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Crystal enigma: Understanding diverse protein conformational dynamics, ligand selectivity and interaction in multi-space group crystals using computational modelling

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Results in Chemistry 2025年 16卷

作者： Mfeka, Mbalenhle Onisuru, Olalekan Pandian, Ramesh Sayed, Yasien Khoza, Thandeka Achilonu, Ikechukwu Department of Biochemistry School of Life Sciences College of Agriculture Engineering & Science University of KwaZulu-Natal Pietermaritzburg 3209 South Africa Protein Structure-Function and Research Laboratory School of Molecular and Cell Biology Faculty of Science University of the Witwatersrand Braamfontein Johannesburg 2000 South Africa

Empirical structural methods have been instrumental in drug design, but they often fall short of capturing protein dynamics. To address this limitation, computer-aided drug design (CADD) is essential. Given that Schistosoma bovis 28 kDa-Glutathione S-Transferase (Sb28GST) is a promising anti-schistosome drug target, a careful selection of crystal structure space groups used for CADD is emphasized in this study. Sb28GST was successfully overexpressed and purified to grow protein crystals with a resolution of 2.4 Å in an orthorhombic space group system. High-throughput virtual screening (HTVS) of a flavonoid compound was performed on monoclinic 8ALS and orthorhombic 8BHZ Sb28GST to identify potential ligands. The results showed a diverse selection of hit compounds with apigenin 7-O-(2G-rhamnosyl)gentiobioside (apigenin) being the common ligand. However, quercetin-3-O-Beta-D-Glucose-7-O-Beta-D-Gentiobioside (quercetin) showed the highest affinity to 8ALS with a Glide gscore of −15.66 kcal/mol. Also, 500-ns molecular dynamics simulations (MDS) of the 8ALS-Sb28GST and 8BHZ-Sb28GST apo systems, as well as their corresponding apigenin and quercetin complexes, show two distinct trajectories which reveal significant differences in their dynamic behaviour and also showed varying interactions. This highlights the need for collective assessment of protein polymorphs to comprehensively understand protein dynamics. The inhibitory potency of apigenin and quercetin via a GSH-CDNB conjugation assay confirmed that they significantly reduced the specific enzyme activity of Sb28GST with both ligands having half-maximal inhibitory concentration (IC₅₀) of 0.13 mM. Extrinsic fluorescence studies and thermal shift assay indicated that these compounds bind to the hydrophobic H-site and allosteric L-site at the dimer interface and have a minimal effect on the protein's thermal stability. © 2025 The Authors

关键词： Binding Empirical, ligand High-throughput virtual screening Molecular dynamics simulations Polymorphs Schistosoma bovis

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DNA nanoflower Oligo-PROTAC for targeted degradation of FUS to treat neurodegenerative diseases

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Nature Communications 2025年第1期16卷 1-15页

作者： Ge, Ruixin Chen, Miao Wu, Sijin Huang, Sirui Zhou, Ping Cao, Minghui Zhang, Fan Zang, Jinzhi Zhu, Yigao Li, Jingrui Ni, Guilin Yang, Zhihao Li, Qingchao Pan, Wei Zhang, Liang Liu, Min Xuan, Chenghao Yu, Haiyang Zhou, Jun Xie, Songbo Center for Cell Structure and Function Collaborative Innovation Center of Cell Biology in Universities of Shandong College of Life Sciences Shandong Normal University Jinan China School of Life Sciences and Medicine Shandong University of Technology Zibo China Wisdom Lake Academy of Pharmacy Xi’an Jiaotong-Liverpool University Suzhou China Jiangsu Province Higher Education Key Laboratory of Cell Therapy Nanoformulation (Construction) Xi’an Jiaotong-Liverpool University Suzhou China The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics Department of Biochemistry and Molecular Biology Tianjin Medical University Tianjin China Research Center of Translational Medicine Jinan Central Hospital Affiliated to Shandong First Medical University Jinan China Laboratory of Tissue Homeostasis Haihe Laboratory of Cell Ecosystem Tianjin China Department of Neuroscience Genentech South San Francisco San Francisco CA United States State Key Laboratory of Medicinal Chemical Biology Tianjin Key Laboratory of Protein Science College of Life Sciences Nankai University Tianjin China Department of Ophthalmology Laboratory of Molecular Ophthalmology and Tianjin Key Laboratory of Ocular Trauma Ministry of Education International Joint Laboratory of Ocular Diseases Tianjin Institute of Eye Health and Eye Diseases China-UK “Belt and Road” Ophthalmology Joint Laboratory Tianjin Medical University General Hospital Tianjin China

Oligonucleotide-based medicine faces challenges in efficiently crossing the blood-brain barrier and rapidly reducing toxic proteins. To address these challenges, here we establish an integrated modality, brain-penetrant DNA nanoflowers incorporated with oligonucleotide-based proteolysis targeting chimeras. Using FUS as a proof-of-concept, mutations of which cause frontotemporal dementia and amyotrophic lateral sclerosis, we demonstrate that a FUS-engaging RNA oligonucleotide crosslinked to a ligand for Cereblon efficiently degrade FUS and its cytoplasmic disease-causing mutants through a ubiquitin-proteasomal pathway. The DNA nanoflower contains hundreds of oligonucleotide binding sites and transferrin receptor-engaging aptamers, allowing efficient loading of the oligonucleotide-based degrader and engaging transferrin receptors for brain delivery. A single dose intravenous injection of this modality reaches brain parenchyma within 2 h and degrades 80% FUS protein there, sustained for two weeks without noticeable toxicity. DNA nanoflower oligonucleotide-based degrader is a therapeutic strategy for neurodegenerative diseases that leverages the advantages of designer oligonucleotides and targeted protein degradation. © The Author(s) 2025.

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Cucumeropsis mannii seed oil shields against cyclophosphamide-induced hepatorenal toxicity by modulating redox imbalance and iNOS/IL-β1 signalling in rats

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Heliyon 2025年第2期11卷 e41624页

作者： Agbara, Amaka Cecilia Eze, Ejike Daniel Offor, Christian Emeka Afodun, Adam Moyosore Ekpono, Ezebuilo Ugbala Agu, Peter Chinedu Aloke, Chinyere Ezeani, Nkeiru Nwaamaka Ikuomola, Emmanuel Orire Etukudo, Ekom Monday Fasogbon, Ilemobayo Victor Musyoka, Angela Mumbua Aja, Patrick Maduabuchi Department of Biochemistry Faculty of Science Ebonyi State University Abakaliki Nigeria Department of Biochemistry Faculty of Biomedical Sciences Kampala International University Uganda Department of Physiology School of Medicine Kabale University Kabale Uganda Department of Anatomy and Cell Biology Faculty of Health Sciences Busitema University Uganda Department of Science Laboratory Technology Biochemistry Option Federal Polytechnic Oko Anambra State Nigeria Department of Medical Biochemistry Faculty of Basic Medical Sciences College of Medicine Alex-Ekwueme Federal University Ndufu-Alike Ikwo Ebonyi State Nigeria Protein Structure-Function and Research Unit School of Molecular and Cell Biology Faculty of Science University of the Witwatersrand Braamfontein Johannesburg 2050 South Africa Department of Physiology Faculty of Biomedical Sciences Kampala International University Uganda Department of Human Anatomy Faculty of Biomedical Sciences Kampala International University Uganda

This study aimed to determine whether C. mannii seed oil (CMSO) could shield rats from cyclophosphamide-induced hepatorenal toxicity. The focus was on its antioxidant and anti-inflammatory properties. We randomly assigned thirty-six (36) male Wistar rats into six groups of six rats each. Groups A and B served as normal and negative controls, respectively. Group C, the standard control, was administered 300 mg/kg body weight (bw) of Omega 3 oil for 27 days, followed by 100 mg/kg bw of cyclophosphamide on day 28. Group D, E, and F received 5, 2.5, and 1.5 ml/kg b.w. of CMSO for 27 days, then 100 ml/kg b.w. of cyclophosphamide on day 28. We measured the body weights of the experimental rats every week. Rats of all groups were sacrificed on day 30 and collected blood for biochemical analysis using standard methods. The phytochemical constituents were determined by the spectrophotometric method. The phytochemical study of CMSO indicated the relative composition of constituents(mg/100g) as phenols (30 %), tannins (20 %), flavonoids (18 %), terpenoids (15 %), glycosides (10 %), alkaloids (5 %), and HCN (2 %) in Cucumeropsis mannii seed oil. When cyclophosphamide was given to Wistar albino rats, it greatly decreased the activities of catalase (CAT) and superoxide dismutase (SOD), but it increased the activities of iNOS and the levels of MDA and IL-1β. Cyclophosphamide increased ALT (52.3 U/L), AST (48.7 U/L), ALP (46.5 U/L), total bilirubin (1.4 mg/dL), conjugated bilirubin (0.8 mg/dL), creatinine (0.8 mg/dL), urea (45.6 mg/dL), and BUN (15.7 mg/dL), with a reduction in the albumin (4.8 g/dL) level. Cyclophosphamide administration also caused hepatocellular necrosis, inflammatory leukocyte infiltration, tubular necrosis, and proteinaceous deposits in Bowman's space in the kidney. However, combining CMSO and Omega 3 oils significantly restored the altered histology architecture, antioxidant, inflammatory markers, and liver and kidney function parameters to levels comparable

关键词： C. mannii seed oil cyclophosphamide Liver and kidney toxicity Prophylactic efficacy

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Cover Image, Volume 88, Issue 4

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proteins: structure, function, and Bioinformatics 2020年第4期88卷

作者： Lan Lan Minli Xing Maithri Kashipathy Justin Douglas Philip Gao Kevin Battaile Robert Hanzlik Scott Lovell Liang Xu Department of Molecular Biosciences The University of Kansas Lawrence Kansas Bio-NMR Core Facility NIH COBRE in Protein Structure and Function The University of Kansas Lawrence Kansas Protein Structure Laboratory NIH COBRE in Protein Structure and Function The University of Kansas Lawrence Kansas Protein Production Group NIH COBRE in Protein Structure and Function The University of Kansas Lawrence Kansas IMCA-CAT Hauptman Woodward Medical Research Institute Argonne Illinois Department of Medicinal Chemistry The University of Kansas Lawrence Kansas Department of Radiation Oncology The University of Kansas Cancer Center Kansas City Kansas

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structures of the glucocorticoid-bound adhesion receptor GPR97-Go complex

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Nature 2021年第7843期589卷 620-626页

作者： Yu-Qi Ping Chunyou Mao Peng Xiao Ru-Jia Zhao Yi Jiang Zhao Yang Wen-Tao An Dan-Dan Shen Fan Yang Huibing Zhang Changxiu Qu Qingya Shen Caiping Tian Zi-Jian Li Shaolong Li Guang-Yu Wang Xiaona Tao Xin Wen Ya-Ni Zhong Jing Yang Fan Yi Xiao Yu H Eric Xu Yan Zhang Jin-Peng Sun CAS Key Laboratory of Receptor Research Center for Structure and Function of Drug Targets Shanghai Institute of Materia Medica Chinese Academy of Sciences Shanghai China. Department of Physiology and Pathophysiology School of Basic Medical Sciences Peking University Key Laboratory of Molecular Cardiovascular Science Ministry of Education Beijing China. Key Laboratory Experimental Teratology of the Ministry of Education Department of Biochemistry and Molecular Biology School of Basic Medical Sciences Cheeloo College of Medicine Shandong University Shandong China. Department of Biophysics and Department of Pathology of Sir Run Run Shaw Hospital Zhejiang University School of Medicine Hangzhou China. Zhejiang Laboratory for Systems and Precision Medicine Zhejiang University Medical Center Hangzhou China. Key Laboratory Experimental Teratology of the Ministry of Education Department of Physiology School of Basic Medical Sciences Cheeloo College of Medicine Shandong University Shandong China. State Key Laboratory of Proteomics Beijing Proteome Research Center National Center for Protein Sciences Beijing Beijing Institute of Lifeomics Beijing China. School of Medicine Tsinghua University Beijing China. Key Laboratory of Molecular Cardiovascular Science Ministry of Education Peking University Beijing China. The Key Laboratory of Infection and Immunity of Shandong Province Department of Pharmacology School of Basic Medical Sciences Shandong University Shandong China. CAS Key Laboratory of Receptor Research Center for Structure and Function of Drug Targets Shanghai Institute of Materia Medica Chinese Academy of Sciences Shanghai China. eric.xu@***. Department of Biophysics and Department of Pathology of Sir Run Run Shaw Hospital Zhejiang University School of Medicine Hangzhou China. zhang_yan@***. Zhejiang Laboratory for Systems and Precision Medicine Zhejiang University Medical Center Hangzhou China. zhang_yan@zju.edu.cn. Zhejiang Provincial Key Laboratory of Immu

Adhesion G-protein-coupled receptors (GPCRs) are a major family of GPCRs, but limited knowledge of their ligand regulation or structure is available. Here we report that glucocorticoid stress hormones activate adhesion G-protein-coupled receptor G3 (ADGRG3; also known as GPR97), a prototypical adhesion GPCR. The cryo-electron microscopy structures of GPR97-G complexes bound to the anti-inflammatory drug beclomethasone or the steroid hormone cortisol revealed that glucocorticoids bind to a pocket within the transmembrane domain. The steroidal core of glucocorticoids is packed against the 'toggle switch' residue W, which senses the binding of a ligand and induces activation of the receptor. Active GPR97 uses a quaternary core and HLY motif to fasten the seven-transmembrane bundle and to mediate G protein coupling. The cytoplasmic side of GPR97 has an open cavity, where all three intracellular loops interact with the G protein, contributing to the high basal activity of GRP97. Palmitoylation at the cytosolic tail of the G protein was found to be essential for efficient engagement with GPR97 but is not observed in other solved GPCR complex structures. Our work provides a structural basis for ligand binding to the seven-transmembrane domain of an adhesion GPCR and subsequent G protein coupling.

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Variation in Polyamine Content among 12 Pollinated Wheat Genotypes under Drought Stress Condition

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Open Journal of Geology 2017年第8期7卷 1094-1109页

作者： Mahdi Seyedsalehi Parisa Sharifi Ombretta Paladino Gassan Hodaifa Elba C. Villegas Randa M. Osman Department of Environmental Engineering Science and Research Branch Islamic Azad University Tehran Iran Department of Agronomy Faculty of Agriculture Urmia University Urmia Iran Department of Civil Chemical and Environmental Engineering Università di Genova Genoa Italy Department of Molecular Biology and Biochemical Engineering Chemical Engineering Area University of Pablo de Olavide Seville Spain Laboratory of Function-Structure and Protein Engineering Center for Research on Biotechnology Autonomous University of Morelos State (UAEM) Cuernavaca Mexico Department of Chemical Engineering and Pilot Plant National Research Centre Cairo Egypt

The present work aims to study the drought stress effects on polyamine content and its relationship with growth and development in seeds, during cell division (from the beginning and until 17 days after pollination) and grain filling (until reaching the physiological maturity) stages. Factorial experiment based on Randomized Complete Block (RCB) design was carried out with three replications. Two factors of the experiment were considered: the level of irrigation (irrigation without and with drought stress during cell division stage and with drought stress during grain filling stage) and the level of wheat genotype (drought-resistant, semi-resistant and sensitive genotypes). As control treatment, soil moisture content of the field was considered. For drought-stress treatment, the 50% of the soil moisture content in control treatment was established. According to the experimental results, Putrescine content value is higher in control treatment which develops seeds of drought-resistant genotypes than that are registered for semi-resistant and sensitive genotypes. Both drought stress treatments induced significant rises in putrescine amount in the different genotypes of the study. The rises of putrescine content in sensitive and semi-resistant genotypes, however, were higher than in resistant ones, and the highest rise in putrescine content appeared in manning semi-resistant genotype during the stage of grain filling (27 days after pollination). Exerting drought stress in both stages of cell division and grain filling led to significant increase in spermine and spermidine contents of developing seeds of entire genotypes of the study. The highest spermidine content during grain filling stage occurred in sensitive genotypes of Shark and Tevee’s, and the lowest occurred in semi-resistant genotype of Sabalan. The highest spermine content during cell division stage, though, happened in semi-resistant genotype of manning. In fact, spermine and spermidine act as analogous to p

关键词： Polyamines Drought Wheat Randomized Complete Block (RCB)

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Author Correction: structure of human GABAB receptor in an inactive state

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Nature 2020年第7818期583卷 E29页

作者： Jinseo Park Ziao Fu Aurel Frangaj Jonathan Liu Lidia Mosyak Tong Shen Vesna N Slavkovich Kimberly M Ray Jaume Taura Baohua Cao Yong Geng Hao Zuo Yongjun Kou Robert Grassucci Shaoxia Chen Zheng Liu Xin Lin Justin P Williams William J Rice Edward T Eng Rick K Huang Rajesh K Soni Brian Kloss Zhiheng Yu Jonathan A Javitch Wayne A Hendrickson Paul A Slesinger Matthias Quick Joseph Graziano Hongtao Yu Oliver Fiehn Oliver B Clarke Joachim Frank Qing R Fan Department of Pharmacology Columbia University New York NY USA. Department of Biochemistry and Molecular Biophysics Columbia University New York NY USA. NIH West Coast Metabolomics Center University of California Davis Davis CA USA. Department of Environmental Health Sciences Columbia University New York NY USA. Nash Family Department of Neuroscience Friedman Brain Institute Icahn School of Medicine at Mount Sinai New York NY USA. Key Laboratory of Receptor Research Center for Structure and Function of Drug Targets Shanghai Institute of Materia Medica Chinese Academy of Sciences Shanghai China. MRC Laboratory of Molecular Biology Cambridge UK. Department of Psychiatry Columbia University New York NY USA. Division of Molecular Therapeutics New York State Psychiatric Institute New York NY USA. Department of Physiology and Cellular Biophysics Columbia University New York NY USA. National Resource for Automated Molecular Microscopy Simons Electron Microscopy Center New York Structural Biology Center New York NY USA. Janelia Research Campus Howard Hughes Medical Institute Ashburn VA USA. Proteomics Shared Resource Herbert Irving Comprehensive Cancer Center Columbia University New York NY USA. Center on Membrane Protein Production and Analysis New York Structural Biology Center New York NY USA. Howard Hughes Medical Institute Department of Pharmacology University of Texas Southwestern Medical Center Dallas TX USA. Department of Physiology and Cellular Biophysics Columbia University New York NY USA. oc2188@cumc.columbia.edu. Department of Anesthesiology and the Irving Institute for Clinical and Translational Research Columbia University New York NY USA. oc2188@cumc.columbia.edu. Department of Biochemistry and Molecular Biophysics Columbia University New York NY USA. jf2192@cumc.columbia.edu. Department of Biological Sciences Columbia University New York NY USA. jf2192@cumc.columbia.edu. Department of Pharmacology Columbia University New Yor

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

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Correction to: Sequence-specific backbone resonance assignments and microsecond timescale molecular dynamics simulation of human eosinophil-derived neurotoxin

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Biomolecular NMR assignments 2018年第2期12卷 365-367页

作者： Donald Gagné Chitra Narayanan Khushboo Bafna Laurie-Anne Charest Pratul K Agarwal Nicolas Doucet INRS-Institut Armand-Frappier Université du Québec 531 Boulevard des Prairies Laval QC H7V 1B7 Canada. Structural Biology Initiative CUNY Advanced Science Research Center New York NY 10031 USA. Graduate School of Genome Science and Technology University of Tennessee Knoxville TN 37996 USA. Computational Biology Institute and Computer Science and Mathematics Division Oak Ridge National Laboratory 1 Bethel Valley Road Oak Ridge TN 37830 USA. Department of Biochemistry Cellular and Molecular Biology University of Tennessee Knoxville TN 37996 USA. INRS-Institut Armand-Frappier Université du Québec 531 Boulevard des Prairies Laval QC H7V 1B7 Canada. nicolas.doucet@iaf.inrs.ca. PROTEO The Québec Network for Research on Protein Function Engineering and Applications Université Laval 1045 Avenue de la Médecine Quebec QC G1V 0A6 Canada. nicolas.doucet@iaf.inrs.ca. GRASP The Groupe de recherche Axé sur la Structure des Protéines McGill University 3649 Promenade Sir William Osler Montreal QC H3G 0B1 Canada. nicolas.doucet@iaf.inrs.ca.

After publication of this article, the authors noticed that a N-C dimension error was unwillingly coded in the 3D NMR spectrum "***" processing script used to perform backbone assignments for this enzyme. The authors noticed that some OBS, CAR and LAB values in the "***" had been switched in the y and z dimensions, probably resulting from a wrong NMRPipe selection when reading the Varian NMR experimental parameters. They have carefully re-processed, re-analyzed, re-assigned, in addition to checking all scripts to evaluate the extent of this processing error on the published assignments. Authors determined that the "***" error resulted in a significant number of incorrect backbone resonance assignments, requiring us to issue corrections in Figs. 2, 3 and 4 of this published manuscript, in addition to Table S1. New versions of these figures and table are provided below. The corresponding BMRB entry has also been revised. The authors note that these modifications do not change the global message, conclusions, and molecular dynamics simulations presented in this article. The authors are grateful to David N. Bernard (INRS) for help with finding and correcting these errors.

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High yield and efficient expression and purification of the human 5-HT3A receptor

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中国药理学报（英文版） 2015年第8期36卷 1024-1032页

作者： Zhong-shan WU Zhi-cheng CUI Hao CHENG Chen FAN Karsten MELCHER Yi JIANG Cheng-hai ZHANG Britton Chance Center for Biomedical Photonics Wuhan National Laboratory for Optoelectronics Huazhong University of Science and Technology Wuhan 430074 China VARI-SIMM Center Center for Structure and Function of Drug Targets CAS-Key Laboratory of Receptor Research Shanghai Institute of Materia Medica Chinese Academy of Sciences Shanghai 201203 China National Center for Protein Science Shanghai State Key Laboratory of Molecular Biology Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Shanghai 201210 China VARI-SIMM Center Center for Structure and Function of Drug Targets CAS-Key Laboratory of Receptor Research Shanghai Institute of Materia Medica Chinese Academy of Sciences Shanghai 201203 China Laboratory of Structural Sciences Van Andel Research Institute Grand Rapids MI 49503 USA

Aim:To establish a method for efficient expression and purification of the human serotonin type 3A receptor (5-HT3A) that is suitable for structural studies.

Aim:To establish a method for efficient expression and purification of the human serotonin type 3A receptor (5-HT_3A) that is suitable for structural studies.

关键词： human 5-HT3A receptor BacMam expression and purification negative stain electron microscopy receptor structure

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Crystallization scale purification of α7 nicotinic acetylcholine receptor from mammalian cells using a BacMam expression system

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中国药理学报（英文版） 2015年第8期36卷 1013-1023页

作者： Hao CHENG Chen FAN Si-wei ZHANG Zhong-shan WU Zhi-cheng CUI Karsten MELCHER Cheng-hai ZHANG VARI-SIMM Center Center for Structure and Function of Drug Targets CAS-Key Laboratory of Receptor Research Shanghai Institute of Materia Medica Chinese Academy of Sciences Shanghai 201203 China National Center for Protein Science Shanghai State Key Laboratory of Molecular Biology Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Shanghai 201210 China VARI-SIMM Center Center for Structure and Function of Drug Targets CAS-Key Laboratory of Receptor Research Shanghai Institute of Materia Medica Chinese Academy of Sciences Shanghai 201203 China Britton Chance Center for Biomedical Photonics Wuhan National Laboratory for Optoelectronics Huazhong University of Science and Technology Wuhan 430074 China Laboratory of Structural Sciences Van Andel Research Institute Grand Rapids MI 49503 USA

Aim:To report our methods for expression and purification of α7 nicotinic acetylcholine receptor (α7-nAChR), a ligand-gated pentameric ion channel and an important drug target.

关键词： α7-nAChR membrane protein receptor expression receptor purification BacMam HEK293F cells

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