of CRPs in neuroprotection.
Correction
Biochemistry & Molecular Biology
Jie Ren, Hongwei Yao, Wanhui Hu, Sarah Perrett, Weibin Gong, Yingang Feng
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
Jie Chen, Sheng Dong, Wenhan Fang, Yiping Jiang, Zhifeng Chen, Xiangquan Qin, Cong Wang, Haifeng Zhou, Longyi Jin, Yingang Feng, Binju Wang, Zhiqi Cong
Summary: We report the selective hydroxylation of alkylbenzenes using an engineered P450 peroxygenase driven by a dual-functional small molecule (DFSM). By combining different P450BM3 variants with DFSMs, more than half of all possible hydroxylated products were obtained from each substrate with high regioselectivity (>99%), enantioselectivity (>99% ee), and high total turnover numbers (up to 80963). Synergistic effects between exogenous DFSMs and the protein environment controlled the regio- and enantioselectivity, as revealed by crystal structure analysis, molecular dynamic simulations, and theoretical calculations. This work has implications for exogenous-molecule-modulated enzymatic regiodivergent and enantioselective hydroxylation with potential applications in synthetic chemistry.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Multidisciplinary
Xiling Wang, Xiaodan Lin, Yiping Jiang, Xiangquan Qin, Nana Ma, Fuquan Yao, Sheng Dong, Chuanfei Liu, Yingang Feng, Longyi Jin, Mo Xian, Zhiqi Cong
Summary: The peroxidase activity of cytochrome P450BM3 was increased through protein engineering by introducing site-directed mutations of key active-site residues. This allowed for efficient regulation of substrate access, leading to a decrease in monooxygenation activity and an increase in peroxidase activity. The P450 peroxidase system was successfully applied for the direct nitration of aromatic compounds and terminal aryl-substituted olefins.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Biochemistry & Molecular Biology
Xuanyan Jia, Leishu Lin, Shun Xu, Lingxuan Li, Zhiyi Wei, Cong Yu, Fengfeng Niu
Summary: This study identified a specific binding interaction between the SH3 domain of ASAP1 and the PRM domain of MICAL1, and revealed the unique structure of the target-binding pocket in ASAP1-SH3. This unique structure was also found in the SH3 domains of GRAF and SKAP1. Furthermore, over 130 proteins with the SH3(AGS)-binding PRM were found in the protein database. Gene ontology analysis suggests that the strong interaction between SH3(AGS)-containing proteins and their targets may play roles in actin cytoskeleton regulation and vesicle trafficking.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Biochemistry & Molecular Biology
Jinsong Xuan, Lingling He, Wen Wen, Yingang Feng
Summary: Biohydrogen production through microbes offers a renewable and abundant hydrogen supply by utilizing raw materials like sunlight, water, and organic waste, thus addressing the issues of energy supply and environmental protection simultaneously.
Review
Chemistry, Physical
Mingzhe Qiu, Sheng Dong, Qiu Cui, Yingang Feng, Jinsong Xuan
Summary: Chiral compounds play an important role in the chemical and pharmaceutical industry, and the production of high enantiopurity chemicals is a major goal in asymmetric catalysis. Enzymatic synthesis, particularly using alpha/beta hydrolases, offers a sustainable and environmentally friendly approach to produce chiral molecules. This review highlights the current understanding of the structures and reaction mechanisms of alpha/beta hydrolases, as well as the efforts in screening and protein engineering to develop biocatalysts for chiral chemicals production. Other strategies, such as whole-cell catalysis and protein immobilization, are also discussed to enhance the performance of alpha/beta hydrolases. The progress in biocatalyst development based on alpha/beta hydrolases will contribute to the green and sustainable development of the chemical and pharmaceutical industry.
Article
Multidisciplinary Sciences
Fengfeng Niu, Yong Liu, Kang Sun, Shun Xu, Jiayuan Dong, Cong Yu, Kaige Yan, Zhiyi Wei
Summary: The study provides insights into the structural and functional regulation of myosin Va, revealing the molecular mechanisms of autoinhibition and activation as well as the specific activation mechanism dependent on multiple cargo adaptors.
Article
Chemistry, Applied
Yuying Zhang, Sheng Dong, Guangning Chen, Siqi Cao, Jingjing Shen, Xuanwei Mei, Qiu Cui, Yingang Feng, Yaoguang Chang, Yanchao Wang, Changhu Xue
Summary: In this study, the structure of GH86 beta-agarase Aga86A_Wa was determined and its methyl-galactose tolerance was investigated. It was found that an accommodation pocket at subsite -1 contributed to the tolerance of methyl-galactose. Similar pockets were also found in two other GH86 enzymes, BuGH86 and BpGH86A, confirming their function in methyl-galactose accommodation. These findings provide insights into the function and mechanism of GH86 agaran degrading enzymes and have implications for the precise preparation of agaran oligosaccharides.
CARBOHYDRATE POLYMERS
(2023)
Review
Biotechnology & Applied Microbiology
Cai You, Ya-Jun Liu, Qiu Cui, Yingang Feng
Summary: GH48 cellulases are widely distributed in cellulolytic microorganisms, especially in the highly efficient cellulose-degrading ruminal system. They hydrolyze cellulose using an inverting mechanism in a processive mode. In addition, GH48 cellulases greatly synergize with endoglucanases to improve cellulose hydrolysis efficiency.
FERMENTATION-BASEL
(2023)
Article
Biology
Su Zhang, Fangfang Wang, Dujuan Zhang, Dongsheng Liu, Wei Ding, Timothy A. Springer, Gaojie Song
Summary: Microneme protein 2 (MIC2) and MIC2-associated protein (M2AP) are essential for the gliding motility and invasion of Toxoplasma gondii. This study reveals the crystal structures of M2AP and its complex with a TSR domain of MIC2 (TSR6). The findings provide insights into the formation and stability of the MIC2-M2AP complex and have implications for developing new therapies against this parasite.
COMMUNICATIONS BIOLOGY
(2023)
Article
Endocrinology & Metabolism
Jia-Le Wang, Xiao-Dong Dou, Jie Cheng, Ming-Xin Gao, Guo-Feng Xu, Wei Ding, Jin-Hui Ding, Yu Li, Si-Han Wang, Zhao-Wei Ji, Xin-Yi Zhao, Tong-Yu Huo, Cai-Fang Zhang, Ya-Meng Liu, Xue-Ying Sha, Jia-Rui Gao, Wen-Hui Zhang, Yong Hao, Cheng Zhang, Jin-Peng Sun, Ning Jiao, Xiao Yu
Summary: This study systematically analyzed the lipid-transmembrane receptor signaling in islet-resident macrophages and identified GPR132-Gi signaling as an important contributor to islet macrophage reprogramming. The researchers successfully designed selective GPR132 antagonists, which could potentially be used for treating refractory diseases such as diabetes.
