1
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Larson NR, Bou-Assaf GM, Laue TM, Berkowitz SA. Using absorbance detection for hs-SV-AUC characterization of adeno-associated virus. Anal Biochem 2024; 694:115617. [PMID: 39019206 DOI: 10.1016/j.ab.2024.115617] [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: 04/09/2024] [Revised: 07/09/2024] [Accepted: 07/11/2024] [Indexed: 07/19/2024]
Abstract
Data are presented demonstrating that absorbance detection can be used during high-speed sedimentation velocity analytical ultracentrifugation (hs-SV-AUC) experiments to characterize the size distribution of adeno-associated virus (AAV) drug products accurately. Advantages and limitations of being able to use this detector in this specific type of SV-AUC experiment are discussed.
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Affiliation(s)
- Nicholas R Larson
- Analytical Development, Biogen, 225 Binney St, Cambridge, MA, 02142, USA
| | - George M Bou-Assaf
- Analytical Development, Biogen, 225 Binney St, Cambridge, MA, 02142, USA
| | - Thomas M Laue
- Carpenter Professor Emeritus, University of New Hampshire, 10 Kelsey Road, Lee, NH, 03861, USA
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2
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Kovalevsky A, Aniana A, Ghirlando R, Coates L, Drago VN, Wear L, Gerlits O, Nashed NT, Louis JM. Effects of SARS-CoV-2 Main Protease Mutations at Positions L50, E166, and L167 Rendering Resistance to Covalent and Noncovalent Inhibitors. J Med Chem 2024. [PMID: 39370853 DOI: 10.1021/acs.jmedchem.4c01781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/08/2024]
Abstract
SARS-CoV-2 propagation under nirmatrelvir and ensitrelvir pressure selects for main protease (MPro) drug-resistant mutations E166V (DRM2), L50F/E166V (DRM3), E166A/L167F (DRM4), and L50F/E166A/L167F (DRM5). DRM2-DRM5 undergoes N-terminal autoprocessing to produce mature MPro with dimer dissociation constants (Kdimer) 2-3 times larger than that of the wildtype. Co-selection of L50F restores catalytic activity of DRM2 and DRM4 from ∼10 to 30%, relative to that of the wild-type enzyme, without altering Kdimer. Binding affinities and thermodynamic profiles that parallel the drug selection pressure, exhibiting significant decreases in affinity through entropy/enthalpy compensation, were compared with GC373. Reorganization of the active sites due to mutations observed in the inhibitor-free DRM3 and DRM4 structures as compared to MProWT may account for the reduced binding affinities, although DRM2 and DRM3 complexes with ensitrelvir are almost identical to MProWT-ensitrelvir. Chemical reactivity changes of the mutant active sites due to differences in electrostatic and protein dynamics effects likely contribute to losses in binding affinities.
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Affiliation(s)
- Andrey Kovalevsky
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, United States
| | - Annie Aniana
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, Maryland 20892-0520, United States
| | - Rodolfo Ghirlando
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, Maryland 20892-0540, United States
| | - Leighton Coates
- Second Target Station, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, United States
| | - Victoria N Drago
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, United States
| | - Lauren Wear
- Department of Natural Sciences, Tennessee Wesleyan University, Athens, Tennessee 37303, United States
| | - Oksana Gerlits
- Department of Natural Sciences, Tennessee Wesleyan University, Athens, Tennessee 37303, United States
| | - Nashaat T Nashed
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, Maryland 20892-0520, United States
| | - John M Louis
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, Maryland 20892-0520, United States
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3
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Zhang J, Liu L, Li M, Liu H, Gong X, Tang Y, Zhang Y, Zhou X, Lin Z, Guo H, Pan L. Molecular basis of the recognition of the active Rab8a by Optineurin. J Mol Biol 2024:168811. [PMID: 39374890 DOI: 10.1016/j.jmb.2024.168811] [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: 07/11/2024] [Revised: 09/25/2024] [Accepted: 09/30/2024] [Indexed: 10/09/2024]
Abstract
Optineurin (OPTN), a multifunctional adaptor protein in mammals, plays critical roles in many cellular processes, such as vesicular trafficking and autophagy. Notably, mutations in optineurin are directly associated with many human diseases, such as amyotrophic lateral sclerosis (ALS). OPTN can specifically recognize Rab8a and the GTPase-activating protein TBC1D17, and facilitates the inactivation of Rab8a mediated by TBC1D17, but with poorly understood mechanism. Here, using biochemical and structural approaches, we systematically characterize the interaction between OPTN and Rab8a, revealing that OPTN selectively recognizes the GTP-bound active Rab8a through its leucine-zipper domain (LZD). The determined crystal structure of OPTN LZD in complex with the active Rab8a not only elucidates the detailed binding mechanism of OPTN with Rab8a but also uncovers a unique binding mode of Rab8a with its effectors. Furthermore, we demonstrate that the central coiled-coil domain of OPTN and the active Rab8a can simultaneously interact with the TBC domain of TBC1D17 to form a ternary complex. Finally, based on the OPTN LZD/Rab8a complex structure and relevant biochemical analyses, we also evaluate several known ALS-associated mutations found in the LZD of OPTN. Collectively, our findings provide mechanistic insights into the interaction of OPTN with Rab8a, expanding our understanding of the binding modes of Rab8a with its effectors and the potential etiology of diseases caused by OPTN mutations.
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Affiliation(s)
- Jing Zhang
- College of Chemistry and Materials Science, Sichuan Normal University, Chengdu, Sichuan 610068, China; State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Lei Liu
- College of Chemistry and Materials Science, Sichuan Normal University, Chengdu, Sichuan 610068, China; State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Miao Li
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200032, China; School of Chemistry and Materials Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, 1 Sub-lane Xiangshan, Hangzhou 310024, China
| | - Haobo Liu
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Xinyu Gong
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yubin Tang
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yuchao Zhang
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Xindi Zhou
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Zhiqiao Lin
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Hanbo Guo
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Lifeng Pan
- College of Chemistry and Materials Science, Sichuan Normal University, Chengdu, Sichuan 610068, China; State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200032, China; School of Chemistry and Materials Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, 1 Sub-lane Xiangshan, Hangzhou 310024, China.
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4
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Mok CY, Chu HY, Lam WWL, Au SWN. Structural insights into the assembly pathway of the Helicobacter pylori CagT4SS outer membrane core complex. Structure 2024; 32:1725-1736.e4. [PMID: 39032488 DOI: 10.1016/j.str.2024.06.019] [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: 03/14/2024] [Revised: 05/16/2024] [Accepted: 06/25/2024] [Indexed: 07/23/2024]
Abstract
Cag type IV secretion system (CagT4SS) translocates oncoprotein cytotoxin-associated gene A (CagA) into host cells and plays a key role in the pathogenesis of Helicobacter pylori. The structure of the outer membrane core complex (OMCC) in CagT4SS consists of CagX, CagY, CagM, CagT, and Cag3 in a stoichiometric ratio of 1:1:2:2:5 with 14-fold symmetry. However, the assembly pathway of OMCC remains elusive. Here, we report the crystal structures of CagT and Cag3-CagT complex, and the structural dynamics of Cag3 and CagT using hydrogen deuterium exchange-mass spectrometry (HDX-MS). The interwoven interaction of Cag3 and CagT involves conformational changes of CagT and β strand swapping. In conjunction with biochemical and biophysical assays, we further demonstrate the different oligomerization states of Cag3 and Cag3-CagT complex. Additionally, the association with CagM requires the pre-formation of Cag3-CagT complex. These results demonstrate the generation of different intermediate sub-assemblies and their structural flexibility, potentially representing different building blocks for OMCC assembly.
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Affiliation(s)
- Chin Yu Mok
- Center for Protein Science and Crystallography, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Hoi Yee Chu
- Center for Protein Science and Crystallography, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Wendy Wai Ling Lam
- Center for Protein Science and Crystallography, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Shannon Wing Ngor Au
- Center for Protein Science and Crystallography, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
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5
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Fan S, Liu J, Chofflet N, Bailey AO, Russell WK, Zhang Z, Takahashi H, Ren G, Rudenko G. Molecular mechanism of contactin 2 homophilic interaction. Structure 2024; 32:1652-1666.e8. [PMID: 38968938 PMCID: PMC11455609 DOI: 10.1016/j.str.2024.06.004] [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: 04/12/2024] [Revised: 05/23/2024] [Accepted: 06/10/2024] [Indexed: 07/07/2024]
Abstract
Contactin 2 (CNTN2) is a cell adhesion molecule involved in axon guidance, neuronal migration, and fasciculation. The ectodomains of CNTN1-CNTN6 are composed of six Ig domains (Ig1-Ig6) and four FN domains. Here, we show that CNTN2 forms transient homophilic interactions (KD ∼200 nM). Cryo-EM structures of full-length CNTN2 and CNTN2_Ig1-Ig6 reveal a T-shaped homodimer formed by intertwined, parallel monomers. Unexpectedly, the horseshoe-shaped Ig1-Ig4 headpieces extend their Ig2-Ig3 tips outwards on either side of the homodimer, while Ig4, Ig5, Ig6, and the FN domains form a central stalk. Cross-linking mass spectrometry and cell-based binding assays confirm the 3D assembly of the CNTN2 homodimer. The interface mediating homodimer formation differs between CNTNs, as do the homophilic versus heterophilic interaction mechanisms. The CNTN family thus encodes a versatile molecular platform that supports a very diverse portfolio of protein interactions and that can be leveraged to strategically guide neural circuit development.
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Affiliation(s)
- Shanghua Fan
- Department of Pharmacology and Toxicology; University of Texas Medical Branch, Galveston, TX 77555, USA; Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Jianfang Liu
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| | - Nicolas Chofflet
- Synapse Development and Plasticity Research Unit, Institut de Recherches Cliniques de Montréal, Montreal, QC H2W 1R7, Canada; Integrated Program in Neuroscience, McGill University, Montreal, QC H3A 2B2, Canada
| | - Aaron O Bailey
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - William K Russell
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Ziqi Zhang
- Synapse Development and Plasticity Research Unit, Institut de Recherches Cliniques de Montréal, Montreal, QC H2W 1R7, Canada
| | - Hideto Takahashi
- Synapse Development and Plasticity Research Unit, Institut de Recherches Cliniques de Montréal, Montreal, QC H2W 1R7, Canada; Department of Medicine, Université de Montréal, Montreal, QC H3T 1J4, Canada; Division of Experimental Medicine, McGill University, Montreal, QC H3A 0G4, Canada.
| | - Gang Ren
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| | - Gabby Rudenko
- Department of Pharmacology and Toxicology; University of Texas Medical Branch, Galveston, TX 77555, USA; Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA.
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6
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Medrano FJ, Hernando-Amado S, Martínez JL, Romero A. A new type of Class C β-lactamases defined by PIB-1. A metal-dependent carbapenem-hydrolyzing β-lactamase, from Pseudomonas aeruginosa: Structural and functional analysis. Int J Biol Macromol 2024; 277:134298. [PMID: 39097051 DOI: 10.1016/j.ijbiomac.2024.134298] [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: 04/03/2024] [Revised: 07/18/2024] [Accepted: 07/28/2024] [Indexed: 08/05/2024]
Abstract
Antibiotic resistance is one of most important health concerns nowadays, and β-lactamases are the most important resistance determinants. These enzymes, based on their structural and functional characteristics, are grouped in four categories (A, B, C and D). We have solved the structure of PIB-1, a Pseudomonas aeruginosa chromosomally-encoded β-lactamase, in its apo form and in complex with meropenem and zinc. These crystal structures show that it belongs to the Class C β-lactamase group, although it shows notable differences, especially in the Ω- and P2-loops, which are important for the enzymatic activity. Functional analysis showed that PIB-1 is able to degrade carbapenems but not cephalosporins, the typical substrate of Class C β-lactamases, and that its catalytic activity increases in the presence of metal ions, especially zinc. They do not bind to the active-site but they induce the formation of trimers that show an increased capacity for the degradation of the antibiotics, suggesting that this oligomer is more active than the other oligomeric species. While PIB-1 is structurally a Class C β-lactamase, the low sequence conservation, substrate profile and its metal-dependence, prompts us to position this enzyme as the founder of a new group inside the Class C β-lactamases. Consequently, its diversity might be wider than expected.
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Affiliation(s)
- Francisco Javier Medrano
- Department of Structural and Chemical Biology, Centro de Investigaciones Biológicas Margarita Salas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain.
| | - Sara Hernando-Amado
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CSIC, Darwin 3, 28043 Madrid, Spain
| | - José Luis Martínez
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CSIC, Darwin 3, 28043 Madrid, Spain
| | - Antonio Romero
- Department of Structural and Chemical Biology, Centro de Investigaciones Biológicas Margarita Salas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain.
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7
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Cho C, Fei C, Jiang B, Yang W, Yuan HS. Molecular mechanisms for DNA methylation defects induced by ICF syndrome-linked mutations in DNMT3B. Protein Sci 2024; 33:e5131. [PMID: 39290110 PMCID: PMC11408749 DOI: 10.1002/pro.5131] [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: 04/23/2024] [Revised: 06/19/2024] [Accepted: 07/14/2024] [Indexed: 09/19/2024]
Abstract
DNA methyltransferase 3B (DNMT3B) plays a crucial role in DNA methylation during mammalian development. Mutations in DNMT3B are associated with human genetic diseases, particularly immunodeficiency, centromere instability, facial anomalies (ICF) syndrome. Although ICF syndrome-related missense mutations in the DNMT3B have been identified, their precise impact on protein structure and function remains inadequately explored. Here, we delve into the impact of four ICF syndrome-linked mutations situated in the DNMT3B dimeric interface (H814R, D817G, V818M, and R823G), revealing that each of these mutations compromises DNA-binding and methyltransferase activities to varying degrees. We further show that H814R, D817G, and V818M mutations severely disrupt the proper assembly of DNMT3B homodimer, whereas R823G does not. We also determined the first crystal structure of the methyltransferase domain of DNMT3B-DNMT3L tetrameric complex hosting the R823G mutation showing that the R823G mutant displays diminished hydrogen bonding interactions around T775, K777, G823, and Q827 in the protein-DNA interface, resulting in reduced DNA-binding affinity and a shift in sequence preference of +1 to +3 flanking positions. Altogether, our study uncovers a wide array of fundamental defects triggered by DNMT3B mutations, including the disassembly of DNMT3B dimers, reduced DNA-binding capacity, and alterations in flanking sequence preferences, leading to aberrant DNA hypomethylation and ICF syndrome.
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Affiliation(s)
- Chao‐Cheng Cho
- Institute of Molecular Biology, Academia SinicaTaipeiTaiwan, ROC
| | - Cheng‐Yin Fei
- Institute of Molecular Biology, Academia SinicaTaipeiTaiwan, ROC
| | - Bo‐Chen Jiang
- Institute of Molecular Biology, Academia SinicaTaipeiTaiwan, ROC
| | - Wei‐Zen Yang
- Institute of Molecular Biology, Academia SinicaTaipeiTaiwan, ROC
| | - Hanna S. Yuan
- Institute of Molecular Biology, Academia SinicaTaipeiTaiwan, ROC
- Graduate Institute of Biochemistry and Molecular BiologyNational Taiwan UniversityTaipeiTaiwan, ROC
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8
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Ramprasad S, Nyarko A. Ensembles of interconverting protein complexes with multiple interaction domains. Curr Opin Struct Biol 2024; 88:102874. [PMID: 38981144 DOI: 10.1016/j.sbi.2024.102874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 05/22/2024] [Accepted: 06/11/2024] [Indexed: 07/11/2024]
Abstract
Many critical biological processes depend on protein complexes that exist as ensembles of subcomplexes rather than a discrete complex. The subcomplexes dynamically interconvert with one another, and the ability to accurately resolve the composition of the diverse molecular species in the ensemble is crucial for understanding the contribution of each subcomplex to the overall function of the protein complex. Advances in computational programs have made it possible to predict the various molecular species in these ensembles, but experimental approaches to identify the pool of subcomplexes and associated stoichiometries are often challenging. This review highlights some experimental approaches that can be used to resolve the diverse molecular species in protein complexes that exist as ensembles of sub complexes.
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Affiliation(s)
- Sanjay Ramprasad
- Department of Biochemistry & Biophysics, Oregon State University, Corvallis, OR 97331, USA
| | - Afua Nyarko
- Department of Biochemistry & Biophysics, Oregon State University, Corvallis, OR 97331, USA.
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9
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Michael Sabo T, Trent JO, Chaires JB, Monsen RC. Strategy for modeling higher-order G-quadruplex structures recalcitrant to NMR determination. Methods 2024; 230:9-20. [PMID: 39032720 DOI: 10.1016/j.ymeth.2024.07.004] [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: 04/05/2024] [Revised: 06/22/2024] [Accepted: 07/17/2024] [Indexed: 07/23/2024] Open
Abstract
Guanine-rich nucleic acids can form intramolecularly folded four-stranded structures known as G-quadruplexes (G4s). Traditionally, G4 research has focused on short, highly modified DNA or RNA sequences that form well-defined homogeneous compact structures. However, the existence of longer sequences with multiple G4 repeats, from proto-oncogene promoters to telomeres, suggests the potential for more complex higher-order structures with multiple G4 units that might offer selective drug-targeting sites for therapeutic development. These larger structures present significant challenges for structural characterization by traditional high-resolution methods like multi-dimensional NMR and X-ray crystallography due to their molecular complexity. To address this current challenge, we have developed an integrated structural biology (ISB) platform, combining experimental and computational methods to determine self-consistent molecular models of higher-order G4s (xG4s). Here we outline our ISB method using two recent examples from our lab, an extended c-Myc promoter and long human telomere G4 repeats, that highlights the utility and generality of our approach to characterizing biologically relevant xG4s.
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Affiliation(s)
- T Michael Sabo
- UofL Health Brown Cancer Center, University of Louisville, Louisville, KY, United States
| | - John O Trent
- UofL Health Brown Cancer Center, University of Louisville, Louisville, KY, United States
| | - Jonathan B Chaires
- UofL Health Brown Cancer Center, University of Louisville, Louisville, KY, United States
| | - Robert C Monsen
- UofL Health Brown Cancer Center, University of Louisville, Louisville, KY, United States.
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10
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Vitoria Gomes M, Landwerlin P, Diebold-Durand ML, Shaik TB, Durand A, Troesch E, Weber C, Brillet K, Lemée MV, Decroos C, Dulac L, Antony P, Watrin E, Ennifar E, Golzio C, Romier C. The cohesin ATPase cycle is mediated by specific conformational dynamics and interface plasticity of SMC1A and SMC3 ATPase domains. Cell Rep 2024; 43:114656. [PMID: 39240714 DOI: 10.1016/j.celrep.2024.114656] [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: 12/15/2023] [Revised: 06/17/2024] [Accepted: 08/02/2024] [Indexed: 09/08/2024] Open
Abstract
Cohesin is key to eukaryotic genome organization and acts throughout the cell cycle in an ATP-dependent manner. The mechanisms underlying cohesin ATPase activity are poorly understood. Here, we characterize distinct steps of the human cohesin ATPase cycle and show that the SMC1A and SMC3 ATPase domains undergo specific but concerted structural rearrangements along this cycle. Specifically, whereas the proximal coiled coil of the SMC1A ATPase domain remains conformationally stable, that of the SMC3 displays an intrinsic flexibility. The ATP-dependent formation of the heterodimeric SMC1A/SMC3 ATPase module (engaged state) favors this flexibility, which is counteracted by NIPBL and DNA binding (clamped state). Opening of the SMC3/RAD21 interface (open-engaged state) stiffens the SMC3 proximal coiled coil, thus constricting together with that of SMC1A the ATPase module DNA-binding chamber. The plasticity of the ATP-dependent interface between the SMC1A and SMC3 ATPase domains enables these structural rearrangements while keeping the ATP gate shut. VIDEO ABSTRACT.
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Affiliation(s)
- Marina Vitoria Gomes
- Université de Strasbourg, IGBMC UMR 7104 - UMR-S 1258, 67400 Illkirch, France; CNRS, UMR 7104, 67400 Illkirch, France; INSERM, UMR-S 1258, 67400 Illkirch, France; Institut de Génétique et de Biologie Moléculaire et Cellulaire, Department of Integrated Structural Biology, 67400 Illkirch, France
| | - Pauline Landwerlin
- Université de Strasbourg, IGBMC UMR 7104 - UMR-S 1258, 67400 Illkirch, France; CNRS, UMR 7104, 67400 Illkirch, France; INSERM, UMR-S 1258, 67400 Illkirch, France; Institut de Génétique et de Biologie Moléculaire et Cellulaire, Department of Integrated Structural Biology, 67400 Illkirch, France
| | - Marie-Laure Diebold-Durand
- Université de Strasbourg, IGBMC UMR 7104 - UMR-S 1258, 67400 Illkirch, France; CNRS, UMR 7104, 67400 Illkirch, France; INSERM, UMR-S 1258, 67400 Illkirch, France; Institut de Génétique et de Biologie Moléculaire et Cellulaire, Department of Integrated Structural Biology, 67400 Illkirch, France
| | - Tajith B Shaik
- Université de Strasbourg, IGBMC UMR 7104 - UMR-S 1258, 67400 Illkirch, France; CNRS, UMR 7104, 67400 Illkirch, France; INSERM, UMR-S 1258, 67400 Illkirch, France; Institut de Génétique et de Biologie Moléculaire et Cellulaire, Department of Integrated Structural Biology, 67400 Illkirch, France
| | - Alexandre Durand
- Université de Strasbourg, IGBMC UMR 7104 - UMR-S 1258, 67400 Illkirch, France; CNRS, UMR 7104, 67400 Illkirch, France; INSERM, UMR-S 1258, 67400 Illkirch, France; Institut de Génétique et de Biologie Moléculaire et Cellulaire, Department of Integrated Structural Biology, 67400 Illkirch, France
| | - Edouard Troesch
- Université de Strasbourg, IGBMC UMR 7104 - UMR-S 1258, 67400 Illkirch, France; CNRS, UMR 7104, 67400 Illkirch, France; INSERM, UMR-S 1258, 67400 Illkirch, France; Institut de Génétique et de Biologie Moléculaire et Cellulaire, Department of Integrated Structural Biology, 67400 Illkirch, France
| | - Chantal Weber
- Université de Strasbourg, IGBMC UMR 7104 - UMR-S 1258, 67400 Illkirch, France; CNRS, UMR 7104, 67400 Illkirch, France; INSERM, UMR-S 1258, 67400 Illkirch, France; Institut de Génétique et de Biologie Moléculaire et Cellulaire, Department of Translational Medicine and Neurogenetics, 67400 Illkirch, France
| | - Karl Brillet
- Architecture et Réactivité de l'ARN, IBMC CNRS UPR 9002, Université de Strasbourg, 67084 Strasbourg Cedex, France
| | - Marianne Victoria Lemée
- Université de Strasbourg, IGBMC UMR 7104 - UMR-S 1258, 67400 Illkirch, France; CNRS, UMR 7104, 67400 Illkirch, France; INSERM, UMR-S 1258, 67400 Illkirch, France; Institut de Génétique et de Biologie Moléculaire et Cellulaire, Department of Translational Medicine and Neurogenetics, 67400 Illkirch, France
| | - Christophe Decroos
- Université de Strasbourg, IGBMC UMR 7104 - UMR-S 1258, 67400 Illkirch, France; CNRS, UMR 7104, 67400 Illkirch, France; INSERM, UMR-S 1258, 67400 Illkirch, France; Institut de Génétique et de Biologie Moléculaire et Cellulaire, Department of Integrated Structural Biology, 67400 Illkirch, France
| | - Ludivine Dulac
- Université de Strasbourg, IGBMC UMR 7104 - UMR-S 1258, 67400 Illkirch, France; CNRS, UMR 7104, 67400 Illkirch, France; INSERM, UMR-S 1258, 67400 Illkirch, France; Institut de Génétique et de Biologie Moléculaire et Cellulaire, Department of Integrated Structural Biology, 67400 Illkirch, France; Institut de Génétique et de Biologie Moléculaire et Cellulaire, Department of Translational Medicine and Neurogenetics, 67400 Illkirch, France
| | - Pierre Antony
- Université de Strasbourg, IGBMC UMR 7104 - UMR-S 1258, 67400 Illkirch, France; CNRS, UMR 7104, 67400 Illkirch, France; INSERM, UMR-S 1258, 67400 Illkirch, France; Institut de Génétique et de Biologie Moléculaire et Cellulaire, Department of Integrated Structural Biology, 67400 Illkirch, France
| | - Erwan Watrin
- CNRS, Université de Rennes, IGDR UMR 6290, 35000 Rennes, France
| | - Eric Ennifar
- Architecture et Réactivité de l'ARN, IBMC CNRS UPR 9002, Université de Strasbourg, 67084 Strasbourg Cedex, France
| | - Christelle Golzio
- Université de Strasbourg, IGBMC UMR 7104 - UMR-S 1258, 67400 Illkirch, France; CNRS, UMR 7104, 67400 Illkirch, France; INSERM, UMR-S 1258, 67400 Illkirch, France; Institut de Génétique et de Biologie Moléculaire et Cellulaire, Department of Translational Medicine and Neurogenetics, 67400 Illkirch, France
| | - Christophe Romier
- Université de Strasbourg, IGBMC UMR 7104 - UMR-S 1258, 67400 Illkirch, France; CNRS, UMR 7104, 67400 Illkirch, France; INSERM, UMR-S 1258, 67400 Illkirch, France; Institut de Génétique et de Biologie Moléculaire et Cellulaire, Department of Integrated Structural Biology, 67400 Illkirch, France.
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11
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Balandin D, Szulc N, Bystranowska D, Gąsior-Głogowska M, Kruszakin R, Szefczyk M. Boosting stability: a hierarchical approach for self-assembling peptide structures. J Mater Chem B 2024. [PMID: 39314115 DOI: 10.1039/d4tb01545b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/25/2024]
Abstract
The primary objective of this study was to implement a hierarchical approach to enhance the conformational stability of a selected group of peptides by incorporating trans-(1S,2S)-2-aminocyclopentanecarboxylic acid (trans-ACPC). The influence of residue mutation on the peptide structures was investigated using circular dichroism, analytical ultracentrifugation, and vibrational spectroscopy. The resulting nanostructures were examined via transmission electron microscopy. The incorporation of trans-ACPC led to increased conformational stability and self-assembling propensity in peptides containing constrained β-amino acid residues.
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Affiliation(s)
- Denys Balandin
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, Wrocław 50-370, Poland.
- Department of Medicinal Chemistry, Otto Loewi Research Center, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010, Graz, Austria
| | - Natalia Szulc
- Department of Physics and Biophysics, Wrocław University of Environmental and Life Sciences, Norwida 25, Wrocław 50-375, Poland
| | - Dominika Bystranowska
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, Wrocław 50-370, Poland
| | - Marlena Gąsior-Głogowska
- Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, Wrocław 50-370, Poland
| | - Roksana Kruszakin
- Laboratory of Instrumental Analysis and Preparation, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Rudolfa Weigla 12, Wrocław 53-114, Poland
| | - Monika Szefczyk
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, Wrocław 50-370, Poland.
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12
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Shafiuddin M, Prather GW, Huang WC, Anton JR, Martin AL, Sillart SB, Tang JZ, Vittori MR, Prinsen MJ, Ninneman JJ, Manithody C, Henderson JP, Aleem AW, Ilagan MXG, McCoy WH. Cutibacterium adaptation to life on humans provides a novel biomarker of C. acnes infections. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.18.613542. [PMID: 39345635 PMCID: PMC11429735 DOI: 10.1101/2024.09.18.613542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/01/2024]
Abstract
The domestication of cattle provided Propionibacteriaceae the opportunity to adapt to human skin. These bacteria constitute a distinct genus ( Cutibacterium ), and a single species within that genus ( C. acnes ) dominates 25% of human skin. C. acnes protects humans from pathogen colonization, but it can also infect indwelling medical devices inserted through human skin. Proteins that help Cutibacteria live on our skin may also act as virulence factors during an opportunistic infection, like a shoulder periprosthetic joint infection (PJI). To better understand the evolution of this commensal and opportunistic pathogen, we sought to extensively characterize one of these proteins, RoxP. This secreted protein is only found in the Cutibacterium genus, helps C. acnes grow in oxic environments, and is required for C. acnes to colonize human skin. Structure-based sequence analysis of twenty-one RoxP orthologs (71-100% identity to C. acnes strain KPA171202 RoxP_1) revealed a high-degree of molecular surface conservation and helped identify a potential heme-binding interface. Biophysical evaluation of a subset of seven RoxP orthologs (71-100% identity) demonstrated that heme-binding is conserved. Computational modeling of these orthologs suggests that RoxP heme-binding is mediated by an invariant molecular surface composed of a surface-exposed tryptophan (W66), adjacent cationic pocket, and nearby potential heme axial ligands. Further, these orthologs were found to undergo heme-dependent oligomerization. To further probe the role of this protein in C. acnes biology, we developed four monoclonal anti-RoxP antibodies, assessed the binding of those antibodies to a subset of ten RoxP orthologs (71-100% identity), developed an anti-RoxP sandwich ELISA (sELISA) with sub-nanogram sensitivity, and adapted that sELISA to quantitate RoxP in human biofluids that can be infected by C. acnes (serum, synovial fluid, cerebrospinal fluid). This study expands our understanding of how an environmental bacterium evolved to live on humans, and the assays developed in this work can now be used to identify this organism when it gains access to sterile sites to cause opportunistic infections. Author Summary The longer humans live, the more they require internal "replacement parts," like prosthetic joints. Increased placement of these and other medical devices has increased their complications, which frequently are infections caused by microbes that live on humans. One of these microbes is Cutibacterium acnes , which dominates 25% of human skin. It appears that when humans domesticated cattle, a C. acnes ancestor adapted from living in cows to living on people. One of these adaptations was RoxP, a protein only found in Cutibacterium and carried by all C. acnes . Here, we describe our extensive characterization of RoxP. We found that distantly related RoxP conserve high stability at the low pH found on human skin. They also conserve the ability to bind heme, a source of iron used by microbes when they infect humans. As a part of this work, we developed tests that measure RoxP to identify C. acnes growth. In a clinic or hospital, these tests could allow a doctor to rapidly identify C. acnes infections, which would improve patient outcomes and lower healthcare costs. This work has helped us better understand how C. acnes adapted to live on humans and to identify C. acnes infections of medical devices.
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13
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Wang Y, Guo H, Lu Y, Yang W, Li T, Ji X. Crystal structure and nucleic acid binding mode of CPV NSP9: implications for viroplasm in Reovirales. Nucleic Acids Res 2024:gkae803. [PMID: 39287123 DOI: 10.1093/nar/gkae803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Revised: 08/28/2024] [Accepted: 09/03/2024] [Indexed: 09/19/2024] Open
Abstract
Cytoplasmic polyhedrosis viruses (CPVs), like other members of the order Reovirales, produce viroplasms, hubs of viral assembly that shield them from host immunity. Our study investigates the potential role of NSP9, a nucleic acid-binding non-structural protein encoded by CPVs, in viroplasm biogenesis. We determined the crystal structure of the NSP9 core (NSP9ΔC), which shows a dimeric organization topologically similar to the P9-1 homodimers of plant reoviruses. The disordered C-terminal region of NSP9 facilitates oligomerization but is dispensable for nucleic acid binding. NSP9 robustly binds to single- and double-stranded nucleic acids, regardless of RNA or DNA origin. Mutagenesis studies further confirmed that the dimeric form of NSP9 is critical for nucleic acid binding due to positively charged residues that form a tunnel during homodimerization. Gel migration assays reveal a unique nucleic acid binding pattern, with the sequential appearance of two distinct complexes dependent on protein concentration. The similar gel migration pattern shared by NSP9 and rotavirus NSP3, coupled with its structural resemblance to P9-1, hints at a potential role in translational regulation or viral genome packaging, which may be linked to viroplasm. This study advances our understanding of viroplasm biogenesis and Reovirales replication, providing insights into potential antiviral drug targets.
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Affiliation(s)
- Yeda Wang
- Department of Infectious Diseases, Nanjing Drum Tower Hospital, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Institute of Viruses and Infectious Diseases, Chemistry and Biomedicine Innovation Center (ChemBIC), Institute of Artificial Intelligence Biomedicine, Nanjing University, Nanjing, China
| | - Hangtian Guo
- Department of Infectious Diseases, Nanjing Drum Tower Hospital, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Institute of Viruses and Infectious Diseases, Chemistry and Biomedicine Innovation Center (ChemBIC), Institute of Artificial Intelligence Biomedicine, Nanjing University, Nanjing, China
| | - Yuhao Lu
- Department of Infectious Diseases, Nanjing Drum Tower Hospital, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Institute of Viruses and Infectious Diseases, Chemistry and Biomedicine Innovation Center (ChemBIC), Institute of Artificial Intelligence Biomedicine, Nanjing University, Nanjing, China
| | - Wanbin Yang
- Department of Infectious Diseases, Nanjing Drum Tower Hospital, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Institute of Viruses and Infectious Diseases, Chemistry and Biomedicine Innovation Center (ChemBIC), Institute of Artificial Intelligence Biomedicine, Nanjing University, Nanjing, China
| | - Tinghan Li
- Department of Infectious Diseases, Nanjing Drum Tower Hospital, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Institute of Viruses and Infectious Diseases, Chemistry and Biomedicine Innovation Center (ChemBIC), Institute of Artificial Intelligence Biomedicine, Nanjing University, Nanjing, China
| | - Xiaoyun Ji
- Department of Infectious Diseases, Nanjing Drum Tower Hospital, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Institute of Viruses and Infectious Diseases, Chemistry and Biomedicine Innovation Center (ChemBIC), Institute of Artificial Intelligence Biomedicine, Nanjing University, Nanjing, China
- Engineering Research Center of Protein and Peptide Medicine, Ministry of Education, China
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14
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Mano K, Noi K, Oe K, Mochizuki T, Morishima K, Inoue R, Sugiyama M, Noguchi K, Shinohara K, Yohda M, Yamada A. Molecular Characterization of the MoxR AAA+ ATPase of Synechococcus sp. Strain NKBG15041c. Int J Mol Sci 2024; 25:9955. [PMID: 39337443 PMCID: PMC11432383 DOI: 10.3390/ijms25189955] [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: 08/16/2024] [Revised: 09/10/2024] [Accepted: 09/12/2024] [Indexed: 09/30/2024] Open
Abstract
We isolated a stress-tolerance-related gene from a genome library of Synechococcus sp. NKBG15041c. The expression of the gene in E. coli confers resistance against various stresses. The gene encodes a MoxR AAA+ ATPase, which was designated SyMRP since it belongs to the MRP subfamily. The recombinant SyMRP showed weak ATPase activity and protected citrate synthase from thermal aggregation. Interestingly, the chaperone activity of SyMRP is ATP-dependent. SyMRP exists as a stable hexamer, and ATP-dependent conformation changes were not detected via analytical ultracentrifugation (AUC) or small-angle X-ray scattering (SAXS). Although the hexameric structure predicted by AlphaFold 3 was the canonical flat-ring structure, the structures observed by atomic force microscopy (AFM) and transmission electron microscopy (TEM) were not the canonical ring structure. In addition, the experimental SAXS profiles did not show a peak that should exist in the symmetric-ring structure. Therefore, SyMRP seems to form a hexameric structure different from the canonical hexameric structure of AAA+ ATPase.
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Affiliation(s)
- Kota Mano
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Tokyo 184-8588, Japan; (K.M.); (K.N.); (K.O.); (T.M.); (K.S.)
| | - Kentaro Noi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Tokyo 184-8588, Japan; (K.M.); (K.N.); (K.O.); (T.M.); (K.S.)
| | - Kumiko Oe
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Tokyo 184-8588, Japan; (K.M.); (K.N.); (K.O.); (T.M.); (K.S.)
| | - Takahiro Mochizuki
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Tokyo 184-8588, Japan; (K.M.); (K.N.); (K.O.); (T.M.); (K.S.)
| | - Ken Morishima
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Osaka 590-0494, Japan; (K.M.); (R.I.); (M.S.)
| | - Rintaro Inoue
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Osaka 590-0494, Japan; (K.M.); (R.I.); (M.S.)
| | - Masaaki Sugiyama
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Osaka 590-0494, Japan; (K.M.); (R.I.); (M.S.)
| | - Keiichi Noguchi
- Instrumentation Analysis Center, Tokyo University of Agriculture and Technology, Tokyo 184-8588, Japan;
| | - Kyosuke Shinohara
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Tokyo 184-8588, Japan; (K.M.); (K.N.); (K.O.); (T.M.); (K.S.)
| | - Masafumi Yohda
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Tokyo 184-8588, Japan; (K.M.); (K.N.); (K.O.); (T.M.); (K.S.)
| | - Akiyo Yamada
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Tokyo 184-8588, Japan; (K.M.); (K.N.); (K.O.); (T.M.); (K.S.)
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15
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Monsen RC, Sabo TM, Gray R, Hopkins JB, Chaires JB. Early Events in G-quadruplex Folding Captured by Time-Resolved Small-Angle X-Ray Scattering. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.05.611539. [PMID: 39282441 PMCID: PMC11398465 DOI: 10.1101/2024.09.05.611539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 09/20/2024]
Abstract
Time-resolved small-angle X-ray experiments (TR-SAXS) are reported here that capture and quantify a previously unknown rapid collapse of the unfolded oligonucleotide as an early step in G4 folding of hybrid 1 and hybrid 2 telomeric G-quadruplex structures. The rapid collapse, initiated by a pH jump, is characterized by an exponential decrease in the radius of gyration from 20.6 to 12.6 Å. The collapse is monophasic and is complete in less than 600 ms. Additional hand-mixing pH-jump kinetic studies show that slower kinetic steps follow the collapse. The folded and unfolded states at equilibrium were further characterized by SAXS studies and other biophysical tools, to show that G4 unfolding was complete at alkaline pH, but not in LiCl solution as is often claimed. The SAXS Ensemble Optimization Method (EOM) analysis reveals models of the unfolded state as a dynamic ensemble of flexible oligonucleotide chains with a variety of transient hairpin structures. These results suggest a G4 folding pathway in which a rapid collapse, analogous to molten globule formation seen in proteins, is followed by a confined conformational search within the collapsed particle to form the native contacts ultimately found in the stable folded form.
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Affiliation(s)
- Robert C Monsen
- Department of Medicine, UofL Health Brown Cancer Center, University of Louisville, Louisville KY, 505 S Hancock St, Louisville, KY 40202
| | - T Michael Sabo
- Department of Medicine, UofL Health Brown Cancer Center, University of Louisville, Louisville KY, 505 S Hancock St, Louisville, KY 40202
| | - Robert Gray
- Department of Medicine, UofL Health Brown Cancer Center, University of Louisville, Louisville KY, 505 S Hancock St, Louisville, KY 40202
| | - Jesse B Hopkins
- The Biophysics Collaborative Access Team (BioCAT) Department of Physics, Illinois Institute of Technology, Chicago, IL 60616
| | - Jonathan B Chaires
- Department of Medicine, UofL Health Brown Cancer Center, University of Louisville, Louisville KY, 505 S Hancock St, Louisville, KY 40202
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16
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He QY, Zhao HF, Meng L, Geng Z, Gao ZQ, Qi XY, Dong YH, Zhang H. A cardioviral 2C-ATP complex structure reveals the essential role of a conserved arginine in regulation of cardioviral 2C activity. J Virol 2024:e0091124. [PMID: 39240112 DOI: 10.1128/jvi.00911-24] [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: 05/23/2024] [Accepted: 08/02/2024] [Indexed: 09/07/2024] Open
Abstract
2C is a highly conserved picornaviral non-structural protein with ATPase activity and plays a multifunctional role in the viral life cycle as a promising target for anti-picornavirus drug development. While the structure-function of enteroviral 2Cs have been well studied, cardioviral 2Cs remain largely uncharacterized. Here, an endogenous ATP molecule was identified in the crystal structure of 2C from encephalomyocarditis virus (EMCV, Cardiovirus A). The ATP is bound into the ATPase active site with a unique compact conformation. Notably, the γ-phosphate of ATP directly interacts with Arg311 (conserved in cardioviral 2Cs), and its mutation significantly inhibits the ATPase activity. Unexpectedly, this mutation remarkably promotes 2C self-oligomerization and viral replication efficiency. Molecular dynamic simulations showed that the Arg311 side chain is highly dynamic, indicating it may function as a switch between the activation state and the inhibition state of ATPase activity. A hexameric ring model of EMCV 2C full length indicated that the C-terminal helix may get close to the N-terminal amphipathic helices to form a continuous positive region for RNA binding. The RNA-binding studies of EMCV 2C revealed that the RNA length is closely associated with the RNA-binding affinities and indicated that the substrate may wrap around the outer surface of the hexamer. Our studies provide a biochemical framework to guide the characterization of EMCV 2C and the essential role of arginine in cardioviral 2C functions. IMPORTANCE Encephalomyocarditis virus (Cardiovirus A) is the causative agent of the homonymous disease, which may induce myocarditis, encephalitis, and reproductive disorders in various mammals. 2C protein is functionally indispensable and a promising target for drug development involving broad-spectrum picornaviral inhibitors. Here, an endogenous ATP molecule with a unique conformation was discovered by a combination of protein crystallography and high-performance liquid chromatography in the encephalomyocarditis virus (EMCV) 2C structure. Biochemical and structural characterization analysis of EMCV 2C revealed the critical role of conserved Arg311 in ATPase activity and self-oligomerization of EMCV 2C. The viral replication kinetics and infectivity study suggested that the residue negatively regulated the infectivity titer and virus encapsulation efficiency of EMCV and is, therefore, crucial for 2C protein to promote viral replication. Our systemic structure-function analysis provides unique insights into the function and regulation mechanism of cardioviral 2C protein.
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Affiliation(s)
- Qing-Yi He
- School of Life Sciences, University of Science and Technology of China, Hefei, China
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, China
| | - Hai-Fan Zhao
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Liang Meng
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Zhi Geng
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Zeng-Qiang Gao
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Xin-Yu Qi
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Yu-Hui Dong
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, China
| | - Heng Zhang
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, China
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17
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Aniana A, Nashed NT, Ghirlando R, Drago VN, Kovalevsky A, Louis JM. Characterization of alternate encounter assemblies of SARS-CoV-2 main protease. J Biol Chem 2024; 300:107675. [PMID: 39128719 PMCID: PMC11416275 DOI: 10.1016/j.jbc.2024.107675] [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: 07/03/2024] [Revised: 08/06/2024] [Accepted: 08/07/2024] [Indexed: 08/13/2024] Open
Abstract
The assembly of two monomeric constructs spanning segments 1-199 (MPro1-199) and 10-306 (MPro10-306) of SARS-CoV-2 main protease (MPro) was examined to assess the existence of a transient heterodimer intermediate in the N-terminal autoprocessing pathway of MPro model precursor. Together, they form a heterodimer population accompanied by a 13-fold increase in catalytic activity. Addition of inhibitor GC373 to the proteins increases the activity further by ∼7-fold with a 1:1 complex and higher order assemblies approaching 1:2 and 2:2 molecules of MPro1-199 and MPro10-306 detectable by analytical ultracentrifugation and native mass estimation by light scattering. Assemblies larger than a heterodimer (1:1) are discussed in terms of alternate pathways of domain III association, either through switching the location of helix 201 to 214 onto a second helical domain of MPro10-306 and vice versa or direct interdomain III contacts like that of the native dimer, based on known structures and AlphaFold 3 prediction, respectively. At a constant concentration of MPro1-199 with molar excess of GC373, the rate of substrate hydrolysis displays first order dependency on the MPro10-306 concentration and vice versa. An equimolar composition of the two proteins with excess GC373 exhibits half-maximal activity at ∼6 μM MPro1-199. Catalytic activity arises primarily from MPro1-199 and is dependent on the interface interactions involving the N-finger residues 1 to 9 of MPro1-199 and E290 of MPro10-306. Importantly, our results confirm that a single N-finger region with its associated intersubunit contacts is sufficient to form a heterodimeric MPro intermediate with enhanced catalytic activity.
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Affiliation(s)
- Annie Aniana
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, Maryland, USA
| | - Nashaat T Nashed
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, Maryland, USA
| | - Rodolfo Ghirlando
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, Maryland, USA
| | - Victoria N Drago
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Andrey Kovalevsky
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - John M Louis
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, Maryland, USA.
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18
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Gao X, Iqbal H, Yu DQ, Gor J, Coker AR, Perkins SJ. The SCR-17 and SCR-18 glycans in human complement factor H enhance its regulatory function. J Biol Chem 2024; 300:107624. [PMID: 39098532 PMCID: PMC11417181 DOI: 10.1016/j.jbc.2024.107624] [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: 04/11/2024] [Revised: 07/10/2024] [Accepted: 07/23/2024] [Indexed: 08/06/2024] Open
Abstract
Human complement factor H (CFH) plays a central role in regulating activated C3b to protect host cells. CFH contain 20 short complement regulator (SCR) domains and eight N-glycosylation sites. The N-terminal SCR domains mediate C3b degradation while the C-terminal CFH domains bind to host cell surfaces to protect these. Our earlier study of Pichia-generated CFH fragments indicated a self-association site at SCR-17/18 that comprises a dimerization site for human factor H. Two N-linked glycans are located on SCR-17 and SCR-18. Here, when we expressed SCR-17/18 without glycans in an Escherichia coli system, analytical ultracentrifugation showed that no dimers were now formed. To investigate this novel finding, full-length CFH and its C-terminal fragments were purified from human plasma and Pichia pastoris respectively, and their glycans were enzymatically removed using PNGase F. Using size-exclusion chromatography, mass spectrometry, and analytical ultracentrifugation, SCR-17/18 from Pichia showed notably less dimer formation without its glycans, confirming that the glycans are necessary for the formation of SCR-17/18 dimers. By surface plasmon resonance, affinity analyses interaction showed decreased binding of deglycosylated full-length CFH to immobilized C3b, showing that CFH glycosylation enhances the key CFH regulation of C3b. We conclude that our study revealed a significant new aspect of CFH regulation based on its glycosylation and its resulting dimerization.
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Affiliation(s)
- Xin Gao
- Division of Biosciences, Department of Structural and Molecular Biology, University College London, London, UK; Division of Medicine, University College London, London, UK
| | - Hina Iqbal
- Division of Biosciences, Department of Structural and Molecular Biology, University College London, London, UK
| | - Ding-Quan Yu
- Division of Biosciences, Department of Structural and Molecular Biology, University College London, London, UK
| | - Jayesh Gor
- Division of Biosciences, Department of Structural and Molecular Biology, University College London, London, UK
| | - Alun R Coker
- Division of Medicine, University College London, London, UK
| | - Stephen J Perkins
- Division of Biosciences, Department of Structural and Molecular Biology, University College London, London, UK.
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19
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Vogt A, Szurgot M, Gardner L, Schultz DC, Marmorstein R. HIRA complex deposition of histone H3.3 is driven by histone tetramerization and histone-DNA binding. J Biol Chem 2024; 300:107604. [PMID: 39059488 PMCID: PMC11388340 DOI: 10.1016/j.jbc.2024.107604] [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: 06/21/2024] [Revised: 07/15/2024] [Accepted: 07/17/2024] [Indexed: 07/28/2024] Open
Abstract
The HIRA histone chaperone complex is comprised of four protein subunits: HIRA, UBN1, CABIN1, and transiently associated ASF1a. All four subunits have been demonstrated to play a role in the deposition of the histone variant H3.3 onto areas of actively transcribed euchromatin in cells. The mechanism by which these subunits function together to drive histone deposition has remained poorly understood. Here we present biochemical and biophysical data supporting a model whereby ASF1a delivers histone H3.3/H4 dimers to the HIRA complex, H3.3/H4 tetramerization drives the association of two HIRA/UBN1 complexes, and the affinity of the histones for DNA drives release of ASF1a and subsequent histone deposition. These findings have implications for understanding how other histone chaperone complexes may mediate histone deposition.
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Affiliation(s)
- Austin Vogt
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA; Abramson Family Cancer Research Center, Perelman School of Medicine at the University of Pennsylvania, Pennsylvania, USA
| | - Mary Szurgot
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA; Abramson Family Cancer Research Center, Perelman School of Medicine at the University of Pennsylvania, Pennsylvania, USA; Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine at the University of Pennsylvania, Pennsylvania, USA
| | - Lauren Gardner
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA; Abramson Family Cancer Research Center, Perelman School of Medicine at the University of Pennsylvania, Pennsylvania, USA
| | - David C Schultz
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Ronen Marmorstein
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA; Abramson Family Cancer Research Center, Perelman School of Medicine at the University of Pennsylvania, Pennsylvania, USA.
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20
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Kuan Y, Chu HF, Hsu PH, Hsu KC, Lin TH, Huang CH, Chen WY. Disulfiram inhibits coronaviral main protease by conjugating to its substrate entry site. Int J Biol Macromol 2024; 276:133955. [PMID: 39025177 DOI: 10.1016/j.ijbiomac.2024.133955] [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: 12/21/2023] [Revised: 07/12/2024] [Accepted: 07/16/2024] [Indexed: 07/20/2024]
Abstract
Coronaviruses (CoV) are highly pathogenic single-strand RNA viruses. CoV infections cause fatal respiratory symptoms and lung injuries in humans and significant economic losses in livestock. Since the SARS-2 outbreak in 2019, the highly conserved main protease (Mpro), also termed 3-chymotrypsin-like protease (3CLpro), has been considered an attractive drug target for treating CoV infections. Mpro mediates the proteolytic cleavage of eleven sites in viral polypeptides necessary for virus replication. Here, we report that disulfiram, an FDA-approved drug for alcoholic treatment, exhibits a broad-spectrum inhibitory effect on CoV Mpros. Analytical ultracentrifugation and circular dichroism analyses indicated that disulfiram treatment blocks the dimeric formation of SARS and PEDV Mpros and decreases the thermostability of SARS, SARS-2, and PEDV Mpros, whereas it facilitates the dimerization and stability of MERS Mpro. Furthermore, mass spectrometry and structural alignment revealed that disulfiram targets the Cys44 residue of Mpros, which is located at the substrate entrance and close to the catalytic His41. In addition, molecular docking analysis suggests that disulfiram conjugation interferes with substrate entry to the catalytic center. In agreement, mutation of Cys44 modulates the disulfiram sensitivity of CoV Mpros. Our study suggests a broad-spectrum inhibitory function of disulfiram against CoV Mpros.
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Affiliation(s)
- Ying Kuan
- Program in Molecular Medicine, National Yang Ming Chiao Tung University and Academia Sinica, Taipei, Taiwan
| | - Hsu-Feng Chu
- Biomedical Industry Ph.D. Program, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Pang-Hung Hsu
- Department of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung 20224, Taiwan
| | - Kai-Cheng Hsu
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Ta-Hsien Lin
- Division of Basic Research, Department of Medical Research, Taipei Veterans General Hospital, Taipei 112, Taiwan; Institute of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
| | - Chun-Hsiang Huang
- National Synchrotron Radiation Research Center, Hsinchu City 30076, Taiwan.
| | - Wei-Yi Chen
- Program in Molecular Medicine, National Yang Ming Chiao Tung University and Academia Sinica, Taipei, Taiwan; Institute of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung University, Taipei 112, Taiwan; Cancer and Immunology Research Center, National Yang Ming Chiao Tung University, Taipei, Taiwan.
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21
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Liao F, Yu G, Zhang C, Liu Z, Li X, He Q, Yin H, Liu X, Li Z, Zhang H. Structural basis for the concerted antiphage activity in the SIR2-HerA system. Nucleic Acids Res 2024:gkae750. [PMID: 39217465 DOI: 10.1093/nar/gkae750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 08/07/2024] [Accepted: 08/19/2024] [Indexed: 09/04/2024] Open
Abstract
Recently, a novel two-gene bacterial defense system against phages, encoding a SIR2 NADase and a HerA ATPase/helicase, has been identified. However, the molecular mechanism of the bacterial SIR2-HerA immune system remains unclear. Here, we determine the cryo-EM structures of SIR2, HerA and their complex from Paenibacillus sp. 453MF in different functional states. The SIR2 proteins oligomerize into a dodecameric ring-shaped structure consisting of two layers of interlocked hexamers, in which each subunit exhibits an auto-inhibited conformation. Distinct from the canonical AAA+ proteins, HerA hexamer alone in this antiphage system adopts a split spiral arrangement, which is stabilized by a unique C-terminal extension. SIR2 and HerA proteins assemble into a ∼1.1 MDa torch-shaped complex to fight against phage infection. Importantly, disruption of the interactions between SIR2 and HerA largely abolishes the antiphage activity. Interestingly, binding alters the oligomer state of SIR2, switching from a dodecamer to a tetradecamer state. The formation of the SIR2-HerA binary complex activates NADase and nuclease activities in SIR2 and ATPase and helicase activities in HerA. Together, our study not only provides a structural basis for the functional communications between SIR2 and HerA proteins, but also unravels a novel concerted antiviral mechanism through NAD+ degradation, ATP hydrolysis, and DNA cleavage.
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Affiliation(s)
- Fumeng Liao
- State Key Laboratory of Experimental Hematology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, International Joint Laboratory of Ocular Diseases (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Cellular Homeostasis and Disease, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Guimei Yu
- State Key Laboratory of Experimental Hematology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, International Joint Laboratory of Ocular Diseases (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Cellular Homeostasis and Disease, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Chendi Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Zhikun Liu
- State Key Laboratory of Experimental Hematology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, International Joint Laboratory of Ocular Diseases (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Cellular Homeostasis and Disease, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Xuzichao Li
- State Key Laboratory of Experimental Hematology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, International Joint Laboratory of Ocular Diseases (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Cellular Homeostasis and Disease, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Qiuqiu He
- State Key Laboratory of Experimental Hematology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, International Joint Laboratory of Ocular Diseases (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Cellular Homeostasis and Disease, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Hang Yin
- Department of Pharmacology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Xiang Liu
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin, China
| | - Zhuang Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Heng Zhang
- State Key Laboratory of Experimental Hematology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, International Joint Laboratory of Ocular Diseases (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Cellular Homeostasis and Disease, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
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22
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Vizjak P, Kamp D, Hepp N, Scacchetti A, Gonzalez Pisfil M, Bartho J, Halic M, Becker PB, Smolle M, Stigler J, Mueller-Planitz F. ISWI catalyzes nucleosome sliding in condensed nucleosome arrays. Nat Struct Mol Biol 2024; 31:1331-1340. [PMID: 38664566 DOI: 10.1038/s41594-024-01290-x] [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: 11/03/2022] [Accepted: 03/25/2024] [Indexed: 05/07/2024]
Abstract
How chromatin enzymes work in condensed chromatin and how they maintain diffusional mobility inside remains unexplored. Here we investigated these challenges using the Drosophila ISWI remodeling ATPase, which slides nucleosomes along DNA. Folding of chromatin fibers did not affect sliding in vitro. Catalytic rates were also comparable in- and outside of chromatin condensates. ISWI cross-links and thereby stiffens condensates, except when ATP hydrolysis is possible. Active hydrolysis is also required for ISWI's mobility in condensates. Energy from ATP hydrolysis therefore fuels ISWI's diffusion through chromatin and prevents ISWI from cross-linking chromatin. Molecular dynamics simulations of a 'monkey-bar' model in which ISWI grabs onto neighboring nucleosomes, then withdraws from one before rebinding another in an ATP hydrolysis-dependent manner, qualitatively agree with our data. We speculate that monkey-bar mechanisms could be shared with other chromatin factors and that changes in chromatin dynamics caused by mutations in remodelers could contribute to pathologies.
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Affiliation(s)
- Petra Vizjak
- Institute of Physiological Chemistry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- Department of Molecular Biology, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
- Early Stage Bioprocess Development, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Dieter Kamp
- Gene Center, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Nicola Hepp
- Institute of Physiological Chemistry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- Department of Molecular Biology, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
- Department of Clinical Genetics, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Alessandro Scacchetti
- Department of Molecular Biology, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
- Epigenetics Institute and Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Mariano Gonzalez Pisfil
- Core Facility Bioimaging and Walter-Brendel-Centre of Experimental Medicine, Biomedical Center, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Joseph Bartho
- Gene Center, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Mario Halic
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Peter B Becker
- Department of Molecular Biology, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Michaela Smolle
- Department of Physiological Chemistry, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
- BioPhysics Core Facility, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
- ViraTherapeutics GmbH, Rum, Austria
| | - Johannes Stigler
- Gene Center, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany.
| | - Felix Mueller-Planitz
- Institute of Physiological Chemistry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.
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23
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Lou J, Deng Q, Zhang X, Bell CC, Das AB, Bediaga NG, Zlatic CO, Johanson TM, Allan RS, Griffin MDW, Paradkar P, Harvey KF, Dawson MA, Hinde E. Heterochromatin protein 1 alpha (HP1α) undergoes a monomer to dimer transition that opens and compacts live cell genome architecture. Nucleic Acids Res 2024:gkae720. [PMID: 39193905 DOI: 10.1093/nar/gkae720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 07/29/2024] [Accepted: 08/07/2024] [Indexed: 08/29/2024] Open
Abstract
Our understanding of heterochromatin nanostructure and its capacity to mediate gene silencing in a living cell has been prevented by the diffraction limit of optical microscopy. Thus, here to overcome this technical hurdle, and directly measure the nucleosome arrangement that underpins this dense chromatin state, we coupled fluorescence lifetime imaging microscopy (FLIM) of Förster resonance energy transfer (FRET) between histones core to the nucleosome, with molecular editing of heterochromatin protein 1 alpha (HP1α). Intriguingly, this super-resolved readout of nanoscale chromatin structure, alongside fluorescence fluctuation spectroscopy (FFS) and FLIM-FRET analysis of HP1α protein-protein interaction, revealed nucleosome arrangement to be differentially regulated by HP1α oligomeric state. Specifically, we found HP1α monomers to impart a previously undescribed global nucleosome spacing throughout genome architecture that is mediated by trimethylation on lysine 9 of histone H3 (H3K9me3) and locally reduced upon HP1α dimerisation. Collectively, these results demonstrate HP1α to impart a dual action on chromatin that increases the dynamic range of nucleosome proximity. We anticipate that this finding will have important implications for our understanding of how live cell heterochromatin structure regulates genome function.
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Affiliation(s)
- Jieqiong Lou
- School of Physics, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Qiji Deng
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC 3000, Australia
| | - Xiaomeng Zhang
- School of Physics, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Charles C Bell
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC 3000, Australia
| | - Andrew B Das
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC 3000, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Naiara G Bediaga
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC 3000, Australia
| | - Courtney O Zlatic
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Timothy M Johanson
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Rhys S Allan
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Michael D W Griffin
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, VIC 3010, Australia
| | - PrasadN Paradkar
- CSIRO Health & Biosecurity, Australian Centre for Disease Preparedness, 5 Portarlington Road, Geelong3220, Australia
| | - Kieran F Harvey
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC 3000, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3010, Australia
- Department of Anatomy and Developmental Biology and Biomedicine Discovery Institute, Monash University, Clayton, VIC 3168, Australia
| | - Mark A Dawson
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC 3000, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3010, Australia
- Centre for Cancer Research, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Elizabeth Hinde
- School of Physics, University of Melbourne, Melbourne, VIC 3010, Australia
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, VIC 3010, Australia
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24
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Shapturenka P, Barnes BK, Mansfield E, Noor MM, Fagan JA. Universalized and robust length separation of carbon and boron nitride nanotubes with improved polymer depletion-based fractionation. RSC Adv 2024; 14:25490-25506. [PMID: 39206342 PMCID: PMC11353058 DOI: 10.1039/d4ra01883d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Accepted: 08/02/2024] [Indexed: 09/04/2024] Open
Abstract
Partitioning nanoparticles by shape and dimension is paramount for advancing nanomaterial standardization, fundamental colloidal investigations, and technologies such as biosensing and digital electronics. Length-separation methods for single-walled carbon nanotubes (SWCNTs) have historically incurred trade-offs in precision and mass throughput, and boron nitride nanotubes (BNNTs) are a rapidly emerging material analogue. We extend and detail a polymer precipitation-based method to fractionate populations of either nanotube type at significant mass scale for four distinct nanotube sources of increasing average diameter (0.7 nm to >2 nm). Such separations result in a supernant phase containing shorter nanotubes and a pellet phase containing the longer nanotubes, with the threshold length for depletion decreasing with increasing polymer concentration. Cross-comparison through analytical ultracentrifugation, spectroscopy, and microscopy versus applied polymer concentration show tailorable and precise length fractionation for 100 nm through >1 μm rod lengths, with fractionation also designable to remove non-nanotube impurities. The threshold length of depletion is further found to increase for decreasing nanotube diameter at fixed polymer concentration, a finding consistent with scaling attributable to nanotube radial excluded volume. The capabilities demonstrated herein promise to significantly advance nanotube implementation within the scientific community.
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Affiliation(s)
- Pavel Shapturenka
- Materials Science and Engineering Division, National Institute of Standards and Technology Gaithersburg MD 20899 USA
| | - Benjamin K Barnes
- Materials Science and Engineering Division, National Institute of Standards and Technology Gaithersburg MD 20899 USA
| | - Elisabeth Mansfield
- Applied Chemicals and Materials Division, National Institute of Standards and Technology Boulder CO 80305 USA
| | - Matthew M Noor
- Materials Science and Engineering Division, National Institute of Standards and Technology Gaithersburg MD 20899 USA
- Department of Mechanical Engineering and Energy Processes, Southern Illinois University Carbondale IL 62901 USA
| | - Jeffrey A Fagan
- Materials Science and Engineering Division, National Institute of Standards and Technology Gaithersburg MD 20899 USA
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25
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Dick A, Mikirtumov V, Fuchs J, Krupp F, Olal D, Bendl E, Sprink T, Diebolder C, Kudryashev M, Kochs G, Roske Y, Daumke O. Structural characterization of Thogoto Virus nucleoprotein provides insights into viral RNA encapsidation and RNP assembly. Structure 2024; 32:1068-1078.e5. [PMID: 38749445 DOI: 10.1016/j.str.2024.04.016] [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: 03/14/2023] [Revised: 03/11/2024] [Accepted: 04/18/2024] [Indexed: 08/11/2024]
Abstract
Orthomyxoviruses, such as influenza and thogotoviruses, are important human and animal pathogens. Their segmented viral RNA genomes are wrapped by viral nucleoproteins (NPs) into helical ribonucleoprotein complexes (RNPs). NP structures of several influenza viruses have been reported. However, there are still contradictory models of how orthomyxovirus RNPs are assembled. Here, we characterize the crystal structure of Thogoto virus (THOV) NP and found striking similarities to structures of influenza viral NPs, including a two-lobed domain architecture, a positively charged RNA-binding cleft, and a tail loop important for trimerization and viral transcription. A low-resolution cryo-electron tomography reconstruction of THOV RNPs elucidates a left-handed double helical assembly. By providing a model for RNP assembly of THOV, our study suggests conserved NP assembly and RNA encapsidation modes for thogoto- and influenza viruses.
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Affiliation(s)
- Alexej Dick
- From Structural Biology, Max-Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Straße 10, 13125 Berlin, Germany; Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustraße 6, 14195 Berlin, Germany
| | - Vasilii Mikirtumov
- From Structural Biology, Max-Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Straße 10, 13125 Berlin, Germany; Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustraße 6, 14195 Berlin, Germany
| | - Jonas Fuchs
- Institute of Virology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Hermann-Herder-Straße 11, 79104 Freiburg, Germany
| | - Ferdinand Krupp
- From Structural Biology, Max-Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Daniel Olal
- From Structural Biology, Max-Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Elias Bendl
- Institute of Virology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Hermann-Herder-Straße 11, 79104 Freiburg, Germany
| | - Thiemo Sprink
- From Structural Biology, Max-Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Straße 10, 13125 Berlin, Germany; Core facility for Cryo-Electron Microscopy, Charité, Berlin, Germany
| | | | - Mikhail Kudryashev
- From Structural Biology, Max-Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Straße 10, 13125 Berlin, Germany; Institute of Medical Physics and Biophysics, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Georg Kochs
- Institute of Virology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Hermann-Herder-Straße 11, 79104 Freiburg, Germany.
| | - Yvette Roske
- From Structural Biology, Max-Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Straße 10, 13125 Berlin, Germany.
| | - Oliver Daumke
- From Structural Biology, Max-Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Straße 10, 13125 Berlin, Germany; Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustraße 6, 14195 Berlin, Germany.
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26
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Sundaram R, Gandhi S, Jonak C, Vasudevan D. Characterization of the Arabidopsis thaliana chromatin remodeler DEK3 for its interaction with histones and DNA. Biochimie 2024:S0300-9084(24)00177-9. [PMID: 39097158 DOI: 10.1016/j.biochi.2024.07.018] [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: 06/03/2024] [Revised: 07/04/2024] [Accepted: 07/31/2024] [Indexed: 08/05/2024]
Abstract
Chromatin structure and dynamics regulate all DNA-templated processes, such as transcription, replication, and repair. Chromatin binding factors, chromatin architectural proteins, and nucleosome remodelers modulate chromatin structure and dynamics and, thereby, the various DNA-dependent processes. Arabidopsis thaliana DEK3, a member of the evolutionarily conserved DEK domain-containing chromatin architectural proteins, is an important factor for chromatin structure and function, involved in transcriptional programming to regulate flowering time and abiotic stress tolerance. AtDEK3 contains an uncharacterized N-terminal domain, a middle SAF domain (winged helix-like domain), and a C-terminal DEK domain, but their role in the interaction of AtDEK3 with histones and DNA remained poorly understood. Using biochemical and biophysical analyses, we provide a comprehensive in vitro characterization of the different AtDEK3 domains for their interaction with histone H3/H4 and DNA. AtDEK3 directly interacts with histone H3/H4 tetramers through its N-terminal domain and the C-terminal DEK domain in a 1:1 stoichiometry. Upon interaction with H3/H4, the unstructured N-terminal domain of AtDEK3 undergoes a conformational change and adopts an alpha-helical conformation. In addition, the in-solution envelope structures of the AtDEK3 domains and their complex with H3/H4 have been characterized. The SAF and DEK domains associate with double-stranded and four-way junction DNA. As DEK3 possesses a histone-interacting domain at the N- and the C-terminus and a DNA-binding domain in the middle and at the C-terminus, the protein might play a complex role as a chromatin remodeler.
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Affiliation(s)
- Rajivgandhi Sundaram
- Institute of Life Sciences, Bhubaneswar, 751023, India; Manipal Academy of Higher Education, Manipal, 576104, India
| | - Surajit Gandhi
- Institute of Life Sciences, Bhubaneswar, 751023, India; Regional Centre for Biotechnology, Faridabad, 121001, India
| | - Claudia Jonak
- AIT Austrian Institute of Technology, Center for Health and Bioresources, Bioresources Unit, Konrad-Lorenz-Strasse 24, 3430 Tulln, Austria
| | - Dileep Vasudevan
- Institute of Life Sciences, Bhubaneswar, 751023, India; Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram, 695014, India.
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27
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Albanese KI, Petrenas R, Pirro F, Naudin EA, Borucu U, Dawson WM, Scott DA, Leggett GJ, Weiner OD, Oliver TAA, Woolfson DN. Rationally seeded computational protein design of ɑ-helical barrels. Nat Chem Biol 2024; 20:991-999. [PMID: 38902458 PMCID: PMC11288890 DOI: 10.1038/s41589-024-01642-0] [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: 08/25/2023] [Accepted: 05/09/2024] [Indexed: 06/22/2024]
Abstract
Computational protein design is advancing rapidly. Here we describe efficient routes starting from validated parallel and antiparallel peptide assemblies to design two families of α-helical barrel proteins with central channels that bind small molecules. Computational designs are seeded by the sequences and structures of defined de novo oligomeric barrel-forming peptides, and adjacent helices are connected by loop building. For targets with antiparallel helices, short loops are sufficient. However, targets with parallel helices require longer connectors; namely, an outer layer of helix-turn-helix-turn-helix motifs that are packed onto the barrels. Throughout these computational pipelines, residues that define open states of the barrels are maintained. This minimizes sequence sampling, accelerating the design process. For each of six targets, just two to six synthetic genes are made for expression in Escherichia coli. On average, 70% of these genes express to give soluble monomeric proteins that are fully characterized, including high-resolution structures for most targets that match the design models with high accuracy.
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Affiliation(s)
- Katherine I Albanese
- School of Chemistry, University of Bristol, Bristol, UK
- Max Planck-Bristol Centre for Minimal Biology, University of Bristol, Bristol, UK
| | | | - Fabio Pirro
- School of Chemistry, University of Bristol, Bristol, UK
| | | | - Ufuk Borucu
- School of Biochemistry, University of Bristol, Medical Sciences Building, Bristol, UK
| | | | - D Arne Scott
- Rosa Biotech, Science Creates St Philips, Bristol, UK
| | | | - Orion D Weiner
- Cardiovascular Research Institute, Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | | | - Derek N Woolfson
- School of Chemistry, University of Bristol, Bristol, UK.
- Max Planck-Bristol Centre for Minimal Biology, University of Bristol, Bristol, UK.
- School of Biochemistry, University of Bristol, Medical Sciences Building, Bristol, UK.
- Bristol BioDesign Institute, University of Bristol, Bristol, UK.
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28
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Stackhouse CI, Pierson KN, Labrecque CL, Mawson C, Berg J, Fuglestad B, Nucci NV. Characterization of 10MAG/LDAO reverse micelles: Understanding versatility for protein encapsulation. Biophys Chem 2024; 311:107269. [PMID: 38815545 PMCID: PMC11225088 DOI: 10.1016/j.bpc.2024.107269] [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: 03/26/2024] [Revised: 05/17/2024] [Accepted: 05/20/2024] [Indexed: 06/01/2024]
Abstract
Reverse micelles (RMs) are spontaneously organizing nanobubbles composed of an organic solvent, surfactants, and an aqueous phase that can encapsulate biological macromolecules for various biophysical studies. Unlike other RM systems, the 1-decanoyl-rac-glycerol (10MAG) and lauryldimethylamine-N-oxide (LDAO) surfactant system has proven to house proteins with higher stability than other RM mixtures with little sensitivity to the water loading (W0, defined by the ratio of water to surfactant). We investigated this unique property by encapsulating three model proteins - cytochrome c, myoglobin, and flavodoxin - in 10MAG/LDAO RMs and applying a variety of experimental methods to characterize this system's behavior. We found that this surfactant system differs greatly from the traditional, spherical, monodisperse RM population model. 10MAG/LDAO RMs were discovered to be oblate ellipsoids at all conditions, and as W0 was increased, surfactants redistributed to form a greater number of increasingly spherical ellipsoidal particles with pools of more bulk-like water. Proteins distinctively influence the thermodynamics of the mixture, encapsulating at their optimal RM size and driving protein-free RM sizes to scale accordingly. These findings inform the future development of similarly malleable encapsulation systems and build a foundation for application of 10MAG/LDAO RMs to analyze biological and chemical processes under nanoscale confinement.
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Affiliation(s)
- Crystal I Stackhouse
- Department of Physics and Astronomy, Rowan University, 201 Mullica Hill Rd, Glassboro, NJ 08028, United States; Department of Biomedical and Biological Sciences, Rowan University, 201 Mullica Hill Rd, Glassboro, NJ 08028, United States.
| | - Kali N Pierson
- Department of Physics and Astronomy, Rowan University, 201 Mullica Hill Rd, Glassboro, NJ 08028, United States; Department of Biomedical and Biological Sciences, Rowan University, 201 Mullica Hill Rd, Glassboro, NJ 08028, United States.
| | - Courtney L Labrecque
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, United States.
| | - Cara Mawson
- Department of Physics and Astronomy, Rowan University, 201 Mullica Hill Rd, Glassboro, NJ 08028, United States; Department of Biomedical and Biological Sciences, Rowan University, 201 Mullica Hill Rd, Glassboro, NJ 08028, United States.
| | - Joshua Berg
- Department of Physics and Astronomy, Rowan University, 201 Mullica Hill Rd, Glassboro, NJ 08028, United States; Department of Biomedical and Biological Sciences, Rowan University, 201 Mullica Hill Rd, Glassboro, NJ 08028, United States
| | - Brian Fuglestad
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, United States; Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, United States.
| | - Nathaniel V Nucci
- Department of Physics and Astronomy, Rowan University, 201 Mullica Hill Rd, Glassboro, NJ 08028, United States; Department of Biomedical and Biological Sciences, Rowan University, 201 Mullica Hill Rd, Glassboro, NJ 08028, United States.
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29
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Prabaharan C, Figiel M, Szczepanowski RH, Skowronek K, Zajko W, Thangaraj V, Chamera S, Nowak E, Nowotny M. Structural and biochemical characterization of cauliflower mosaic virus reverse transcriptase. J Biol Chem 2024; 300:107555. [PMID: 39002684 PMCID: PMC11363490 DOI: 10.1016/j.jbc.2024.107555] [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: 12/01/2023] [Revised: 06/19/2024] [Accepted: 06/30/2024] [Indexed: 07/15/2024] Open
Abstract
Reverse transcriptases (RTs) are enzymes with DNA polymerase and RNase H activities. They convert ssRNA into dsDNA and are key enzymes for the replication of retroviruses and retroelements. Caulimoviridae is a major family of plant-infecting viruses. Caulimoviruses have a circular dsDNA genome that is replicated by reverse transcription, but in contrast to retroviruses, they lack integrase. Caulimoviruses are related to Ty3 retroelements. Ty3 RT has been extensively studied structurally and biochemically, but corresponding information for caulimoviral RTs is unavailable. In the present study, we report the first crystal structure of cauliflower mosaic virus (CaMV) RT in complex with a duplex made of RNA and DNA strands (RNA/DNA hybrid). CaMV RT forms a monomeric complex with the hybrid, unlike Ty3 RT, which does so as a dimer. Results of the RNA-dependent DNA polymerase and DNA-dependent DNA polymerase activity assays showed that individual CaMV RT molecules are able to perform full polymerase functions. However, our analyses showed that an additional CaMV RT molecule needs to transiently associate with a polymerase-competent RT molecule to execute RNase H cuts of the RNA strand. Collectively, our results provide details into the structure and function of CaMV RT and describe how the enzyme compares to other related RTs.
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Affiliation(s)
- Chandrasekaran Prabaharan
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Małgorzata Figiel
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Roman H Szczepanowski
- Biophysics and Bioanalytics Facility, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Krzysztof Skowronek
- Biophysics and Bioanalytics Facility, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Weronika Zajko
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Vinuchakkaravarthy Thangaraj
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Sebastian Chamera
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Elżbieta Nowak
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland.
| | - Marcin Nowotny
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland.
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30
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Rossi V, Nielson SE, Ortolano A, Lonardo I, Haroldsen E, Comer D, Price OM, Wallace N, Hevel JM. Oligomerization of protein arginine methyltransferase 1 and its effect on methyltransferase activity and substrate specificity. Protein Sci 2024; 33:e5118. [PMID: 39022984 PMCID: PMC11255602 DOI: 10.1002/pro.5118] [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: 04/04/2024] [Revised: 06/30/2024] [Accepted: 07/02/2024] [Indexed: 07/20/2024]
Abstract
Proper protein arginine methylation by protein arginine methyltransferase 1 (PRMT1) is critical for maintaining cellular health, while dysregulation is often associated with disease. How the activity of PRMT1 is regulated is therefore paramount, but is not clearly understood. Several studies have observed higher order oligomeric species of PRMT1, but it is unclear if these exist at physiological concentrations and there is confusion in the literature about how oligomerization affects activity. We therefore sought to determine which oligomeric species of PRMT1 are physiologically relevant, and quantitatively correlate activity with specific oligomer forms. Through quantitative western blotting, we determined that concentrations of PRMT1 available in a variety of human cell lines are in the sub-micromolar to low micromolar range. Isothermal spectral shift binding data were modeled to a monomer/dimer/tetramer equilibrium with an EC50 for tetramer dissociation of ~20 nM. A combination of sedimentation velocity and Native polyacrylamide gel electrophoresis experiments directly confirmed that the major oligomeric species of PRMT1 at physiological concentrations would be dimers and tetramers. Surprisingly, the methyltransferase activity of a dimeric PRMT1 variant is similar to wild type, tetrameric PRMT1 with some purified substrates, but dimer and tetramer forms of PRMT1 show differences in catalytic efficiencies and substrate specificity for other substrates. Our results define an oligomerization paradigm for PRMT1, show that the biophysical characteristics of PRMT1 are poised to support a monomer/dimer/tetramer equilibrium in vivo, and suggest that the oligomeric state of PRMT1 could be used to regulate substrate specificity.
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Affiliation(s)
- Vincent Rossi
- Department of Chemistry and BiochemistryUtah State UniversityLoganUtahUSA
| | - Sarah E. Nielson
- Department of Chemistry and BiochemistryUtah State UniversityLoganUtahUSA
| | - Ariana Ortolano
- Department of Chemistry and BiochemistryUtah State UniversityLoganUtahUSA
| | - Isabella Lonardo
- Department of Chemistry and BiochemistryUtah State UniversityLoganUtahUSA
| | - Emeline Haroldsen
- Department of Chemistry and BiochemistryUtah State UniversityLoganUtahUSA
| | - Drake Comer
- Department of Chemistry and BiochemistryUtah State UniversityLoganUtahUSA
| | - Owen M Price
- Department of Chemistry and BiochemistryUtah State UniversityLoganUtahUSA
| | | | - Joan M. Hevel
- Department of Chemistry and BiochemistryUtah State UniversityLoganUtahUSA
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31
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Janc M, Zevnik K, Dolinar A, Jakomin T, Štalekar M, Bačnik K, Kutnjak D, Žnidarič MT, Zentilin L, Fedorov D, Dobnik D. In-Depth Comparison of Adeno-Associated Virus Containing Fractions after CsCl Ultracentrifugation Gradient Separation. Viruses 2024; 16:1235. [PMID: 39205208 PMCID: PMC11360810 DOI: 10.3390/v16081235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 07/24/2024] [Accepted: 07/25/2024] [Indexed: 09/04/2024] Open
Abstract
Recombinant adeno-associated viruses (rAAVs) play a pivotal role in the treatment of genetic diseases. However, current production and purification processes yield AAV-based preparations that often contain unwanted empty, partially filled or damaged viral particles and impurities, including residual host cell DNA and proteins, plasmid DNA, and viral aggregates. To precisely understand the composition of AAV preparations, we systematically compared four different single-stranded AAV (ssAAV) and self-complementary (scAAV) fractions extracted from the CsCl ultracentrifugation gradient using established methods (transduction efficiency, analytical ultracentrifugation (AUC), quantitative and digital droplet PCR (qPCR and ddPCR), transmission electron microscopy (TEM) and enzyme-linked immunosorbent assay (ELISA)) alongside newer techniques (multiplex ddPCR, multi-angle light-scattering coupled to size-exclusion chromatography (SEC-MALS), multi-angle dynamic light scattering (MADLS), and high-throughput sequencing (HTS)). Suboptimal particle separation within the fractions resulted in unexpectedly similar infectivity levels. No single technique could simultaneously provide comprehensive insights in the presence of both bioactive particles and contaminants. Notably, multiplex ddPCR revealed distinct vector genome fragmentation patterns, differing between ssAAV and scAAV. This highlights the urgent need for innovative analytical and production approaches to optimize AAV vector production and enhance therapeutic outcomes.
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Affiliation(s)
- Mojca Janc
- National Institute of Biology, Večna pot 121, 1000 Ljubljana, Slovenia (D.D.)
- Jožef Stefan International Postgraduate School, Jamova cesta 39, 1000 Ljubljana, Slovenia
| | - Kaja Zevnik
- National Institute of Biology, Večna pot 121, 1000 Ljubljana, Slovenia (D.D.)
| | - Ana Dolinar
- National Institute of Biology, Večna pot 121, 1000 Ljubljana, Slovenia (D.D.)
| | - Tjaša Jakomin
- National Institute of Biology, Večna pot 121, 1000 Ljubljana, Slovenia (D.D.)
| | - Maja Štalekar
- National Institute of Biology, Večna pot 121, 1000 Ljubljana, Slovenia (D.D.)
| | - Katarina Bačnik
- National Institute of Biology, Večna pot 121, 1000 Ljubljana, Slovenia (D.D.)
| | - Denis Kutnjak
- National Institute of Biology, Večna pot 121, 1000 Ljubljana, Slovenia (D.D.)
| | | | - Lorena Zentilin
- International Center for Genetic Engineering and Biotechnology, Area Science Park, Padriciano 99, 34149 Trieste, Italy
| | - Dmitrii Fedorov
- Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, 00076 Aalto, Finland
- Center of Excellence in Life-Inspired Hybrid Materials (LIBER) Aalto University, P.O. Box 16100, 00076 Aalto, Finland
| | - David Dobnik
- National Institute of Biology, Večna pot 121, 1000 Ljubljana, Slovenia (D.D.)
- Niba Labs d.o.o., Litostrojska cesta 52, 1000 Ljubljana, Slovenia
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32
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Umuhire Juru A, Ghirlando R, Zhang J. Structural basis of tRNA recognition by the widespread OB fold. Nat Commun 2024; 15:6385. [PMID: 39075051 PMCID: PMC11286949 DOI: 10.1038/s41467-024-50730-1] [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: 03/28/2024] [Accepted: 07/18/2024] [Indexed: 07/31/2024] Open
Abstract
The widespread oligonucleotide/oligosaccharide-binding (OB)-fold recognizes diverse substrates from sugars to nucleic acids and proteins, and plays key roles in genome maintenance, transcription, translation, and tRNA metabolism. OB-containing bacterial Trbp and yeast Arc1p proteins are thought to recognize the tRNA elbow or anticodon regions. Here we report a 2.6 Å co-crystal structure of Aquifex aeolicus Trbp111 bound to tRNAIle, which reveals that Trbp recognizes tRNAs solely by capturing their 3' ends. Structural, mutational, and biophysical analyses show that the Trbp/EMAPII-like OB fold precisely recognizes the single-stranded structure, 3' terminal location, and specific sequence of the 3' CA dinucleotide - a universal feature of mature tRNAs. Arc1p supplements its OB - tRNA 3' end interaction with additional contacts that involve an adjacent basic region and the tRNA body. This study uncovers a previously unrecognized mode of tRNA recognition by an ancient protein fold, and provides insights into protein-mediated tRNA aminoacylation, folding, localization, trafficking, and piracy.
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Affiliation(s)
- Aline Umuhire Juru
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, USA
| | - Rodolfo Ghirlando
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, USA
| | - Jinwei Zhang
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, USA.
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33
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Barros-Medina I, Robles-Ramos MÁ, Sobrinos-Sanguino M, Luque-Ortega JR, Alfonso C, Margolin W, Rivas G, Monterroso B, Zorrilla S. Bacterial cell cycle regulator MatP forms biomolecular condensates and directly interacts with cell division protein FtsZ. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.23.604758. [PMID: 39211257 PMCID: PMC11361077 DOI: 10.1101/2024.07.23.604758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Bacterial cytokinesis is driven by a contractile ring of FtsZ protein polymers at midcell. FtsZ can also form phase-separated biomolecular condensates with potential implications for cytokinesis and development of antibiotic-tolerant persister cells. In Escherichia coli , FtsZ ring positioning depends in part on the MatP protein, which binds DNA sites ( matS ) in the chromosome terminus region and indirectly interacts with FtsZ through two other proteins. We report here that MatP also forms biomolecular condensates in reconstituted systems that mimic the crowded bacterial cytoplasm, on its own or with FtsZ. Our biophysical analyses uncover a direct MatP-FtsZ interaction, which is disrupted by matS sites that also regulate MatP condensate formation. These condensates preferentially locate at the surface of lipid droplets, a behavior probably mediated by MatP-lipid binding. GTP triggers assembly of FtsZ polymers from FtsZ-MatP condensates. These polymers are decorated with MatP, but exposure to matS sites releases MatP. Such matS -responsive MatP biomolecular condensates, regulated by GTP when coassembled with FtsZ, may provide a mechanism for MatP storage and rapid mobilization that could facilitate MatP's role in spatially regulating cytokinesis. Moreover, sequestration of MatP through phase separation could promote cell entry into dormant states that are able to survive antibiotic treatments. GRAPHICAL ABSTRACT
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34
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Wang R, Xu Q, Wu Z, Li J, Guo H, Liao T, Shi Y, Yuan L, Gao H, Yang R, Shi Z, Li F. The structural basis of the activation and inhibition of DSR2 NADase by phage proteins. Nat Commun 2024; 15:6185. [PMID: 39039073 PMCID: PMC11263360 DOI: 10.1038/s41467-024-50410-0] [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: 01/29/2024] [Accepted: 07/09/2024] [Indexed: 07/24/2024] Open
Abstract
DSR2, a Sir2 domain-containing protein, protects bacteria from phage infection by hydrolyzing NAD+. The enzymatic activity of DSR2 is triggered by the SPR phage tail tube protein (TTP), while suppressed by the SPbeta phage-encoded DSAD1 protein, enabling phages to evade the host defense. However, the molecular mechanisms of activation and inhibition of DSR2 remain elusive. Here, we report the cryo-EM structures of apo DSR2, DSR2-TTP-NAD+ and DSR2-DSAD1 complexes. DSR2 assembles into a head-to-head tetramer mediated by its Sir2 domain. The C-terminal helical regions of DSR2 constitute four partner-binding cavities with opened and closed conformation. Two TTP molecules bind to two of the four C-terminal cavities, inducing conformational change of Sir2 domain to activate DSR2. Furthermore, DSAD1 competes with the activator for binding to the C-terminal cavity of DSR2, effectively suppressing its enzymatic activity. Our results provide the mechanistic insights into the DSR2-mediated anti-phage defense system and DSAD1-dependent phage immune evasion.
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Affiliation(s)
- Ruiwen Wang
- MOE Key Laboratory of Rare Pediatric Diseases, Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Qi Xu
- Zhejiang Key Laboratory of Structural Biology, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
| | - Zhuoxi Wu
- MOE Key Laboratory of Rare Pediatric Diseases, Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Jialu Li
- Zhejiang Key Laboratory of Structural Biology, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
| | - Hao Guo
- MOE Key Laboratory of Rare Pediatric Diseases, Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Tianzhui Liao
- MOE Key Laboratory of Rare Pediatric Diseases, Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Yuan Shi
- Zhejiang Key Laboratory of Structural Biology, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
| | - Ling Yuan
- MOE Key Laboratory of Rare Pediatric Diseases, Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Haishan Gao
- Zhejiang Key Laboratory of Structural Biology, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
| | - Rong Yang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China.
| | - Zhubing Shi
- Zhejiang Key Laboratory of Structural Biology, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China.
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China.
| | - Faxiang Li
- MOE Key Laboratory of Rare Pediatric Diseases, Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China.
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35
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Webb JA, Farrow E, Cain B, Yuan Z, Yarawsky A, Schoch E, Gagliani E, Herr A, Gebelein B, Kovall R. Cooperative Gsx2-DNA binding requires DNA bending and a novel Gsx2 homeodomain interface. Nucleic Acids Res 2024; 52:7987-8002. [PMID: 38874471 PMCID: PMC11260452 DOI: 10.1093/nar/gkae522] [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: 12/11/2023] [Revised: 05/28/2024] [Accepted: 06/05/2024] [Indexed: 06/15/2024] Open
Abstract
The conserved Gsx homeodomain (HD) transcription factors specify neural cell fates in animals from flies to mammals. Like many HD proteins, Gsx factors bind A/T-rich DNA sequences prompting the following question: How do HD factors that bind similar DNA sequences in vitro regulate specific target genes in vivo? Prior studies revealed that Gsx factors bind DNA both as a monomer on individual A/T-rich sites and as a cooperative homodimer to two sites spaced precisely 7 bp apart. However, the mechanistic basis for Gsx-DNA binding and cooperativity is poorly understood. Here, we used biochemical, biophysical, structural and modeling approaches to (i) show that Gsx factors are monomers in solution and require DNA for cooperative complex formation, (ii) define the affinity and thermodynamic binding parameters of Gsx2/DNA interactions, (iii) solve a high-resolution monomer/DNA structure that reveals that Gsx2 induces a 20° bend in DNA, (iv) identify a Gsx2 protein-protein interface required for cooperative DNA binding and (v) determine that flexible spacer DNA sequences enhance Gsx2 cooperativity on dimer sites. Altogether, our results provide a mechanistic basis for understanding the protein and DNA structural determinants that underlie cooperative DNA binding by Gsx factors.
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Affiliation(s)
- Jordan A Webb
- Department of Molecular and Cellular Biosciences, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Edward Farrow
- Graduate Program in Molecular and Developmental Biology, Cincinnati Children’s Hospital Research Foundation, Cincinnati, OH 45229, USA
- Medical-Scientist Training Program, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Brittany Cain
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, 3333 Burnet Avenue, MLC 7007, Cincinnati, OH 45229, USA
| | - Zhenyu Yuan
- Department of Molecular and Cellular Biosciences, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Alexander E Yarawsky
- Division of Immunobiology, Cincinnati Children’s Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Emma Schoch
- Department of Medical Education, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Ellen K Gagliani
- Department of Chemistry, Xavier University, Cincinnati, OH 45207, USA
| | - Andrew B Herr
- Division of Immunobiology, Cincinnati Children’s Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Brian Gebelein
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, 3333 Burnet Avenue, MLC 7007, Cincinnati, OH 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Rhett A Kovall
- Department of Molecular and Cellular Biosciences, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
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36
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Zdanowicz R, Afanasyev P, Pruška A, Harrison JA, Giese C, Boehringer D, Leitner A, Zenobi R, Glockshuber R. Stoichiometry and architecture of the human pyruvate dehydrogenase complex. SCIENCE ADVANCES 2024; 10:eadn4582. [PMID: 39018392 PMCID: PMC466950 DOI: 10.1126/sciadv.adn4582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 06/05/2024] [Indexed: 07/19/2024]
Abstract
The pyruvate dehydrogenase complex (PDHc) is a key megaenzyme linking glycolysis with the citric acid cycle. In mammalian PDHc, dihydrolipoamide acetyltransferase (E2) and the dihydrolipoamide dehydrogenase-binding protein (E3BP) form a 60-subunit core that associates with the peripheral subunits pyruvate dehydrogenase (E1) and dihydrolipoamide dehydrogenase (E3). The structure and stoichiometry of the fully assembled, mammalian PDHc or its core remained elusive. Here, we demonstrate that the human PDHc core is formed by 48 E2 copies that bind 48 E1 heterotetramers and 12 E3BP copies that bind 12 E3 homodimers. Cryo-electron microscopy, together with native and cross-linking mass spectrometry, confirmed a core model in which 8 E2 homotrimers and 12 E2-E2-E3BP heterotrimers assemble into a pseudoicosahedral particle such that the 12 E3BP molecules form six E3BP-E3BP intertrimer interfaces distributed tetrahedrally within the 60-subunit core. The even distribution of E3 subunits in the peripheral shell of PDHc guarantees maximum enzymatic activity of the megaenzyme.
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Affiliation(s)
- Rafal Zdanowicz
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Otto-Stern-Weg 5, 8093 Zürich, Switzerland
| | - Pavel Afanasyev
- Cryo-EM Knowledge Hub, ETH Zurich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland
| | - Adam Pruška
- Department of Chemistry and Applied Biosciences, Laboratory of Organic Chemistry, ETH Zurich, Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland
| | - Julian A. Harrison
- Department of Chemistry and Applied Biosciences, Laboratory of Organic Chemistry, ETH Zurich, Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland
| | - Christoph Giese
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Otto-Stern-Weg 5, 8093 Zürich, Switzerland
| | - Daniel Boehringer
- Cryo-EM Knowledge Hub, ETH Zurich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland
| | - Alexander Leitner
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland
| | - Renato Zenobi
- Department of Chemistry and Applied Biosciences, Laboratory of Organic Chemistry, ETH Zurich, Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland
| | - Rudi Glockshuber
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Otto-Stern-Weg 5, 8093 Zürich, Switzerland
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37
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Shweta H, Gupta K, Zhou Y, Cui X, Li S, Lu Z, Goldman YE, Dantzig JA. Characterization and structural basis for the brightness of mCLIFY: a novel monomeric and circularly permuted bright yellow fluorescent protein. RESEARCH SQUARE 2024:rs.3.rs-4638282. [PMID: 39070629 PMCID: PMC11276004 DOI: 10.21203/rs.3.rs-4638282/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
We present mCLIFY: a monomeric, bright, yellow, and long-lived fluorescent protein (FP) created by circular permutation of YPet, the brightest yellow FP from Aequorea Victoria for use in cellular and in vitro single molecule studies. mCLIFY retains the enhanced photophysical properties of YPET as a monomer at concentrations ≤ 40 μM. In contrast, we determined that YPet has a dimerization dissociation constant (K D 1-2) of 3.4 μM. Dimerization of YPet can cause homo-FRET, which underlies quantitative errors due to dimerization and homo-FRET. We determined the atomic structure of mCLIFY at 1.57 Å resolution and used its similarity with Venus for guided chromophore-targeted substitution studies to provide insights into its enhanced photophysical properties. The mutation V58L within the chromophore pocket improved quantum yield and extinction coefficient, making mCLIFY ~30% brighter than Venus. The extensive characterization of the photophysical and structural properties of YPet and mCLIFY presented here allowed us to reveal the basis of their long lifetimes and enhanced brightness and the basis of YPet's dimerization.
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Affiliation(s)
- Him Shweta
- Pennsylvania Muscle Institute, University of Pennsylvania, Philadelphia, PA-19104, United States of America
- Center for Engineering Mechanobiology (CEMB), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA-19104, United States of America
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA-19104, United States of America
- Present address: Departments of Pharmacology and Cellular and Molecular Biology, University of California, Davis, CA-95616
| | - Kushol Gupta
- Department of Biochemistry & Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA-19104, United States of America
| | - Yufeng Zhou
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA-19104, United States of America
| | - Xiaonan Cui
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA-19104, United States of America
| | - Selene Li
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA-19104, United States of America
| | - Zhe Lu
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA-19104, United States of America
| | - Yale E. Goldman
- Pennsylvania Muscle Institute, University of Pennsylvania, Philadelphia, PA-19104, United States of America
- Center for Engineering Mechanobiology (CEMB), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA-19104, United States of America
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA-19104, United States of America
- Present address: Departments of Pharmacology and Cellular and Molecular Biology, University of California, Davis, CA-95616
| | - Jody A. Dantzig
- Pennsylvania Muscle Institute, University of Pennsylvania, Philadelphia, PA-19104, United States of America
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA-19104, United States of America
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38
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Zhao H, Sousa AA, Schuck P. Flotation Coefficient Distributions of Lipid Nanoparticles by Sedimentation Velocity Analytical Ultracentrifugation. ACS NANO 2024; 18:18663-18672. [PMID: 38967176 PMCID: PMC11256894 DOI: 10.1021/acsnano.4c05322] [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: 04/22/2024] [Revised: 06/24/2024] [Accepted: 06/27/2024] [Indexed: 07/06/2024]
Abstract
The robust characterization of lipid nanoparticles (LNPs) encapsulating therapeutics or vaccines is an important and multifaceted translational problem. Sedimentation velocity analytical ultracentrifugation (SV-AUC) has proven to be a powerful approach in the characterization of size-distribution, interactions, and composition of various types of nanoparticles across a large size range, including metal nanoparticles (NPs), polymeric NPs, and also nucleic acid loaded viral capsids. Similar potential of SV-AUC can be expected for the characterization of LNPs, but is hindered by the flotation of LNPs being incompatible with common sedimentation analysis models. To address this gap, we developed a high-resolution, diffusion-deconvoluted sedimentation/flotation distribution analysis approach analogous to the most widely used sedimentation analysis model c(s). The approach takes advantage of independent measurements of the average particle size or diffusion coefficient, which can be conveniently determined, for example, by dynamic light scattering (DLS). We demonstrate the application to an experimental model of extruded liposomes as well as a commercial LNP product and discuss experimental potential and limitations of SV-AUC. The method is implemented analogously to the sedimentation models in the free, widely used SEDFIT software.
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Affiliation(s)
- Huaying Zhao
- Laboratory
of Dynamics of Macromolecular Assembly, National Institute of Biomedical
Imaging and Bioengineering, National Institutes
of Health, Bethesda, Maryland 20892, United States
| | - Alioscka A. Sousa
- Department
of Biochemistry, Federal University of São
Paulo, São Paulo, SP 04044, Brazil
| | - Peter Schuck
- Laboratory
of Dynamics of Macromolecular Assembly, National Institute of Biomedical
Imaging and Bioengineering, National Institutes
of Health, Bethesda, Maryland 20892, United States
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39
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Beaufort N, Ingendahl L, Merdanovic M, Schmidt A, Podlesainski D, Richter T, Neumann T, Kuszner M, Vetter IR, Stege P, Burston SG, Filipovic A, Ruiz-Blanco YB, Bravo-Rodriguez K, Mieres-Perez J, Beuck C, Uebel S, Zobawa M, Schillinger J, Malik R, Todorov-Völgyi K, Rey J, Roberti A, Hagemeier B, Wefers B, Müller SA, Wurst W, Sanchez-Garcia E, Zimmermann A, Hu XY, Clausen T, Huber R, Lichtenthaler SF, Schmuck C, Giese M, Kaiser M, Ehrmann M, Dichgans M. Rational correction of pathogenic conformational defects in HTRA1. Nat Commun 2024; 15:5944. [PMID: 39013852 PMCID: PMC11252331 DOI: 10.1038/s41467-024-49982-8] [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: 01/21/2021] [Accepted: 06/24/2024] [Indexed: 07/18/2024] Open
Abstract
Loss-of-function mutations in the homotrimeric serine protease HTRA1 cause cerebral vasculopathy. Here, we establish independent approaches to achieve the functional correction of trimer assembly defects. Focusing on the prototypical R274Q mutation, we identify an HTRA1 variant that promotes trimer formation thus restoring enzymatic activity in vitro. Genetic experiments in Htra1R274Q mice further demonstrate that expression of this protein-based corrector in trans is sufficient to stabilize HtrA1-R274Q and restore the proteomic signature of the brain vasculature. An alternative approach employs supramolecular chemical ligands that shift the monomer-trimer equilibrium towards proteolytically active trimers. Moreover, we identify a peptidic ligand that activates HTRA1 monomers. Our findings open perspectives for tailored protein repair strategies.
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Affiliation(s)
- Nathalie Beaufort
- Institute for Stroke and Dementia Research (ISD), University Hospital, Ludwig Maximilian University of Munich, Munich, Germany
| | - Linda Ingendahl
- Center of Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Essen, Germany
| | - Melisa Merdanovic
- Center of Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Essen, Germany
| | - Andree Schmidt
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- Graduate School of Systemic Neurosciences (GSN), LMU Munich, Munich, Germany
| | - David Podlesainski
- Center of Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Essen, Germany
| | - Tim Richter
- Center of Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Essen, Germany
| | - Thorben Neumann
- Organic Chemistry, Faculty of Chemistry, University Duisburg-Essen, Essen, Germany
| | - Michael Kuszner
- Center of Medical Biotechnology, Faculty of Chemistry, University Duisburg-Essen, Essen, Germany
| | - Ingrid R Vetter
- Max-Planck-Institute of Molecular Physiology, Dortmund, Germany
| | - Patricia Stege
- Max-Planck-Institute of Molecular Physiology, Dortmund, Germany
| | - Steven G Burston
- School of Biochemistry, University of Bristol, Biomedical Sciences Building, Bristol, UK
| | - Anto Filipovic
- Center of Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Essen, Germany
| | - Yasser B Ruiz-Blanco
- Center of Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Essen, Germany
| | - Kenny Bravo-Rodriguez
- Center of Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Essen, Germany
- Max-Planck-Institute of Molecular Physiology, Dortmund, Germany
| | - Joel Mieres-Perez
- Center of Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Essen, Germany
- Department of Biochemical and Chemical Engineering, Technical University Dortmund, Dortmund, Germany
| | - Christine Beuck
- Center of Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Essen, Germany
| | - Stephan Uebel
- Max-Planck-Institute of Biochemistry, Martinsried, Germany
| | - Monika Zobawa
- Max-Planck-Institute of Biochemistry, Martinsried, Germany
| | - Jasmin Schillinger
- Center of Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Essen, Germany
| | - Rainer Malik
- Institute for Stroke and Dementia Research (ISD), University Hospital, Ludwig Maximilian University of Munich, Munich, Germany
| | - Katalin Todorov-Völgyi
- Institute for Stroke and Dementia Research (ISD), University Hospital, Ludwig Maximilian University of Munich, Munich, Germany
| | - Juliana Rey
- Center of Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Essen, Germany
| | - Annabell Roberti
- Center of Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Essen, Germany
| | - Birte Hagemeier
- Center of Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Essen, Germany
| | - Benedikt Wefers
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- Institute of Developmental Genetics (IDG), Helmholtz Zentrum München, Neuherberg, Germany
| | - Stephan A Müller
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- Neuroproteomics, School of Medicine, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Wolfgang Wurst
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- Institute of Developmental Genetics (IDG), Helmholtz Zentrum München, Neuherberg, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
- Technische Universität München-Weihenstephan, Freising, Germany
| | - Elsa Sanchez-Garcia
- Department of Biochemical and Chemical Engineering, Technical University Dortmund, Dortmund, Germany
| | - Alexander Zimmermann
- Center of Medical Biotechnology, Faculty of Chemistry, University Duisburg-Essen, Essen, Germany
| | - Xiao-Yu Hu
- College of Material Science and Technology, Nanjing University of Aeronautics and Astronautics, Nanjing, China
| | - Tim Clausen
- Research Institute of Molecular Pathology (IMP), Vienna, Austria
| | - Robert Huber
- Center of Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Essen, Germany
- Max-Planck-Institute of Biochemistry, Martinsried, Germany
| | - Stefan F Lichtenthaler
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- Neuroproteomics, School of Medicine, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Carsten Schmuck
- Center of Medical Biotechnology, Faculty of Chemistry, University Duisburg-Essen, Essen, Germany
| | - Michael Giese
- Organic Chemistry, Faculty of Chemistry, University Duisburg-Essen, Essen, Germany
| | - Markus Kaiser
- Center of Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Essen, Germany
| | - Michael Ehrmann
- Center of Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Essen, Germany.
| | - Martin Dichgans
- Institute for Stroke and Dementia Research (ISD), University Hospital, Ludwig Maximilian University of Munich, Munich, Germany.
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany.
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany.
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40
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Fu J, Li S, Guan H, Li C, Zhao YB, Chen TT, Xian W, Zhang Z, Liu Y, Guan Q, Wang J, Lu Q, Kang L, Zheng SR, Li J, Cao S, Das C, Liu X, Song L, Ouyang S, Luo ZQ. Legionella maintains host cell ubiquitin homeostasis by effectors with unique catalytic mechanisms. Nat Commun 2024; 15:5953. [PMID: 39009586 PMCID: PMC11251166 DOI: 10.1038/s41467-024-50311-2] [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: 04/01/2024] [Accepted: 07/05/2024] [Indexed: 07/17/2024] Open
Abstract
The intracellular bacterial pathogen Legionella pneumophila modulates host cell functions by secreting multiple effectors with diverse biochemical activities. In particular, effectors of the SidE family interfere with host protein ubiquitination in a process that involves production of phosphoribosyl ubiquitin (PR-Ub). Here, we show that effector LnaB converts PR-Ub into ADP-ribosylated ubiquitin, which is further processed to ADP-ribose and functional ubiquitin by the (ADP-ribosyl)hydrolase MavL, thus maintaining ubiquitin homeostasis in infected cells. Upon being activated by actin, LnaB also undergoes self-AMPylation on tyrosine residues. The activity of LnaB requires a motif consisting of Ser, His and Glu (SHxxxE) present in a large family of toxins from diverse bacterial pathogens. Thus, our study sheds light on the mechanisms by which a pathogen maintains ubiquitin homeostasis and identifies a family of enzymes capable of protein AMPylation.
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Affiliation(s)
- Jiaqi Fu
- Department of Respiratory Medicine, Center for Infectious Diseases and Pathogen Biology, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, The First Hospital of Jilin University, Changchun, China
| | - Siying Li
- Department of Respiratory Medicine, Center for Infectious Diseases and Pathogen Biology, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, The First Hospital of Jilin University, Changchun, China
| | - Hongxin Guan
- Key Laboratory of Microbial Pathogenesis and Interventions of Fujian Province University, the Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Chuang Li
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Yan-Bo Zhao
- Key Laboratory of Microbial Pathogenesis and Interventions of Fujian Province University, the Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Tao-Tao Chen
- Key Laboratory of Microbial Pathogenesis and Interventions of Fujian Province University, the Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Wei Xian
- Department of Microbiology, NHC Key Laboratory of Medical Immunology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Zhengrui Zhang
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | - Yao Liu
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Qingtian Guan
- Department of Respiratory Medicine, Center for Infectious Diseases and Pathogen Biology, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, The First Hospital of Jilin University, Changchun, China
| | - Jingting Wang
- Key Laboratory of Microbial Pathogenesis and Interventions of Fujian Province University, the Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Qiuhua Lu
- Key Laboratory of Microbial Pathogenesis and Interventions of Fujian Province University, the Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Lina Kang
- Key Laboratory of Microbial Pathogenesis and Interventions of Fujian Province University, the Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Si-Ru Zheng
- Key Laboratory of Microbial Pathogenesis and Interventions of Fujian Province University, the Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Jinyu Li
- College of Chemistry, Fuzhou University, Fuzhou, Fujian, China
| | - Shoujing Cao
- College of Chemistry, Fuzhou University, Fuzhou, Fujian, China
| | - Chittaranjan Das
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | - Xiaoyun Liu
- Department of Microbiology, NHC Key Laboratory of Medical Immunology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China.
| | - Lei Song
- Department of Respiratory Medicine, Center for Infectious Diseases and Pathogen Biology, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, The First Hospital of Jilin University, Changchun, China.
| | - Songying Ouyang
- Key Laboratory of Microbial Pathogenesis and Interventions of Fujian Province University, the Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, China.
| | - Zhao-Qing Luo
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA.
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41
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Palmer N, Agnew C, Benn C, Buffham WJ, Castro JN, Chessari G, Clark M, Cons BD, Coyle JE, Dawson LA, Hamlett CCF, Hodson C, Holding F, Johnson CN, Liebeschuetz JW, Mahajan P, McCarthy JM, Murray CW, O'Reilly M, Peakman T, Price A, Rapti M, Reeks J, Schöpf P, St-Denis JD, Valenzano C, Wallis NG, Walser R, Weir H, Wilsher NE, Woodhead A, Bento CF, Tisi D. Fragment-Based Discovery of a Series of Allosteric-Binding Site Modulators of β-Glucocerebrosidase. J Med Chem 2024; 67:11168-11181. [PMID: 38932616 DOI: 10.1021/acs.jmedchem.4c00702] [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: 06/28/2024]
Abstract
β-Glucocerebrosidase (GBA/GCase) mutations leading to misfolded protein cause Gaucher's disease and are a major genetic risk factor for Parkinson's disease and dementia with Lewy bodies. The identification of small molecule pharmacological chaperones that can stabilize the misfolded protein and increase delivery of degradation-prone mutant GCase to the lysosome is a strategy under active investigation. Here, we describe the first use of fragment-based drug discovery (FBDD) to identify pharmacological chaperones of GCase. The fragment hits were identified by using X-ray crystallography and biophysical techniques. This work led to the discovery of a series of compounds that bind GCase with nM potency and positively modulate GCase activity in cells.
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Affiliation(s)
- Nick Palmer
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Christopher Agnew
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Caroline Benn
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - William J Buffham
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Joan N Castro
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Gianni Chessari
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Mellissa Clark
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Benjamin D Cons
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Joseph E Coyle
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Lee A Dawson
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | | | - Charlotte Hodson
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Finn Holding
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Christopher N Johnson
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - John W Liebeschuetz
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Pravin Mahajan
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - James M McCarthy
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Christopher W Murray
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Marc O'Reilly
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Torren Peakman
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Amanda Price
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Magdalini Rapti
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Judith Reeks
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Patrick Schöpf
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Jeffrey D St-Denis
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Chiara Valenzano
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Nicola G Wallis
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Reto Walser
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Heather Weir
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Nicola E Wilsher
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Andrew Woodhead
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Carla F Bento
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Dominic Tisi
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
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42
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Mišković MZ, Wojtyś M, Winiewska-Szajewska M, Wielgus-Kutrowska B, Matković M, Domazet Jurašin D, Štefanić Z, Bzowska A, Leščić Ašler I. Location Is Everything: Influence of His-Tag Fusion Site on Properties of Adenylosuccinate Synthetase from Helicobacter pylori. Int J Mol Sci 2024; 25:7613. [PMID: 39062851 PMCID: PMC11276676 DOI: 10.3390/ijms25147613] [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: 04/30/2024] [Revised: 07/05/2024] [Accepted: 07/08/2024] [Indexed: 07/28/2024] Open
Abstract
The requirement for fast and dependable protein purification methods is constant, either for functional studies of natural proteins or for the production of biotechnological protein products. The original procedure has to be formulated for each individual protein, and this demanding task was significantly simplified by the introduction of affinity tags. Helicobacter pylori adenylosuccinate synthetase (AdSS) is present in solution in a dynamic equilibrium of monomers and biologically active homodimers. The addition of the His6-tag on the C-terminus (C-His-AdSS) was proven to have a negligible effect on the characteristics of this enzyme. This paper shows that the same enzyme with the His6-tag fused on its N-terminus (N-His-AdSS) has a high tendency to precipitate. Circular dichroism and X-ray diffraction studies do not detect any structural change that could explain this propensity. However, the dynamic light scattering, differential scanning fluorimetry, and analytical ultracentrifugation measurements indicate that the monomer of this construct is prone to aggregation, which shifts the equilibrium towards the insoluble precipitant. In agreement, enzyme kinetics measurements showed reduced enzyme activity, but preserved affinity for the substrates, in comparison with the wild-type and C-His-AdSS. The presented results reinforce the notion that testing the influence of the tag on protein properties should not be overlooked.
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Affiliation(s)
- Marija Zora Mišković
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, HR-10000 Zagreb, Croatia;
| | - Marta Wojtyś
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland; (M.W.); (M.W.-S.); (B.W.-K.)
| | - Maria Winiewska-Szajewska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland; (M.W.); (M.W.-S.); (B.W.-K.)
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Beata Wielgus-Kutrowska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland; (M.W.); (M.W.-S.); (B.W.-K.)
| | - Marija Matković
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, HR-10000 Zagreb, Croatia;
| | - Darija Domazet Jurašin
- Division of Physical Chemistry, Ruđer Bošković Institute, Bijenička cesta 54, HR-10000 Zagreb, Croatia; (D.D.J.); (Z.Š.)
| | - Zoran Štefanić
- Division of Physical Chemistry, Ruđer Bošković Institute, Bijenička cesta 54, HR-10000 Zagreb, Croatia; (D.D.J.); (Z.Š.)
| | - Agnieszka Bzowska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland; (M.W.); (M.W.-S.); (B.W.-K.)
| | - Ivana Leščić Ašler
- Division of Physical Chemistry, Ruđer Bošković Institute, Bijenička cesta 54, HR-10000 Zagreb, Croatia; (D.D.J.); (Z.Š.)
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43
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Soulié M, Deletraz A, Wehbie M, Mahler F, Chantemargue B, Bouchemal I, Le Roy A, Petit-Härtlein I, Fieschi F, Breyton C, Ebel C, Keller S, Durand G. Rigid Cyclic Fluorinated Detergents: Fine-Tuning the Hydrophilic-Lipophilic Balance Controls Self-Assembling and Biochemical Properties. ACS APPLIED MATERIALS & INTERFACES 2024; 16:32971-32982. [PMID: 38885044 DOI: 10.1021/acsami.4c03359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
We report herein the synthesis of three detergents bearing a perfluorinated cyclohexyl group connected through a short, hydrogenated spacer (i.e., propyl, butyl, or pentyl) to a β-maltoside polar head that are, respectively, called FCymal-3, FCymal-4, and FCymal-5. Increasing the length of the spacer decreased the critical micellar concentration (CMC), as demonstrated by surface tension (SFT) and isothermal titration calorimetry (ITC), from 5 mM for FCymal-3 to 0.7 mM for FCymal-5. The morphology of the micelles was studied by dynamic light scattering (DLS), analytical ultracentrifugation (AUC), and small-angle X-ray scattering (SAXS), indicating heterogeneous rod-like shapes. While micelles of FCymal-3 and -4 have similar hydrodynamic diameters of ∼10 nm, those of FCymal-5 were twice as large. We also investigated the ability of the detergents to solubilize lipid membranes made of 1-palmitoyl-2-oleyl-sn-glycero-3-phosphocholine (POPC). Molecular modeling indicated that the FCymal detergents generate disorder in lipid bilayers, with FCymal-3 being inserted more deeply into bilayers than FCymal-4 and -5. This was experimentally confirmed using POPC vesicles that were completely solubilized within 2 h with FCymal-3, whereas FCymal-5 required >8 h. A similar trend was noticed for the direct extraction of membrane proteins from E. coli membranes, with FCymal-3 being more potent than FCymal-5. An opposite trend was observed in terms of stabilization of the two model membrane proteins bacteriorhodopsin (bR) and SpNOX. In all three FCymal detergents, bR was stable for at least 2 months with no signs of aggregation. However, while the structural integrity of bR was fully preserved in FCymal-4 and -5, minor bleaching was observed in FCymal-3. Similarly, SpNOX exhibited the least activity in FCymal-3 and the highest activity in FCymal-5. By combining solubilizing and stabilizing potency, FCymal detergents push forward our expectations of the usefulness of fluorinated detergents for handling and investigating membrane proteins.
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Affiliation(s)
- Marine Soulié
- Institut des Biomolécules Max Mousseron (UMR 5247 UM-CNRS-ENSCM), Equipe Chimie Bioorganique et Systèmes amphiphiles, 301 Rue Baruch de Spinoza, 84916 Avignon Cedex 9, France
- Avignon Université, Unité Propre de Recherche et d'Innovation, Equipe Synthèse et Systèmes Colloïdaux Bio-organiques, 301 Rue Baruch de Spinoza, 84916 Avignon Cedex 9, France
| | - Anais Deletraz
- Institut des Biomolécules Max Mousseron (UMR 5247 UM-CNRS-ENSCM), Equipe Chimie Bioorganique et Systèmes amphiphiles, 301 Rue Baruch de Spinoza, 84916 Avignon Cedex 9, France
| | - Moheddine Wehbie
- Institut des Biomolécules Max Mousseron (UMR 5247 UM-CNRS-ENSCM), Equipe Chimie Bioorganique et Systèmes amphiphiles, 301 Rue Baruch de Spinoza, 84916 Avignon Cedex 9, France
| | - Florian Mahler
- Molecular Biophysics, Technische Universität Kaiserslautern (TUK), Erwin-Schrödinger-Str. 13, 67663 Kaiserslautern, Germany
| | | | - Ilham Bouchemal
- Univ. Grenoble Alpes, CNRS, CEA, CNRS, IBS, F-38000 Grenoble, France
| | - Aline Le Roy
- Univ. Grenoble Alpes, CNRS, CEA, CNRS, IBS, F-38000 Grenoble, France
| | | | - Franck Fieschi
- Univ. Grenoble Alpes, CNRS, CEA, CNRS, IBS, F-38000 Grenoble, France
- Institut Universitaire de France (IUF), 75005 Paris, France
| | - Cécile Breyton
- Univ. Grenoble Alpes, CNRS, CEA, CNRS, IBS, F-38000 Grenoble, France
| | - Christine Ebel
- Univ. Grenoble Alpes, CNRS, CEA, CNRS, IBS, F-38000 Grenoble, France
| | - Sandro Keller
- Biophysics, Institute of Molecular Biosciences (IMB), NAWI Graz, University of Graz, Humboldtstr. 50/III, 8010 Graz, Austria
- Field of Excellence BioHealth, University of Graz, 8010 Graz, Austria
- BioTechMed-Graz, 8010 Graz, Austria
| | - Grégory Durand
- Institut des Biomolécules Max Mousseron (UMR 5247 UM-CNRS-ENSCM), Equipe Chimie Bioorganique et Systèmes amphiphiles, 301 Rue Baruch de Spinoza, 84916 Avignon Cedex 9, France
- Avignon Université, Unité Propre de Recherche et d'Innovation, Equipe Synthèse et Systèmes Colloïdaux Bio-organiques, 301 Rue Baruch de Spinoza, 84916 Avignon Cedex 9, France
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Nasiri F, Ebrahimi P, Shahsavani MB, Barati A, Zarei I, Hong J, Hoshino M, Moosavi-Movahedi AA, Yousefi R. Unraveling the impact of the p.R107L mutation on the structure and function of human αB-Crystallin: Implications for cataract formation. Biochimie 2024; 222:151-168. [PMID: 38494110 DOI: 10.1016/j.biochi.2024.03.004] [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: 12/15/2023] [Revised: 03/01/2024] [Accepted: 03/04/2024] [Indexed: 03/19/2024]
Abstract
To date, several pathogenic mutations have been identified in the primary structure of human α-Crystallin, frequently involving the substitution of arginine with a different amino acid. These mutations can lead to the incidence of cataracts and myopathy. Recently, an important cataract-associated mutation has been reported in the functional α-Crystallin domain (ACD) of human αB-Crystallin protein, where arginine 107 (R107) is replaced by a leucine. In this study, we investigated the structure, chaperone function, stability, oligomerization, and amyloidogenic properties of the p.R107L human αB-Crystallin using a number of different techniques. Our results suggest that the p.R107L mutation can cause significant changes in the secondary, tertiary, and quaternary structures of αB-Crystallin. This cataractogenic mutation led to the formation of protein oligomers with larger sizes than the wild-type protein and reduced the chemical and thermal stability of the mutant chaperone. Both fluorescence and microscopic assessments indicated that this mutation significantly altered the amyloidogenic properties of human αB-Crystallin. Furthermore, the mutant protein indicated an attenuated in vitro chaperone activity. The molecular dynamics (MD) simulation confirmed the experimental results and indicated that p.R107L mutation could alter the proper conformation of human αB-Crystallin dimers. In summary, our results indicated that the p.R107L mutation could promote the formation of larger oligomers, diminish the stability and chaperone activity of human αB-Crystallin, and these changes, in turn, can play a crucial role in the development of cataract disorder.
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Affiliation(s)
- Farid Nasiri
- Protein Chemistry Laboratory (PCL), Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran
| | - Parisa Ebrahimi
- Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran
| | | | - Anis Barati
- Protein Chemistry Laboratory (PCL), Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran
| | - Issa Zarei
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, 1416634793, Iran
| | - Jun Hong
- School of Life Sciences, Henan University, Kaifeng, 475000, People's Republic of China
| | - Masaru Hoshino
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, 606-8501, Japan
| | | | - Reza Yousefi
- Protein Chemistry Laboratory (PCL), Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran.
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45
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Goto Y, Miyafusa T, Honda S. Designing monomeric IFNγ: The significance of domain-swapped dimer structure in IFNγ immune responses. J Biol Chem 2024; 300:107464. [PMID: 38879015 DOI: 10.1016/j.jbc.2024.107464] [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: 02/22/2024] [Revised: 05/21/2024] [Accepted: 06/03/2024] [Indexed: 07/12/2024] Open
Abstract
Interferon (IFN) γ can initiate immune responses by inducing the expression of major histocompatibility complex molecules, suggesting its potential for cancer immunotherapy. However, it also has an immunosuppressive function that limits its application as a therapeutic agent. IFNγ has a characteristic domain-swapped dimer structure with two of the six α-helices exchanged with each other. As we hypothesized that the contrasting functions of IFNγ could be attributed to its unique domain-swapped structure, we designed monomeric IFNγ by transforming the domain-swapped dimer structure of WT IFNγ. We conjectured the evolution of this domain-swapped dimer and hypothesized that the current IFNγ structure emerged through shortening of the loop structure at the base of the swapped domain and the accumulation of hydrophobic amino acids at the newly generated interface during domain-swapping. We then designed and generated a stable monomeric IFNγ by retracing this evolutionary process, complementing the lost loop structure with a linker, and replacing the accumulated hydrophobic amino acids with hydrophilic ones. We determined that the designed variant was a monomer based on molecular size and number of epitopes and exhibited activity in cell-based assays. Notably, the monomeric IFNγ showed a qualitatively similar balance between immunostimulatory and immunosuppressive gene expression as WT IFNγ. This study demonstrates that the structural format of IFNγ affects the strength of its activity rather than regulating the fate of downstream gene expression.
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Affiliation(s)
- Yota Goto
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan; Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
| | - Takamitsu Miyafusa
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
| | - Shinya Honda
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan; Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan.
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46
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Sun J, Morishima K, Inoue R, Sugiyama M, Takata T. Characterization of βB2-crystallin tryptophan mutants reveals two different folding states in solution. Protein Sci 2024; 33:e5092. [PMID: 38924206 PMCID: PMC11201810 DOI: 10.1002/pro.5092] [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: 03/30/2024] [Revised: 06/07/2024] [Accepted: 06/11/2024] [Indexed: 06/28/2024]
Abstract
Conserved tryptophan residues are critical for the structure and the stability of β/γ-crystallin in the lenses of vertebrates. During aging, in which the lenses are continuously exposed to ultraviolet irradiation and other environmental stresses, oxidation of tryptophan residues in β/γ-crystallin is triggered and impacts the lens proteins to varying degrees. Kynurenine derivatives, formed by oxidation of tryptophan, accumulate, resulting in destabilization and insolubilization of β/γ-crystallin, which correlates with age-related cataract formation. To understand the contribution of tryptophan modification on the structure and stability of human βB2-crystallin, five tryptophan residues were mutated to phenylalanine considering its similarity in structure and hydrophilicity to kynurenine. Among all mutants, W59F and W151F altered the stability and homo-oligomerization of βB2-crystallin-W59F promoted tetramerization whereas W151F blocked oligomerization. Most W59F dimers transformed into tetramer in a month, and the separated dimer and tetramer of W59F demonstrated different structures and hydrophobicity, implying that the biochemical properties of βB2-crystallin vary over time. By using SAXS, we found that the dimer of βB2-crystallin in solution resembled the lattice βB1-crystallin dimer (face-en-face), whereas the tetramer of βB2-crystallin in solution resembled its lattice tetramer (domain-swapped). Our results suggest that homo-oligomerization of βB2-crystallin includes potential inter-subunit reactions, such as dissociation, unfolding, and re-formation of the dimers into a tetramer in solution. The W>F mutants are useful in studying different folding states of βB2-crystallin in lens.
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Affiliation(s)
- Jiayue Sun
- Department of Chemistry, Graduate School of ScienceKyoto UniversityKyotoJapan
| | - Ken Morishima
- Institute for Integrated Radiation and Nuclear ScienceKyoto UniversityOsakaJapan
| | - Rintaro Inoue
- Institute for Integrated Radiation and Nuclear ScienceKyoto UniversityOsakaJapan
| | - Masaaki Sugiyama
- Institute for Integrated Radiation and Nuclear ScienceKyoto UniversityOsakaJapan
| | - Takumi Takata
- Institute for Integrated Radiation and Nuclear ScienceKyoto UniversityOsakaJapan
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47
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Lučić M, Allport T, Clarke TA, Williams LJ, Wilson MT, Chaplin AK, Worrall JAR. The oligomeric states of dye-decolorizing peroxidases from Streptomyces lividans and their implications for mechanism of substrate oxidation. Protein Sci 2024; 33:e5073. [PMID: 38864770 PMCID: PMC11168072 DOI: 10.1002/pro.5073] [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: 02/22/2024] [Revised: 05/18/2024] [Accepted: 05/25/2024] [Indexed: 06/13/2024]
Abstract
A common evolutionary mechanism in biology to drive function is protein oligomerization. In prokaryotes, the symmetrical assembly of repeating protein units to form homomers is widespread, yet consideration in vitro of whether such assemblies have functional or mechanistic consequences is often overlooked. Dye-decolorizing peroxidases (DyPs) are one such example, where their dimeric α + β barrel units can form various oligomeric states, but the oligomer influence, if any, on mechanism and function has received little attention. In this work, we have explored the oligomeric state of three DyPs found in Streptomyces lividans, each with very different mechanistic behaviors in their reactions with hydrogen peroxide and organic substrates. Using analytical ultracentrifugation, we reveal that except for one of the A-type DyPs where only a single sedimenting species is detected, oligomer states ranging from homodimers to dodecamers are prevalent in solution. Using cryo-EM on preparations of the B-type DyP, we determined a 3.02 Å resolution structure of a hexamer assembly that corresponds to the dominant oligomeric state in solution as determined by analytical ultracentrifugation. Furthermore, cryo-EM data detected sub-populations of higher-order oligomers, with one of these formed by an arrangement of two B-type DyP hexamers to give a dodecamer assembly. Our solution and structural insights of these oligomer states provide a new framework to consider previous mechanistic studies of these DyP members and are discussed in terms of long-range electron transfer for substrate oxidation and in the "storage" of oxidizable equivalents on the heme until a two-electron donor is available.
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Affiliation(s)
- Marina Lučić
- School of Life SciencesUniversity of EssexColchesterUK
| | - Thomas Allport
- Leicester Institute for Structural and Chemical Biology, Department of Molecular and Cell BiologyUniversity of LeicesterLeicesterUK
| | | | | | | | - Amanda K. Chaplin
- Leicester Institute for Structural and Chemical Biology, Department of Molecular and Cell BiologyUniversity of LeicesterLeicesterUK
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48
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Carriles AA, Muzzolini L, Minici C, Tornaghi P, Patrone M, Degano M. Structure-Function Insights into the Dual Role in Nucleobase and Nicotinamide Metabolism and a Possible Use in Cancer Gene Therapy of the URH1p Riboside Hydrolase. Int J Mol Sci 2024; 25:7032. [PMID: 39000137 PMCID: PMC11241417 DOI: 10.3390/ijms25137032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 06/14/2024] [Accepted: 06/24/2024] [Indexed: 07/16/2024] Open
Abstract
The URH1p enzyme from the yeast Saccharomyces cerevisiae has gained significant interest due to its role in nitrogenous base metabolism, particularly involving uracil and nicotinamide salvage. Indeed, URH1p was initially classified as a nucleoside hydrolase (NH) with a pronounced preference for uridine substrate but was later shown to also participate in a Preiss-Handler-dependent pathway for recycling of both endogenous and exogenous nicotinamide riboside (NR) towards NAD+ synthesis. Here, we present the detailed enzymatic and structural characterisation of the yeast URH1p enzyme, a member of the group I NH family of enzymes. We show that the URH1p has similar catalytic efficiencies for hydrolysis of NR and uridine, advocating a dual role of the enzyme in both NAD+ synthesis and nucleobase salvage. We demonstrate that URH1p has a monomeric structure that is unprecedented for members of the NH homology group I, showing that oligomerisation is not strictly required for the N-ribosidic activity in this family of enzymes. The size, thermal stability and activity of URH1p towards the synthetic substrate 5-fluoruridine, a riboside precursor of the antitumoral drug 5-fluorouracil, make the enzyme an attractive tool to be employed in gene-directed enzyme-prodrug activation therapy against solid tumours.
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Affiliation(s)
- Alejandra Angela Carriles
- Biocrystallography Group, IRCCS San Raffaele Scientific Institute, Via Olgettina 60, 20132 Milano, Italy
| | - Laura Muzzolini
- Biocrystallography Group, IRCCS San Raffaele Scientific Institute, Via Olgettina 60, 20132 Milano, Italy
| | - Claudia Minici
- Biocrystallography Group, IRCCS San Raffaele Scientific Institute, Via Olgettina 60, 20132 Milano, Italy
| | - Paola Tornaghi
- Biocrystallography Group, IRCCS San Raffaele Scientific Institute, Via Olgettina 60, 20132 Milano, Italy
| | - Marco Patrone
- Biocrystallography Group, IRCCS San Raffaele Scientific Institute, Via Olgettina 60, 20132 Milano, Italy
| | - Massimo Degano
- Biocrystallography Group, IRCCS San Raffaele Scientific Institute, Via Olgettina 60, 20132 Milano, Italy
- Faculty of Medicine and Surgery, Università Vita-Salute San Raffaele, Via Olgettina 58, 20132 Milano, Italy
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Tang S, Huang CH, Ko TP, Lin KF, Chang YC, Lin PY, Sun L, Chen CY. Dual dimeric interactions in the nucleic acid-binding protein Sac10b lead to multiple bridging of double-stranded DNA. Heliyon 2024; 10:e31630. [PMID: 38867953 PMCID: PMC11167270 DOI: 10.1016/j.heliyon.2024.e31630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 04/26/2024] [Accepted: 05/20/2024] [Indexed: 06/14/2024] Open
Abstract
Nucleoid-associated proteins play a crucial role in the compaction and regulation of genetic material across organisms. The Sac10b family, also known as Alba, comprises widely distributed and highly conserved nucleoid-associated proteins found in archaea. Sac10b is identified as the first 10 kDa DNA-binding protein in the thermoacidophile Sulfolobus acidocaldarius. Here, we present the crystal structures of two homologous proteins, Sac10b1 and Sac10b2, as well as the Sac10b1 mutant F59A, determined at a resolution of 1.4-2.0 Å. Electron microscopic images reveal the DNA-bridging capabilities of both Sac10b1 and Sac10b2, albeit to varying extents. Analyses of crystal packing and electron microscopic results suggest that Sac10b1 facilitates cooperative DNA binding, forming extensive bridged filaments via the conserved R58 and F59 residues at the dimer-dimer interface. Substitutions at R58 or F59 of Sac10b1 attenuate end-to-end association, resulting in non-cooperative DNA binding, and formation of small, bridged DNA segments in a way similar to Sac10b2. Analytical ultracentrifuge and circular dichroism confirm the presence of thermostable, acid-tolerant dimers in both Sac10b1 and Sac10b2. These findings attest to the functional role of Sac10b in organizing and stabilizing chromosomal DNA through distinct bridging interactions, particularly under extreme growth conditions.
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Affiliation(s)
- Songqiang Tang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Chun-Hsiang Huang
- Protein Diffraction Group, Experimental Facility Division, National Synchrotron Radiation Research Center, Hsinchu, 30076, Taiwan
| | - Tzu-Ping Ko
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan
| | - Kuan-Fu Lin
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Yuan-Chih Chang
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan
| | - Po-Yen Lin
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Liuchang Sun
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Chin-Yu Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, China
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50
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Barylko B, Taylor CA, Wang J, Hedde PN, Chen Y, Hur KH, Binns DD, Brautigam CA, DeMartino GN, Mueller JD, Jameson DM, Albanesi JP. Analysis of Arc/Arg3.1 Oligomerization In Vitro and in Living Cells. Int J Mol Sci 2024; 25:6454. [PMID: 38928159 PMCID: PMC11203824 DOI: 10.3390/ijms25126454] [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: 05/24/2024] [Accepted: 06/06/2024] [Indexed: 06/28/2024] Open
Abstract
Arc (also known as Arg3.1) is an activity-dependent immediate early gene product enriched in neuronal dendrites. Arc plays essential roles in long-term potentiation, long-term depression, and synaptic scaling. Although its mechanisms of action in these forms of synaptic plasticity are not completely well established, the activities of Arc include the remodeling of the actin cytoskeleton, the facilitation of AMPA receptor (AMPAR) endocytosis, and the regulation of the transcription of AMPAR subunits. In addition, Arc has sequence and structural similarity to retroviral Gag proteins and self-associates into virus-like particles that encapsulate mRNA and perhaps other cargo for intercellular transport. Each of these activities is likely to be influenced by Arc's reversible self-association into multiple oligomeric species. Here, we used mass photometry to show that Arc exists predominantly as monomers, dimers, and trimers at approximately 20 nM concentration in vitro. Fluorescence fluctuation spectroscopy revealed that Arc is almost exclusively present as low-order (monomer to tetramer) oligomers in the cytoplasm of living cells, over a 200 nM to 5 μM concentration range. We also confirmed that an α-helical segment in the N-terminal domain contains essential determinants of Arc's self-association.
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Affiliation(s)
- Barbara Barylko
- Department of Pharmacology, University of Texas Southwestern Medical Center, 6001 Forest Park, Dallas, TX 75390, USA; (B.B.); (C.A.T.4th); (D.D.B.)
| | - Clinton A. Taylor
- Department of Pharmacology, University of Texas Southwestern Medical Center, 6001 Forest Park, Dallas, TX 75390, USA; (B.B.); (C.A.T.4th); (D.D.B.)
| | - Jason Wang
- Department of Physiology, University of Texas Southwestern Medical Center, 6001 Forest Park, Dallas, TX 75390, USA; (J.W.); (G.N.D.)
| | - Per Niklas Hedde
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii, 651 Ilalo St., BSB 222, Honolulu, HI 96813, USA;
- Laboratory for Fluorescence Dynamics, University of California, Irvine, CA 92697, USA
| | - Yan Chen
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN 55455, USA; (Y.C.); (K.-H.H.); (J.D.M.)
| | - Kwang-Ho Hur
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN 55455, USA; (Y.C.); (K.-H.H.); (J.D.M.)
| | - Derk D. Binns
- Department of Pharmacology, University of Texas Southwestern Medical Center, 6001 Forest Park, Dallas, TX 75390, USA; (B.B.); (C.A.T.4th); (D.D.B.)
| | - Chad A. Brautigam
- Department of Biophysics, University of Texas Southwestern Medical Center, 6001 Forest Park, Dallas, TX 75390, USA;
| | - George N. DeMartino
- Department of Physiology, University of Texas Southwestern Medical Center, 6001 Forest Park, Dallas, TX 75390, USA; (J.W.); (G.N.D.)
| | - Joachim D. Mueller
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN 55455, USA; (Y.C.); (K.-H.H.); (J.D.M.)
| | - David M. Jameson
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii, 651 Ilalo St., BSB 222, Honolulu, HI 96813, USA;
| | - Joseph P. Albanesi
- Department of Pharmacology, University of Texas Southwestern Medical Center, 6001 Forest Park, Dallas, TX 75390, USA; (B.B.); (C.A.T.4th); (D.D.B.)
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