1
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Rooney J, Rivera-de-Torre E, Li R, Mclean K, Price DR, Nisbet AJ, Laustsen AH, Jenkins TP, Hofmann A, Bakshi S, Zarkan A, Cantacessi C. Structural and functional analyses of nematode-derived antimicrobial peptides support the occurrence of direct mechanisms of worm-microbiota interactions. Comput Struct Biotechnol J 2024; 23:1522-1533. [PMID: 38633385 PMCID: PMC11021794 DOI: 10.1016/j.csbj.2024.04.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 04/07/2024] [Accepted: 04/09/2024] [Indexed: 04/19/2024] Open
Abstract
The complex relationships between gastrointestinal (GI) nematodes and the host gut microbiota have been implicated in key aspects of helminth disease and infection outcomes. Nevertheless, the direct and indirect mechanisms governing these interactions are, thus far, largely unknown. In this proof-of-concept study, we demonstrate that the excretory-secretory products (ESPs) and extracellular vesicles (EVs) of key GI nematodes contain peptides that, when recombinantly expressed, exert antimicrobial activity in vitro against Bacillus subtilis. In particular, using time-lapse microfluidics microscopy, we demonstrate that exposure of B. subtilis to a recombinant saposin-domain containing peptide from the 'brown stomach worm', Teladorsagia circumcincta, and a metridin-like ShK toxin from the 'barber's pole worm', Haemonchus contortus, results in cell lysis and significantly reduced growth rates. Data from this study support the hypothesis that GI nematodes may modulate the composition of the vertebrate gut microbiota directly via the secretion of antimicrobial peptides, and pave the way for future investigations aimed at deciphering the impact of such changes on the pathophysiology of GI helminth infection and disease.
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Affiliation(s)
- James Rooney
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | | | - Ruizhe Li
- Department of Engineering, University of Cambridge, Cambridge, United Kingdom
| | - Kevin Mclean
- Moredun Research Institute, Penicuik Midlothian, United Kingdom
| | | | | | - Andreas H. Laustsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Timothy P. Jenkins
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Andreas Hofmann
- Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Kulmbach, Germany
- Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Somenath Bakshi
- Department of Engineering, University of Cambridge, Cambridge, United Kingdom
| | - Ashraf Zarkan
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Cinzia Cantacessi
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
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2
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Wang X, Gao X, Fan X, Huai Z, Zhang G, Yao M, Wang T, Huang X, Lai L. WUREN: Whole-modal union representation for epitope prediction. Comput Struct Biotechnol J 2024; 23:2122-2131. [PMID: 38817963 PMCID: PMC11137340 DOI: 10.1016/j.csbj.2024.05.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 05/14/2024] [Accepted: 05/14/2024] [Indexed: 06/01/2024] Open
Abstract
B-cell epitope identification plays a vital role in the development of vaccines, therapies, and diagnostic tools. Currently, molecular docking tools in B-cell epitope prediction are heavily influenced by empirical parameters and require significant computational resources, rendering a great challenge to meet large-scale prediction demands. When predicting epitopes from antigen-antibody complex, current artificial intelligence algorithms cannot accurately implement the prediction due to insufficient protein feature representations, indicating novel algorithm is desperately needed for efficient protein information extraction. In this paper, we introduce a multimodal model called WUREN (Whole-modal Union Representation for Epitope predictioN), which effectively combines sequence, graph, and structural features. It achieved AUC-PR scores of 0.213 and 0.193 on the solved structures and AlphaFold-generated structures, respectively, for the independent test proteins selected from DiscoTope3 benchmark. Our findings indicate that WUREN is an efficient feature extraction model for protein complexes, with the generalizable application potential in the development of protein-based drugs. Moreover, the streamlined framework of WUREN could be readily extended to model similar biomolecules, such as nucleic acids, carbohydrates, and lipids.
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Affiliation(s)
| | | | - Xuezhe Fan
- XtalPi Innovation Center, Beijing, China
| | - Zhe Huai
- XtalPi Innovation Center, Beijing, China
| | | | | | | | | | - Lipeng Lai
- XtalPi Innovation Center, Beijing, China
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3
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Sabuakham S, Nasoontorn S, Kongtaworn N, Rungrotmongkol T, Silsirivanit A, Pingaew R, Mahalapbutr P. Anilino-1,4-naphthoquinones as potent mushroom tyrosinase inhibitors: in vitro and in silico studies. J Enzyme Inhib Med Chem 2024; 39:2357174. [PMID: 38814149 PMCID: PMC11141316 DOI: 10.1080/14756366.2024.2357174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 05/14/2024] [Indexed: 05/31/2024] Open
Abstract
Tyrosinase, a pivotal enzyme in melanin synthesis, is a primary target for the development of depigmenting agents. In this work, in vitro and in silico techniques were employed to identify novel tyrosinase inhibitors from a set of 12 anilino-1,4-naphthoquinone derivatives. Results from the mushroom tyrosinase activity assay indicated that, among the 12 derivatives, three compounds (1, 5, and 10) demonstrated the most significant inhibitory activity against mushroom tyrosinase, surpassing the effectiveness of the kojic acid. Molecular docking revealed that all studied derivatives interacted with copper ions and amino acid residues at the enzyme active site. Molecular dynamics simulations provided insights into the stability of enzyme-inhibitor complexes, in which compounds 1, 5, and particularly 10 displayed greater stability, atomic contacts, and structural compactness than kojic acid. Drug likeness prediction further strengthens the potential of anilino-1,4-naphthoquinones as promising candidates for the development of novel tyrosinase inhibitors for the treatment of hyperpigmentation disorders.
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Affiliation(s)
- Sahachai Sabuakham
- Department of Biochemistry, Center for Translational Medicine, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Sutita Nasoontorn
- Department of Biochemistry, Center for Translational Medicine, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Napat Kongtaworn
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok, Thailand
| | - Thanyada Rungrotmongkol
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok, Thailand
- Center of Excellence in Structural and Computational Biology, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Atit Silsirivanit
- Department of Biochemistry, Center for Translational Medicine, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Ratchanok Pingaew
- Department of Chemistry, Faculty of Science, Srinakharinwirot University, Bangkok, Thailand
| | - Panupong Mahalapbutr
- Department of Biochemistry, Center for Translational Medicine, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
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4
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Kuo BJ, Lin SC, Tu YF, Huang PH, Lo YC. Study of individual domains contributing to MALT1 dimerization in BCL10-independent and dependent assembly. Biochem Biophys Res Commun 2024; 717:150029. [PMID: 38714015 DOI: 10.1016/j.bbrc.2024.150029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 04/17/2024] [Accepted: 04/28/2024] [Indexed: 05/09/2024]
Abstract
The CARMA-BCL10-MALT1 (CBM) signalosome functions as a pivotal supramolecular module, integrating diverse receptor-induced signaling pathways to regulate BCL10-dependent NF-kB activation in innate and adaptive immunity. Conversely, the API2-MALT1 fusion protein in t(11; 18)(q21; q21) MALT lymphoma constitutively induces BCL10-independent NF-kB activation. MALT1 dimer formation is indispensable for the requisite proteolytic activity and is critical for NF-kB activation regulation in both scenarios. However, the molecular assembly of MALT1 individual domains in CBM activation remains elusive. Here we report the crystal structure of the MALT1 death domain (DD) at a resolution of 2.1 Å, incorporating reconstructed residues in previously disordered loops 1 and 2. Additionally, we observe a conformational regulation element (CRE) regulating stem-helix formation in NLRPs pyrin (PYD) within the MALT1 DD structure. The structure reveals a stem-helix-mediated dimer further corroborated in solution. To elucidate how the BCL10 filament facilitates MALT1 dimerization, we reconstitute a BCL10-CARD-MALT1-DD-IG1-IG2 complex model. We propose a N+7 rule for BCL10-dependent MALT1 dimerization via the IG1-IG2 domain and for MALT1-dependent cleavage in trans. Biochemical data further indicates concentration-dependent dimerization of the MALT1 IG1-IG2 domain, facilitating MALT1 dimerization in BCL10-independent manner. Our findings provide a structural and biochemical foundation for understanding MALT1 dimeric mechanisms, shedding light on potential BCL10-independent MALT1 dimer formation and high-order BCL10-MALT1 assembly.
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Affiliation(s)
- Bai-Jiun Kuo
- Department of Biotechnology and Bioindustry Sciences, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan, 70101, Taiwan
| | - Su-Chang Lin
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Yi-Fan Tu
- Department of Biotechnology and Bioindustry Sciences, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan, 70101, Taiwan; Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Po-Hui Huang
- Department of Biotechnology and Bioindustry Sciences, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan, 70101, Taiwan
| | - Yu-Chih Lo
- Department of Biotechnology and Bioindustry Sciences, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan, 70101, Taiwan.
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5
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Deng C, Wang X, Wang T, Liu W, Yuan X, Huang Y, Cao S. Virtual screening and molecular growth guide the design of inhibitors for the influenza virus drug-resistant mutant M2-V27A/S31N. J Biomol Struct Dyn 2024; 42:5253-5267. [PMID: 37424098 DOI: 10.1080/07391102.2023.2233026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 06/09/2023] [Indexed: 07/11/2023]
Abstract
The influenza A virus matrix protein 2 (AM2) protein is a proton-gated, proton-selective ion channel essential for influenza replication that has been identified as an antiviral target. The drug-resistance of the M2-V27A/S31N strain, which has been growing more prevalent in recent years and has the potential to spread globally, prevents current amantadine inhibitors from having the desired impact. In this study, we compiled the most common influenza A virus strains from 2001-2020 from the U.S. National Center for Biotechnology Information database and hypothesized that M2-V27A/S31N would become a common strain. The lead compound ZINC299830590 was screened for M2-V27A/S31N in the ZINC15 database using a pharmacophore model and molecular descriptors. This lead compound was then optimized by molecular growth, which allowed us to identify important amino acid residues and create interactions with them to produce compound 4. Molecular dynamics simulation showed that the complex of compound 4 and M2-V27A/S31N had certain degrees of stability and flexibility. The binding free energy of compound 4 was calculated using the MM/PB(GB)SA method and totaled -106.525 kcal/mol. Finally, physicochemical and pharmacokinetic profiles were predicted using the Absorption, Distribution, Metabolism, Excretion, and Toxicity model, which indicated the good bioavailability of compound 4. These results provide the basis for further in vivo and in vitro studies to demonstrate that compound 4 is a promising drug candidate against M2-V27A/S31N.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Changyong Deng
- Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan, China
| | - Xiaobo Wang
- School of Pharmacy, Xianning Medical College, Hubei University of Science and Technology, Xianning, China
| | - Tangle Wang
- Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan, China
| | - Wei Liu
- Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan, China
| | - Xiaolan Yuan
- Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan, China
| | - Yan Huang
- Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan, China
| | - Shuang Cao
- Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan, China
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6
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Pérez-Pérez ME, Mallén-Ponce MJ, Odriozola-Gil Y, Rubio A, Salas JJ, Martínez-Force E, Pérez-Pulido AJ, Crespo JL. Lipid turnover through lipophagy in the newly identified extremophilic green microalga Chlamydomonas urium. THE NEW PHYTOLOGIST 2024; 243:284-298. [PMID: 38730535 DOI: 10.1111/nph.19811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 04/19/2024] [Indexed: 05/13/2024]
Abstract
Autophagy is a central degradative pathway highly conserved among eukaryotes, including microalgae, which remains unexplored in extremophilic organisms. In this study, we described and characterized autophagy in the newly identified extremophilic green microalga Chlamydomonas urium, which was isolated from an acidic environment. The nuclear genome of C. urium was sequenced, assembled and annotated in order to identify autophagy-related genes. Transmission electron microscopy, immunoblotting, metabolomic and photosynthetic analyses were performed to investigate autophagy in this extremophilic microalga. The analysis of the C. urium genome revealed the conservation of core autophagy-related genes. We investigated the role of autophagy in C. urium by blocking autophagic flux with the vacuolar ATPase inhibitor concanamycin A. Our results indicated that inhibition of autophagic flux in this microalga resulted in a pronounced accumulation of triacylglycerols and lipid droplets (LDs). Metabolomic and photosynthetic analyses indicated that C. urium cells with impaired vacuolar function maintained an active metabolism. Such effects were not observed in the neutrophilic microalga Chlamydomonas reinhardtii. Inhibition of autophagic flux in C. urium uncovered an active recycling of LDs through lipophagy, a selective autophagy pathway for lipid turnover. This study provided the metabolic basis by which extremophilic algae are able to catabolize lipids in the vacuole.
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Affiliation(s)
- María Esther Pérez-Pérez
- Instituto de Bioquímica Vegetal y Fotosíntesis (CSIC-Universidad de Sevilla), 41092, Sevilla, Spain
| | - Manuel J Mallén-Ponce
- Instituto de Bioquímica Vegetal y Fotosíntesis (CSIC-Universidad de Sevilla), 41092, Sevilla, Spain
| | - Yosu Odriozola-Gil
- Instituto de Bioquímica Vegetal y Fotosíntesis (CSIC-Universidad de Sevilla), 41092, Sevilla, Spain
| | - Alejandro Rubio
- Centro Andaluz de Biología del Desarrollo (CABD, UPO-CSIC-JA), Faculty of Experimental Sciences (Genetics Department), University Pablo de Olavide, 41013, Sevilla, Spain
| | - Joaquín J Salas
- Instituto de la Grasa (CSIC), Ctra Utrera Km1, Ed. 46, 41013, Sevilla, Spain
| | | | - Antonio J Pérez-Pulido
- Centro Andaluz de Biología del Desarrollo (CABD, UPO-CSIC-JA), Faculty of Experimental Sciences (Genetics Department), University Pablo de Olavide, 41013, Sevilla, Spain
| | - José L Crespo
- Instituto de Bioquímica Vegetal y Fotosíntesis (CSIC-Universidad de Sevilla), 41092, Sevilla, Spain
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7
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Aute R, Waghela N, Deshmukh MV. Key arginine residues in R2D2 dsRBD1 and dsRBD2 lead the siRNA recognition in Drosophila melanogaster RNAi pathway. Biophys Chem 2024; 310:107247. [PMID: 38663122 DOI: 10.1016/j.bpc.2024.107247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 04/04/2024] [Accepted: 04/16/2024] [Indexed: 05/23/2024]
Abstract
In Drosophila melanogaster, Dcr-2:R2D2 heterodimer binds to the 21 nucleotide siRNA duplex to form the R2D2/Dcr-2 Initiator (RDI) complex, which is critical for the initiation of siRNA-induced silencing complex (RISC) assembly. During RDI complex formation, R2D2, a protein that contains three dsRNA binding domains (dsRBD), senses two aspects of the siRNA: thermodynamically more stable end (asymmetry sensing) and the 5'-phosphate (5'-P) recognition. Despite several detailed studies to date, the molecular determinants arising from R2D2 for performing these two tasks remain elusive. In this study, we have performed structural, biophysical, and biochemical characterization of R2D2 dsRBDs. We found that the solution NMR-derived structure of R2D2 dsRBD1 yielded a canonical α1-β1-β2-β3-α2 fold, wherein two arginine salt bridges provide additional stability to the R2D2 dsRBD1. Furthermore, we show that R2D2 dsRBD1 interacts with thermodynamically asymmetric siRNA duplex independent of its 5'-phosphorylation state, whereas R2D2 dsRBD2 prefers to interact with 5'-P siRNA duplex. The mutation of key arginine residues, R53 and R101, in concatenated dsRBDs of R2D2 results in a significant loss of siRNA duplex recognition. Our study deciphers the active roles of R2D2 dsRBDs by showing that dsRBD1 initiates siRNA recognition, whereas dsRBD2 senses 5'-phosphate as an authentic mark on functional siRNA.
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Affiliation(s)
- Ramdas Aute
- CSIR - Centre for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Uppal Road, Hyderabad 500007, Telangana, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Nilam Waghela
- CSIR - Centre for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Uppal Road, Hyderabad 500007, Telangana, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Mandar V Deshmukh
- CSIR - Centre for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Uppal Road, Hyderabad 500007, Telangana, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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8
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Prakinee K, Lawan N, Phintha A, Visitsatthawong S, Chitnumsub P, Jitkaroon W, Chaiyen P. On the Mechanisms of Hypohalous Acid Formation and Electrophilic Halogenation by Non-Native Halogenases. Angew Chem Int Ed Engl 2024; 63:e202403858. [PMID: 38606607 DOI: 10.1002/anie.202403858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Revised: 03/29/2024] [Accepted: 04/10/2024] [Indexed: 04/13/2024]
Abstract
Enzymatic electrophilic halogenation is a mild tool for functionalization of diverse organic compounds. Only a few groups of native halogenases are capable of catalyzing such a reaction. In this study, we used a mechanism-guided strategy to discover the electrophilic halogenation activity catalyzed by non-native halogenases. As the ability to form a hypohalous acid (HOX) is key for halogenation, flavin-dependent monooxygenases/oxidases capable of forming C4a-hydroperoxyflavin (FlC4a-OOH), such as dehalogenase, hydroxylases, luciferase and pyranose-2-oxidase (P2O), and flavin reductase capable of forming H2O2 were explored for their abilities to generate HOX in situ. Transient kinetic analyses using stopped-flow spectrophotometry/fluorometry and product analysis indicate that FlC4a-OOH in dehalogenases, selected hydroxylases and luciferases, but not in P2O can form HOX; however, the HOX generated from FlC4a-OOH cannot halogenate their substrates. Remarkably, in situ H2O2 generated by P2O can form HOI and also iodinate various compounds. Because not all enzymes capable of forming FlC4a-OOH can react with halides to form HOX, QM/MM calculations, site-directed mutagenesis and structural analysis were carried out to elucidate the mechanism underlying HOX formation and characterize the active site environment. Our findings shed light on identifying new halogenase scaffolds besides the currently known enzymes and have invoked a new mode of chemoenzymatic halogenation.
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Affiliation(s)
- Kridsadakorn Prakinee
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC) Wangchan Valley, Rayong, 21210, Thailand
| | - Narin Lawan
- Department of Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Aisaraphon Phintha
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC) Wangchan Valley, Rayong, 21210, Thailand
| | - Surawit Visitsatthawong
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC) Wangchan Valley, Rayong, 21210, Thailand
| | - Penchit Chitnumsub
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC) Wangchan Valley, Rayong, 21210, Thailand
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA) Thailand Science Park, Pathum Thani, 12120, Thailand
| | - Watcharapa Jitkaroon
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC) Wangchan Valley, Rayong, 21210, Thailand
| | - Pimchai Chaiyen
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC) Wangchan Valley, Rayong, 21210, Thailand
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9
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Jungnickel KEJ, Guelle O, Iguchi M, Dong W, Kotov V, Gabriel F, Debacker C, Dairou J, McCort-Tranchepain I, Laqtom NN, Chan SH, Ejima A, Sato K, Massa López D, Saftig P, Mehdipour AR, Abu-Remaileh M, Gasnier B, Löw C, Damme M. MFSD1 with its accessory subunit GLMP functions as a general dipeptide uniporter in lysosomes. Nat Cell Biol 2024:10.1038/s41556-024-01436-5. [PMID: 38839979 DOI: 10.1038/s41556-024-01436-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 05/07/2024] [Indexed: 06/07/2024]
Abstract
The lysosomal degradation of macromolecules produces diverse small metabolites exported by specific transporters for reuse in biosynthetic pathways. Here we deorphanized the major facilitator superfamily domain containing 1 (MFSD1) protein, which forms a tight complex with the glycosylated lysosomal membrane protein (GLMP) in the lysosomal membrane. Untargeted metabolomics analysis of MFSD1-deficient mouse lysosomes revealed an increase in cationic dipeptides. Purified MFSD1 selectively bound diverse dipeptides, while electrophysiological, isotope tracer and fluorescence-based studies in Xenopus oocytes and proteoliposomes showed that MFSD1-GLMP acts as a uniporter for cationic, neutral and anionic dipeptides. Cryoelectron microscopy structure of the dipeptide-bound MFSD1-GLMP complex in outward-open conformation characterized the heterodimer interface and, in combination with molecular dynamics simulations, provided a structural basis for its selectivity towards diverse dipeptides. Together, our data identify MFSD1 as a general lysosomal dipeptide uniporter, providing an alternative route to recycle lysosomal proteolysis products when lysosomal amino acid exporters are overloaded.
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Affiliation(s)
| | - Océane Guelle
- Saints-Pères Paris Institute for the Neurosciences, Université Paris Cité, Centre National de la Recherche Scientifique, Paris, France
| | - Miharu Iguchi
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
- The Institute for Chemistry, Engineering and Medicine for Human Health, Stanford University, Stanford, CA, USA
| | - Wentao Dong
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
- The Institute for Chemistry, Engineering and Medicine for Human Health, Stanford University, Stanford, CA, USA
| | - Vadim Kotov
- Centre for Structural Systems Biology, Hamburg, Germany
- European Molecular Biology Laboratory Hamburg, Hamburg, Germany
| | - Florian Gabriel
- Centre for Structural Systems Biology, Hamburg, Germany
- European Molecular Biology Laboratory Hamburg, Hamburg, Germany
| | - Cécile Debacker
- Saints-Pères Paris Institute for the Neurosciences, Université Paris Cité, Centre National de la Recherche Scientifique, Paris, France
| | - Julien Dairou
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, CNRS UMR 8601, Université Paris Cité, Paris, France
| | - Isabelle McCort-Tranchepain
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, CNRS UMR 8601, Université Paris Cité, Paris, France
| | - Nouf N Laqtom
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
- The Institute for Chemistry, Engineering and Medicine for Human Health, Stanford University, Stanford, CA, USA
| | - Sze Ham Chan
- Department of Pharmacology, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Akika Ejima
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Kenji Sato
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - David Massa López
- Institute of Biochemistry, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Paul Saftig
- Institute of Biochemistry, Christian-Albrechts-University Kiel, Kiel, Germany
| | | | - Monther Abu-Remaileh
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
- The Institute for Chemistry, Engineering and Medicine for Human Health, Stanford University, Stanford, CA, USA
| | - Bruno Gasnier
- Saints-Pères Paris Institute for the Neurosciences, Université Paris Cité, Centre National de la Recherche Scientifique, Paris, France.
| | - Christian Löw
- Centre for Structural Systems Biology, Hamburg, Germany.
- European Molecular Biology Laboratory Hamburg, Hamburg, Germany.
| | - Markus Damme
- Institute of Biochemistry, Christian-Albrechts-University Kiel, Kiel, Germany.
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10
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Yu B, Wang X, Tan KN, Iwahara J. Influence of an Intrinsically Disordered Region on Protein Domains Revealed by NMR-Based Electrostatic Potential Measurements. J Am Chem Soc 2024; 146:14922-14926. [PMID: 38771003 DOI: 10.1021/jacs.4c03254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Many human proteins possess intrinsically disordered regions containing consecutive aspartate or glutamate residues ("D/E repeats"). Approximately half of them are DNA/RNA-binding proteins. In this study, using nuclear magnetic resonance (NMR) spectroscopy, we investigated the electrostatic properties of D/E repeats and their influence on folded domains within the same protein. Local electrostatic potentials were directly measured for the HMGB1 protein, its isolated D/E repeats, and DNA-binding domains by NMR. The data provide quantitative information about the electrostatic interactions between distinct segments of HMGB1. Due to the interactions between the D/E repeats and the DNA-binding domains, local electrostatic potentials of the DNA-binding domains within the full-length HMGB1 protein were largely negative despite the presence of many positively charged residues. Our NMR data on counterions and electrostatic potentials show that the D/E repeats and DNA have similar electrostatic properties and compete for the DNA-binding domains. The competition promotes dissociation of the protein-DNA complex and influences the molecular behavior of the HMGB1 protein. These effects may be general among the DNA/RNA-binding proteins with D/E repeats.
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Affiliation(s)
- Binhan Yu
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555-1068, United States
| | - Xi Wang
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555-1068, United States
| | - Kyle N Tan
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555-1068, United States
| | - Junji Iwahara
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555-1068, United States
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11
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Oliva B, Velasco J, Leila Berto G, Polikarpov I, Cristante de Oliveira L, Segato F. Recombinant cellobiose dehydrogenase from Thermothelomyces thermophilus: Its functional characterization and applicability in cellobionic acid production. BIORESOURCE TECHNOLOGY 2024; 402:130763. [PMID: 38692377 DOI: 10.1016/j.biortech.2024.130763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 04/10/2024] [Accepted: 04/28/2024] [Indexed: 05/03/2024]
Abstract
The fungus Thermothelomyces thermophilus is a thermotolerant microorganism that has been explored as a reservoir for enzymes (hydrolytic enzymes and oxidoreductases). The functional analysis of a recombinant cellobiose dehydrogenase (MtCDHB) from T. thermophilus demonstrated a thermophilic behavior, an optimal pH in alkaline conditions for inter-domain electron transfer, and catalytic activity on cellooligosaccharides with different degree of polymerization. Its applicability was evaluated to the sustainable production of cellobionic acid (CBA), a potential pharmaceutical and cosmetic ingredient rarely commercialized. Dissolving pulp was used as a disaccharide source for MtCDHB. Initially, recombinant exoglucanases (MtCBHI and MtCBHII) from T. thermophilus hydrolyzed the dissolving pulp, resulting in 87% cellobiose yield, which was subsequently converted into CBA by MtCDHB, achieving a 66% CBA yield after 24 h. These findings highlight the potential of MtCDHB as a novel approach to obtaining CBA through the bioconversion of a plant-based source.
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Affiliation(s)
- Bianca Oliva
- Department of Biotechnology, Lorena School of Engineering, University of São Paulo, Lorena, SP, Brazil
| | - Josman Velasco
- Department of Biotechnology, Lorena School of Engineering, University of São Paulo, Lorena, SP, Brazil; Biological Sciences Department, Universidad de los Andes, Bogotá DC, Colombia
| | - Gabriela Leila Berto
- Department of Biotechnology, Lorena School of Engineering, University of São Paulo, Lorena, SP, Brazil
| | - Igor Polikarpov
- São Carlos Institute of Physics, University of São Paulo, São Carlos, SP, Brazil
| | - Leandro Cristante de Oliveira
- Department of Physics, Institute of Biosciences, Humanities and Exact Sciences (IBILCE) São Paulo State University "Júlio de Mesquita Filho" - Unesp - São José do Rio Preto, SP, Brazil
| | - Fernando Segato
- Department of Biotechnology, Lorena School of Engineering, University of São Paulo, Lorena, SP, Brazil.
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12
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Trofimov YA, Krylov NA, Minakov AS, Nadezhdin KD, Neuberger A, Sobolevsky AI, Efremov RG. Dynamic molecular portraits of ion-conducting pores characterize functional states of TRPV channels. Commun Chem 2024; 7:119. [PMID: 38824263 PMCID: PMC11144267 DOI: 10.1038/s42004-024-01198-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Accepted: 05/06/2024] [Indexed: 06/03/2024] Open
Abstract
Structural biology is solving an ever-increasing number of snapshots of ion channel conformational ensembles. Deciphering ion channel mechanisms, however, requires understanding the ensemble dynamics beyond the static structures. Here, we present a molecular modeling-based approach characterizing the ion channel structural intermediates, or their "dynamic molecular portraits", by assessing water and ion conductivity along with the detailed evaluation of pore hydrophobicity and residue packing. We illustrate the power of this approach by analyzing structures of few vanilloid-subfamily transient receptor potential (TRPV) channels. Based on the pore architecture, there are three major states that are common for TRPVs, which we call α-closed, π-closed, and π-open. We show that the pore hydrophobicity and residue packing for the open state is most favorable for the pore conductance. On the contrary, the α-closed state is the most hydrophobic and always non-conducting. Our approach can also be used for structural and functional classification of ion channels.
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Affiliation(s)
- Yury A Trofimov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Nikolay A Krylov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | | | - Kirill D Nadezhdin
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Arthur Neuberger
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Alexander I Sobolevsky
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Roman G Efremov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.
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13
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Bonanata J. The role of the active site lysine residue on FAD reduction by NADPH in glutathione reductase. Comput Biol Chem 2024; 110:108075. [PMID: 38678729 DOI: 10.1016/j.compbiolchem.2024.108075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 04/01/2024] [Accepted: 04/11/2024] [Indexed: 05/01/2024]
Abstract
Glutathione reductase (GR) is a two dinucleotide binding domain flavoprotein (tDBDF) that catalyzes the reduction of glutathione disulfide to glutathione coupled to the oxidation of NADPH to NADP+. An interesting feature of GR and other tDBDFs is the presence of a lysine residue (Lys-66 in human GR) at the active site, which interacts with the flavin group, but has an unknown function. To better understand the role of this residue, the dynamics of GR was studied using molecular dynamics simulations, and the reaction mechanism of FAD reduction by NADPH was studied using QM/MM molecular modeling. The two possible protonation states of Lys-66 were considered: neutral and protonated. Molecular dynamics results suggest that the active site is more structured for neutral Lys-66 than for protonated Lys-66. QM/MM modeling results suggest that Lys-66 should be in its neutral state for a thermodynamically favorable reduction of FAD by NADPH. Since the reaction is unfavorable with protonated Lys-66, the reverse reaction (the reduction of NADP+ by FADH-) is expected to take place. A phylogenetic analysis of various tDBDFs was performed, finding that an active site lysine is present in different the tDBDFs enzymes, suggesting that it has a conserved biological role. Overall, these results suggest that the protonation state of the active site lysine determines the energetics of the reaction, controlling its reversibility.
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Affiliation(s)
- Jenner Bonanata
- Laboratorio de Química Teórica y Computacional, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Uruguay; Centro de Investigaciones Biomédicas, Universidad de la República, Uruguay.
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14
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Penteado AB, de Oliveira Ribeiro G, Lima Araújo EL, Kato RB, de Melo Freire CC, de Araújo JMG, da Luz Wallau G, Salvato RS, de Jesus R, Bosco GG, Franz HF, da Silva PEA, de Souza Leal E, Goulart Trossini GH, de Lima Neto DF. Binding Evolution of the Dengue Virus Envelope Against DC-SIGN: A Combined Approach of Phylogenetics and Molecular Dynamics Analyses Over 30 Years of Dengue Virus in Brazil. J Mol Biol 2024; 436:168577. [PMID: 38642883 DOI: 10.1016/j.jmb.2024.168577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 04/12/2024] [Accepted: 04/15/2024] [Indexed: 04/22/2024]
Abstract
The Red Queen Hypothesis (RQH), derived from Lewis Carroll's "Through the Looking-Glass", postulates that organisms must continually adapt in response to each other to maintain relative fitness. Within the context of host-pathogen interactions, the RQH implies an evolutionary arms race, wherein viruses evolve to exploit hosts and hosts evolve to resist viral invasion. This study delves into the dynamics of the RQH in the context of virus-cell interactions, specifically focusing on virus receptors and cell receptors. We observed multiple virus-host systems and noted patterns of co-evolution. As viruses evolved receptor-binding proteins to effectively engage with cell receptors, cells countered by altering their receptor genes. This ongoing mutual adaptation cycle has influenced the molecular intricacies of receptor-ligand interactions. Our data supports the RQH as a driving force behind the diversification and specialization of both viral and host cell receptors. Understanding this co-evolutionary dance offers insights into the unpredictability of emerging viral diseases and potential therapeutic interventions. Future research is crucial to dissect the nuanced molecular changes and the broader ecological consequences of this ever-evolving battle. Here, we combine phylogenetic inferences, structural modeling, and molecular dynamics analyses to describe the epidemiological characteristics of major Brazilian DENV strains that circulated from 1990 to 2022 from a combined perspective, thus providing us with a more detailed picture on the dynamics of such interactions over time.
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MESH Headings
- Dengue Virus/genetics
- Dengue Virus/metabolism
- Receptors, Cell Surface/metabolism
- Receptors, Cell Surface/genetics
- Receptors, Cell Surface/chemistry
- Phylogeny
- Molecular Dynamics Simulation
- Humans
- Cell Adhesion Molecules/metabolism
- Cell Adhesion Molecules/genetics
- Cell Adhesion Molecules/chemistry
- Brazil
- Lectins, C-Type/metabolism
- Lectins, C-Type/genetics
- Lectins, C-Type/chemistry
- Evolution, Molecular
- Dengue/virology
- Host-Pathogen Interactions/genetics
- Protein Binding
- Viral Envelope/metabolism
- Receptors, Virus/metabolism
- Receptors, Virus/chemistry
- Receptors, Virus/genetics
- Viral Envelope Proteins/genetics
- Viral Envelope Proteins/metabolism
- Viral Envelope Proteins/chemistry
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Affiliation(s)
- André Berndt Penteado
- School of Pharmaceutical Sciences, University of São Paulo, Department of Pharmacy, Av. Prof. Lineu Prestes, 580, Cidade Universitária, São Paulo, SP 05508-000, Brazil
| | - Geovani de Oliveira Ribeiro
- General-Coordination of Public Health Laboratories, Department of Strategic Coordination and Surveillance in Health and the Environment, Ministry of Health, Brasilia, Brazil; Department of Cellular Biology, University of Brasilia (UNB), Brasilia, Distrito Federal, Brazil
| | - Emerson Luiz Lima Araújo
- General Coordination of Attention to Communicable Diseases in Primary Care of the Department of Comprehensive Care Management of the Secretariat of Primary Health Care of the Ministry of Health (CDTAP/DGCI/SAPS-MS), Brazil
| | - Rodrigo Bentes Kato
- General-Coordination of Public Health Laboratories, Department of Strategic Coordination and Surveillance in Health and the Environment, Ministry of Health, Brasilia, Brazil
| | - Caio Cesar de Melo Freire
- Department of Genetics and Evolution, Centre of Biological and Health Sciences, Federal University of Sao Carlos, PO Box 676, Washington Luis Road, km 235, São Carlos, SP 13565-905, Brazil
| | - Joselio Maria Galvão de Araújo
- Federal University of Rio Grande do Norte, Biosciences Center, Department of Microbiology and Parasitology, Campus Universitário, S/N Lagoa Nova 59078900, Natal, RN, Brazil
| | - Gabriel da Luz Wallau
- Department of Entomology and Bioinformatics Center of the Aggeu Magalhães Institute - FIOCRUZ - IAM, Brazil
| | - Richard Steiner Salvato
- Center for Scientific and Technological Development, State Center for Health Surveillance of Rio Grande do Sul, State Department of Health of Rio Grande do Sul, Porto Alegre, Brazil
| | - Ronaldo de Jesus
- General-Coordination of Public Health Laboratories, Department of Strategic Coordination and Surveillance in Health and the Environment, Ministry of Health, Brasilia, Brazil
| | - Geraldine Goés Bosco
- University of São Paulo, Faculty of Philosophy Sciences and Letters of Ribeirão Preto. Av. Bandeirantes, 3900 Ribeirão Preto, SP, Brazil
| | - Helena Ferreira Franz
- General-Coordination of Public Health Laboratories, Department of Strategic Coordination and Surveillance in Health and the Environment, Ministry of Health, Brasilia, Brazil
| | - Pedro Eduardo Almeida da Silva
- General-Coordination of Public Health Laboratories, Department of Strategic Coordination and Surveillance in Health and the Environment, Ministry of Health, Brasilia, Brazil
| | - Elcio de Souza Leal
- Federal University of Pará, Faculty of Biotechnology, Institute of Biological Sciences, Rua Augusto Corrêa, Guamá, 04039-032 Belem, PA, Brazil
| | - Gustavo Henrique Goulart Trossini
- School of Pharmaceutical Sciences, University of São Paulo, Department of Pharmacy, Av. Prof. Lineu Prestes, 580, Cidade Universitária, São Paulo, SP 05508-000, Brazil
| | - Daniel Ferreira de Lima Neto
- School of Pharmaceutical Sciences, University of São Paulo, Department of Pharmacy, Av. Prof. Lineu Prestes, 580, Cidade Universitária, São Paulo, SP 05508-000, Brazil.
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15
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Oliva B, Zervas A, Stougaard P, Westh P, Thøgersen MS. Metagenomic exploration of cold-active enzymes for detergent applications: Characterization of a novel, cold-active and alkali-stable GH8 endoglucanase from ikaite columns in SW Greenland. Microb Biotechnol 2024; 17:e14466. [PMID: 38829370 PMCID: PMC11146146 DOI: 10.1111/1751-7915.14466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 03/12/2024] [Accepted: 03/20/2024] [Indexed: 06/05/2024] Open
Abstract
Microbial communities from extreme environments are largely understudied, but are essential as producers of metabolites, including enzymes, for industrial processes. As cultivation of most microorganisms remains a challenge, culture-independent approaches for enzyme discovery in the form of metagenomics to analyse the genetic potential of a community are rapidly becoming the way forward. This study focused on analysing a metagenome from the cold and alkaline ikaite columns in Greenland, identifying 282 open reading frames (ORFs) that encoded putative carbohydrate-modifying enzymes with potential applications in, for example detergents and other processes where activity at low temperature and high pH is desired. Seventeen selected ORFs, representing eight enzyme families were synthesized and expressed in two host organisms, Escherichia coli and Aliivibrio wodanis. Aliivibrio wodanis demonstrated expression of a more diverse range of enzyme classes compared to E. coli, emphasizing the importance of alternative expression systems for enzymes from extremophilic microorganisms. To demonstrate the validity of the screening strategy, we chose a recombinantly expressed cellulolytic enzyme from the metagenome for further characterization. The enzyme, Cel240, exhibited close to 40% of its relative activity at low temperatures (4°C) and demonstrated endoglucanase characteristics, with a preference for cellulose substrates. Despite low sequence similarity with known enzymes, computational analysis and structural modelling confirmed its cellulase-family affiliation. Cel240 displayed activity at low temperatures and good stability at 25°C, activity at alkaline pH and increased activity in the presence of CaCl2, making it a promising candidate for detergent and washing industry applications.
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Affiliation(s)
- Bianca Oliva
- Section for Protein Chemistry and Enzyme Technology, Department of Biotechnology and BiomedicineTechnical University of DenmarkLyngbyDenmark
- Present address:
Synthetic and Molecular Biology Laboratory, Department of Biotechnology, Lorena School of EngineeringUniversity of São PauloLorenaSPBrazil
| | - Athanasios Zervas
- Section for Environmental Microbiology, Department of Environmental ScienceAarhus UniversityRoskildeDenmark
| | - Peter Stougaard
- Section for Environmental Microbiology, Department of Environmental ScienceAarhus UniversityRoskildeDenmark
| | - Peter Westh
- Section for Protein Chemistry and Enzyme Technology, Department of Biotechnology and BiomedicineTechnical University of DenmarkLyngbyDenmark
| | - Mariane Schmidt Thøgersen
- Section for Environmental Microbiology, Department of Environmental ScienceAarhus UniversityRoskildeDenmark
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16
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Saura MLP, Cajachagua CL, Balan A, General IJ. Phosphate uptake in PhoX: Molecular mechanisms. Int J Biol Macromol 2024; 269:131993. [PMID: 38705335 DOI: 10.1016/j.ijbiomac.2024.131993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 04/25/2024] [Accepted: 04/28/2024] [Indexed: 05/07/2024]
Abstract
PhoX is a high-affinity phosphate binding protein, present in Xanthomonas citri, a phytopathogen responsible for the citrus canker disease. Performing molecular dynamics simulations and different types of computational analyses, we study the molecular mechanisms at play in relation to phosphate binding, revealing the global functioning of the protein: PhoX naturally oscillates along its global normal modes, which allow it to explore both bound and unbound conformations, eventually attracting a nearby negative phosphate ion to the highly positive electrostatic potential on its surface, particularly close to the binding pocket. There, several hydrogen bonds are formed with the two main domains of the structure. Phosphate creates, in this way, a strong bridge that connects the domains, keeping itself between them, in a tight closed conformation, explaining its high binding affinity.
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Affiliation(s)
- María Luz Perez Saura
- School of Science and Technology, Universidad Nacional de San Martin, 25 de Mayo y Francia, San Martín 1650, Buenos Aires, Argentina
| | - Cindy Lee Cajachagua
- Universidade de São Paulo (USP), Instituto de Ciências Biomédicas II (ICBII), São Paulo,São Paulo, Brazil
| | - Andrea Balan
- Universidade de São Paulo (USP), Instituto de Ciências Biomédicas II (ICBII), São Paulo,São Paulo, Brazil
| | - Ignacio J General
- School of Science and Technology, Universidad Nacional de San Martin, ICIFI and CONICET, 25 de Mayo y Francia, San Martín 1650, Buenos Aires, Argentina.
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17
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Kaya S, Tatar-Yılmaz G, Aktar BSK, Emre EEO. Discovery of New Dual-Target Agents Against PPAR-γ and α-Glucosidase Enzymes with Molecular Modeling Methods: Molecular Docking, Molecular Dynamic Simulations, and MM/PBSA Analysis. Protein J 2024; 43:577-591. [PMID: 38642318 DOI: 10.1007/s10930-024-10196-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/23/2024] [Indexed: 04/22/2024]
Abstract
Type 2 diabetes mellitus (T2DM) has become a serious public health problem both in our country and worldwide, being the most prevalent type of diabetes. The combined use of drugs in the treatment of T2DM leads to serious side effects, including gastrointestinal problems, liver toxicity, hypoglycemia, and treatment costs. Hence, there has been a growing emphasis on drugs that demonstrate dual interactions. Several studies have suggested that dual-target agents for peroxisome proliferator-activated receptor-γ (PPAR-γ) and alpha-glucosidase (α-glucosidase) could be a potent approach for treating patients with diabetes. We aim to develop new antidiabetic agents that target PPAR-γ and α-glucosidase enzymes using molecular modeling techniques. These compounds show dual interactions, are more effective, and have fewer side effects. The molecular docking method was employed to investigate the enzyme-ligand interaction mechanisms of 159 newly designed compounds with target enzymes. Additionally, we evaluated the ADME properties and pharmacokinetic suitability of these compounds based on Lipinski and Veber's rules. Compound 70, which exhibited favorable ADME properties, demonstrated more effective binding energy with both PPAR-γ and α-glucosidase enzymes (-12,16 kcal/mol, -10.07 kcal/mol) compared to the reference compounds of Acetohexamide (-9.31 kcal/mol, -7.48 kcal/mol) and Glibenclamide (-11.12 kcal/mol, -8.66 kcal/mol). Further, analyses of MM/PBSA binding free energy and molecular dynamics (MD) simulations were conducted for target enzymes with compound 70, which exhibited the most favorable binding affinities with both enzymes. Based on this information, our study aims to contribute to the development of new dual-target antidiabetic agents with improved efficacy, reduced side effects, and enhanced reliability for diabetes treatment.
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Affiliation(s)
- Süleyman Kaya
- Department of Biostatistics and Medical Informatics, Faculty of Medicine, Karadeniz Technical University, Trabzon, Turkey
| | - Gizem Tatar-Yılmaz
- Department of Biostatistics and Medical Informatics, Faculty of Medicine, Karadeniz Technical University, Trabzon, Turkey.
| | - Bedriye Seda Kurşun Aktar
- Department of Hair Care and Beauty Services, Yeşilyurt Vocational School, Malatya Turgut Özal University, 44900, Malatya, Turkey
| | - Emine Elçin Oruç Emre
- Department of Chemistry, Faculty of Art and Sciences, Gaziantep University, Gaziantep, 27310, Turkey
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18
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Kotova PD, Dymova EA, Lyamin OO, Rogachevskaja OA, Kolesnikov SS. PI3 kinase inhibitor PI828 uncouples aminergic GPCRs and Ca 2+ mobilization irrespectively of its primary target. Biochim Biophys Acta Gen Subj 2024; 1868:130649. [PMID: 38823731 DOI: 10.1016/j.bbagen.2024.130649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 04/20/2024] [Accepted: 05/29/2024] [Indexed: 06/03/2024]
Abstract
The phosphoinositide 3-kinase (PI3K) is involved in regulation of multiple intracellular processes. Although the inhibitory analysis is generally employed for validating a physiological role of PI3K, increasing body of evidence suggests that PI3K inhibitors can exhibit PI3K-unrelated activity as well. Here we studied Ca2+ signaling initiated by aminergic agonists in a variety of different cells and analyzed effects of the PI3K inhibitor PI828 on cell responsiveness. It turned out that PI828 inhibited Ca2+ transients elicited by acetylcholine (ACh), histamine, and serotonin, but did not affect Ca2+ responses to norepinephrine and ATP. Another PI3K inhibitor wortmannin negligibly affected Ca2+ signaling initiated by any one of the tested agonists. Using the genetically encoded PIP3 sensor PH(Akt)-Venus, we confirmed that both PI828 and wortmannin effectively inhibited PI3K and ascertained that this kinase negligibly contributed to ACh transduction. These findings suggested that PI828 inhibited Ca2+ responses to aminergic agonists tested, involving an unknown cellular mechanism unrelated to the PI3K inhibition. Complementary physiological experiments provided evidence that PI828 could inhibit Ca2+ signals induced by certain agonists, by acting extracellularly, presumably, through their surface receptors. For the muscarinic M3 receptor, this possibility was verified with molecular docking and molecular dynamics. As demonstrated with these tools, wortmannin could be bound in the extracellular vestibule at the muscarinic M3 receptor but this did not preclude binding of ACh to the M3 receptor followed by its activation. In contrast, PI828 could sterically block the passage of ACh into the allosteric site, preventing activation of the muscarinic M3 receptor.
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Affiliation(s)
- Polina D Kotova
- Institute of Cell Biophysics of the Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Institutskaya Street 3, Pushchino, Russia.
| | - Ekaterina A Dymova
- Institute of Cell Biophysics of the Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Institutskaya Street 3, Pushchino, Russia
| | - Oleg O Lyamin
- Institute of Cell Biophysics of the Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Institutskaya Street 3, Pushchino, Russia
| | - Olga A Rogachevskaja
- Institute of Cell Biophysics of the Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Institutskaya Street 3, Pushchino, Russia
| | - Stanislav S Kolesnikov
- Institute of Cell Biophysics of the Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Institutskaya Street 3, Pushchino, Russia
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19
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Stanevich V, Oyeniran O, Somani S. Modeling Chromatography Binding through Molecular Dynamics Simulations with Resin Fragments. J Phys Chem B 2024. [PMID: 38809811 DOI: 10.1021/acs.jpcb.4c00578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2024]
Abstract
Accurate atomistic modeling of the interactions of a chromatography resin with a solute can inform the selection of purification conditions for a product, an important problem in the biotech and pharmaceutical industries. We present a molecular dynamics simulation-based approach for the qualitative prediction of interaction sites (specificity) and retention times (affinity) of a protein for a given chromatography resin. We mimicked the resin with an unrestrained ligand composed of the resin headgroup coupled with successively larger fragments of the agarose backbone. The interactions of the ligand with the protein are simulated in an explicit solvent using the Replica Exchange Molecular Dynamics enhanced sampling approach in conjunction with Hydrogen Mass Repartitioning (REMD-HMR). We computed the ligand interaction surface from the simulation trajectories and correlated the features of the interaction surface with experimentally determined retention times. The simulation and analysis protocol were first applied to a series of ubiquitin mutants for which retention times on Capto MMC resin are available. The ubiquitin simulations helped identify the optimal ligand that was used in subsequent simulations on six proteins for which Capto MMC elution times are available. For each of the six proteins, we computed the interaction surface and characterized it in terms of a range of simulation-averaged residue-level physicochemical descriptors. Modeling of the salt concentrations required for elution with respect to the descriptors resulted in a linear fit in terms of aromaphilicity and Kyte-Doolittle hydrophobicity that was robust to outliers, showed high correlation, and correctly ranked the protein elution order. The physics-based model building approach described here does not require a large experimental data set and can be readily applied to different resins and diverse biomolecules.
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Affiliation(s)
- Vitali Stanevich
- Protein Therapeutics API Development, Janssen Research & Development, LLC, a Johnson & Johnson company, Malvern, Pennsylvania 19355, United States
| | - Oluyemi Oyeniran
- Statistics and Decision Sciences, Janssen Research & Development, LLC, a Johnson & Johnson company, Spring House, Pennsylvania 19002, United States
| | - Sandeep Somani
- In Silico Discovery, Janssen Research & Development, LLC, a Johnson & Johnson company, Spring House, Pennsylvania 19002, United States
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20
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Liu G, Mei X, Zhang Y, Chen G, Li J, Tao W, Sun M, Zheng L, Chang Y, Xue C. Characterization and Structural Analysis of a Novel Carbohydrate-Binding Module from Family 96 with Chondroitin Sulfate-Specific Binding Capacity. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024. [PMID: 38805590 DOI: 10.1021/acs.jafc.4c00090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2024]
Abstract
Chondroitin sulfate (CS) is the predominant glycosaminoglycan within the human body and is widely applied in various industries. Carbohydrate-binding modules (CBMs) possessing the capacity for carbohydrate recognition are verified to be important tools for polysaccharide investigation. Only one CS-specific CBM, PhCBM100, has hitherto been characterized. In the present study, two CBM96 domains present in the same putative PL8_3 chondroitin AC lyase were discovered and recombinantly expressed. The results of microtiter plate assays and affinity gel electrophoresis assays showed that the two corresponding proteins, DmCBM96-1 and DmCBM96-2, bind specifically to CSs. The crystal structure of DmCBM96-1 was determined at a 2.20 Å resolution. It adopts a β-sandwich fold comprising two antiparallel β-sheets, showing structural similarities to TM6-N4, which is the founding member of the CBM96 family. Site mutagenesis analysis revealed that the residues of Arg27, Lys45, Tyr51, Arg53, and Arg157 are critical for CS binding. The characterization of the two CBM96 proteins demonstrates the diverse ligand specificity of the CBM96 family and provides promising tools for CS investigation.
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Affiliation(s)
- Guanchen Liu
- College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao 266404, China
| | - Xuanwei Mei
- College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao 266404, China
| | - Yuying Zhang
- College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao 266404, China
| | - Guangning Chen
- College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao 266404, China
| | - Jiajing Li
- College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao 266404, China
| | - Wenwen Tao
- College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao 266404, China
| | - Menghui Sun
- College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao 266404, China
| | - Long Zheng
- College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao 266404, China
| | - Yaoguang Chang
- College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao 266404, China
| | - Changhu Xue
- College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao 266404, China
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21
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Lefèbre J, Falk T, Ning Y, Rademacher C. Secondary Sites of the C-type Lectin-Like Fold. Chemistry 2024; 30:e202400660. [PMID: 38527187 DOI: 10.1002/chem.202400660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Revised: 03/23/2024] [Accepted: 03/25/2024] [Indexed: 03/27/2024]
Abstract
C-type lectins are a large superfamily of proteins involved in a multitude of biological processes. In particular, their involvement in immunity and homeostasis has rendered them attractive targets for diverse therapeutic interventions. They share a characteristic C-type lectin-like domain whose adaptability enables them to bind a broad spectrum of ligands beyond the originally defined canonical Ca2+-dependent carbohydrate binding. Together with variable domain architecture and high-level conformational plasticity, this enables C-type lectins to meet diverse functional demands. Secondary sites provide another layer of regulation and are often intricately linked to functional diversity. Located remote from the canonical primary binding site, secondary sites can accommodate ligands with other physicochemical properties and alter protein dynamics, thus enhancing selectivity and enabling fine-tuning of the biological response. In this review, we outline the structural determinants allowing C-type lectins to perform a large variety of tasks and to accommodate the ligands associated with it. Using the six well-characterized Ca2+-dependent and Ca2+-independent C-type lectin receptors DC-SIGN, langerin, MGL, dectin-1, CLEC-2 and NKG2D as examples, we focus on the characteristics of non-canonical interactions and secondary sites and their potential use in drug discovery endeavors.
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Affiliation(s)
- Jonathan Lefèbre
- Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
- Vienna Doctoral School of Pharmaceutical, Nutritional and Sport, Sciences, University of Vienna, Vienna, Austria
- Department of Microbiology, Immunology and Genetics, University of Vienna, Max F. Perutz Labs, Vienna, Austria
| | - Torben Falk
- Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
- Vienna Doctoral School of Pharmaceutical, Nutritional and Sport, Sciences, University of Vienna, Vienna, Austria
- Department of Microbiology, Immunology and Genetics, University of Vienna, Max F. Perutz Labs, Vienna, Austria
| | - Yunzhan Ning
- Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
- Vienna Doctoral School of Pharmaceutical, Nutritional and Sport, Sciences, University of Vienna, Vienna, Austria
- Department of Microbiology, Immunology and Genetics, University of Vienna, Max F. Perutz Labs, Vienna, Austria
| | - Christoph Rademacher
- Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
- Department of Microbiology, Immunology and Genetics, University of Vienna, Max F. Perutz Labs, Vienna, Austria
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22
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Irwin NAT, Richards TA. Self-assembling viral histones are evolutionary intermediates between archaeal and eukaryotic nucleosomes. Nat Microbiol 2024:10.1038/s41564-024-01707-9. [PMID: 38806669 DOI: 10.1038/s41564-024-01707-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 04/19/2024] [Indexed: 05/30/2024]
Abstract
Nucleosomes are DNA-protein complexes composed of histone proteins that form the basis of eukaryotic chromatin. The nucleosome was a key innovation during eukaryotic evolution, but its origin from histone homologues in Archaea remains unclear. Viral histone repeats, consisting of multiple histone paralogues within a single protein, may reflect an intermediate state. Here we examine the diversity of histones encoded by Nucleocytoviricota viruses. We identified 258 histones from 168 viral metagenomes with variable domain configurations including histone singlets, doublets, triplets and quadruplets, the latter comprising the four core histones arranged in series. Viral histone repeats branch phylogenetically between Archaea and eukaryotes and display intermediate functions in Escherichia coli, self-assembling into eukaryotic-like nucleosomes that stack into archaeal-like oligomers capable of impacting genomic activity and condensing DNA. Histone linkage also facilitates nucleosome formation, promoting eukaryotic histone assembly in E. coli. These data support the hypothesis that viral histone repeats originated in stem-eukaryotes and that nucleosome evolution proceeded through histone repeat intermediates.
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Affiliation(s)
- Nicholas A T Irwin
- Merton College, University of Oxford, Oxford, UK.
- Department of Biology, University of Oxford, Oxford, UK.
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria.
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23
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Grelet E, Tortora MMC. Elucidating chirality transfer in liquid crystals of viruses. NATURE MATERIALS 2024:10.1038/s41563-024-01897-x. [PMID: 38783105 DOI: 10.1038/s41563-024-01897-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 04/11/2024] [Indexed: 05/25/2024]
Abstract
Chirality is ubiquitous in nature across all length scales, with major implications spanning fields from biology, chemistry and physics to materials science. How chirality propagates from nanoscale building blocks to meso- and macroscopic helical structures remains an open issue. Here, working with a canonical system of filamentous viruses, we demonstrate that their self-assembly into chiral liquid crystal phases quantitatively results from the interplay between two main mechanisms of chirality transfer: electrostatic interactions from the helical charge patterns on the virus surface, and fluctuation-based helical deformations leading to viral backbone helicity. Our experimental and theoretical approach provides a comprehensive framework for deciphering how chirality is hierarchically and quantitatively propagated across spatial scales. Our work highlights the ways in which supramolecular helicity may arise from subtle chiral contributions of opposite handedness that act either cooperatively or competitively, thus accounting for the multiplicity of chiral behaviours observed for nearly identical molecular systems.
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Affiliation(s)
- Eric Grelet
- Centre de Recherche Paul Pascal (CRPP, UMR 5031), Univ. Bordeaux, CNRS, Pessac, France.
| | - Maxime M C Tortora
- Laboratoire de Biologie et Modélisation de la Cellule (LBMC, UMR 5239, Inserm 1293), Univ. Claude Bernard Lyon 1, ENS de Lyon, CNRS, Lyon, France.
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA.
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24
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Suladze S, Sustay Martinez C, Rodriguez Camargo DC, Engler J, Rodina N, Sarkar R, Zacharias M, Reif B. Structural Insights into Seeding Mechanisms of hIAPP Fibril Formation. J Am Chem Soc 2024; 146:13783-13796. [PMID: 38723619 PMCID: PMC11117405 DOI: 10.1021/jacs.3c14233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 04/26/2024] [Accepted: 04/29/2024] [Indexed: 05/23/2024]
Abstract
The deposition of islet amyloid polypeptide (hIAPP) fibrils is a hallmark of β-cell death in type II diabetes. In this study, we employ state-of-the-art MAS solid-state spectroscopy to investigate the previously elusive N-terminal region of hIAPP fibrils, uncovering both rigidity and heterogeneity. Comparative analysis between wild-type hIAPP and a disulfide-deficient variant (hIAPPC2S,C7S) unveils shared fibril core structures yet strikingly distinct dynamics in the N-terminus. Specifically, the variant fibrils exhibit extended β-strand conformations, facilitating surface nucleation. Moreover, our findings illuminate the pivotal roles of specific residues in modulating secondary nucleation rates. These results deepen our understanding of hIAPP fibril assembly and provide critical insights into the molecular mechanisms underpinning type II diabetes, holding promise for future therapeutic strategies.
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Affiliation(s)
- Saba Suladze
- Bayerisches
NMR Zentrum (BNMRZ) at the Department of Biosciences, School of Natural
Sciences, Technische Universität
München, 85747 Garching, Germany
- Helmholtz-Zentrum
München (HMGU), Deutsches Forschungszentrum für Gesundheit
und Umwelt, Institute of Structural Biology
(STB), Ingolstädter
Landstraße 1, 85764 Neuherberg, Germany
| | - Christian Sustay Martinez
- Center
for
Functional Protein Assemblies (CPA), Department of Bioscience, TUM
School of Natural Sciences, Technische Universität
München, Ernst-Otto-Fischer-Straße
8, 85747 Garching, Germany
| | - Diana C. Rodriguez Camargo
- Bayerisches
NMR Zentrum (BNMRZ) at the Department of Biosciences, School of Natural
Sciences, Technische Universität
München, 85747 Garching, Germany
- Helmholtz-Zentrum
München (HMGU), Deutsches Forschungszentrum für Gesundheit
und Umwelt, Institute of Structural Biology
(STB), Ingolstädter
Landstraße 1, 85764 Neuherberg, Germany
| | - Jonas Engler
- Bayerisches
NMR Zentrum (BNMRZ) at the Department of Biosciences, School of Natural
Sciences, Technische Universität
München, 85747 Garching, Germany
- Helmholtz-Zentrum
München (HMGU), Deutsches Forschungszentrum für Gesundheit
und Umwelt, Institute of Structural Biology
(STB), Ingolstädter
Landstraße 1, 85764 Neuherberg, Germany
| | - Natalia Rodina
- Bayerisches
NMR Zentrum (BNMRZ) at the Department of Biosciences, School of Natural
Sciences, Technische Universität
München, 85747 Garching, Germany
- Helmholtz-Zentrum
München (HMGU), Deutsches Forschungszentrum für Gesundheit
und Umwelt, Institute of Structural Biology
(STB), Ingolstädter
Landstraße 1, 85764 Neuherberg, Germany
| | - Riddhiman Sarkar
- Bayerisches
NMR Zentrum (BNMRZ) at the Department of Biosciences, School of Natural
Sciences, Technische Universität
München, 85747 Garching, Germany
- Helmholtz-Zentrum
München (HMGU), Deutsches Forschungszentrum für Gesundheit
und Umwelt, Institute of Structural Biology
(STB), Ingolstädter
Landstraße 1, 85764 Neuherberg, Germany
| | - Martin Zacharias
- Center
for
Functional Protein Assemblies (CPA), Department of Bioscience, TUM
School of Natural Sciences, Technische Universität
München, Ernst-Otto-Fischer-Straße
8, 85747 Garching, Germany
| | - Bernd Reif
- Bayerisches
NMR Zentrum (BNMRZ) at the Department of Biosciences, School of Natural
Sciences, Technische Universität
München, 85747 Garching, Germany
- Helmholtz-Zentrum
München (HMGU), Deutsches Forschungszentrum für Gesundheit
und Umwelt, Institute of Structural Biology
(STB), Ingolstädter
Landstraße 1, 85764 Neuherberg, Germany
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25
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Gomes LS, Costa ÉDO, Duarte TG, Charret TS, Castiglione RC, Simões RL, Pascoal VDB, Döring TH, da Silva FDC, Ferreira VF, S. de Oliveira A, Pascoal ACRF, Cruz AL, Nascimento V. New Chalcogen-Functionalized Naphthoquinones: Design, Synthesis, and Evaluation, In Vitro and In Silico, against Squamous Cell Carcinoma. ACS OMEGA 2024; 9:21948-21963. [PMID: 38799368 PMCID: PMC11112715 DOI: 10.1021/acsomega.3c10134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 04/24/2024] [Accepted: 04/29/2024] [Indexed: 05/29/2024]
Abstract
Due to the growth in the number of patients and the complexity involved in anticancer therapies, new therapeutic approaches are urgent and necessary. In this context, compounds containing the selenium atom can be employed in developing new medicines due to their potential therapeutic efficacy and unique modes of action. Furthermore, tellurium, a previously unknown element, has emerged as a promising possibility in chalcogen-containing compounds. In this study, 13 target compounds (9a-i, 10a-c, and 11) were effectively synthesized as potential anticancer agents, employing a CuI-catalyzed Csp-chalcogen bond formation procedure. The developed methodology yielded excellent results, ranging from 30 to 85%, and the compounds were carefully characterized. Eight of these compounds showed promise as potential therapeutic drugs due to their high yields and remarkable selectivity against SCC-9 cells (squamous cell carcinoma). Compound 10a, in particular, demonstrated exceptional selectivity, making it an excellent choice for cancer cell targeting while sparing healthy cells. Furthermore, complementing in silico and molecular docking studies shed light on their physical features and putative modes of action. This research highlights the potential of these compounds in anticancer treatments and lays the way for future drug development efforts.
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Affiliation(s)
- Luana
da Silva Gomes
- SupraSelen
Laboratory, Department of Organic Chemistry, Institute of Chemistry, Federal University Fluminense, Campus of Valonguinho, Niterói-RJ 24020-141, Brazil
| | - Érica de Oliveira Costa
- SupraSelen
Laboratory, Department of Organic Chemistry, Institute of Chemistry, Federal University Fluminense, Campus of Valonguinho, Niterói-RJ 24020-141, Brazil
| | - Thuany G. Duarte
- SupraSelen
Laboratory, Department of Organic Chemistry, Institute of Chemistry, Federal University Fluminense, Campus of Valonguinho, Niterói-RJ 24020-141, Brazil
| | - Thiago S. Charret
- Research
Laboratory of Natural Products and Bioactive Molecules, Nova Friburgo
Health Institute, Fluminense Federal University
(ISNF-UFF), Nova Friburgo-RJ 28625-650, Brazil
| | - Raquel C. Castiglione
- Laboratory
for Clinical and Experimental Research on Vascular Biology, Biomedical
Center, State University of Rio de Janeiro, Rio de Janeiro-RJ 20550-900, Brazil
| | - Rafael L. Simões
- Laboratory
of Molecular and Cellular Pharmacology, Roberto Alcântara Gomes
Biology Institute, State University of Rio
de Janeiro, Rio de Janeiro 20551-030, Brazil
| | - Vinicius D. B. Pascoal
- Research
Laboratory of Natural Products and Bioactive Molecules, Nova Friburgo
Health Institute, Fluminense Federal University
(ISNF-UFF), Nova Friburgo-RJ 28625-650, Brazil
| | - Thiago H. Döring
- Department
of Exact Sciences and Education, Federal
University of Santa Catarina, Campus Blumenau, Blumenau-SC, 89036-256, Brazil
| | - Fernando de C. da Silva
- Applied Organic
Synthesis Laboratory (LabSOA), Institute of Chemistry, Universidade Federal Fluminense, Niterói-RJ 24020-141, Brazil
| | - Vitor F. Ferreira
- Department
of Exact Sciences and Education, Federal
University of Santa Catarina, Campus Blumenau, Blumenau-SC 89036-256, Brazil
| | - Aldo S. de Oliveira
- Department
of Exact Sciences and Education, Federal
University of Santa Catarina, Campus Blumenau, Blumenau-SC, 89036-256, Brazil
| | - Aislan C. R. F. Pascoal
- Research
Laboratory of Natural Products and Bioactive Molecules, Nova Friburgo
Health Institute, Fluminense Federal University
(ISNF-UFF), Nova Friburgo-RJ 28625-650, Brazil
| | - André L.
S. Cruz
- Physiopathology
Laboratory, Institute of Medical Sciences, Multidisciplinary Center
UFRJ, Federal University of Rio De Janeiro
(UFRJ), Macaé-RJ 27930-560, Brazil
| | - Vanessa Nascimento
- SupraSelen
Laboratory, Department of Organic Chemistry, Institute of Chemistry, Federal University Fluminense, Campus of Valonguinho, Niterói-RJ 24020-141, Brazil
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26
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Yuan L, Liang X, He L. Unveiling dissociation mechanisms and binding patterns in the UHRF1-DPPA3 complex via multi-replica molecular dynamics simulations. J Mol Model 2024; 30:173. [PMID: 38767734 DOI: 10.1007/s00894-024-05946-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Accepted: 04/16/2024] [Indexed: 05/22/2024]
Abstract
CONTEXT Ubiquitin-like with PHD and RING finger domain containing protein 1 (UHRF1) is responsible for preserving the stability of genomic methylation through the recruitment of DNA methyltransferase 1 (DNMT1). However, the interaction between Developmental pluripotency associated 3 (DPPA3) and the pre-PHD-PHD (PPHD) domain of UHRF1 hinders the nuclear localization of UHRF1. This disruption has implications for potential cancer treatment strategies. Drugs that mimic the binding pattern between DPPA3 and PPHD could offer a promising approach to cancer treatment. Our study reveals that DPPA3 undergoes dissociation from the C-terminal through three different modes of helix unfolding. Furthermore, we have identified key residue pairs involved in this dissociation process and potential drug-targeting residues. These findings offer valuable insights into the dissociation mechanism of DPPA3 from PPHD and have the potential to inform the design of novel drugs targeting UHRF1 for cancer therapy. METHODS To comprehend the dissociation process and binding patterns of PPHD-DPPA3, we employed enhanced sampling techniques, including steered molecular dynamics (SMD) and conventional molecular dynamics (cMD). Additionally, we utilized self-organizing maps (SOM) and time-resolved force distribution analysis (TRFDA) methodologies. The Gromacs software was used for performing molecular dynamics simulations, and the AMBER FF14SB force field was applied to the protein.
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Affiliation(s)
- Longxiao Yuan
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Tianjin, 300353, China
| | - Xiaodan Liang
- School of Computer Sciences and Technology, Tiangong University, Tianjin, 300387, China.
| | - Lei He
- Institute for Fetology, The First Affiliated Hospital of Soochow University, Suzhou, 215006, China.
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27
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Pham PC, Taylor M, Nguyen GTH, Beltran J, Bennett JL, Ho J, Donald WA. Binding of Per- and Polyfluoroalkyl Substances to β-Lactoglobulin from Bovine Milk. Chem Res Toxicol 2024; 37:757-770. [PMID: 38625865 DOI: 10.1021/acs.chemrestox.4c00021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/18/2024]
Abstract
Per- and polyfluoroalkyl substances (PFAS) are known for their high environmental persistence and potential toxicity. The presence of PFAS has been reported in many dairy products. However, the mechanisms underlying the accumulation of PFAS in these products remain unclear. Here, we used native mass spectrometry and molecular dynamics simulations to probe the interactions between 19 PFAS of environmental concern and two isoforms of the major bovine whey protein β-lactoglobulin (β-LG). We observed that six of these PFAS bound to both protein isoforms with low- to mid-micromolar dissociation constants. Based on quantitative, competitive binding experiments with endogenous ligands, PFAS can bind orthosterically and preferentially to β-LG's hydrophobic ligand-binding calyx. β-Cyclodextrin can also suppress binding of PFAS to β-LG owing to the ability of β-cyclodextrin to directly sequester PFAS from solution. This research sheds light on PFAS-β-LG binding, suggesting that such interactions could impact lipid-fatty acid transport in bovine mammary glands at high PFAS concentrations. Furthermore, our results highlight the potential use of β-cyclodextrin in mitigating PFAS binding, providing insights toward the development of strategies to reduce PFAS accumulation in dairy products and other biological systems.
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Affiliation(s)
- P Chi Pham
- School of Chemistry, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Mackenzie Taylor
- School of Chemistry, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Giang T H Nguyen
- School of Chemistry, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Jeunesse Beltran
- School of Chemistry, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Jack L Bennett
- School of Chemistry, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Junming Ho
- School of Chemistry, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - William A Donald
- School of Chemistry, University of New South Wales, Sydney, New South Wales 2052, Australia
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28
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Bai Q, Xu T, Huang J, Pérez-Sánchez H. Geometric deep learning methods and applications in 3D structure-based drug design. Drug Discov Today 2024; 29:104024. [PMID: 38759948 DOI: 10.1016/j.drudis.2024.104024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 05/02/2024] [Accepted: 05/10/2024] [Indexed: 05/19/2024]
Abstract
3D structure-based drug design (SBDD) is considered a challenging and rational way for innovative drug discovery. Geometric deep learning is a promising approach that solves the accurate model training of 3D SBDD through building neural network models to learn non-Euclidean data, such as 3D molecular graphs and manifold data. Here, we summarize geometric deep learning methods and applications that contain 3D molecular representations, equivariant graph neural networks (EGNNs), and six generative model methods [diffusion model, flow-based model, generative adversarial networks (GANs), variational autoencoder (VAE), autoregressive models, and energy-based models]. Our review provides insights into geometric deep learning methods and advanced applications of 3D SBDD that will be of relevance for the drug discovery community.
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Affiliation(s)
- Qifeng Bai
- School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, Gansu, PR China.
| | | | - Junzhou Huang
- Department of Computer Science and Engineering, the University of Texas at Arlington, Arlington, TX 76019, USA
| | - Horacio Pérez-Sánchez
- Structural Bioinformatics and High Performance Computing Research Group (BIO-HPC), Computer Engineering Department, UCAM Universidad Católica de Murcia, Murcia 30107, Spain.
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29
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Mignon J, Leyder T, Mottet D, Uversky VN, Michaux C. In-depth investigation of the effect of pH on the autofluorescence properties of DPF3b and DPF3a amyloid fibrils. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 313:124156. [PMID: 38508075 DOI: 10.1016/j.saa.2024.124156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 03/10/2024] [Accepted: 03/12/2024] [Indexed: 03/22/2024]
Abstract
Double PHD fingers 3 (DPF3) protein exists as two splicing variants, DPF3b and DPF3a, the involvement of which in human cancer and neurodegeneration is beginning to be increasingly recognised. Both isoforms have recently been identified as intrinsically disordered proteins able to undergo amyloid fibrillation. Upon their aggregation, DPF3 proteins exhibit an intrinsic fluorescence in the visible range, referred to as deep-blue autofluorescence (dbAF). Comprehension of such phenomenon remaining elusive, we investigated in the present study the influence of pH on the optical properties of DPF3b and DPF3a fibrils. By varying the excitation wavelength and the pH condition, the two isoforms were revealed to display several autofluorescence modes that were defined as violet, deep-blue, and blue-green according to their emission range. Complementarily, analysis of excitation spectra and red edge shift plots allowed to better decipher their photoselection mechanism and to highlight isoform-specific excitation-emission features. Furthermore, the observed violation to Kasha-Vavilov's rule was attributed to red edge excitation shift effects, which were impacted by pH-mediated H-bond disruption, leading to changes in intramolecular charge and proton transfer, or π-electrons delocalisation. Finally, emergence of different autofluorescence emitters was likely related to structurally distinct fibrillar assemblies between isoforms, as well as to discrepancies in the amino acid composition of their aggregation prone regions.
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Affiliation(s)
- Julien Mignon
- Laboratoire de Chimie Physique des Biomolécules, UCPTS, University of Namur, 61 rue de Bruxelles, 5000 Namur, Belgium; Namur Institute of Structured Matter (NISM), University of Namur, 61 rue de Bruxelles, 5000 Namur, Belgium; Namur Research Institute for Life Sciences (NARILIS), University of Namur, 61 rue de Bruxelles, 5000 Namur, Belgium.
| | - Tanguy Leyder
- Laboratoire de Chimie Physique des Biomolécules, UCPTS, University of Namur, 61 rue de Bruxelles, 5000 Namur, Belgium.
| | - Denis Mottet
- Gene Expression and Cancer Laboratory, GIGA-Molecular Biology of Diseases, University of Liège, B34, Avenue de l'Hôpital, 4000 Liège, Belgium.
| | - Vladimir N Uversky
- Department of Molecular Medicine, USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, United States.
| | - Catherine Michaux
- Laboratoire de Chimie Physique des Biomolécules, UCPTS, University of Namur, 61 rue de Bruxelles, 5000 Namur, Belgium; Namur Institute of Structured Matter (NISM), University of Namur, 61 rue de Bruxelles, 5000 Namur, Belgium; Namur Research Institute for Life Sciences (NARILIS), University of Namur, 61 rue de Bruxelles, 5000 Namur, Belgium.
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30
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Szulc N, Gąsior-Głogowska M, Żyłka P, Szefczyk M, Wojciechowski JW, Żak AM, Dyrka W, Kaczorowska A, Burdukiewicz M, Tarek M, Kotulska M. Structural effects of charge destabilization and amino acid substitutions in amyloid fragments of CsgA. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 313:124094. [PMID: 38503257 DOI: 10.1016/j.saa.2024.124094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 02/20/2024] [Accepted: 02/27/2024] [Indexed: 03/21/2024]
Abstract
The most studied functional amyloid is the CsgA, major curli subunit protein, which is produced by numerous strains of Enterobacteriaceae. Although CsgA sequences are highly conserved, they exhibit species diversity, which reflects the specific evolutionary and functional adaptability of the major curli subunit. Herein, we performed bioinformatics analyses to uncover the differences in the amyloidogenic properties of the R4 fragments in Escherichia coli and Salmonella enterica and proposed four mutants for more detailed studies: M1, M2, M3, and M4. The mutated sequences were characterized by various experimental techniques, such as circular dichroism, ATR-FTIR, FT-Raman, thioflavin T, transmission electron microscopy and confocal microscopy. Additionally, molecular dynamics simulations were performed to determine the role of buffer ions in the aggregation process. Our results demonstrated that the aggregation kinetics, fibril morphology, and overall structure of the peptide were significantly affected by the positions of charged amino acids within the repeat sequences of CsgA. Notably, substituting glycine with lysine resulted in the formation of distinctive spherically packed globular aggregates. The differences in morphology observed are attributed to the influence of phosphate ions, which disrupt the local electrostatic interaction network of the polypeptide chains. This study provides knowledge on the preferential formation of amyloid fibrils based on charge states within the polypeptide chain.
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Affiliation(s)
- Natalia Szulc
- Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland; CNRS, University of Lorraine, F-5400 Nancy, France; Department of Physics and Biophysics, Faculty of Biotechnology and Food Science, Wrocław University of Environmental and Life Sciences, Norwida 25, 50-375 Wrocław, Poland
| | - Marlena Gąsior-Głogowska
- Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Paweł Żyłka
- Department of Electrical Engineering Fundamentals, Faculty of Electrical Engineering, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Monika Szefczyk
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Jakub W Wojciechowski
- Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Andrzej M Żak
- Institute of Advanced Materials, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Witold Dyrka
- Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Aleksandra Kaczorowska
- Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland; Laboratory of Cytobiochemistry, Faculty of Biotechnology, University of Wroclaw, F. Joliot-Curie 14a, 50-383 Wroclaw, Poland
| | - Michał Burdukiewicz
- Institute of Biotechnology and Biomedicine, Autonomous University of Barcelona, Campus Universitat Autònoma de Barcelona Plaça Cívica Bellaterra, s/n, 08193 Cerdanyola del Vallès, Barcelona, Spain; Clinical Research Centre, Medical University of Bialystok, Jana Kilinskiego 1, 15-089 Bialystok, Poland
| | - Mounir Tarek
- CNRS, University of Lorraine, F-5400 Nancy, France.
| | - Malgorzata Kotulska
- Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland.
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31
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Yuan L, Liang X, He L. Insights into the Dissociation Process and Binding Pattern of the BRCT7/8-PHF8 Complex. ACS OMEGA 2024; 9:20819-20831. [PMID: 38764655 PMCID: PMC11097150 DOI: 10.1021/acsomega.3c09433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 02/27/2024] [Accepted: 04/24/2024] [Indexed: 05/21/2024]
Abstract
DNA topoisomerase 2-binding protein 1 (Topbp1) plays a crucial role in activating the ataxia-telangiectasia mutated and rad3-related (ATR) complex to initiate DNA damage repair responses. For this process to occur, it is necessary for PHF8 to dissociate from Topbp1. Topbp1 binds to the acidic patch sequence (APS) of PHF8 through its C-terminal BRCT7/8 domain, and disrupting this interaction could be a promising strategy for cancer treatment. To investigate the dissociation process and binding pattern of BRCT7/8-PHF8, we employed enhanced sampling techniques, such as steered molecular dynamics (SMD) simulations and accelerated molecular dynamics (aMD) simulations, along with self-organizing maps (SOM) and time-resolved force distribution analysis (TRFDA) methodologies. Our results demonstrate that the dissociation of PHF8 from BRCT7/8 starts from the N-terminus, leading to the unfolding of the N-terminal helix. Additionally, we identified critical residues that play a pivotal role in this dissociation process. These findings provide valuable insights into the disassociation of PHF8 from BRCT7/8, which could potentially guide the development of novel drugs targeting Topbp1 for cancer therapy.
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Affiliation(s)
- Longxiao Yuan
- State
Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Tianjin 300353, China
| | - Xiaodan Liang
- School
of Computer Sciences and Technology, Tiangong
University, Tianjin 300387, China
| | - Lei He
- Institute
for Fetology, The First Affiliated Hospital
of Soochow University, Suzhou 215006, China
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32
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Britton D, Legocki J, Paul D, Katsara O, Aristizabal O, Pandya N, Mishkit O, Xiao Y, Aristizabal M, Rahman N, Schneider R, Wadghiri YZ, Montclare JK. Coiled-Coil Protein Hydrogels Engineered with Minimized Fiber Diameters for Sustained Release of Doxorubicin in Triple-Negative Breast Cancer. ACS Biomater Sci Eng 2024; 10:3425-3437. [PMID: 38622760 PMCID: PMC11094684 DOI: 10.1021/acsbiomaterials.4c00349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 03/31/2024] [Accepted: 04/03/2024] [Indexed: 04/17/2024]
Abstract
Triple-negative breast cancer (TNBC) lacks expressed protein targets, making therapy development challenging. Hydrogels offer a promising new route in this regard by improving the chemotherapeutic efficacy through increased solubility and sustained release. Moreover, subcutaneous hydrogel administration reduces patient burden by requiring less therapy and shorter treatment times. We recently established the design principles for the supramolecular assembly of single-domain coiled-coils into hydrogels. Using a modified computational design algorithm, we designed Q8, a hydrogel with rapid assembly for faster therapeutic hydrogel preparation. Q8 encapsulates and releases doxorubicin (Dox), enabling localized sustained release via subcutaneous injection. Remarkably, a single subcutaneous injection of Dox-laden Q8 (Q8•Dox) significantly suppresses tumors within just 1 week. This work showcases the bottom-up engineering of a fully protein-based drug delivery vehicle for improved TBNC treatment via noninvasive localized therapy.
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Affiliation(s)
- Dustin Britton
- Department
of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
| | - Jakub Legocki
- Department
of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
| | - Deven Paul
- Department
of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
| | - Olga Katsara
- Department
of Microbiology, New York University Grossman
School of Medicine, New York, New York 10016, United States
| | - Orlando Aristizabal
- Center
for Advanced Imaging Innovation and Research (CAI2R), New York University Grossman School of Medicine, New York, New York 10016, United States
- Bernard
and Irene Schwartz Center for Biomedical Imaging, Department of Radiology, New York University Grossman School of Medicine, New York, New York 10016, United States
| | - Neelam Pandya
- Center
for Advanced Imaging Innovation and Research (CAI2R), New York University Grossman School of Medicine, New York, New York 10016, United States
- Bernard
and Irene Schwartz Center for Biomedical Imaging, Department of Radiology, New York University Grossman School of Medicine, New York, New York 10016, United States
| | - Orin Mishkit
- Center
for Advanced Imaging Innovation and Research (CAI2R), New York University Grossman School of Medicine, New York, New York 10016, United States
- Bernard
and Irene Schwartz Center for Biomedical Imaging, Department of Radiology, New York University Grossman School of Medicine, New York, New York 10016, United States
| | - Yingxin Xiao
- Department
of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
| | - Matias Aristizabal
- Center
for Advanced Imaging Innovation and Research (CAI2R), New York University Grossman School of Medicine, New York, New York 10016, United States
- Bernard
and Irene Schwartz Center for Biomedical Imaging, Department of Radiology, New York University Grossman School of Medicine, New York, New York 10016, United States
| | - Neha Rahman
- Center
for Advanced Imaging Innovation and Research (CAI2R), New York University Grossman School of Medicine, New York, New York 10016, United States
- Bernard
and Irene Schwartz Center for Biomedical Imaging, Department of Radiology, New York University Grossman School of Medicine, New York, New York 10016, United States
| | - Robert Schneider
- Department
of Microbiology, New York University Grossman
School of Medicine, New York, New York 10016, United States
- Department
of Radiation Oncology, New York University
Grossman School of Medicine, New
York, New York 10016, United States
| | - Youssef Z. Wadghiri
- Center
for Advanced Imaging Innovation and Research (CAI2R), New York University Grossman School of Medicine, New York, New York 10016, United States
- Bernard
and Irene Schwartz Center for Biomedical Imaging, Department of Radiology, New York University Grossman School of Medicine, New York, New York 10016, United States
| | - Jin Kim Montclare
- Department
of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
- Bernard
and Irene Schwartz Center for Biomedical Imaging, Department of Radiology, New York University Grossman School of Medicine, New York, New York 10016, United States
- Department
of Biomedical Engineering, New York University
Tandon School of Engineering, Brooklyn ,New York11201, United States
- Department
of Chemistry, New York University, New York, New York 10012, United States
- Department
of Biomaterials, New York University College
of Dentistry, New York, New York 10010, United States
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33
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das Neves MA, do Nascimento JR, Maciel-Silva VL, Dos Santos AM, Junior JDJGV, Coelho AJS, Lima MIS, Pereira SRF, da Rocha CQ. Anti-Leishmania activity and molecular docking of unusual flavonoids-rich fraction from Arrabidaea brachypoda (Bignoniaceae). Mol Biochem Parasitol 2024; 259:111629. [PMID: 38750697 DOI: 10.1016/j.molbiopara.2024.111629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 04/30/2024] [Accepted: 05/09/2024] [Indexed: 05/20/2024]
Abstract
Leishmaniases comprise a group of infectious parasitic diseases caused by various species of Leishmania and are considered a significant public health problem worldwide. Only a few medications, including miltefosine, amphotericin B, and meglumine antimonate, are used in current therapy. These medications are associated with severe side effects, low efficacy, high cost, and the need for hospital support. Additionally, there have been occurrences of drug resistance. Additionally, only a limited number of drugs, such as meglumine antimonate, amphotericin B, and miltefosine, are available, all of which are associated with severe side effects. In this context, the need for new effective drugs with fewer adverse effects is evident. Therefore, this study investigated the anti-Leishmania activity of a dichloromethane fraction (DCMF) extracted from Arrabidaea brachypoda roots. This fraction inhibited the viability of L. infantum, L. braziliensis, and L. Mexicana promastigotes, with IC50 values of 10.13, 11.44, and 11.16 µg/mL, respectively, and against L. infantum amastigotes (IC50 = 4.81 µg/mL). Moreover, the DCMF exhibited moderate cytotoxicity (CC50 = 25.15) towards RAW264.7 macrophages, with a selectivity index (SI) of 5.2. Notably, the DCMF caused damage to the macrophage genome only at 40 µg/mL, which is greater than the IC50 found for all Leishmania species. The results suggest that DCMF demonstrates similar antileishmanial effectiveness to isolated brachydin B, without causing genotoxic effects on mammalian cells. This finding is crucial because the isolation of the compounds relies on several steps and is very costly while obtaining the DCMF fraction is a simple and cost-effective process. Furthermore, In addition, the potential mechanisms of action of brachydins were also investigated. The computational analysis indicates that brachydin compounds bind to the Triosephosphate isomerase (TIM) enzyme via two main mechanisms: destabilizing the interface between the homodimers and interacting with catalytic residues situated at the site of binding. Based on all the results, DCMF exhibits promise as a therapeutic agent for leishmaniasis due to its significantly reduced toxicity in comparison to the adverse effects associated with current reference treatments.
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Affiliation(s)
- Monica A das Neves
- UFMA-Federal University of Maranhão, Center for Exact Sciences and Technology (CCET), Post Graduate Program in Chemistry, São Luís CEP 65080-805, Brazil
| | - Jessyane R do Nascimento
- UNESP, São Paulo State University Júlio de Mesquita Filho, Institute of Chemistry, Post Graduate Program in Chemistry, Araraquara CEP 14800-060, Brazil
| | - Vera Lucia Maciel-Silva
- UEMA, Maranhão State University, Center for Education, Exact and Natural Sciences (CECEN), Department of Biology, CEP: 65055-310, São Luís, Brazil
| | - Alberto M Dos Santos
- UNICAMP - University of Campinas, Institute of Chemistry and Center for Computer in Engineering and Sciences, Campinas CEP 13084-862, Brazil
| | | | - Ana Jessica S Coelho
- UFMA-Federal University of Maranhão, Laboratory of Genetics and Molecular Biology, Department of Biology, São Luís CEP 65080-805, Brazil
| | - Mayara Ingrid S Lima
- UFMA-Federal University of Maranhão, Laboratory of Genetics and Molecular Biology, Department of Biology, São Luís CEP 65080-805, Brazil
| | - Silma Regina F Pereira
- UFMA-Federal University of Maranhão, Laboratory of Genetics and Molecular Biology, Department of Biology, São Luís CEP 65080-805, Brazil
| | - Cláudia Q da Rocha
- UFMA-Federal University of Maranhão, Center for Exact Sciences and Technology (CCET), Post Graduate Program in Chemistry, São Luís CEP 65080-805, Brazil.
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34
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Gupta P, Hiller A, Chowdhury J, Lim D, Lim DY, Saeij JPJ, Babaian A, Rodriguez F, Pereira L, Morales-Tapia A. A parasite odyssey: An RNA virus concealed in Toxoplasma gondii. Virus Evol 2024; 10:veae040. [PMID: 38817668 PMCID: PMC11137675 DOI: 10.1093/ve/veae040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 03/05/2024] [Accepted: 05/10/2024] [Indexed: 06/01/2024] Open
Abstract
We are entering a 'Platinum Age of Virus Discovery', an era marked by exponential growth in the discovery of virus biodiversity, and driven by advances in metagenomics and computational analysis. In the ecosystem of a human (or any animal) there are more species of viruses than simply those directly infecting the animal cells. Viruses can infect all organisms constituting the microbiome, including bacteria, fungi, and unicellular parasites. Thus the complexity of possible interactions between host, microbe, and viruses is unfathomable. To understand this interaction network we must employ computationally assisted virology as a means of analyzing and interpreting the millions of available samples to make inferences about the ways in which viruses may intersect human health. From a computational viral screen of human neuronal datasets, we identified a novel narnavirus Apocryptovirus odysseus (Ao) which likely infects the neurotropic parasite Toxoplasma gondii. Previously, several parasitic protozoan viruses (PPVs) have been mechanistically established as triggers of host innate responses, and here we present in silico evidence that Ao is a plausible pro-inflammatory factor in human and mouse cells infected by T. gondii. T. gondii infects billions of people worldwide, yet the prognosis of toxoplasmosis disease is highly variable, and PPVs like Ao could function as a hitherto undescribed hypervirulence factor. In a broader screen of over 7.6 million samples, we explored phylogenetically proximal viruses to Ao and discovered nineteen Apocryptovirus species, all found in libraries annotated as vertebrate transcriptome or metatranscriptomes. While samples containing this genus of narnaviruses are derived from sheep, goat, bat, rabbit, chicken, and pigeon samples, the presence of virus is strongly predictive of parasitic Apicomplexa nucleic acid co-occurrence, supporting the fact that Apocryptovirus is a genus of parasite-infecting viruses. This is a computational proof-of-concept study in which we rapidly analyze millions of datasets from which we distilled a mechanistically, ecologically, and phylogenetically refined hypothesis. We predict that this highly diverged Ao RNA virus is biologically a T. gondii infection, and that Ao, and other viruses like it, will modulate this disease which afflicts billions worldwide.
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Affiliation(s)
- Purav Gupta
- The Woodlands Secondary School, 3225 Erindale Station Rd,Mississauga, ON L5C 1Y5, Canada
- Department of Molecular Genetics, University of Toronto, 1 King’s College Circle, Toronto, ON M5S 1A8, Canada
- The Donnelly Centre for Cellular + Biomolecular Research, University of Toronto, 160 College St, Toronto, ON M5S 3E1, Canada
- The Woodlands Secondary School, 3225 Erindale Station Rd, Mississauga, ON L5C 1Y5, Canada
| | - Aiden Hiller
- Department of Molecular Genetics, University of Toronto, 1 King’s College Circle, Toronto, ON M5S 1A8, Canada
- The Donnelly Centre for Cellular + Biomolecular Research, University of Toronto, 160 College St, Toronto, ON M5S 3E1, Canada
- The Woodlands Secondary School, 3225 Erindale Station Rd, Mississauga, ON L5C 1Y5, Canada
| | - Jawad Chowdhury
- Department of Molecular Genetics, University of Toronto, 1 King’s College Circle, Toronto, ON M5S 1A8, Canada
- The Donnelly Centre for Cellular + Biomolecular Research, University of Toronto, 160 College St, Toronto, ON M5S 3E1, Canada
- The Woodlands Secondary School, 3225 Erindale Station Rd, Mississauga, ON L5C 1Y5, Canada
| | - Declan Lim
- Department of Molecular Genetics, University of Toronto, 1 King’s College Circle, Toronto, ON M5S 1A8, Canada
- The Donnelly Centre for Cellular + Biomolecular Research, University of Toronto, 160 College St, Toronto, ON M5S 3E1, Canada
- The Woodlands Secondary School, 3225 Erindale Station Rd, Mississauga, ON L5C 1Y5, Canada
| | - Dillon Yee Lim
- The Woodlands Secondary School, 3225 Erindale Station Rd, Mississauga, ON L5C 1Y5, Canada
- Department of Physiology, Anatomy and Genetics, University of Oxford, Sherrington Building, Sherrington Road, Oxford, Oxfordshire, OX1 3PT, UK
| | - Jeroen P J Saeij
- The Woodlands Secondary School, 3225 Erindale Station Rd, Mississauga, ON L5C 1Y5, Canada
- Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California, 1 Shields Ave, Davis, CA 95616, USA
| | - Artem Babaian
- Department of Molecular Genetics, University of Toronto, 1 King’s College Circle, Toronto, ON M5S 1A8, Canada
- The Donnelly Centre for Cellular + Biomolecular Research, University of Toronto, 160 College St, Toronto, ON M5S 3E1, Canada
- The Woodlands Secondary School, 3225 Erindale Station Rd, Mississauga, ON L5C 1Y5, Canada
| | - Felipe Rodriguez
- The Woodlands Secondary School, 3225 Erindale Station Rd, Mississauga, ON L5C 1Y5, Canada
- Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California, 1 Shields Ave, Davis, CA 95616, USA
| | - Luke Pereira
- Department of Molecular Genetics, University of Toronto, 1 King’s College Circle, Toronto, ON M5S 1A8, Canada
- The Donnelly Centre for Cellular + Biomolecular Research, University of Toronto, 160 College St, Toronto, ON M5S 3E1, Canada
- The Woodlands Secondary School, 3225 Erindale Station Rd, Mississauga, ON L5C 1Y5, Canada
| | - Alejandro Morales-Tapia
- Department of Molecular Genetics, University of Toronto, 1 King’s College Circle, Toronto, ON M5S 1A8, Canada
- The Donnelly Centre for Cellular + Biomolecular Research, University of Toronto, 160 College St, Toronto, ON M5S 3E1, Canada
- The Woodlands Secondary School, 3225 Erindale Station Rd, Mississauga, ON L5C 1Y5, Canada
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35
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Adams MC, Schiltz C, Sun J, Hosford C, Johnson V, Pan H, Borbat P, Freed J, Thomason L, Court C, Court D, Chappie J. The crystal structure of bacteriophage λ RexA provides novel insights into the DNA binding properties of Rex-like phage exclusion proteins. Nucleic Acids Res 2024; 52:4659-4675. [PMID: 38554102 PMCID: PMC11077077 DOI: 10.1093/nar/gkae212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 03/07/2024] [Accepted: 03/12/2024] [Indexed: 04/01/2024] Open
Abstract
RexA and RexB function as an exclusion system that prevents bacteriophage T4rII mutants from growing on Escherichia coli λ phage lysogens. Recent data established that RexA is a non-specific DNA binding protein that can act independently of RexB to bias the λ bistable switch toward the lytic state, preventing conversion back to lysogeny. The molecular interactions underlying these activities are unknown, owing in part to a dearth of structural information. Here, we present the 2.05-Å crystal structure of the λ RexA dimer, which reveals a two-domain architecture with unexpected structural homology to the recombination-associated protein RdgC. Modelling suggests that our structure adopts a closed conformation and would require significant domain rearrangements to facilitate DNA binding. Mutagenesis coupled with electromobility shift assays, limited proteolysis, and double electron-electron spin resonance spectroscopy support a DNA-dependent conformational change. In vivo phenotypes of RexA mutants suggest that DNA binding is not a strict requirement for phage exclusion but may directly contribute to modulation of the bistable switch. We further demonstrate that RexA homologs from other temperate phages also dimerize and bind DNA in vitro. Collectively, these findings advance our mechanistic understanding of Rex functions and provide new evolutionary insights into different aspects of phage biology.
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Affiliation(s)
- Myfanwy C Adams
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Carl J Schiltz
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Jing Sun
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA
| | | | - Virginia M Johnson
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Hao Pan
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Peter P Borbat
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
- National Biomedical Resource for Advanced Electron Spin Resonance Spectroscopy, Cornell University, Ithaca, NY 14853, USA
| | - Jack H Freed
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
- National Biomedical Resource for Advanced Electron Spin Resonance Spectroscopy, Cornell University, Ithaca, NY 14853, USA
| | - Lynn C Thomason
- Center for Cancer Research, National Cancer Institute, Frederick, MD21702, USA
| | - Carolyn Court
- Center for Cancer Research, National Cancer Institute, Frederick, MD21702, USA
| | - Donald L Court
- Center for Cancer Research, National Cancer Institute, Frederick, MD21702, USA
| | - Joshua S Chappie
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA
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36
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Brytan W, Shortall K, Duarte F, Soulimane T, Padrela L. Contribution of a C-Terminal Extension to the Substrate Affinity and Oligomeric Stability of Aldehyde Dehydrogenase from Thermus thermophilus HB27. Biochemistry 2024; 63:1075-1088. [PMID: 38602394 PMCID: PMC11080044 DOI: 10.1021/acs.biochem.3c00698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 03/22/2024] [Accepted: 03/25/2024] [Indexed: 04/12/2024]
Abstract
Aldehyde dehydrogenase enzymes (ALDHs) are widely studied for their roles in disease propagation and cell metabolism. Their use in biocatalysis applications, for the conversion of aldehydes to carboxylic acids, has also been recognized. Understanding the structural features and functions of both prokaryotic and eukaryotic ALDHs is key to uncovering novel applications of the enzyme and probing its role in disease propagation. The thermostable enzyme ALDHTt originating fromThermus thermophilus, strain HB27, possesses a unique extension of its C-terminus, which has been evolutionarily excluded from mesophilic counterparts and other thermophilic enzymes in the same genus. In this work, the thermophilic adaptation is studied by the expression and optimized purification of mutant ALDHTt-508, with a 22-amino acid truncation of the C-terminus. The mutant shows increased activity throughout production compared to native ALDHTt, indicating an opening of the active site upon C-terminus truncation and giving rationale into the evolutionary exclusion of the C-terminal extension from similar thermophilic and mesophilic ALDH proteins. Additionally, the C-terminus is shown to play a role in controlling substrate specificity of native ALDH, particularly in excluding catalysis of certain large and certain aromatic ortho-substituted aldehydes, as well as modulating the protein's pH tolerance by increasing surface charge. Dynamic light scattering and size-exclusion HPLC methods are used to show the role of the C-terminus in ALDHTt oligomeric stability at the cost of catalytic efficiency. Studying the aggregation rate of ALDHTt with and without a C-terminal extension leads to the conclusion that ALDHTt follows a monomolecular reaction aggregation mechanism.
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Affiliation(s)
- Wiktoria Brytan
- Department
of Chemical Sciences, Bernal Institute,
University of Limerick, Limerick V94 T9PX, Ireland
| | - Kim Shortall
- Department
of Chemical Sciences, Bernal Institute,
University of Limerick, Limerick V94 T9PX, Ireland
| | - Francisco Duarte
- Department
of Chemical Sciences, Bernal Institute,
University of Limerick, Limerick V94 T9PX, Ireland
| | - Tewfik Soulimane
- Department
of Chemical Sciences, Bernal Institute,
University of Limerick, Limerick V94 T9PX, Ireland
- SSPC
− The Science Foundation Ireland Research Centre for Pharmaceuticals, Limerick V94 T9PX,Ireland
| | - Luis Padrela
- Department
of Chemical Sciences, Bernal Institute,
University of Limerick, Limerick V94 T9PX, Ireland
- SSPC
− The Science Foundation Ireland Research Centre for Pharmaceuticals, Limerick V94 T9PX,Ireland
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37
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Gulotta A, Polimeni M, Lenton S, Starr CG, Stradner A, Zaccarelli E, Schurtenberger P. Combining Scattering Experiments and Colloid Theory to Characterize Charge Effects in Concentrated Antibody Solutions. Mol Pharm 2024; 21:2250-2271. [PMID: 38661388 PMCID: PMC11080060 DOI: 10.1021/acs.molpharmaceut.3c01023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 04/08/2024] [Accepted: 04/08/2024] [Indexed: 04/26/2024]
Abstract
Charges and their contribution to protein-protein interactions are essential for the key structural and dynamic properties of monoclonal antibody (mAb) solutions. In fact, they influence the apparent molecular weight, the static structure factor, the collective diffusion coefficient, or the relative viscosity, and their concentration dependence. Further, charges play an important role in the colloidal stability of mAbs. There exist standard experimental tools to characterize mAb net charges, such as the measurement of the electrophoretic mobility, the second virial coefficient, or the diffusion interaction parameter. However, the resulting values are difficult to directly relate to the actual overall net charge of the antibody and to theoretical predictions based on its known molecular structure. Here, we report the results of a systematic investigation of the solution properties of a charged IgG1 mAb as a function of concentration and ionic strength using a combination of electrophoretic measurements, static and dynamic light scattering, small-angle X-ray scattering, and tracer particle-based microrheology. We analyze and interpret the experimental results using established colloid theory and coarse-grained computer simulations. We discuss the potential and limits of colloidal models for the description of the interaction effects of charged mAbs, in particular pointing out the importance of incorporating shape and charge anisotropy when attempting to predict structural and dynamic solution properties at high concentrations.
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Affiliation(s)
- Alessandro Gulotta
- Physical
Chemistry, Department of Chemistry, Lund
University, Lund SE-221 00, Sweden
| | - Marco Polimeni
- Physical
Chemistry, Department of Chemistry, Lund
University, Lund SE-221 00, Sweden
| | - Samuel Lenton
- Physical
Chemistry, Department of Chemistry, Lund
University, Lund SE-221 00, Sweden
| | - Charles G. Starr
- Biologics
Drug Product Development and Manufacturing, CMC Development, Sanofi, Framingham, Massachusetts 01701, United States
| | - Anna Stradner
- Physical
Chemistry, Department of Chemistry, Lund
University, Lund SE-221 00, Sweden
- LINXS
Institute of Advanced Neutron and X-ray Science, Scheelevägen 19, Lund SE-223 70, Sweden
| | - Emanuela Zaccarelli
- Institute
for Complex Systems, National Research Council (ISC−CNR), Piazzale Aldo Moro 5, Rome 00185, Italy
- Department
of Physics, Sapienza University of Rome, Piazzale Aldo Moro 2, Rome 00185, Italy
| | - Peter Schurtenberger
- Physical
Chemistry, Department of Chemistry, Lund
University, Lund SE-221 00, Sweden
- LINXS
Institute of Advanced Neutron and X-ray Science, Scheelevägen 19, Lund SE-223 70, Sweden
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38
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Kladova OA, Tyugashev TE, Miroshnikov AA, Novopashina DS, Kuznetsov NA, Kuznetsova AA. SNP-Associated Substitutions of Amino Acid Residues in the dNTP Selection Subdomain Decrease Polβ Polymerase Activity. Biomolecules 2024; 14:547. [PMID: 38785954 PMCID: PMC11117729 DOI: 10.3390/biom14050547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 04/18/2024] [Accepted: 04/30/2024] [Indexed: 05/25/2024] Open
Abstract
In the cell, DNA polymerase β (Polβ) is involved in many processes aimed at maintaining genome stability and is considered the main repair DNA polymerase participating in base excision repair (BER). Polβ can fill DNA gaps formed by other DNA repair enzymes. Single-nucleotide polymorphisms (SNPs) in the POLB gene can affect the enzymatic properties of the resulting protein, owing to possible amino acid substitutions. For many SNP-associated Polβ variants, an association with cancer, owing to changes in polymerase activity and fidelity, has been shown. In this work, kinetic analyses and molecular dynamics simulations were used to examine the activity of naturally occurring polymorphic variants G274R, G290C, and R333W. Previously, the amino acid substitutions at these positions have been found in various types of tumors, implying a specific role of Gly-274, Gly-290, and Arg-333 in Polβ functioning. All three polymorphic variants had reduced polymerase activity. Two substitutions-G274R and R333W-led to the almost complete disappearance of gap-filling and primer elongation activities, a decrease in the deoxynucleotide triphosphate-binding ability, and a lower polymerization constant, due to alterations of local contacts near the replaced amino acid residues. Thus, variants G274R, G290C, and R333W may be implicated in an elevated level of unrepaired DNA damage.
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Affiliation(s)
- Olga A. Kladova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (T.E.T.); (D.S.N.); (N.A.K.)
| | - Timofey E. Tyugashev
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (T.E.T.); (D.S.N.); (N.A.K.)
| | | | - Daria S. Novopashina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (T.E.T.); (D.S.N.); (N.A.K.)
| | - Nikita A. Kuznetsov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (T.E.T.); (D.S.N.); (N.A.K.)
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia;
| | - Aleksandra A. Kuznetsova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (T.E.T.); (D.S.N.); (N.A.K.)
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Tatar Yilmaz G, Yayli N, Tüzüner T, Bozdal G, Salmanli M, Renda G, Korkmaz B, Bozdeveci A, Alpay Karaoğlu Ş. Synthesis, Antimicrobial Activities, and Molecular Modeling Studies of Agents for the Sortase A Enzyme. Chem Biodivers 2024; 21:e202301659. [PMID: 38407541 DOI: 10.1002/cbdv.202301659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 02/21/2024] [Accepted: 02/24/2024] [Indexed: 02/27/2024]
Abstract
Sortase A (SrtA) is an attractive target for developing new anti-infective drugs that aim to interfere with essential virulence mechanisms, such as adhesion to host cells and biofilm formation. Herein, twenty hydroxy, nitro, bromo, fluoro, and methoxy substituted chalcone compounds were synthesized, antimicrobial activities and molecular modeling strategies against the SrtA enzyme were investigated. The most active compounds were found to be T2, T4, and T19 against Streptococcus mutans (S. mutans) with MIC values of 1.93, 3.8, 3.94 μg/mL, and docking scores of -6.46, -6.63, -6.73 kcal/mol, respectively. Also, these three active compounds showed better activity than the chlorohexidine (CHX) (MIC value: 4.88 μg/mL, docking score: -6.29 kcal/mol) in both in vitro and in silico. Structural stability and binding free energy analysis of S.mutans SrtA with active compounds were measured by molecular dynamic (MD) simulations throughout 100 nanoseconds (ns) time. It was observed that the stability of the critical interactions between these compounds and the target enzyme was preserved. To prove further, in vivo biological evaluation studies could be conducted for the most promising precursor compounds T2, T4, and T19, and it might open new avenues to the discovery of more potent SrtA inhibitors.
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Affiliation(s)
- Gizem Tatar Yilmaz
- Department of Biostatistics and Medical Informatics, Faculty of Medicine, Karadeniz Technical University, 61080, Trabzon, Turkiye
| | - Nurettin Yayli
- Department of Pharmacognosy, Faculty of Pharmacy, Karadeniz Technical University, 61080, Trabzon, Turkiye
| | - Tamer Tüzüner
- Department of Pediatric Dentistry, Faculty of Dentistry, Karadeniz Technical University, 61080, Trabzon, Turkiye
| | - Gözde Bozdal
- Department of Pharmacognosy, Faculty of Pharmacy, Karadeniz Technical University, 61080, Trabzon, Turkiye
| | - Merve Salmanli
- Department of Pediatric Dentistry, Faculty of Dentistry, Karadeniz Technical University, 61080, Trabzon, Turkiye
| | - Gülin Renda
- Department of Pharmacognosy, Faculty of Pharmacy, Karadeniz Technical University, 61080, Trabzon, Turkiye
| | - Büşra Korkmaz
- Department of Pharmacognosy, Faculty of Pharmacy, Karadeniz Technical University, 61080, Trabzon, Turkiye
| | - Arif Bozdeveci
- Department of Biology, Faculty of Arts and Sciences, Recep Tayyip Erdoğan University, 53100, Rize, Turkiye
| | - Şengül Alpay Karaoğlu
- Department of Biology, Faculty of Arts and Sciences, Recep Tayyip Erdoğan University, 53100, Rize, Turkiye
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Korasick DA, Buckley DP, Palpacelli A, Cursio I, Cesaroni E, Cheng J, Tanner JJ. Biochemical, structural, and computational analyses of two new clinically identified missense mutations of ALDH7A1. Chem Biol Interact 2024; 394:110993. [PMID: 38604394 PMCID: PMC11073572 DOI: 10.1016/j.cbi.2024.110993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 03/30/2024] [Accepted: 04/04/2024] [Indexed: 04/13/2024]
Abstract
Aldehyde dehydrogenase 7A1 (ALDH7A1) catalyzes a step of lysine catabolism. Certain missense mutations in the ALDH7A1 gene cause pyridoxine dependent epilepsy (PDE), a rare autosomal neurometabolic disorder with recessive inheritance that affects almost 1:65,000 live births and is classically characterized by recurrent seizures from the neonatal period. We report a biochemical, structural, and computational study of two novel ALDH7A1 missense mutations that were identified in a child with rare recurrent seizures from the third month of life. The mutations affect two residues in the oligomer interfaces of ALDH7A1, Arg134 and Arg441 (Arg162 and Arg469 in the HGVS nomenclature). The corresponding enzyme variants R134S and R441C (p.Arg162Ser and p.Arg469Cys in the HGVS nomenclature) were expressed in Escherichia coli and purified. R134S and R441C have 10,000- and 50-fold lower catalytic efficiency than wild-type ALDH7A1, respectively. Sedimentation velocity analytical ultracentrifugation shows that R134S is defective in tetramerization, remaining locked in a dimeric state even in the presence of the tetramer-inducing coenzyme NAD+. Because the tetramer is the active form of ALDH7A1, the defect in oligomerization explains the very low catalytic activity of R134S. In contrast, R441C exhibits wild-type oligomerization behavior, and the 2.0 Å resolution crystal structure of R441C complexed with NAD+ revealed no obvious structural perturbations when compared to the wild-type enzyme structure. Molecular dynamics simulations suggest that the mutation of Arg441 to Cys may increase intersubunit ion pairs and alter the dynamics of the active site gate. Our biochemical, structural, and computational data on two novel clinical variants of ALDH7A1 add to the complexity of the molecular determinants underlying pyridoxine dependent epilepsy.
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Affiliation(s)
- David A Korasick
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, United States
| | - David P Buckley
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, United States
| | | | - Ida Cursio
- Child Neurology and Psychiatric Unit, Pediatric Hospital G. Salesi, United Hospitals of Marche, Ancona, Italy
| | - Elisabetta Cesaroni
- Child Neurology and Psychiatric Unit, Pediatric Hospital G. Salesi, United Hospitals of Marche, Ancona, Italy
| | - Jianlin Cheng
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, 65211, United States
| | - John J Tanner
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, United States; Department of Chemistry, University of Missouri, Columbia, MO, 65211, United States.
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Lahfa M, Barthe P, de Guillen K, Cesari S, Raji M, Kroj T, Le Naour—Vernet M, Hoh F, Gladieux P, Roumestand C, Gracy J, Declerck N, Padilla A. The structural landscape and diversity of Pyricularia oryzae MAX effectors revisited. PLoS Pathog 2024; 20:e1012176. [PMID: 38709846 PMCID: PMC11132498 DOI: 10.1371/journal.ppat.1012176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 05/28/2024] [Accepted: 04/08/2024] [Indexed: 05/08/2024] Open
Abstract
Magnaporthe AVRs and ToxB-like (MAX) effectors constitute a family of secreted virulence proteins in the fungus Pyricularia oryzae (syn. Magnaporthe oryzae), which causes blast disease on numerous cereals and grasses. In spite of high sequence divergence, MAX effectors share a common fold characterized by a ß-sandwich core stabilized by a conserved disulfide bond. In this study, we investigated the structural landscape and diversity within the MAX effector repertoire of P. oryzae. Combining experimental protein structure determination and in silico structure modeling we validated the presence of the conserved MAX effector core domain in 77 out of 94 groups of orthologs (OG) identified in a previous population genomic study. Four novel MAX effector structures determined by NMR were in remarkably good agreement with AlphaFold2 (AF2) predictions. Based on the comparison of the AF2-generated 3D models we propose a classification of the MAX effectors superfamily in 20 structural groups that vary in the canonical MAX fold, disulfide bond patterns, and additional secondary structures in N- and C-terminal extensions. About one-third of the MAX family members remain singletons, without strong structural relationship to other MAX effectors. Analysis of the surface properties of the AF2 MAX models also highlights the high variability within the MAX family at the structural level, potentially reflecting the wide diversity of their virulence functions and host targets.
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Affiliation(s)
- Mounia Lahfa
- Centre de Biologie Structurale, Univ Montpellier, CNRS UMR 5048, INSERM U 1054, Montpellier, France
| | - Philippe Barthe
- Centre de Biologie Structurale, Univ Montpellier, CNRS UMR 5048, INSERM U 1054, Montpellier, France
| | - Karine de Guillen
- Centre de Biologie Structurale, Univ Montpellier, CNRS UMR 5048, INSERM U 1054, Montpellier, France
| | - Stella Cesari
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Mouna Raji
- Centre de Biologie Structurale, Univ Montpellier, CNRS UMR 5048, INSERM U 1054, Montpellier, France
| | - Thomas Kroj
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Marie Le Naour—Vernet
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - François Hoh
- Centre de Biologie Structurale, Univ Montpellier, CNRS UMR 5048, INSERM U 1054, Montpellier, France
| | - Pierre Gladieux
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Christian Roumestand
- Centre de Biologie Structurale, Univ Montpellier, CNRS UMR 5048, INSERM U 1054, Montpellier, France
| | - Jérôme Gracy
- Centre de Biologie Structurale, Univ Montpellier, CNRS UMR 5048, INSERM U 1054, Montpellier, France
| | - Nathalie Declerck
- Centre de Biologie Structurale, Univ Montpellier, CNRS UMR 5048, INSERM U 1054, Montpellier, France
| | - André Padilla
- Centre de Biologie Structurale, Univ Montpellier, CNRS UMR 5048, INSERM U 1054, Montpellier, France
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Tindall CA, Möhlis K, Rapöhn I, Dommel S, Riedl V, Schneekönig M, Höfling C, Roßner S, Stichel J, Beck-Sickinger AG, Weiner J, Heiker JT. LRP1 is the cell-surface endocytosis receptor for vaspin in adipocytes. FEBS J 2024; 291:2134-2154. [PMID: 37921063 DOI: 10.1111/febs.16991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 09/12/2023] [Accepted: 10/31/2023] [Indexed: 11/04/2023]
Abstract
Vaspin is a serine protease inhibitor that protects against adipose tissue inflammation and insulin resistance, two key drivers of adipocyte dysfunction and metabolic disorders in obesity. Inhibition of target proteases such as KLK7 has been shown to reduce adipose tissue inflammation in obesity, while vaspin binding to cell surface GRP78 has been linked to reduced obesity-induced ER stress and insulin resistance in the liver. However, the molecular mechanisms by which vaspin directly affects cellular processes in adipocytes remain unknown. Using fluorescently labeled vaspin, we found that vaspin is rapidly internalized by mouse and human adipocytes, but less efficiently by endothelial, kidney, liver, and neuronal cells. Internalization occurs by active, clathrin-mediated endocytosis, which is dependent on vaspin binding to the LRP1 receptor, rather than GRP78 as previously thought. This was demonstrated by competition experiments and RNAi-mediated knock-down in adipocytes and by rescuing vaspin internalization in LRP1-deficient Pea13 cells after transfection with a functional LRP1 minireceptor. Vaspin internalization is further increased in mature adipocytes after insulin-stimulated translocation of LRP1. Although vaspin has nanomolar affinity for LRP1 clusters II-IV, binding to cell surface heparan sulfates is required for efficient LRP1-mediated internalization. Native, but not cleaved vaspin, and also vaspin polymers are efficiently endocytosed, and ultimately targeted for lysosomal degradation. Our study provides mechanistic insight into the uptake and degradation of vaspin in adipocytes, thereby broadening our understanding of its functional repertoire. We hypothesize the vaspin-LRP1 axis to be an important mediator of vaspin effects not only in adipose tissue but also in other LRP1-expressing cells.
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Affiliation(s)
- Catherine A Tindall
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Zentrum München at the University of Leipzig and University Hospital Leipzig, Germany
- Faculty of Life Sciences, Institute of Biochemistry, University of Leipzig, Germany
| | - Kevin Möhlis
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Zentrum München at the University of Leipzig and University Hospital Leipzig, Germany
| | - Inka Rapöhn
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Zentrum München at the University of Leipzig and University Hospital Leipzig, Germany
| | - Sebastian Dommel
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Zentrum München at the University of Leipzig and University Hospital Leipzig, Germany
- Faculty of Life Sciences, Institute of Biochemistry, University of Leipzig, Germany
| | - Veronika Riedl
- Faculty of Life Sciences, Institute of Biochemistry, University of Leipzig, Germany
| | - Michael Schneekönig
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Zentrum München at the University of Leipzig and University Hospital Leipzig, Germany
| | - Corinna Höfling
- Paul Flechsig Institute for Brain Research, University of Leipzig, Germany
| | - Steffen Roßner
- Paul Flechsig Institute for Brain Research, University of Leipzig, Germany
| | - Jan Stichel
- Faculty of Life Sciences, Institute of Biochemistry, University of Leipzig, Germany
| | | | - Juliane Weiner
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Germany
| | - John T Heiker
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Zentrum München at the University of Leipzig and University Hospital Leipzig, Germany
- Faculty of Life Sciences, Institute of Biochemistry, University of Leipzig, Germany
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Ślusarz MJ, Lipińska AD. An intrinsic network of polar interactions is responsible for binding of UL49.5 C-degron by the CRL2 KLHDC3 ubiquitin ligase. Proteins 2024; 92:610-622. [PMID: 38069558 DOI: 10.1002/prot.26651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 11/14/2023] [Accepted: 11/27/2023] [Indexed: 04/13/2024]
Abstract
Bovine herpesvirus type 1 (BoHV-1) is a pathogen of cattle responsible for infectious bovine rhinotracheitis. The BoHV-1 UL49.5 is a transmembrane protein that binds to the transporter associated with antigen processing (TAP) and downregulates cell surface expression of the antigenic peptide complexes with the major histocompatibility complex class I (MHC-I). KLHDC3 is a kelch domain-containing protein 3 and a substrate receptor of a cullin2-RING (CRL2) E3 ubiquitin ligase. Recently, it has been identified that CRL2KLHDC3 is responsible for UL49.5-triggered TAP degradation via a C-degron pathway and the presence of the degron sequence does not lead to the degradation of UL49.5 itself. The molecular modeling of KLHDC3 in complexes with four UL49.5 C-terminal decapeptides (one native protein and three mutants) revealed their activity to be closely correlated with the conformation which they adopt in KLHDC3 binding cleft. To analyze the interaction between UL49.5 and KLHDC3 in detail, in this work a total of 3.6 μs long molecular dynamics simulations have been performed. The complete UL49.5-KLHDC3 complexes were embedded into the fully hydrated all-atom lipid membrane model with explicit water molecules. The network of polar interactions has been proposed to be responsible for the recognition and binding of the degron in KLHDC3. The interaction network within the binding pocket appeared to be very similar between two CRL2 substrate receptors: KLHDC3 and KLHDC2.
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Affiliation(s)
| | - Andrea D Lipińska
- Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, Gdańsk, Poland
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Kathe NC, Novakovic M, Allain FHT. Buffer choice and pH strongly influence phase separation of SARS-CoV-2 nucleocapsid with RNA. Mol Biol Cell 2024; 35:ar73. [PMID: 38568799 DOI: 10.1091/mbc.e23-12-0500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2024] Open
Abstract
The SARS-CoV-2 nucleocapsid (N) protein is crucial for virus replication and genome packaging. N protein forms biomolecular condensates both in vitro and in vivo in a process known as liquid-liquid phase separation (LLPS), but the exact factors regulating LLPS of N protein are not fully understood. Here, we show that pH and buffer choice have a profound impact on LLPS of N protein. The degree of phase separation is highly dependent on the pH of the solution, which is correlated with histidine protonation in N protein. Specifically, we demonstrate that protonation of H356 is essential for LLPS in phosphate buffer. Moreover, electrostatic interactions of buffer molecules with specific amino acid residues are able to alter the net charge of N protein, thus influencing its ability to undergo phase separation in the presence of RNA. Overall, these findings reveal that even subtle changes in amino acid protonation or surface charge caused by the pH and buffer system can strongly influence the LLPS behavior, and point to electrostatic interactions as the main driving forces of N protein phase separation. Further, our findings emphasize the importance of these experimental parameters when studying phase separation of biomolecules, especially in the context of viral infections where the intracellular milieu undergoes drastic changes and intracellular pH normally decreases.
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Affiliation(s)
- Nina C Kathe
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - Mihajlo Novakovic
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - Frédéric H-T Allain
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
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45
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Motsa BB, Sharma T, Cioffi MD, Chapagain PP, Stahelin RV. Minor electrostatic changes robustly increase VP40 membrane binding, assembly, and budding of Ebola virus matrix protein derived virus-like particles. J Biol Chem 2024; 300:107213. [PMID: 38522519 PMCID: PMC11061732 DOI: 10.1016/j.jbc.2024.107213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 03/05/2024] [Accepted: 03/15/2024] [Indexed: 03/26/2024] Open
Abstract
Ebola virus (EBOV) is a filamentous negative-sense RNA virus, which causes severe hemorrhagic fever. There are limited vaccines or therapeutics for prevention and treatment of EBOV, so it is important to get a detailed understanding of the virus lifecycle to illuminate new drug targets. EBOV encodes for the matrix protein, VP40, which regulates assembly and budding of new virions from the inner leaflet of the host cell plasma membrane (PM). In this work, we determine the effects of VP40 mutations altering electrostatics on PM interactions and subsequent budding. VP40 mutations that modify surface electrostatics affect viral assembly and budding by altering VP40 membrane-binding capabilities. Mutations that increase VP40 net positive charge by one (e.g., Gly to Arg or Asp to Ala) increase VP40 affinity for phosphatidylserine and phosphatidylinositol 4,5-bisphosphate in the host cell PM. This increased affinity enhances PM association and budding efficiency leading to more effective formation of virus-like particles. In contrast, mutations that decrease net positive charge by one (e.g., Gly to Asp) lead to a decrease in assembly and budding because of decreased interactions with the anionic PM. Taken together, our results highlight the sensitivity of slight electrostatic changes on the VP40 surface for assembly and budding. Understanding the effects of single amino acid substitutions on viral budding and assembly will be useful for explaining changes in the infectivity and virulence of different EBOV strains, VP40 variants that occur in nature, and for long-term drug discovery endeavors aimed at EBOV assembly and budding.
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Affiliation(s)
- Balindile B Motsa
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, Purdue Institute of Inflammation, Immunology, and Infectious Disease, Purdue University, West Lafayette, Indiana, USA
| | - Tej Sharma
- Department of Physics, Florida International University, Miami, Florida, USA
| | - Michael D Cioffi
- Department of Physics, Florida International University, Miami, Florida, USA
| | - Prem P Chapagain
- Department of Physics, Florida International University, Miami, Florida, USA; Biomolecular Sciences Institute, Florida International University, Miami, Florida, USA
| | - Robert V Stahelin
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, Purdue Institute of Inflammation, Immunology, and Infectious Disease, Purdue University, West Lafayette, Indiana, USA.
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46
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Bosy M, Scroggs MW, Betcke T, Burman E, Cooper CD. Coupling finite and boundary element methods to solve the Poisson-Boltzmann equation for electrostatics in molecular solvation. J Comput Chem 2024; 45:787-797. [PMID: 38126925 DOI: 10.1002/jcc.27262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 10/03/2023] [Accepted: 11/05/2023] [Indexed: 12/23/2023]
Abstract
The Poisson-Boltzmann equation is widely used to model electrostatics in molecular systems. Available software packages solve it using finite difference, finite element, and boundary element methods, where the latter is attractive due to the accurate representation of the molecular surface and partial charges, and exact enforcement of the boundary conditions at infinity. However, the boundary element method is limited to linear equations and piecewise constant variations of the material properties. In this work, we present a scheme that couples finite and boundary elements for the linearised Poisson-Boltzmann equation, where the finite element method is applied in a confined solute region and the boundary element method in the external solvent region. As a proof-of-concept exercise, we use the simplest methods available: Johnson-Nédélec coupling with mass matrix and diagonal preconditioning, implemented using the Bempp-cl and FEniCSx libraries via their Python interfaces. We showcase our implementation by computing the polar component of the solvation free energy of a set of molecules using a constant and a Gaussian-varying permittivity. As validation, we compare against well-established finite difference solvers for an extensive binding energy data set, and with the finite difference code APBS (to 0.5%) for Gaussian permittivities. We also show scaling results from protein G B1 (955 atoms) up to immunoglobulin G (20,148 atoms). For small problems, the coupled method was efficient, outperforming a purely boundary integral approach. For Gaussian-varying permittivities, which are beyond the applicability of boundary elements alone, we were able to run medium to large-sized problems on a single workstation. The development of better preconditioning techniques and the use of distributed memory parallelism for larger systems remains an area for future work. We hope this work will serve as inspiration for future developments that consider space-varying field parameters, and mixed linear-nonlinear schemes for molecular electrostatics with implicit solvent models.
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Affiliation(s)
- Michał Bosy
- School of Computer Science and Mathematics, Kingston University London, Kingston upon Thames, UK
| | | | - Timo Betcke
- Department of Mathematics, University College London, London, UK
| | - Erik Burman
- Department of Mathematics, University College London, London, UK
| | - Christopher D Cooper
- Department of Mechanical Engineering and Centro Científico Tecnológico de Valparaíso, Universidad Técnica Federico Santa María, Valparaíso, Chile
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47
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Johann F, Wöll S, Gieseler H. "Negative" Impact: The Role of Payload Charge in the Physicochemical Stability of Auristatin Antibody-Drug Conjugates. J Pharm Sci 2024:S0022-3549(24)00150-3. [PMID: 38679233 DOI: 10.1016/j.xphs.2024.04.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 04/21/2024] [Accepted: 04/22/2024] [Indexed: 05/01/2024]
Abstract
Antibody-drug conjugates (ADCs) tend to be less stable than their parent antibodies, which is often attributed to the hydrophobic nature of their drug payloads. This study investigated how the payload charge affects ADC stability by comparing two interchain cysteine ADCs that had matched drug-to-antibody ratios and identical linkers but differently charged auristatin payloads, vcMMAE (neutral) and vcMMAF (negative). Both ADCs exhibited higher aggregation than their parent antibody under shaking stress and thermal stress conditions. However, conjugation with vcMMAF increased the aggregation rates to a greater extent than conjugation with uncharged but more hydrophobic vcMMAE. Consistent with the payload logD values, ADC-vcMMAE showed the greatest increase in hydrophobicity but minor changes in charge compared with the parent antibody, as indicated by hydrophobic interaction chromatography and capillary electrophoresis data. In contrast, ADC-vcMMAF showed a decrease in net charge and isoelectric point along with an increase in charge heterogeneity. This charge alteration likely contributed to a reduced electrostatic repulsion and increased surface activity in ADC-vcMMAF, thus affecting its aggregation propensity. These findings suggest that not only the hydrophobicity of the payload, but also its charge should be considered as a critical factor affecting the stability of ADCs.
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Affiliation(s)
- Florian Johann
- Friedrich-Alexander University (FAU) Erlangen-Nürnberg, Department of Pharmaceutical Technology and Biopharmacy, Freeze Drying Focus Group (FDFG), Cauerstraße 4, 91058 Erlangen, Germany; Merck KGaA, Global CMC Development, Frankfurter Straße 250, 64293 Darmstadt, Germany
| | - Steffen Wöll
- Merck KGaA, Global CMC Development, Frankfurter Straße 250, 64293 Darmstadt, Germany
| | - Henning Gieseler
- Friedrich-Alexander University (FAU) Erlangen-Nürnberg, Department of Pharmaceutical Technology and Biopharmacy, Freeze Drying Focus Group (FDFG), Cauerstraße 4, 91058 Erlangen, Germany; GILYOS GmbH, Friedrich-Bergius-Ring 15, 97076 Würzburg, Germany.
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48
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Toyama Y, Shimada I. NMR characterization of RNA binding property of the DEAD-box RNA helicase DDX3X and its implications for helicase activity. Nat Commun 2024; 15:3303. [PMID: 38664397 PMCID: PMC11045745 DOI: 10.1038/s41467-024-47659-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 04/05/2024] [Indexed: 04/28/2024] Open
Abstract
The DEAD-box RNA helicase (DDX) plays a central role in many aspects of RNA metabolism by remodeling the defined structure of RNA molecules. While a number of structural studies have revealed the atomistic details of the interaction between DDX and RNA ligands, the molecular mechanism of how this molecule unwinds a structured RNA into an unstructured single-stranded RNA (ssRNA) has largely remained elusive. This is due to challenges in structurally characterizing the unwinding intermediate state and the lack of thermodynamic details underlying this process. In this study, we use solution nuclear magnetic resonance (NMR) spectroscopy to characterize the interaction of human DDX3X, a member of the DDX family, with various RNA ligands. Our results show that the inherent binding affinity of DDX3X for ssRNA is significantly higher than that for structured RNA elements. This preferential binding, accompanied by the formation of a domain-closed conformation in complex with ssRNA, effectively stabilizes the denatured ssRNA state and thus underlies the unwinding activity of DDX3X. Our results provide a thermodynamic and structural basis for the DDX function, whereby DDX can recognize and remodel a distinct set of structured RNAs to participate in a wide range of physiological processes.
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Affiliation(s)
- Yuki Toyama
- RIKEN Center for Biosystems Dynamics Research (BDR), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.
| | - Ichio Shimada
- RIKEN Center for Biosystems Dynamics Research (BDR), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-4-4 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8528, Japan.
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49
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Mahalingan KK, Grotjahn DA, Li Y, Lander GC, Zehr EA, Roll-Mecak A. Structural basis for α-tubulin-specific and modification state-dependent glutamylation. Nat Chem Biol 2024:10.1038/s41589-024-01599-0. [PMID: 38658656 DOI: 10.1038/s41589-024-01599-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 03/06/2024] [Indexed: 04/26/2024]
Abstract
Microtubules have spatiotemporally complex posttranslational modification patterns. Tubulin tyrosine ligase-like (TTLL) enzymes introduce the most prevalent modifications on α-tubulin and β-tubulin. How TTLLs specialize for specific substrate recognition and ultimately modification-pattern generation is largely unknown. TTLL6, a glutamylase implicated in ciliopathies, preferentially modifies tubulin α-tails in microtubules. Cryo-electron microscopy, kinetic analysis and single-molecule biochemistry reveal an unprecedented quadrivalent recognition that ensures simultaneous readout of microtubule geometry and posttranslational modification status. By binding to a β-tubulin subunit, TTLL6 modifies the α-tail of the longitudinally adjacent tubulin dimer. Spanning two tubulin dimers along and across protofilaments (PFs) ensures fidelity of recognition of both the α-tail and the microtubule. Moreover, TTLL6 reads out and is stimulated by glutamylation of the β-tail of the laterally adjacent tubulin dimer, mediating crosstalk between α-tail and β-tail. This positive feedback loop can generate localized microtubule glutamylation patterns. Our work uncovers general principles that generate tubulin chemical and topographic complexity.
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Affiliation(s)
- Kishore K Mahalingan
- Cell Biology and Biophysics Unit, Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Danielle A Grotjahn
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute La Jolla, La Jolla, CA, USA
| | - Yan Li
- Proteomics Core Facility, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Gabriel C Lander
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute La Jolla, La Jolla, CA, USA
| | - Elena A Zehr
- Cell Biology and Biophysics Unit, Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Antonina Roll-Mecak
- Cell Biology and Biophysics Unit, Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA.
- Biochemistry & Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, MD, USA.
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50
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Arifuzzaman M, Kwon E, Kim DY. Structural insights into the regulation of protein-arginine kinase McsB by McsA. Proc Natl Acad Sci U S A 2024; 121:e2320312121. [PMID: 38625935 PMCID: PMC11046695 DOI: 10.1073/pnas.2320312121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Accepted: 03/17/2024] [Indexed: 04/18/2024] Open
Abstract
In gram-positive bacteria, phosphorylated arginine functions as a protein degradation signal in a similar manner as ubiquitin in eukaryotes. The protein-arginine phosphorylation is mediated by the McsAB complex, where McsB possesses kinase activity and McsA modulates McsB activity. Although mcsA and mcsB are regulated within the same operon, the role of McsA in kinase activity has not yet been clarified. In this study, we determined the molecular mechanism by which McsA regulates kinase activity. The crystal structure of the McsAB complex shows that McsA binds to the McsB kinase domain through a second zinc-coordination domain and the subsequent loop region. This binding activates McsB kinase activity by rearranging the catalytic site, preventing McsB self-assembly, and enhancing stoichiometric substrate binding. The first zinc-coordination and coiled-coil domains of McsA further activate McsB by reassembling the McsAB oligomer. These results demonstrate that McsA is the regulatory subunit for the reconstitution of the protein-arginine kinase holoenzyme. This study provides structural insight into how protein-arginine kinase directs the cellular protein degradation system.
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Affiliation(s)
- Md Arifuzzaman
- College of Pharmacy, Yeungnam University, Gyeongsan38541, Republic of Korea
| | - Eunju Kwon
- Division of Life Science, Gyeongsang National University, Jinju52828, Republic of Korea
- Research Institute of Molecular Alchemy, Gyeongsang National University, Jinju52828, Republic of Korea
| | - Dong Young Kim
- College of Pharmacy, Yeungnam University, Gyeongsan38541, Republic of Korea
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