1
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Lu Z, Hu Y, Wang J, Zhang B, Zhang Y, Cui Z, Zhang L, Zhang A. Structure of the exopolyphosphatase (PPX) from Zymomonas mobilis reveals a two-magnesium-ions PPX. Int J Biol Macromol 2024; 262:129796. [PMID: 38311144 DOI: 10.1016/j.ijbiomac.2024.129796] [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: 08/14/2023] [Revised: 01/23/2024] [Accepted: 01/25/2024] [Indexed: 02/10/2024]
Abstract
Rapid adaptation of metabolic capabilities is crucial for bacterial survival in habitats with fluctuating nutrient availability. In such conditions, the bacterial stringent response is a central regulatory mechanism activated by nutrient starvation or other stressors. This response is primarily controlled by exopolyphosphatase/guanosine pentaphosphate phosphohydrolase (PPX/GPPA) enzymes. To gain further insight into these enzymes, the high-resolution crystal structure of PPX from Zymomonas mobilis (ZmPPX) was determined at 1.8 Å. The phosphatase activity of PPX was strictly dependent on the presence of divalent metal cations. Notably, the structure of ZmPPX revealed the presence of two magnesium ions in the active site center, which is atypical compared to other PPX structures where only one divalent ion is observed. ZmPPX exists as a dimer in solution and belongs to the "long" PPX group consisting of four domains. Remarkably, the dimer configuration exhibits a substantial and deep aqueduct with positive potential along its interface. This aqueduct appears to extend towards the active site region, suggesting that this positively charged aqueduct could potentially serve as a binding site for polyP.
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Affiliation(s)
- Zuokun Lu
- Food and Pharmacy College, Xuchang University, Xuchang 461000, Henan, China; Key Laboratory of Biomarker-Based Rapid Detection Technology for Food Safety of Henan Province, Xuchang University, Xuchang 461000, Henan, China
| | - Yongsheng Hu
- Food and Pharmacy College, Xuchang University, Xuchang 461000, Henan, China
| | - Jiazhan Wang
- Food and Pharmacy College, Xuchang University, Xuchang 461000, Henan, China
| | - Bingyang Zhang
- Food and Pharmacy College, Xuchang University, Xuchang 461000, Henan, China
| | - Yanyan Zhang
- Food and Pharmacy College, Xuchang University, Xuchang 461000, Henan, China
| | - Zhaohui Cui
- Food and Pharmacy College, Xuchang University, Xuchang 461000, Henan, China; Key Laboratory of Biomarker-Based Rapid Detection Technology for Food Safety of Henan Province, Xuchang University, Xuchang 461000, Henan, China
| | - Liang Zhang
- Food and Pharmacy College, Xuchang University, Xuchang 461000, Henan, China; Key Laboratory of Biomarker-Based Rapid Detection Technology for Food Safety of Henan Province, Xuchang University, Xuchang 461000, Henan, China
| | - Aili Zhang
- Food and Pharmacy College, Xuchang University, Xuchang 461000, Henan, China.
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2
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Hsu MF, Sriramoju MK, Lai CH, Chen YR, Huang JS, Ko TP, Huang KF, Hsu STD. Structure, dynamics, and stability of the smallest and most complex 7 1 protein knot. J Biol Chem 2024; 300:105553. [PMID: 38072060 PMCID: PMC10840475 DOI: 10.1016/j.jbc.2023.105553] [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: 06/29/2023] [Revised: 11/21/2023] [Accepted: 12/04/2023] [Indexed: 12/29/2023] Open
Abstract
Proteins can spontaneously tie a variety of intricate topological knots through twisting and threading of the polypeptide chains. Recently developed artificial intelligence algorithms have predicted several new classes of topological knotted proteins, but the predictions remain to be authenticated experimentally. Here, we showed by X-ray crystallography and solution-state NMR spectroscopy that Q9PR55, an 89-residue protein from Ureaplasma urealyticum, possesses a novel 71 knotted topology that is accurately predicted by AlphaFold 2, except for the flexible N terminus. Q9PR55 is monomeric in solution, making it the smallest and most complex knotted protein known to date. In addition to its exceptional chemical stability against urea-induced unfolding, Q9PR55 is remarkably robust to resist the mechanical unfolding-coupled proteolysis by a bacterial proteasome, ClpXP. Our results suggest that the mechanical resistance against pulling-induced unfolding is determined by the complexity of the knotted topology rather than the size of the molecule.
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Affiliation(s)
- Min-Feng Hsu
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | | | - Chih-Hsuan Lai
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Yun-Ru Chen
- Academia Sinica Protein Clinic, Academia Sinica, Taipei, Taiwan
| | - Jing-Siou Huang
- Academia Sinica Protein Clinic, Academia Sinica, Taipei, Taiwan
| | - Tzu-Ping Ko
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Kai-Fa Huang
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan; Academia Sinica Protein Clinic, Academia Sinica, Taipei, Taiwan
| | - Shang-Te Danny Hsu
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan; Academia Sinica Protein Clinic, Academia Sinica, Taipei, Taiwan; Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan; International Institute for Sustainability with Knotted Chiral Meta Matter (WPI-SKCM(2)), Hiroshima University, Higashihiroshima, Japan.
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3
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Jacob PL, Brugnoli B, Del Giudice A, Phan H, Chauhan VM, Beckett L, Gillis RB, Moloney C, Cavanagh RJ, Krumins E, Reynolds-Green M, Lentz JC, Conte C, Cuzzucoli Crucitti V, Couturaud B, Galantini L, Francolini I, Howdle SM, Taresco V. Poly (diglycerol adipate) variants as enhanced nanocarrier replacements in drug delivery applications. J Colloid Interface Sci 2023; 641:1043-1057. [PMID: 36996683 DOI: 10.1016/j.jcis.2023.03.124] [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: 12/02/2022] [Revised: 02/17/2023] [Accepted: 03/19/2023] [Indexed: 03/30/2023]
Abstract
Sustainably derived poly(glycerol adipate) (PGA) has been deemed to deliver all the desirable features expected in a polymeric scaffold for drug-delivery, including biodegradability, biocompatibility, self-assembly into nanoparticles (NPs) and a functionalisable pendant group. Despite showing these advantages over commercial alkyl polyesters, PGA suffers from a series of key drawbacks caused by poor amphiphilic balance. This leads to weak drug-polymer interactions and subsequent low drug-loading in NPs, as well as low NPs stability. To overcome this, in the present work, we applied a more significant variation of the polyester backbone while maintaining mild and sustainable polymerisation conditions. We have investigated the effect of the variation of both hydrophilic and hydrophobic segments upon physical properties and drug interactions as well as self-assembly and NPs stability. For the first time we have replaced glycerol with the more hydrophilic diglycerol, as well as adjusting the final amphiphilic balance of the polyester repetitive units by incorporating the more hydrophobic 1,6-n-hexanediol (Hex). The properties of the novel poly(diglycerol adipate) (PDGA) variants have been compared against known polyglycerol-based polyesters. Interestingly, while the bare PDGA showed improved water solubility and diminished self-assembling ability, the Hex variation demonstrated enhanced features as a nanocarrier. In this regard, PDGAHex NPs were tested for their stability in different environments and for their ability to encode enhanced drug loading. Moreover, the novel materials have shown good biocompatibility in both in vitro and in vivo (whole organism) experiments.
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Affiliation(s)
- Philippa L Jacob
- School of Chemistry, University Park, Nottingham NG7 2RD, United Kingdom
| | - Benedetta Brugnoli
- Dept. of Chemistry, Sapienza University of Rome, Piazzale A. Moro 5, 00185 Rome, Italy
| | | | - Hien Phan
- Institut de Chimie et des Matériaux Paris-Est, Université de Paris-Est Créteil, CNRS UMR 7182, 2 rue Henri Dunant, 94320 Thiais, France
| | - Veeren M Chauhan
- Laboratory of Biophysics and Surface Analysis, School of Pharmacy, University of Nottingham, Boots Sciences Building, University Park, Nottingham NG7 2RD, United Kingdom
| | - Laura Beckett
- Laboratory of Biophysics and Surface Analysis, School of Pharmacy, University of Nottingham, Boots Sciences Building, University Park, Nottingham NG7 2RD, United Kingdom
| | - Richard B Gillis
- National Centre for Macromolecular Hydrodynamics, University of Nottingham, Sutton Bonington LE12 5RD, United Kingdom; Biomaterials Group, School of Biosciences, University of Nottingham, Sutton Bonington LE12 5RD, United Kingdom; College of Business, Technology and Engineering, Sheffield Hallam University, Food and Nutrition Group, Sheffield S1 1WB, United Kingdom
| | - Cara Moloney
- School of Medicine, BioDiscovery Institute-3, University Park, Nottingham NG7 2RD, United Kingdom
| | - Robert J Cavanagh
- School of Medicine, BioDiscovery Institute-3, University Park, Nottingham NG7 2RD, United Kingdom
| | - Eduards Krumins
- School of Chemistry, University Park, Nottingham NG7 2RD, United Kingdom
| | | | - Joachim C Lentz
- School of Chemistry, University Park, Nottingham NG7 2RD, United Kingdom
| | - Claudia Conte
- Department of Pharmacy, University of Napoli Federico II, Napoli, Italy
| | - Valentina Cuzzucoli Crucitti
- Centre for Additive Manufacturing and Department of Chemical and Environmental Engineering, Faculty of Engineering, University of Nottingham, Nottingham NG7 2RD, United Kingdom
| | - Benoit Couturaud
- Institut de Chimie et des Matériaux Paris-Est, Université de Paris-Est Créteil, CNRS UMR 7182, 2 rue Henri Dunant, 94320 Thiais, France
| | - Luciano Galantini
- Dept. of Chemistry, Sapienza University of Rome, Piazzale A. Moro 5, 00185 Rome, Italy
| | - Iolanda Francolini
- Dept. of Chemistry, Sapienza University of Rome, Piazzale A. Moro 5, 00185 Rome, Italy
| | - Steven M Howdle
- School of Chemistry, University Park, Nottingham NG7 2RD, United Kingdom
| | - Vincenzo Taresco
- School of Chemistry, University Park, Nottingham NG7 2RD, United Kingdom.
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4
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Abu Hammad K, Dinu V, MacCalman TE, Pattem J, Goodall M, Gillis RB, Jefferis R, Harding SE. Comparative sedimentation equilibrium analysis of two IgG1 glycoforms: IgGCri and IgGWid. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2023; 52:439-443. [PMID: 37195494 PMCID: PMC10444637 DOI: 10.1007/s00249-023-01656-x] [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: 01/07/2023] [Accepted: 03/14/2023] [Indexed: 05/18/2023]
Abstract
The solution properties of two different glycoforms of IgG1 (IgG1Cri and IgG1Wid) are compared using primarily sedimentation equilibrium analysis with two complementary analysis routines: SEDFIT-MSTAR and MULTISIG. IgGCri bears diantennary complex-type glycans on its Fc domain that are fully core fucosylated and partially sialylated, whilst on IgGWid, they are non-fucosylated, partially galactosylated and non-sialylated. IgGWid is also Fab glycosylated. Despite these differences, SEDFIT-MSTAR analysis shows similar weight average molar masses Mw of ~ (150 ± 5) kDa for IgGCri and ~ (154 ± 5) kDa for IgGWid and both glycoforms show evidence of the presence of a small fraction of dimer confirmed by MULTISIG analysis and also by sedimentation coefficient distributions from supportive sedimentation velocity measurements. The closeness of the sedimentation equilibrium behaviour and sedimentation coefficient distributions with a main peak sedimentation coefficient of ~ 6.4S for both glycoforms at different concentrations suggest that the different glycosylation profiles do not significantly impact on molar mass (molecular weight) nor conformation in solution.
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Affiliation(s)
- Khalil Abu Hammad
- National Centre for Macromolecular Hydrodynamics (NCMH), School of Biosciences, University of Nottingham, Sutton Bonington, LE12 5RD, UK
| | - Vlad Dinu
- National Centre for Macromolecular Hydrodynamics (NCMH), School of Biosciences, University of Nottingham, Sutton Bonington, LE12 5RD, UK
| | - Thomas E MacCalman
- National Centre for Macromolecular Hydrodynamics (NCMH), School of Biosciences, University of Nottingham, Sutton Bonington, LE12 5RD, UK
- School of Biosciences, University of Nottingham, Sutton Bonington, LE12 5RD, UK
| | - Jacob Pattem
- National Centre for Macromolecular Hydrodynamics (NCMH), School of Biosciences, University of Nottingham, Sutton Bonington, LE12 5RD, UK
- School of Biosciences, University of Nottingham, Sutton Bonington, LE12 5RD, UK
| | - Margaret Goodall
- Institute of Immunology & Immunotherapy, College of Medical & Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Richard B Gillis
- National Centre for Macromolecular Hydrodynamics (NCMH), School of Biosciences, University of Nottingham, Sutton Bonington, LE12 5RD, UK
- School of Biosciences, University of Nottingham, Sutton Bonington, LE12 5RD, UK
- College of Business, Technology and Engineering, Food and Nutrition Group, Sheffield Hallam University, Sheffield, S1 1WB, UK
| | - Roy Jefferis
- Institute of Immunology & Immunotherapy, College of Medical & Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Stephen E Harding
- National Centre for Macromolecular Hydrodynamics (NCMH), School of Biosciences, University of Nottingham, Sutton Bonington, LE12 5RD, UK.
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5
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Tjia-Fleck S, Readnour BM, Ayinuola YA, Castellino FJ. High-Resolution Single-Particle Cryo-EM Hydrated Structure of Streptococcus pyogenes Enolase Offers Insights into Its Function as a Plasminogen Receptor. Biochemistry 2023; 62:735-746. [PMID: 36701429 DOI: 10.1021/acs.biochem.2c00637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Cellular plasminogen (Pg) receptors (PgRs) are utilized to recruit Pg; stimulate its activation to the serine protease, plasmin (Pm); and sterically protect the surface Pm from inactivation by host inhibitors. One such PgR is the moonlighting enzyme, enolase, some of which leaves the cytoplasm and resides at the cell surface to potentially function as a PgR. Since microbes employ conscription of host Pg by PgRs as one virulence mechanism, we explored the structural basis of the ability of Streptococcus pyogenes enolase (Sen) to function in this manner. Employing single-particle cryo-electron microscopy (cryo-EM), recombinant Sen from S. pyogenes was modeled at 2.6 Å as a stable symmetrical doughnut-shaped homooctamer with point group 422 (D4) symmetry, with a monomeric subunit molecular weight of ∼49 kDa. Binding sites for hPg were reported in other studies to include an internal K252,255 and the COOH-terminal K434,435 residues of Sen. However, in native Sen, the latter are buried within the minor interfaces of the octamer and do not function as a Pg-binding epitope. Whereas Sen and hPg do not interact in solution, when Sen is bound to a surface, hPg interacts with Sen independently of K252,255,434,435. PgRs devoid of COOH-terminal lysine utilize lysine isosteres comprising a basic residue, "i", and an anionic residue at "i + 3" around one turn of an α-helix. We highlight a number of surface-exposed potential hPg-binding lysine isosteres and further conclude that while the octameric structure of Sen is critical for hPg binding, disruption of this octamer without dissociation exposes hPg-binding epitopes.
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Affiliation(s)
- Sheiny Tjia-Fleck
- W.M. Keck Center for Transgene Research, University of Notre Dame, Notre Dame, Indiana 46556, United States.,Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Bradley M Readnour
- W.M. Keck Center for Transgene Research, University of Notre Dame, Notre Dame, Indiana 46556, United States.,Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Yetunde A Ayinuola
- W.M. Keck Center for Transgene Research, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Francis J Castellino
- W.M. Keck Center for Transgene Research, University of Notre Dame, Notre Dame, Indiana 46556, United States.,Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
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6
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Self-association of the glycopeptide antibiotic teicoplanin A2 in aqueous solution studied by molecular hydrodynamics. Sci Rep 2023; 13:1969. [PMID: 36737502 PMCID: PMC9895975 DOI: 10.1038/s41598-023-28740-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 01/24/2023] [Indexed: 02/05/2023] Open
Abstract
The natural glycopeptide antibiotic teicoplanin is used for the treatment of serious Gram-positive related bacterial infections and can be administered intravenously, intramuscularly, topically (ocular infections), or orally. It has also been considered for targeting viral infection by SARS-CoV-2. The hydrodynamic properties of teicoplanin A2 (M1 = 1880 g/mol) were examined in phosphate chloride buffer (pH 6.8, I = 0.10 M) using sedimentation velocity and sedimentation equilibrium in the analytical ultracentrifuge together with capillary (rolling ball) viscometry. In the concentration range, 0-10 mg/mL teicoplanin A2 was found to self-associate plateauing > 1 mg/mL to give a molar mass of (35,400 ± 1000) g/mol corresponding to ~ (19 ± 1) mers, with a sedimentation coefficient s20, w = ~ 4.65 S. The intrinsic viscosity [[Formula: see text]] was found to be (3.2 ± 0.1) mL/g: both this, the value for s20,w and the hydrodynamic radius from dynamic light scattering are consistent with a globular macromolecular assembly, with a swelling ratio through dynamic hydration processes of ~ 2.
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7
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Wang Q, Lu D, Liu H, Li C. Tetramerization of GH2 β-Glucuronidases is Essential for Catalyzing the Hydrolysis of the Large Substrate Glycyrrhizin. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:16286-16297. [PMID: 36516995 DOI: 10.1021/acs.jafc.2c06859] [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: 06/17/2023]
Abstract
In this study, structural analysis was employed to identify three hotspot residues that contribute most to the tetramer formation of a glycoside hydrolase family 2 (GH2) β-glucuronidase (GUS) from Aspergillus oryzae Li-3. Single-point mutation at these sites completely disrupted the tetramer structure and abolished the glycyrrhizin (GL)-hydrolyzing activity. Then, the W522A dimer was refactored into a tetramer by disulfide bonding, and partial GL activity was restored. Further saturated mutation showed a strong correlation between the GL activity of the mutants and their tetramer ratios. Molecular simulations were employed to illustrate the critical role of the tetramer interface in maintaining a functional active-site structure. The three highly conserved tetramer-forming residues were finally applied to two other GH2 GUSs for tetramer dissociation and demonstrated the significance of the homotetramerization for GL-hydrolyzing activity of GH2 GUSs. This study lays foundation for engineering GL-hydrolyzing GUSs at the quaternary structure level for function regulations.
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Affiliation(s)
- Qibin Wang
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 10081, PR China
| | - Dingyuan Lu
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 10081, PR China
| | - Hu Liu
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 10081, PR China
| | - Chun Li
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 10081, PR China
- Key Laboratory for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing 10084, PR China
- Center for Synthetic & Systems Biology, Tsinghua University, Beijing 10084, PR China
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8
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Ye X, Chen Y, Wu C. How is the
z
‐Average Molar Mass Related to the Sedimentation Data? MACROMOL CHEM PHYS 2022. [DOI: 10.1002/macp.202200331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Xiaodong Ye
- The Hefei National Research Center for Physical Sciences at Microscale Department of Chemical Physics The University of Science and Technology of China Hefei Anhui 230026 China
- The CAS Key Laboratory of Soft Matter Chemistry The University of Science and Technology of China Hefei Anhui 230026 China
| | - Yonggang Chen
- The Hefei National Research Center for Physical Sciences at Microscale Department of Chemical Physics The University of Science and Technology of China Hefei Anhui 230026 China
| | - Chi Wu
- The Hefei National Research Center for Physical Sciences at Microscale Department of Chemical Physics The University of Science and Technology of China Hefei Anhui 230026 China
- The Center of Food Science and Processing and the Shenzhen Key Laboratory of Food Science and Processing The Shenzhen University Shenzhen 518060 China
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9
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Comparative hydrodynamic characterisation of two hydroxylated polymers based on α-pinene- or oleic acid-derived monomers for potential use as archaeological consolidants. Sci Rep 2022; 12:18411. [PMID: 36319651 PMCID: PMC9626589 DOI: 10.1038/s41598-022-21027-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 09/21/2022] [Indexed: 11/07/2022] Open
Abstract
The Oseberg Viking ship burial is one of the most extensive collections of Viking wooden artefacts ever excavated in Norway. In the early twentieth century, many of these artefacts were treated with alum in order to preserve them, inadvertently leading to their current degraded state. It is therefore crucial to develop new bioinspired polymers which could be used to conserve these artefacts and prevent further disintegration. Two hydroxylated polymers were synthesised (TPA6 and TPA7), using α-pinene- and oleic acid-derived monomers functionalised with an acrylate moiety. Characterisation using biomolecular hydrodynamics (analytical ultracentrifugation and high precision viscometry) has shown that these polymers have properties which would potentially make them good wood consolidants. Conformation analyses with the viscosity increment (ν) universal hydrodynamic parameter and ELLIPS1 software showed that both polymers had extended conformations, facilitating in situ networking when applied to wood. SEDFIT-MSTAR analyses of sedimentation equilibrium data indicates a weight average molar mass Mw of (3.9 ± 0.8) kDa and (4.2 ± 0.2) kDa for TPA6 and TPA7 respectively. Analyses with SEDFIT (sedimentation velocity) and MultiSig however revealed that TPA7 had a much greater homogeneity and a lower proportion of aggregation. These studies suggest that both these polymers-particularly TPA7-have characteristics suitable for wood consolidation, such as an optimal molar mass, conformation and a hydroxylated nature, making them interesting leads for further research.
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Dinu V, Borah PK, Muleya M, Scott DJ, Lithgo R, Pattem J, Harding SE, Yakubov GE, Fisk ID. Flavour compounds affect protein structure: The effect of methyl anthranilate on bovine serum albumin conformation. Food Chem 2022; 388:133013. [PMID: 35483284 DOI: 10.1016/j.foodchem.2022.133013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 03/15/2022] [Accepted: 04/17/2022] [Indexed: 11/27/2022]
Abstract
This study aims to understand possible effects of flavour compounds on the structure and conformation of endogenous proteins. Using methyl anthranilate (a grape flavour compound added to drinks, confectionery, and vape-liquids) and bovine serum albumin (BSA, a model serum protein) we designed experimental investigations using analytical ultracentrifugation, size exclusion chromatography small angle X-ray scattering, and fluorescence spectroscopy to reveal that methyl anthranilate spontaneously binds to BSA (ΔG°, ca. -21 KJ mol-1) which induces a conformational compactness (ca. 10 %) in the monomer structure. Complementary molecular modelling and dynamics simulations suggested the binding occurs at Sudlow II of BSA via establishment of hydrogen bonds with arginine409, lysine413 and serine488 leading to an increased conformational order in domains IA, IIB and IIIB. This work aims to set the foundation for future research on flavour-protein interactions and offer new sets of opportunities for understanding the effects of small compounds on protein structure.
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Affiliation(s)
- Vlad Dinu
- National Centre for Macromolecular Hydrodynamics, School of Biosciences, University of Nottingham, Sutton Bonington Campus, LE12 5RD, United Kingdom; Division of Food, Nutrition and Dietetics, School of Biosciences, University of Nottingham, Sutton Bonington Campus, LE12 5RD, United Kingdom.
| | - Pallab Kumar Borah
- Division of Food, Nutrition and Dietetics, School of Biosciences, University of Nottingham, Sutton Bonington Campus, LE12 5RD, United Kingdom
| | - Molly Muleya
- Division of Food, Nutrition and Dietetics, School of Biosciences, University of Nottingham, Sutton Bonington Campus, LE12 5RD, United Kingdom
| | - David J Scott
- Division of Microbiology, Brewing and Biotechnology, School of Biosciences, University of Nottingham, Sutton Bonington Campus, LE12 5RD, United Kingdom; Research Complex at Harwell, Rutherford Appleton Laboratory, Oxfordshire OX11 0FA. United Kingdom
| | - Ryan Lithgo
- Division of Microbiology, Brewing and Biotechnology, School of Biosciences, University of Nottingham, Sutton Bonington Campus, LE12 5RD, United Kingdom; Research Complex at Harwell, Rutherford Appleton Laboratory, Oxfordshire OX11 0FA. United Kingdom
| | - Jacob Pattem
- Division of Food, Nutrition and Dietetics, School of Biosciences, University of Nottingham, Sutton Bonington Campus, LE12 5RD, United Kingdom
| | - Stephen E Harding
- National Centre for Macromolecular Hydrodynamics, School of Biosciences, University of Nottingham, Sutton Bonington Campus, LE12 5RD, United Kingdom
| | - Gleb E Yakubov
- National Centre for Macromolecular Hydrodynamics, School of Biosciences, University of Nottingham, Sutton Bonington Campus, LE12 5RD, United Kingdom; Division of Food, Nutrition and Dietetics, School of Biosciences, University of Nottingham, Sutton Bonington Campus, LE12 5RD, United Kingdom
| | - Ian D Fisk
- Division of Food, Nutrition and Dietetics, School of Biosciences, University of Nottingham, Sutton Bonington Campus, LE12 5RD, United Kingdom; University of Adelaide, North Terrace, Adelaide SA 5005, Australia
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11
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Zhao YB, Liu MX, Chen TT, Ma X, Li ZK, Zheng Z, Zheng SR, Chen L, Li YZ, Tang LR, Chen Q, Wang P, Ouyang S. Pathogen effector AvrSr35 triggers Sr35 resistosome assembly via a direct recognition mechanism. SCIENCE ADVANCES 2022; 8:eabq5108. [PMID: 36083908 PMCID: PMC9462685 DOI: 10.1126/sciadv.abq5108] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 07/26/2022] [Indexed: 05/20/2023]
Abstract
Nucleotide-binding, leucine-rich repeat receptors (NLRs) perceive pathogen effectors to trigger plant immunity. The direct recognition mechanism of pathogen effectors by coiled-coil NLRs (CNLs) remains unclear. We demonstrate that the Triticum monococcum CNL Sr35 directly recognizes the pathogen effector AvrSr35 from Puccinia graminis f. sp. tritici and report a cryo-electron microscopy structure of Sr35 resistosome and a crystal structure of AvrSr35. We show that AvrSr35 forms homodimers that are disassociated into monomers upon direct recognition by the leucine-rich repeat domain of Sr35, which induces Sr35 resistosome assembly and the subsequent immune response. The first 20 amino-terminal residues of Sr35 are indispensable for immune signaling but not for plasma membrane association. Our findings reveal the direct recognition and activation mechanism of a plant CNL and provide insights into biochemical function of Sr35 resistosome.
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Affiliation(s)
- Yan-Bo Zhao
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, 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 350117, China
| | - Meng-Xi Liu
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, 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 350117, China
| | - Tao-Tao Chen
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, 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 350117, China
| | - Xiaomin Ma
- Cryo-EM Centre, Southern University of Science and Technology, Shenzhen 515055, China
| | - Ze-Kai Li
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, 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 350117, China
| | - Zichao Zheng
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Plant Immunity Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Si-Ru Zheng
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, 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 350117, China
| | - Lifei Chen
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, 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 350117, China
| | - You-Zhi Li
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, 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 350117, China
| | - Li-Rui Tang
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, 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 350117, China
| | - Qi Chen
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, 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 350117, China
| | - Peiyi Wang
- Cryo-EM Centre, Southern University of Science and Technology, Shenzhen 515055, China
- Corresponding author. (S.O.); (P.W.)
| | - Songying Ouyang
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, 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 350117, China
- Corresponding author. (S.O.); (P.W.)
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12
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Hua F, Fu Z, Cheng Y. A simplified and effective molecular-level kinetic model for plastic pyrolysis. Chem Eng Sci 2022. [DOI: 10.1016/j.ces.2022.118146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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13
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Biophysical Reviews’ “meet the editors series”—a profile of Steve Harding’s career in macromolecular hydrodynamics. Biophys Rev 2022; 14:605-610. [DOI: 10.1007/s12551-022-00963-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 05/24/2022] [Indexed: 01/14/2023] Open
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14
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Discovery of a New Microbial Origin Cold-Active Neopullulanase Capable for Effective Conversion of Pullulan to Panose. Int J Mol Sci 2022; 23:ijms23136928. [PMID: 35805929 PMCID: PMC9267027 DOI: 10.3390/ijms23136928] [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: 05/24/2022] [Revised: 06/20/2022] [Accepted: 06/21/2022] [Indexed: 11/26/2022] Open
Abstract
Panose is a type of functional sugar with diverse bioactivities. The enzymatic conversion bioprocess to produce high purity panose with high efficiency has become increasingly important. Here, a new neopullulanase (NPase), Amy117 from B. pseudofirmus 703, was identified and characterized. Amy117 presented the optimal activity at pH 7.0 and 30 °C, its activity is over 40% at 10 °C and over 80% at 20 °C, which is cold-active. The enzyme cleaved α-1, 4-glycosidic linkages of pullulan to generate panose as the only hydrolysis product, and degraded cyclodextrins (CDs) and starch to glucose and maltose, with an apparent preference for CDs. Furthermore, Amy117 can produce 72.7 mg/mL panose with a conversion yield of 91% (w/w) based on 80 mg/mL pullulan. The sequence and structure analysis showed that the low proportion of Arg, high proportion of Asn and Gln, and high α-helix levels in Amy117 may contribute to its cold-active properties. Root mean square deviation (RMSD) analysis also showed that Amy117 is more flexible than two mesophilic homologues. Hence, we discovered a new high-efficiency panose-producing NPase, which so far achieves the highest panose production and would be an ideal candidate in the food industry.
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15
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Subramanian C, Cuypers MG, Radka CD, White SW, Rock CO. Domain architecture and catalysis of the Staphylococcus aureus fatty acid kinase. J Biol Chem 2022; 298:101993. [PMID: 35490779 PMCID: PMC9136124 DOI: 10.1016/j.jbc.2022.101993] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 04/25/2022] [Accepted: 04/26/2022] [Indexed: 12/02/2022] Open
Abstract
Fatty acid kinase (Fak) is a two-component enzyme that generates acyl-phosphate for phospholipid synthesis. Fak consists of a kinase domain protein (FakA) that phosphorylates a fatty acid enveloped by a fatty acid binding protein (FakB). The structural basis for FakB function has been established, but little is known about FakA. Here, we used limited proteolysis to define three separate FakA domains: the amino terminal FakA_N, the central FakA_L, and the carboxy terminal FakA_C. The isolated domains lack kinase activity, but activity is restored when FakA_N and FakA_L are present individually or connected as FakA_NL. The X-ray structure of the monomeric FakA_N captures the product complex with ADP and two Mg2+ ions bound at the nucleotide site. The FakA_L domain encodes the dimerization interface along with conserved catalytic residues Cys240, His282, and His284. AlphaFold analysis of FakA_L predicts the catalytic residues are spatially clustered and pointing away from the dimerization surface. Furthermore, the X-ray structure of FakA_C shows that it consists of two subdomains that are structurally related to FakB. Analytical ultracentrifugation demonstrates that FakA_C binds FakB, and site-directed mutagenesis confirms that a positively charged wedge on FakB meshes with a negatively charged groove on FakA_C. Finally, small angle X-ray scattering analysis is consistent with freely rotating FakA_N and FakA_C domains tethered by flexible linkers to FakA_L. These data reveal specific roles for the three independently folded FakA protein domains in substrate binding and catalysis.
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Affiliation(s)
- Chitra Subramanian
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Maxime G Cuypers
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Christopher D Radka
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Stephen W White
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Charles O Rock
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.
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16
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Comparative Hydrodynamic Study on Non-Aqueous Soluble Archaeological Wood Consolidants: Butvar B-98 and PDMS-OH Siloxanes. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27072133. [PMID: 35408530 PMCID: PMC9000765 DOI: 10.3390/molecules27072133] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 03/16/2022] [Accepted: 03/20/2022] [Indexed: 11/17/2022]
Abstract
Butvar B-98 and PDMS-OH both have a demonstrable ability as consolidants for archaeological wood. This makes them both potential treatment options for the Oseberg collection, which is one of the most important archaeological finds from the Viking era. Both Butvar B-98 and PDMS-OH are soluble in organic solvents, offering a useful alternative to aqueous-based consolidants. Extensive characterisation studies were carried out on both of these polymers, with the use of analytical ultracentrifugation and viscometry, for the benefit of conservators wanting to know more about the physical properties of these materials. Short column sedimentation equilibrium analysis using SEDFIT-MSTAR revealed a weight-average molar mass (weight-average molecular weight) Mw of (54.0 ± 1.5) kDa (kg · mol-1) for Butvar B-98, while four samples of PDMS-OH siloxanes (each with a different molar mass) had an Mw of (52.5 ± 3.0) kDa, (38.8 ± 1.5) kDa, (6.2 ± 0.7) kDa and (1.6 ± 0.1) kDa. Sedimentation velocity confirmed that all polymers were heterogeneous, with a wide range of molar masses. All molecular species showed considerable conformational asymmetry from measurements of intrinsic viscosity, which would facilitate networking interactions as consolidants. It is anticipated that the accumulated data on these two consolidants will enable conservators to make a more informed decision when it comes to choosing which treatment to administer to archaeological artefacts.
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17
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Michna A, Płaziński W, Lupa D, Wasilewska M, Adamczyk Z. Carrageenan molecule conformations and electrokinetic properties in electrolyte solutions: Modeling and experimental measurements. Food Hydrocoll 2021. [DOI: 10.1016/j.foodhyd.2021.107033] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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18
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Ayinuola O, Ayinuola YA, Qiu C, Lee SW, Ploplis VA, Castellino FJ. Binding of the kringle-2 domain of human plasminogen to streptococcal PAM-type M-protein causes dissociation of PAM dimers. Microbiologyopen 2021; 10:e1252. [PMID: 34964287 PMCID: PMC8633249 DOI: 10.1002/mbo3.1252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 11/03/2021] [Indexed: 11/24/2022] Open
Abstract
The direct binding of human plasminogen (hPg), via its kringle-2 domain (K2hPg ), to streptococcal M-protein (PAM), largely contributes to the pathogenesis of Pattern D Group A Streptococcus pyogenes (GAS). However, the mechanism of complex formation is unknown. In a system consisting of a Class II PAM from Pattern D GAS isolate NS88.2 (PAMNS88.2 ), with one K2hPg binding a-repeat in its A-domain, we employed biophysical techniques to analyze the mechanism of the K2hPg /PAMNS88.2 interaction. We show that apo-PAMNS88.2 is a coiled-coil homodimer (M.Wt. ~80 kDa) at 4°C-25°C, and is monomeric (M.Wt. ~40 kDa) at 37°C, demonstrating a temperature-dependent dissociation of PAMNS88.2 over a narrow temperature range. PAMNS88.2 displayed a single tight binding site for K2hPg at 4°C, which progressively increased at 25°C through 37°C. We isolated the K2hPg /PAMNS88.2 complexes at 4°C, 25°C, and 37°C and found molecular weights of ~50 kDa at each temperature, corresponding to a 1:1 (m:m) K2hPg /PAMNS88.2 monomer complex. hPg activation experiments by streptokinase demonstrated that the hPg/PAMNS88.2 monomer complexes are fully functional. The data show that PAM dimers dissociate into functional monomers at physiological temperatures or when presented with the active hPg module (K2hPg ) showing that PAM is a functional monomer at 37°C.
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Affiliation(s)
- Olawole Ayinuola
- W. M. Keck Center for Transgene ResearchUniversity of Notre DameNotre DameIndianaUSA
| | - Yetunde A. Ayinuola
- W. M. Keck Center for Transgene ResearchUniversity of Notre DameNotre DameIndianaUSA
| | - Cunjia Qiu
- W. M. Keck Center for Transgene ResearchUniversity of Notre DameNotre DameIndianaUSA
- Department of Chemistry and BiochemistryUniversity of Notre DameNotre DameIndianaUSA
| | - Shaun W. Lee
- W. M. Keck Center for Transgene ResearchUniversity of Notre DameNotre DameIndianaUSA
- Department of Biological SciencesUniversity of Notre DameNotre DameIndianaUSA
| | - Victoria A. Ploplis
- W. M. Keck Center for Transgene ResearchUniversity of Notre DameNotre DameIndianaUSA
- Department of Chemistry and BiochemistryUniversity of Notre DameNotre DameIndianaUSA
| | - Francis J. Castellino
- W. M. Keck Center for Transgene ResearchUniversity of Notre DameNotre DameIndianaUSA
- Department of Chemistry and BiochemistryUniversity of Notre DameNotre DameIndianaUSA
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19
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Harding SE. Analytical Ultracentrifugation as a Matrix-Free Probe for the Study of Kinase Related Cellular and Bacterial Membrane Proteins and Glycans. Molecules 2021; 26:molecules26196080. [PMID: 34641622 PMCID: PMC8512968 DOI: 10.3390/molecules26196080] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 09/28/2021] [Accepted: 09/30/2021] [Indexed: 11/16/2022] Open
Abstract
Analytical ultracentrifugation is a versatile approach for analysing the molecular mass, molecular integrity (degradation/aggregation), oligomeric state and association/dissociation constants for self-association, and assay of ligand binding of kinase related membrane proteins and glycans. It has the great property of being matrix free-providing separation and analysis of macromolecular species without the need of a separation matrix or membrane or immobilisation onto a surface. This short review-designed for the non-hydrodynamic expert-examines the potential of modern sedimentation velocity and sedimentation equilibrium and the challenges posed for these molecules particularly those which have significant cytoplasmic or extracellular domains in addition to the transmembrane region. These different regions can generate different optimal requirements in terms of choice of the appropriate solvent (aqueous/detergent). We compare how analytical ultracentrifugation has contributed to our understanding of two kinase related cellular or bacterial protein/glycan systems (i) the membrane erythrocyte band 3 protein system-studied in aqueous and detergent based solvent systems-and (ii) what it has contributed so far to our understanding of the enterococcal VanS, the glycan ligand vancomycin and interactions of vancomycin with mucins from the gastrointestinal tract.
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Affiliation(s)
- Stephen E. Harding
- National Centre for Macromolecular Hydrodynamics, School of Biosciences, University of Nottingham, Sutton Bonington LE12 5RD, UK;
- Science for Cultural History (SciCult) Laboratory, Kulturhistorisk Museum, University of Oslo, St. Olavs Plass, 0130 Oslo, Norway
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20
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Lu Y, Joosten L, Donkers J, Andriulo F, Slaghek TM, Phillips-Jones MK, Gosselink RJA, Harding SE. Characterisation of mass distributions of solvent-fractionated lignins using analytical ultracentrifugation and size exclusion chromatography methods. Sci Rep 2021; 11:13937. [PMID: 34230572 PMCID: PMC8260654 DOI: 10.1038/s41598-021-93424-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 06/18/2021] [Indexed: 11/13/2022] Open
Abstract
Lignins are valuable renewable resources for the potential production of a large array of biofuels, aromatic chemicals and biopolymers. Yet native and industrial lignins are complex, highly branched and heterogenous macromolecules, properties that have to date often undermined their use as starting materials in lignin valorisation strategies. Reliable knowledge of weight average molar mass, conformation and polydispersity of lignin starting materials can be proven to be crucial to and improve the prospects for the success of such strategies. Here we evaluated the use of commonly-used size exclusion chromatography (SEC)-calibrated with polystyrene sulphonate standards-and under-used analytical ultracentrifugation-which does not require calibration-to characterise a series of lignin fractions sequentially extracted from soda and Kraft alkaline lignins using ethyl acetate, methyl ethyl ketone (MEK), methanol and acetone:water (fractions F01-F04, respectively). Absolute values of weight average molar mass (Mw) determined using sedimentation equilibrium in the analytical ultracentrifuge of (3.0 ± 0.1) kDa and (4.2 ± 0.2) kDa for soda and Kraft lignins respectively, agreed closely with previous SEC-determined Mws and reasonably with the size exclusion chromatography measurements employed here, confirming the appropriateness of the standards (with the possible exceptions of fraction F05 for soda P1000 and F03 for Indulin). Both methods revealed the presence of low (~ 1 kDa) Mw material in F01 and F02 fractions followed by progressively higher Mw in subsequent fractions. Compositional analysis confirmed > 90% (by weight) total lignins successively extracted from both lignins using MEK, methanol and acetone:water (F02 to F04). Considerable heterogeneity of both unfractionated and fractionated lignins was revealed through determinations of both sedimentation coefficient distributions and polydispersity indices. The study also demonstrates the advantages of using analytical ultracentrifugation, both alongside SEC as well as in its own right, for determining absolute Mw, heterogeneity and conformation information for characterising industrial lignins.
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Affiliation(s)
- Yudong Lu
- National Centre for Macromolecular Hydrodynamics, School of Biosciences, University of Nottingham, Sutton Bonington, Leicestershire, LE12 5RD, UK
| | - Lionard Joosten
- Wageningen Food and Biobased Research, 6708 WG, Wageningen, The Netherlands
| | - Jacqueline Donkers
- Wageningen Food and Biobased Research, 6708 WG, Wageningen, The Netherlands
| | - Fabrizio Andriulo
- SciCult Laboratory, Department of Collection Management, Museum of Cultural History, University of Oslo, St. Olavs Plass, 0130, Oslo, Norway
| | - Ted M Slaghek
- Wageningen Food and Biobased Research, 6708 WG, Wageningen, The Netherlands
| | - Mary K Phillips-Jones
- National Centre for Macromolecular Hydrodynamics, School of Biosciences, University of Nottingham, Sutton Bonington, Leicestershire, LE12 5RD, UK.
| | | | - Stephen E Harding
- National Centre for Macromolecular Hydrodynamics, School of Biosciences, University of Nottingham, Sutton Bonington, Leicestershire, LE12 5RD, UK.
- SciCult Laboratory, Department of Collection Management, Museum of Cultural History, University of Oslo, St. Olavs Plass, 0130, Oslo, Norway.
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21
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Terpene polyacrylate TPA5 shows favorable molecular hydrodynamic properties as a potential bioinspired archaeological wood consolidant. Sci Rep 2021; 11:7343. [PMID: 33795726 PMCID: PMC8016987 DOI: 10.1038/s41598-021-86543-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 02/25/2021] [Indexed: 02/01/2023] Open
Abstract
There is currently a pressing need for the development of novel bioinspired consolidants for waterlogged, archaeological wood. Bioinspired materials possess many advantages, such as biocompatibility and sustainability, which makes them ideal to use in this capacity. Based on this, a polyhydroxylated monomer was synthesised from α-pinene, a sustainable terpene feedstock derived from pine trees, and used to prepare a low molar mass polymer TPA5 through free radical polymerisation. This polymer was extensively characterised by NMR spectroscopy (chemical composition) and molecular hydrodynamics, primarily using analytical ultracentrifugation reinforced by gel filtration chromatography and viscometry, in order to investigate whether it would be suitable for wood consolidation purposes. Sedimentation equilibrium indicated a weight average molar mass Mw of (4.3 ± 0.2) kDa, with minimal concentration dependence. Further analysis with MULTISIG revealed a broad distribution of molar masses and this heterogeneity was further confirmed by sedimentation velocity. Conformation analyses with the Perrin P and viscosity increment ν universal hydrodynamic parameters indicated that the polymer had an elongated shape, with both factors giving consistent results and a consensus axial ratio of ~ 4.5. These collective properties-hydrogen bonding potential enhanced by an elongated shape, together with a small injectable molar mass-suggest this polymer is worthy of further consideration as a potential consolidant.
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22
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Romanov RS, Kurilova SA, Baykov AA, Rodina EV. Effect of Structure Variations in the Inter-subunit Contact Zone on the Activity and Allosteric Regulation of Inorganic Pyrophosphatase from Mycobacterium tuberculosis. BIOCHEMISTRY (MOSCOW) 2021; 85:326-333. [PMID: 32564737 DOI: 10.1134/s0006297920030086] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Hexameric inorganic pyrophosphatase from Mycobacterium tuberculosis (Mt-PPase) has a number of structural and functional features that distinguish it from homologous enzymes widely occurring in living organisms. In particular, it has unusual zones of inter-subunit contacts and lacks the N-terminal region common for other PPases. In this work, we constructed two mutant forms of the enzyme, Ec-Mt-PPase and R14Q-Mt-PPase. In Ec-Mt-PPase, the missing part of the polypeptide chain was compensated with a fragment of PPase from Escherichia coli (Ec-PPase). In R14Q-Mt-PPase, a point mutation was introduced to the contact interface between the two trimers of the hexamer. Both modifications significantly improved the catalytic activity of the enzyme and abolished its inhibition by the cofactor (Mg2+ ion) excess. Activation of Mt-PPase by low (~10 μM) concentrations of ATP, fructose-1-phosphate, L-malate, and non-hydrolyzable substrate analogue methylene bisphosphonate (PCP) was observed. At concentrations of 100 μM and higher, the first three compounds acted as inhibitors. The activating effect of PCP was absent in both mutant forms, and the inhibitory effect of fructose-1-phosphate was absent in Ec-Mt-PPase. The effects of other modulators varied only quantitatively among the mutants. The obtained data indicate the presence of allosteric sites in Mt-PPase, which are located in the zones of inter-subunit contact or associated with them.
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Affiliation(s)
- R S Romanov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - S A Kurilova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - A A Baykov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - E V Rodina
- Lomonosov Moscow State University, Faculty of Chemistry, Moscow, 119991, Russia.
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23
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Gillis RB, Solomon HV, Govada L, Oldham NJ, Dinu V, Jiwani SI, Gyasi-Antwi P, Coffey F, Meal A, Morgan PS, Harding SE, Helliwell JR, Chayen NE, Adams GG. Analysis of insulin glulisine at the molecular level by X-ray crystallography and biophysical techniques. Sci Rep 2021; 11:1737. [PMID: 33462295 PMCID: PMC7814034 DOI: 10.1038/s41598-021-81251-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 12/09/2020] [Indexed: 11/16/2022] Open
Abstract
This study concerns glulisine, a rapid-acting insulin analogue that plays a fundamental role in diabetes management. We have applied a combination of methods namely X-ray crystallography, and biophysical characterisation to provide a detailed insight into the structure and function of glulisine. X-ray data provided structural information to a resolution of 1.26 Å. Crystals belonged to the H3 space group with hexagonal (centred trigonal) cell dimensions a = b = 82.44 and c = 33.65 Å with two molecules in the asymmetric unit. A unique position of D21Glu, not present in other fast-acting analogues, pointing inwards rather than to the outside surface was observed. This reduces interactions with neighbouring molecules thereby increasing preference of the dimer form. Sedimentation velocity/equilibrium studies revealed a trinary system of dimers and hexamers/dihexamers in dynamic equilibrium. This new information may lead to better understanding of the pharmacokinetic and pharmacodynamic behaviour of glulisine which might aid in improving formulation regarding its fast-acting role and reducing side effects of this drug.
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Affiliation(s)
- Richard B Gillis
- Faculty of Medicine and Health Sciences, Queen's Medical Centre, University of Nottingham, Nottingham, NG7 2HA, UK.
| | - Hodaya V Solomon
- Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, Sir Alexander Fleming Building, London, SW7 2AZ, UK
| | - Lata Govada
- Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, Sir Alexander Fleming Building, London, SW7 2AZ, UK
| | - Neil J Oldham
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Vlad Dinu
- National Centre for Macromolecular Hydrodynamics, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK
| | - Shahwar Imran Jiwani
- Faculty of Medicine and Health Sciences, Queen's Medical Centre, University of Nottingham, Nottingham, NG7 2HA, UK
| | - Philemon Gyasi-Antwi
- Faculty of Medicine and Health Sciences, Queen's Medical Centre, University of Nottingham, Nottingham, NG7 2HA, UK
| | - Frank Coffey
- Faculty of Medicine and Health Sciences, Queen's Medical Centre, University of Nottingham, Nottingham, NG7 2HA, UK
| | - Andy Meal
- Faculty of Medicine and Health Sciences, Queen's Medical Centre, University of Nottingham, Nottingham, NG7 2HA, UK
| | - Paul S Morgan
- Faculty of Medicine and Health Sciences, Queen's Medical Centre, University of Nottingham, Nottingham, NG7 2HA, UK
| | - Stephen E Harding
- National Centre for Macromolecular Hydrodynamics, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK.,Universitetet I Oslo, St. Olavs plass, Postboks 6762, 0130, Oslo, Norway
| | - John R Helliwell
- Department of Chemistry, University of Manchester, Manchester, M13 9PL, UK
| | - Naomi E Chayen
- Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, Sir Alexander Fleming Building, London, SW7 2AZ, UK.
| | - Gary G Adams
- Faculty of Medicine and Health Sciences, Queen's Medical Centre, University of Nottingham, Nottingham, NG7 2HA, UK.
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24
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Kondyli E, Pappa EC, Kremmyda A, Arapoglou D, Metafa M, Eliopoulos C, Israilides C. Manufacture of Reduced Fat White-Brined Cheese with the Addition of β-Glucans Biobased Polysaccharides as Textural Properties Improvements. Polymers (Basel) 2020; 12:polym12112647. [PMID: 33182804 PMCID: PMC7696168 DOI: 10.3390/polym12112647] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 11/05/2020] [Accepted: 11/06/2020] [Indexed: 12/02/2022] Open
Abstract
β-Glucan, isolated from the mushroom Pleurotus ostreatus, at a concentration of 0.4%, was used in the manufacture of reduced-fat white-brined cheese from sheep milk. Control reduced-fat cheese was also produced from the same milk without the addition of β-glucan. The resultant cheeses were examined for their physicochemical characteristics, color and textural properties, and level of proteolysis and lipolysis. Furthermore, cheeses were evaluated organoleptically. In general, there were no statistical differences in the physicochemical characteristics and proteolysis levels found between both cheeses. The addition of β-glucan improved textural properties, and the cheeses received favorable grades for all the organoleptic characteristics. There were no flavor defects (such as a bitter taste) described by the panellists in this study. Generally, the addition of β-glucan did not significantly affect total free fatty acid content; however, at 180 days of ripening and storage, cheeses with the addition of β-glucan had a higher (p < 0.05) content than cheeses without β-glucan. The major fatty acids were acetic acid and capric acid.
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Affiliation(s)
- Efthymia Kondyli
- Dairy Research Department, Institute of Technology of Agricultural Products, Hellenic Agricultural Organization-DEMETER, Katsikas, 45221 Ioannina, Greece;
- Correspondence: ; Tel.: +30-265-109-4780
| | - Eleni C. Pappa
- Dairy Research Department, Institute of Technology of Agricultural Products, Hellenic Agricultural Organization-DEMETER, Katsikas, 45221 Ioannina, Greece;
| | - Alexandra Kremmyda
- Division of Food, Nutrition and Dietetics, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK;
| | - Dimitris Arapoglou
- Institute of Technology of Agricultural Products, Hellenic Agricultural Organisation-DEMETER, 1 S.Venizelou, 14123 Lycovrysi, Greece; (D.A.); (M.M.); (C.E.); (C.I.)
| | - Maria Metafa
- Institute of Technology of Agricultural Products, Hellenic Agricultural Organisation-DEMETER, 1 S.Venizelou, 14123 Lycovrysi, Greece; (D.A.); (M.M.); (C.E.); (C.I.)
| | - Christos Eliopoulos
- Institute of Technology of Agricultural Products, Hellenic Agricultural Organisation-DEMETER, 1 S.Venizelou, 14123 Lycovrysi, Greece; (D.A.); (M.M.); (C.E.); (C.I.)
| | - Cleanthes Israilides
- Institute of Technology of Agricultural Products, Hellenic Agricultural Organisation-DEMETER, 1 S.Venizelou, 14123 Lycovrysi, Greece; (D.A.); (M.M.); (C.E.); (C.I.)
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25
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Patil SM, Nguyen J, Keire DA, Chen K. Sedimentation Velocity Analytical Ultracentrifugation Analysis of Marketed Rituximab Drug Product Size Distribution. Pharm Res 2020; 37:238. [PMID: 33155155 DOI: 10.1007/s11095-020-02961-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 10/22/2020] [Indexed: 10/23/2022]
Abstract
PURPOSE Analytical methods suitable for intact drug products are often necessary to evaluate the equivalence in physicochemical properties between two drug products (DP) containing the same drug substance (DS), e.g., an innovator biologic drug and its proposed biosimilar. Analytical Ultracentrifugation (AUC) is a biophysics technique applied to the analysis of size and shape of biomolecules. However, the application of AUC to formulated monoclonal antibody (mAb) DP at high concentration has not been reported. METHODS A sedimentation velocity (SV) AUC procedure with a short-pathlength centerpiece was applied to two marketed rituximab DPs, Rituxan® (US) and Reditux® (India), without any buffer exchange or dilution. Detailed precision analysis was performed. RESULTS Highly reproducible sedimentation coefficient values (S) and peak areas were obtained for the dominant (> 84%) monomeric rituximab peak. The minor mAb fragment peaks had large variation in both S values and peak areas (3-12%). The identification of oligomer peaks was only reproducible once the abundance was higher than 2%. CONCLUSIONS SV-AUC provides an orthogonal characterization tool for protein size distribution, composition and assay, which could be informative for biosimilar drug developers who mostly only have access to formulated mAb. However, AUC needs thorough validation on its accuracy, precision and sensitivity.
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Affiliation(s)
- Sharadrao M Patil
- Division of Complex Drug Analysis, Office of Testing and Research, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland, 20993, USA.
| | - John Nguyen
- Division of Complex Drug Analysis, Office of Testing and Research, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland, 20993, USA
| | - David A Keire
- Office of Testing and Research, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, St. Louis, Missouri, 63110, USA
| | - Kang Chen
- Division of Complex Drug Analysis, Office of Testing and Research, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland, 20993, USA.
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26
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Huang Q, Duan B, Dong X, Fan S, Xia B. GapR binds DNA through dynamic opening of its tetrameric interface. Nucleic Acids Res 2020; 48:9372-9386. [PMID: 32756896 PMCID: PMC7498317 DOI: 10.1093/nar/gkaa644] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Revised: 07/13/2020] [Accepted: 07/24/2020] [Indexed: 01/27/2023] Open
Abstract
GapR is a nucleoid-associated protein that is an essential regulator of chromosome replication in the cell cycle model Caulobacter crescentus. Here, we demonstrate that free GapR is a homotetramer, but not a dimer as previously reported (Guo et al., Cell 175: 583–597, 2018). We have determined the crystal structure of GapR in complex with a 10-bp A-tract DNA, which has an open tetrameric conformation, different from the closed clamp conformation in the previously reported crystal structure of GapR/DNA complex. The free GapR adopts multiple conformations in dynamic exchange equilibrium, with the major conformation resembling the closed tetrameric conformation, while the open tetrameric conformation is a representative of minor conformers. As it is impossible for the circular genomic DNA to get into the central DNA binding tunnel of the major conformation, we propose that GapR initially binds DNA through the open conformation, and then undergoes structural rearrangement to form the closed conformation which fully encircles the DNA. GapR prefers to bind DNA with 10-bp consecutive A/T base pairs nonselectively (Kd ∼12 nM), while it can also bind GC-rich DNA sequence with a reasonable affinity of about 120 nM. Besides, our results suggest that GapR binding results in widening the minor groove of AT-rich DNA, instead of overtwisting DNA.
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Affiliation(s)
- Qian Huang
- Beijing Nuclear Magnetic Resonance Center, School of Life Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Bo Duan
- Beijing Nuclear Magnetic Resonance Center, School of Life Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Xianzhi Dong
- Institute of Biophysics, Chinese Academy of Science, Beijing 100101, China
| | - Shilong Fan
- The Technology Center for Protein Sciences, Tsinghua University, Beijing 100084, China
| | - Bin Xia
- Beijing Nuclear Magnetic Resonance Center, School of Life Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
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27
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Grube M, Dinu V, Lindemann H, Pielenz F, Festag G, Schubert US, Heinze T, Harding S, Nischang I. Polysaccharide valproates: Structure - property relationships in solution. Carbohydr Polym 2020; 246:116652. [PMID: 32747284 DOI: 10.1016/j.carbpol.2020.116652] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 06/07/2020] [Accepted: 06/15/2020] [Indexed: 12/30/2022]
Abstract
Polysaccharides are promising macromolecular platforms for use in the life sciences. Here, bioactive cellulose, pullulan, and dextran valproates are characterized hydrodynamically by sedimentation velocity and thermodynamically by sedimentation equilibrium analytical ultracentrifugation. Using sedimentation-diffusion analysis of sedimentation velocity experiments by numerical solution of the Lamm equation enabled the calculation of sedimentation and diffusion coefficients, and consequently molar masses. Sedimentation equilibrium experiments were then also used to determine the average molar masses. The corresponding set of data, with independently performed self-diffusion measurements by nuclear magnetic resonance spectroscopy, and together with size exclusion chromatography molar masses by coupling to refractive index-, viscometric-, and multi-angle laser light scattering detection, were subsequently correlated to each other by the hydrodynamic invariant and sedimentation parameter. We assess statistically most relevant average values of the molar masses of these polysaccharide valproates with relevant macromolecular conformational characteristics.
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Affiliation(s)
- Mandy Grube
- Laboratory of Organic and Macromolecular Chemistry (IOMC), Friedrich Schiller University Jena, Humboldtstraße 10, 07743 Jena, Germany; Jena Center for Soft Matter (JCSM), Friedrich Schiller University Jena, Philosophenweg 7, 07743 Jena, Germany
| | - Vlad Dinu
- National Centre for Macromolecular Hydrodynamics, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, United Kingdom
| | - Henry Lindemann
- Laboratory of Organic and Macromolecular Chemistry (IOMC), Friedrich Schiller University Jena, Humboldtstraße 10, 07743 Jena, Germany; Jena Center for Soft Matter (JCSM), Friedrich Schiller University Jena, Philosophenweg 7, 07743 Jena, Germany
| | - Friederike Pielenz
- Laboratory of Organic and Macromolecular Chemistry (IOMC), Friedrich Schiller University Jena, Humboldtstraße 10, 07743 Jena, Germany
| | - Grit Festag
- Laboratory of Organic and Macromolecular Chemistry (IOMC), Friedrich Schiller University Jena, Humboldtstraße 10, 07743 Jena, Germany; Jena Center for Soft Matter (JCSM), Friedrich Schiller University Jena, Philosophenweg 7, 07743 Jena, Germany
| | - Ulrich S Schubert
- Laboratory of Organic and Macromolecular Chemistry (IOMC), Friedrich Schiller University Jena, Humboldtstraße 10, 07743 Jena, Germany; Jena Center for Soft Matter (JCSM), Friedrich Schiller University Jena, Philosophenweg 7, 07743 Jena, Germany
| | - Thomas Heinze
- Laboratory of Organic and Macromolecular Chemistry (IOMC), Friedrich Schiller University Jena, Humboldtstraße 10, 07743 Jena, Germany; Jena Center for Soft Matter (JCSM), Friedrich Schiller University Jena, Philosophenweg 7, 07743 Jena, Germany
| | - Stephen Harding
- National Centre for Macromolecular Hydrodynamics, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, United Kingdom
| | - Ivo Nischang
- Laboratory of Organic and Macromolecular Chemistry (IOMC), Friedrich Schiller University Jena, Humboldtstraße 10, 07743 Jena, Germany; Jena Center for Soft Matter (JCSM), Friedrich Schiller University Jena, Philosophenweg 7, 07743 Jena, Germany.
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Kim G, Lee SG, Han S, Jung J, Jeong HS, Hyun JK, Rhee DK, Kim HM, Lee S. ClpL is a functionally active tetradecameric AAA+ chaperone, distinct from hexameric/dodecameric ones. FASEB J 2020; 34:14353-14370. [PMID: 32910525 DOI: 10.1096/fj.202000843r] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 07/23/2020] [Accepted: 08/11/2020] [Indexed: 01/17/2023]
Abstract
AAA+ (ATPases associated with diverse cellular activities) chaperones are involved in a plethora of cellular activities to ensure protein homeostasis. The function of AAA+ chaperones is mostly modulated by their hexameric/dodecameric quaternary structures. Here we report the structural and biochemical characterizations of a tetradecameric AAA+ chaperone, ClpL from Streptococcus pneumoniae. ClpL exists as a tetradecamer in solution in the presence of ATP. The cryo-EM structure of ClpL at 4.5 Å resolution reveals a striking tetradecameric arrangement. Solution structures of ClpL derived from small-angle X-ray scattering data suggest that the tetradecameric ClpL could assume a spiral conformation found in active hexameric/dodecameric AAA+ chaperone structures. Vertical positioning of the middle domain accounts for the head-to-head arrangement of two heptameric rings. Biochemical activity assays with site-directed mutagenesis confirmed the critical roles of residues both in the integrity of the tetradecameric arrangement and activities of ClpL. Non-conserved Q321 and R670 are crucial in the heptameric ring assembly of ClpL. These results establish that ClpL is a functionally active tetradecamer, clearly distinct from hexameric/dodecameric AAA+ chaperones.
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Affiliation(s)
- Gyuhee Kim
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Korea
| | - Seong-Gyu Lee
- Center for Biomolecular and Cellular Structure, Institute for Basic Science (IBS), Daejeon, Korea.,Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Korea
| | - Seungsu Han
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Korea
| | - Jaeeun Jung
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Korea
| | | | - Jae-Kyung Hyun
- Korea Basic Science Institute, Cheongju, Korea.,Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Dong-Kwon Rhee
- School of Pharmacy, Sungkyunkwan University, Suwon, Korea
| | - Ho Min Kim
- Center for Biomolecular and Cellular Structure, Institute for Basic Science (IBS), Daejeon, Korea.,Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Korea
| | - Sangho Lee
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Korea.,Biomedical Institute for Convergence at SKKU, Sungkyunkwan University, Suwon, Korea
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Tert-butyldimethylsilyl chitosan synthesis and characterization by analytical ultracentrifugation, for archaeological wood conservation. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2020; 49:781-789. [PMID: 32845350 PMCID: PMC7701062 DOI: 10.1007/s00249-020-01450-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 07/10/2020] [Accepted: 07/17/2020] [Indexed: 11/24/2022]
Abstract
The Oseberg ship is one of the most important archaeological testimonies of the Vikings. After excavation in 1904, the wooden gravegoods were conserved using alum salts. This resulted in extreme degradation of a number of the objects a hundred years later through acid depolymerisation of cellulose and lignin. The fragile condition of the artefacts requires a reconsolidation which has to be done avoiding water as solvent. We synthesized tert-butyldimethylsilyl (TBDMS) chitosan which is soluble in a 50:50 solution of ethyl acetate and toluene. Measurement of its molecular weight, to anticipate its penetration, provided a challenge as the density difference of the polymer and solvent was too small to provide adequate solute redistribution under a centrifugal field, so a two-stage process was implemented (i) determination of the weight-average molar mass of the aqueous soluble activated precursor, chitosan mesylate, Mw,mc using sedimentation equilibrium with the SEDFIT-MSTAR algorithm, and determination of the degree of polymerisation DP; (ii) measurement of the average degree of substitution DSTBDMS of the TBDMS group on each chitosan monosaccharide monomer unit using NMR, to augment the Mw,mc value to give the molar mass of the TBDMS-chitosan. For the preparation, we find Mw = 9.8 kg·mol−1, which is within the acceptable limit for penetration and consolidation of degraded wood. Future work will test this on archaeological wood from different sources.
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30
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Jiwani SI, Gillis RB, Besong D, Almutairi F, Erten T, Kök MS, Harding SE, Paulsen BS, Adams GG. Isolation and Biophysical Characterisation of Bioactive Polysaccharides from Cucurbita Moschata (Butternut Squash). Polymers (Basel) 2020; 12:polym12081650. [PMID: 32722155 PMCID: PMC7466094 DOI: 10.3390/polym12081650] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 07/15/2020] [Accepted: 07/22/2020] [Indexed: 11/16/2022] Open
Abstract
Cucurbits are plants that have been used frequently as functional foods. This study includes the extraction, isolation, and characterisation of the mesocarp polysaccharide of Cucurbita moschata. The polysaccharide component was purified by gel filtration into three fractions (NJBTF1, NJBTF2, and NJBTF3) of different molecular weights. Characterisation includes the hydrodynamic properties, identification of monosaccharide composition, and bioactivity. Sedimentation velocity also indicated the presence of small amounts of additional discrete higher molecular weight components even after fractionation. Sedimentation equilibrium revealed respective weight average molecular weights of 90, 31, and 19 kDa, with the higher fractions (NJBTF1 and NJBTF2) indicating a tendency to self-associate. Based on the limited amount of data (combinations of 3 sets of viscosity and sedimentation data corresponding to the 3 fractions), HYDFIT indicates an extended, semi-flexible coil conformation. Of all the fractions obtained, NJBTF1 showed the highest bioactivity. All fractions contained galacturonic acid and variable amounts of neutral sugars. To probe further, the extent of glycosidic linkages in NJBTF1 was estimated using gas chromatography–mass spectrometry (GCMS), yielding a high galacturonic acid content (for pectin polysaccharide) and the presence of fructans—the first evidence of fructans (levan) in the mesocarp. Our understanding of the size and structural flexibility together with the high bioactivity suggests that the polysaccharide obtained from C. moschata has the potential to be developed into a therapeutic agent.
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Affiliation(s)
- Shahwar Imran Jiwani
- Queen’s Medical Centre, Faculty of Medicine and Health Sciences, University of Nottingham, Clifton Boulevard, Nottingham NG7 2UH, UK;
- Correspondence: (S.I.J.); (G.G.A.); Tel.: +44-(0)-115-748-4098 (S.I.J.); +44-(0)-115-823-0901 (G.G.A.)
| | - Richard B. Gillis
- Queen’s Medical Centre, Faculty of Medicine and Health Sciences, University of Nottingham, Clifton Boulevard, Nottingham NG7 2UH, UK;
| | - David Besong
- Solar and Photovoltaics Engineering Center, King Abdullah University of Science and Technology, Thuwal, Makkah 23955-6900, Saudi Arabia;
| | - Fahad Almutairi
- Department of Biochemistry, Faculty of Science, University of Tabuk, P.O. Box 741, Tabuk 71491, Saudi Arabia;
| | - Tayyibe Erten
- Department of Nutrition and Dietetics, Faculty of Health Sciences, Bayburt University, 69000 Bayburt, Turkey;
| | - M. Samil Kök
- Department of Food Engineering, Faculty of Engineering & Architecture, Abant Izzet Baysal University, Gölköy, 14300 Bolu, Turkey;
| | - Stephen E. Harding
- National Centre for Macromolecular Hydrodynamics (NCMH), School of Biosciences, Sutton Bonington Campus, The University of Nottingham, Sutton Bonington, Leicestershire LE12 5RD, UK;
| | - Berit S. Paulsen
- Department of Pharmaceutical Chemistry, School of Pharmacy, Section Pharmacognosy, University of Oslo, PB 1068, Blindern, N-0316 Oslo, Norway;
| | - Gary G. Adams
- Queen’s Medical Centre, Faculty of Medicine and Health Sciences, University of Nottingham, Clifton Boulevard, Nottingham NG7 2UH, UK;
- Correspondence: (S.I.J.); (G.G.A.); Tel.: +44-(0)-115-748-4098 (S.I.J.); +44-(0)-115-823-0901 (G.G.A.)
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31
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Li X, Lu Y, Adams GG, Zobel H, Ballance S, Wolf B, Harding SE. Characterisation of the molecular properties of scleroglucan as an alternative rigid rod molecule to xanthan gum for oropharyngeal dysphagia. Food Hydrocoll 2020; 101:105446. [PMID: 32255886 PMCID: PMC7015278 DOI: 10.1016/j.foodhyd.2019.105446] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Scleroglucan, a neutral β(1–3) glucan with β(1–6) glucan branches every third residue, is being considered as an alternative rod-like, shear thinning high molecular weight β-glucan based polysaccharide to xanthan gum for the management of patients with oropharyngeal dysphagia. It is therefore important to understand more fully its hydrodynamic properties in solution, in particular heterogeneity, molecular weight distribution and its behaviour in the presence of mucin glycoproteins. A commercially purified scleroglucan preparation produced by fermentation of the filamentous fungus Sclerotium rolfsii was analysed in deionised distilled water with 0.02% added azide. Sedimentation velocity in the analytical ultracentrifuge showed the scleroglucan preparation to be unimodal at concentrations >0.75 mg/ml which resolved into two components at lower concentration and with partial reversibility between the components. Sedimentation coefficient versus concentration plots showed significant hydrodynamic non-ideality. Self-association behaviour was confirmed by sedimentation equilibrium experiments with molecular weights between ~3 × 106 g/mol to ~5 × 106 g/mol after correcting for thermodynamic non-ideality. SEC-MALS-viscosity experiments showed a transition between a rod-shape at lower molar masses to a more flexible structure at higher masses consistent with previous observations. Sedimentation velocity experiments also showed no evidence for potentially problematic interactions with submaxillary mucin. Scleroglucan considered as alternative to xanthan. Sedimentation velocity shows partial reversible self-association. Associative behaviour confirmed by sedimentation equilibrium. SEC-MALS and viscosity show transition between a rod to more flexible structure. No problematic interactions with submaxillary mucin.
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Affiliation(s)
- Xinxin Li
- National Centre for Macromolecular Hydrodynamics, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK
- Division of Food, Nutrition and Dietectics, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK
| | - Yudong Lu
- National Centre for Macromolecular Hydrodynamics, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK
| | - Gary G. Adams
- School of Health Sciences, University of Nottingham, Queen's Medical Centre, Nottingham, NG7 2HA, UK
| | - Hanne Zobel
- Nofima AS, Norwegian Institute of Food, Fisheries and Aquaculture Research, Ås, Norway
| | - Simon Ballance
- Nofima AS, Norwegian Institute of Food, Fisheries and Aquaculture Research, Ås, Norway
| | - Bettina Wolf
- Division of Food, Nutrition and Dietectics, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK
- Corresponding author.
| | - Stephen E. Harding
- National Centre for Macromolecular Hydrodynamics, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK
- Kulturhistorisk Museum, Universitetet i Oslo, Postboks 6762, St. Olavs Plass, 0130, Oslo, Norway
- Corresponding author. National Centre for Macromolecular Hydrodynamics, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK.
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32
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Simonova YA, Topchiy MA, Filatova MP, Yevlampieva NP, Slyusarenko MA, Bondarenko GN, Asachenko AF, Nechaev MS, Timofeeva LM. Impact of the RAFT/MADIX agent on protonated diallylammonium monomer cyclopolymerization with efficient chain transfer to monomer. Eur Polym J 2020. [DOI: 10.1016/j.eurpolymj.2019.109363] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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33
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Acton O, Grant T, Nicastro G, Ball NJ, Goldstone DC, Robertson LE, Sader K, Nans A, Ramos A, Stoye JP, Taylor IA, Rosenthal PB. Structural basis for Fullerene geometry in a human endogenous retrovirus capsid. Nat Commun 2019; 10:5822. [PMID: 31862888 PMCID: PMC6925226 DOI: 10.1038/s41467-019-13786-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 11/28/2019] [Indexed: 01/09/2023] Open
Abstract
The HML2 (HERV-K) group constitutes the most recently acquired family of human endogenous retroviruses, with many proviruses less than one million years old. Many maintain intact open reading frames and provirus expression together with HML2 particle formation are observed in early stage human embryo development and are associated with pluripotency as well as inflammatory disease, cancers and HIV-1 infection. Here, we reconstruct the core structural protein (CA) of an HML2 retrovirus, assemble particles in vitro and employ single particle cryogenic electron microscopy (cryo-EM) to determine structures of four classes of CA Fullerene shell assemblies. These icosahedral and capsular assemblies reveal at high-resolution the molecular interactions that allow CA to form both pentamers and hexamers and show how invariant pentamers and structurally plastic hexamers associate to form the unique polyhedral structures found in retroviral cores.
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Affiliation(s)
- Oliver Acton
- Structural Biology of Cells and Viruses Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Tim Grant
- Structural Biology of Cells and Viruses Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA, 20147, USA
| | - Giuseppe Nicastro
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Neil J Ball
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - David C Goldstone
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Laura E Robertson
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Kasim Sader
- Structural Biology of Cells and Viruses Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Thermo Fisher Scientific Materials and Structural Analysis, Eindhoven, Netherlands
| | - Andrea Nans
- Structural Biology of Cells and Viruses Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Andres Ramos
- Division of Molecular Structure, MRC National Institute for Medical Research, London, NW7 1AA, UK
- Institute of Structural and Molecular Biology, University College London, London, UK
| | - Jonathan P Stoye
- Retrovirus-Host Interactions Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Department of Medicine, Imperial College London, London, SW7 2AZ, UK
| | - Ian A Taylor
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
| | - Peter B Rosenthal
- Structural Biology of Cells and Viruses Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
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34
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Gadon A, Linforth R, Harding SE, Cook D. Characterisation of high molecular weight hop proanthocyanidins using Analytical Ultracentrifugation. Sci Rep 2019; 9:12650. [PMID: 31477789 PMCID: PMC6718571 DOI: 10.1038/s41598-019-49171-4] [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: 03/20/2019] [Accepted: 08/16/2019] [Indexed: 11/09/2022] Open
Abstract
We report the novel application of Analytical Ultracentrifugation (AUCF) to characterise the polymeric proanthocyanidin fraction of hops. Extraction of hop samples with 70% acetone (aq) followed by a C-18 Solid Phase Extraction yielded polyphenolic fractions for AUCF analysis. Sedimentation velocity experiments demonstrated the presence of discrete molecular weight bands of proanthocyanidins, as opposed to a continuous distribution of molecular weights. There were 4 such bands for Saaz hop (0.15, 1.1, 2.7 and 4.4S) and 3 bands for Magnum (0.15, 1.6 and 3.0S). The method resulted in a reproducible size (sedimentation coefficient) distribution for replicate runs of the same extract and for extracts prepared from different samples of the same hop variety. Sedimentation equilibrium experiments were then used to fit molecular weight distributions using the new SEDFIT-MSTAR method for the same samples. Thus we report for the first time polymeric proanthocyanidins in hops with molecular weights of up to 100 kDa in Saaz hop (or up to 56 kDa in Magnum). This represents the first application of AUCF to characterise complex fractions of polyphenolics extracted from botanical sources and the methodology developed should find wider application in the study of this diverse and bioactive class of compounds.
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Affiliation(s)
- Arthur Gadon
- International Centre for Brewing Science, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Sutton Bonington, Leicestershire, UK
| | - Robert Linforth
- Division of Food Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Sutton Bonington, Leicestershire, UK
| | - Stephen E Harding
- National Centre for Molecular Hydrodynamics, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Sutton Bonington, Leicestershire, UK. .,Kulturhistoriskmuseum, Universitetet i Oslo, Postboks 6762, St. Olavs plass, 0130, Oslo, Norway.
| | - David Cook
- International Centre for Brewing Science, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Sutton Bonington, Leicestershire, UK.
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35
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Zeigler DF, Gage E, Roque R, Clegg CH. Epitope targeting with self-assembled peptide vaccines. NPJ Vaccines 2019; 4:30. [PMID: 31341647 PMCID: PMC6642127 DOI: 10.1038/s41541-019-0125-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 06/26/2019] [Indexed: 12/16/2022] Open
Abstract
Nanoparticle-based delivery systems are being used to simplify and accelerate new vaccine development. Previously, we described the solid-phase synthesis of a 61-amino acid conjugate vaccine carrier comprising a α-helical domain followed by two universal T cell epitopes. Circular dichroism, analytical centrifugation, and dynamic light scattering indicate that this carrier forms coiled-coil nanoparticles. Here we expand the potential of this carrier by appending B cell epitopes to its amino acid sequence, thereby eliminating the need for traditional conjugation reactions. Peptides containing Tau or amyloid-β epitopes at either terminus assemble into ~20 nm particles and induce antibody responses in outbred mice. Vaccine function was verified in three experiments. The first targeted gonadotropin-releasing hormone, a 10-amino acid neuropeptide that regulates sexual development. Induction of peak antibody titers in male mice stimulated a dramatic loss in fertility and marked testis degeneration. The second experiment generated antibodies to an epitope on the murine IgE heavy chain analogous to human IgE sequence recognized by omalizumab, the first monoclonal antibody approved for the treatment of allergic asthma. Like omalizumab, the anti-IgE antibodies in immunized mice reduced the concentrations of circulating free IgE and prevented IgE-induced anaphylaxis. Finally, a peptide containing the highly conserved Helix A epitope within the influenza hemagglutinin stem domain induced antibodies that successfully protected mice against a lethal H1N1 challenge. These results establish the utility of a new vaccine platform for eliciting prophylactic and therapeutic antibodies to linear and helical B cell epitopes. Synthetic nanoparticles have the potential to be a simple, efficacious, and customizable platform for vaccine delivery. Christopher H. Clegg and colleagues include B cell epitopes on a self-assembling α-helical peptide nanoparticle carrier in order to elicit robust antibody generation. This novel vaccine platform is validated in vivo to produce physiologically-relevant antibodies in three different settings: an antibody-mediated ‘castration’ approach (anti-gonadotropin-releasing hormone), depletion of IgE (by generation of anti-IgE), and finally production of antibodies to a conserved H1N1 influenza epitope that mediates a protective effect in mice.
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Affiliation(s)
- David F Zeigler
- 1TRIA Bioscience Corp, Suite 260, 1616 Eastlake Avenue East, Seattle, WA 98102 USA
| | - Emily Gage
- 1TRIA Bioscience Corp, Suite 260, 1616 Eastlake Avenue East, Seattle, WA 98102 USA
| | - Richard Roque
- 1TRIA Bioscience Corp, Suite 260, 1616 Eastlake Avenue East, Seattle, WA 98102 USA.,2Present Address: MedImmune, One MedImmune Way, Gaithersburg, MD 20878 USA
| | - Christopher H Clegg
- 1TRIA Bioscience Corp, Suite 260, 1616 Eastlake Avenue East, Seattle, WA 98102 USA
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36
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Paxman JJ, Lo AW, Sullivan MJ, Panjikar S, Kuiper M, Whitten AE, Wang G, Luan CH, Moriel DG, Tan L, Peters KM, Phan MD, Gee CL, Ulett GC, Schembri MA, Heras B. Unique structural features of a bacterial autotransporter adhesin suggest mechanisms for interaction with host macromolecules. Nat Commun 2019; 10:1967. [PMID: 31036849 PMCID: PMC6488583 DOI: 10.1038/s41467-019-09814-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 03/28/2019] [Indexed: 12/31/2022] Open
Abstract
Autotransporters are the largest family of outer membrane and secreted proteins in Gram-negative bacteria. Most autotransporters are localised to the bacterial surface where they promote colonisation of host epithelial surfaces. Here we present the crystal structure of UpaB, an autotransporter that is known to contribute to uropathogenic E. coli (UPEC) colonisation of the urinary tract. We provide evidence that UpaB can interact with glycosaminoglycans and host fibronectin. Unique modifications to its core β-helical structure create a groove on one side of the protein for interaction with glycosaminoglycans, while the opposite face can bind fibronectin. Our findings reveal far greater diversity in the autotransporter β-helix than previously thought, and suggest that this domain can interact with host macromolecules. The relevance of these interactions during infection remains unclear.
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Affiliation(s)
- Jason J Paxman
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, 3086, VIC, Australia
| | - Alvin W Lo
- School of Chemistry and Molecular Biosciences, and Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, 4072, QLD, Australia
| | - Matthew J Sullivan
- School of Medical Science, and Menzies Health Institute Queensland, Griffith University, Gold Coast, 4222, QLD, Australia
| | - Santosh Panjikar
- Macromolecular Crystallography, Australian Synchrotron, Clayton, 3168, VIC, Australia
- Department of Molecular Biology and Biochemistry, Monash University, Melbourne, 3800, VIC, Australia
| | - Michael Kuiper
- Molecular & Materials Modelling group Data61, CSIRO, Docklands, Melbourne, 8012, VIC, Australia
| | - Andrew E Whitten
- Australian Centre for Neutron Scattering, Australian Nuclear Science and Technology Organisation, Lucas Heights, 2234, NSW, Australia
| | - Geqing Wang
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, 3086, VIC, Australia
| | - Chi-Hao Luan
- High Throughput Analysis Laboratory and Department of Molecular Biosciences, Northwestern University, Chicago, 60208, IL, USA
| | - Danilo G Moriel
- School of Chemistry and Molecular Biosciences, and Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, 4072, QLD, Australia
| | - Lendl Tan
- School of Chemistry and Molecular Biosciences, and Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, 4072, QLD, Australia
| | - Kate M Peters
- School of Chemistry and Molecular Biosciences, and Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, 4072, QLD, Australia
| | - Minh-Duy Phan
- School of Chemistry and Molecular Biosciences, and Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, 4072, QLD, Australia
| | - Christine L Gee
- Macromolecular Crystallography, Australian Synchrotron, Clayton, 3168, VIC, Australia
| | - Glen C Ulett
- School of Medical Science, and Menzies Health Institute Queensland, Griffith University, Gold Coast, 4222, QLD, Australia
| | - Mark A Schembri
- School of Chemistry and Molecular Biosciences, and Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, 4072, QLD, Australia.
| | - Begoña Heras
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, 3086, VIC, Australia.
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37
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Watanabe S, Hayashi K, Toh K, Kim HJ, Liu X, Chaya H, Fukushima S, Katsushima K, Kondo Y, Uchida S, Ogura S, Nomoto T, Takemoto H, Cabral H, Kinoh H, Tanaka HY, Kano MR, Matsumoto Y, Fukuhara H, Uchida S, Nangaku M, Osada K, Nishiyama N, Miyata K, Kataoka K. In vivo rendezvous of small nucleic acid drugs with charge-matched block catiomers to target cancers. Nat Commun 2019; 10:1894. [PMID: 31019193 PMCID: PMC6482185 DOI: 10.1038/s41467-019-09856-w] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 03/29/2019] [Indexed: 11/13/2022] Open
Abstract
Stabilisation of fragile oligonucleotides, typically small interfering RNA (siRNA), is one of the most critical issues for oligonucleotide therapeutics. Many previous studies encapsulated oligonucleotides into ~100-nm nanoparticles. However, such nanoparticles inevitably accumulate in liver and spleen. Further, some intractable cancers, e.g., tumours in pancreas and brain, have inherent barrier characteristics preventing the penetration of such nanoparticles into tumour microenvironments. Herein, we report an alternative approach to cancer-targeted oligonucleotide delivery using a Y-shaped block catiomer (YBC) with precisely regulated chain length. Notably, the number of positive charges in YBC is adjusted to match that of negative charges in each oligonucleotide strand (i.e., 20). The YBC rendezvouses with a single oligonucleotide in the bloodstream to generate a dynamic ion-pair, termed unit polyion complex (uPIC). Owing to both significant longevity in the bloodstream and appreciably small size (~18 nm), the uPIC efficiently delivers oligonucleotides into pancreatic tumour and brain tumour models, exerting significant antitumour activity.
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MESH Headings
- Animals
- Antineoplastic Agents/chemical synthesis
- Antineoplastic Agents/metabolism
- Antineoplastic Agents/pharmacokinetics
- Brain Neoplasms/genetics
- Brain Neoplasms/metabolism
- Brain Neoplasms/mortality
- Brain Neoplasms/therapy
- Carbocyanines/chemistry
- Cell Cycle Proteins/antagonists & inhibitors
- Cell Cycle Proteins/genetics
- Cell Cycle Proteins/metabolism
- Cell Line, Tumor
- Drug Carriers/chemical synthesis
- Drug Carriers/pharmacokinetics
- Fluorescent Dyes/chemistry
- Gene Expression Regulation, Neoplastic
- Humans
- Injections, Intravenous
- Male
- Mice
- Nanostructures/administration & dosage
- Nanostructures/chemistry
- Oligonucleotides/chemical synthesis
- Oligonucleotides/genetics
- Oligonucleotides/metabolism
- Oligonucleotides/pharmacokinetics
- Pancreatic Neoplasms/genetics
- Pancreatic Neoplasms/metabolism
- Pancreatic Neoplasms/mortality
- Pancreatic Neoplasms/therapy
- Polyethylene Glycols/chemistry
- Polylysine/chemistry
- Protein Serine-Threonine Kinases/antagonists & inhibitors
- Protein Serine-Threonine Kinases/genetics
- Protein Serine-Threonine Kinases/metabolism
- Proto-Oncogene Proteins/antagonists & inhibitors
- Proto-Oncogene Proteins/genetics
- Proto-Oncogene Proteins/metabolism
- RNA, Long Noncoding/antagonists & inhibitors
- RNA, Long Noncoding/genetics
- RNA, Long Noncoding/metabolism
- RNA, Small Interfering/chemical synthesis
- RNA, Small Interfering/genetics
- RNA, Small Interfering/metabolism
- RNA, Small Interfering/pharmacokinetics
- Static Electricity
- Survival Analysis
- Xenograft Model Antitumor Assays
- Polo-Like Kinase 1
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Affiliation(s)
- Sumiyo Watanabe
- Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
- Division of Nephrology, Department of Internal Medicine, Teikyo University School of Medicine, 2-11-1 Kaga, Itabashi-ku, Tokyo, 173-8605, Japan
- Division of Nephrology and Endocrinology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8544, Japan
| | - Kotaro Hayashi
- Innovation Center of NanoMedicine, Kawasaki Institute of Industrial Promotion, 3-25-14 Tonomachi, Kawasaki-ku, Kawasaki, 210-0821, Japan
| | - Kazuko Toh
- Innovation Center of NanoMedicine, Kawasaki Institute of Industrial Promotion, 3-25-14 Tonomachi, Kawasaki-ku, Kawasaki, 210-0821, Japan
| | - Hyun Jin Kim
- Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Xueying Liu
- Innovation Center of NanoMedicine, Kawasaki Institute of Industrial Promotion, 3-25-14 Tonomachi, Kawasaki-ku, Kawasaki, 210-0821, Japan
| | - Hiroyuki Chaya
- Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
- Department of Materials Engineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Shigeto Fukushima
- Innovation Center of NanoMedicine, Kawasaki Institute of Industrial Promotion, 3-25-14 Tonomachi, Kawasaki-ku, Kawasaki, 210-0821, Japan
| | - Keisuke Katsushima
- Division of Cancer Biology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Yutaka Kondo
- Division of Cancer Biology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Satoshi Uchida
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Satomi Ogura
- Innovation Center of NanoMedicine, Kawasaki Institute of Industrial Promotion, 3-25-14 Tonomachi, Kawasaki-ku, Kawasaki, 210-0821, Japan
- Department of Materials Engineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Takahiro Nomoto
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, R1-11, 4259 Nagatsuta, Midori-ku, Yokohama, 226-8503, Japan
| | - Hiroyasu Takemoto
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, R1-11, 4259 Nagatsuta, Midori-ku, Yokohama, 226-8503, Japan
| | - Horacio Cabral
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Hiroaki Kinoh
- Innovation Center of NanoMedicine, Kawasaki Institute of Industrial Promotion, 3-25-14 Tonomachi, Kawasaki-ku, Kawasaki, 210-0821, Japan
| | - Hiroyoshi Y Tanaka
- Department of Pharmaceutical Biomedicine, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, 1-1-1 Tsushima-naka, Kita-ku, Okayama-shi, Okayama Prefecture, 700-8530, Japan
| | - Mitsunobu R Kano
- Department of Pharmaceutical Biomedicine, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, 1-1-1 Tsushima-naka, Kita-ku, Okayama-shi, Okayama Prefecture, 700-8530, Japan
- Department of Pharmaceutical Biomedicine, Okayama University Graduate School of Interdisciplinary Science and Engineering in Health Systems, 1-1-1 Tsushima-naka, Kita-ku, Okayama-shi, Okayama Prefecture, 700-8530, Japan
| | - Yu Matsumoto
- Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Hiroshi Fukuhara
- Department of Urology, Kyorin University Faculty of Medicine, 6-20-2 Shinkawa, Mitaka, Tokyo, 181-8611, Japan
| | - Shunya Uchida
- Division of Nephrology, Department of Internal Medicine, Teikyo University School of Medicine, 2-11-1 Kaga, Itabashi-ku, Tokyo, 173-8605, Japan
| | - Masaomi Nangaku
- Division of Nephrology and Endocrinology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8544, Japan
| | - Kensuke Osada
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Nobuhiro Nishiyama
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, R1-11, 4259 Nagatsuta, Midori-ku, Yokohama, 226-8503, Japan
| | - Kanjiro Miyata
- Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
- Department of Materials Engineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.
| | - Kazunori Kataoka
- Innovation Center of NanoMedicine, Kawasaki Institute of Industrial Promotion, 3-25-14 Tonomachi, Kawasaki-ku, Kawasaki, 210-0821, Japan.
- Institute for Future Initiatives, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
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38
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Barak R, Yom-Tov G, Guez-Haddad J, Gasri-Plotnitsky L, Maimon R, Cohen-Berkman M, McCarthy AA, Perlson E, Henis-Korenblit S, Isupov MN, Opatowsky Y. Structural Principles in Robo Activation and Auto-inhibition. Cell 2019; 177:272-285.e16. [PMID: 30853216 DOI: 10.1016/j.cell.2019.02.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Revised: 12/06/2018] [Accepted: 02/06/2019] [Indexed: 01/28/2023]
Abstract
Proper brain function requires high-precision neuronal expansion and wiring, processes controlled by the transmembrane Roundabout (Robo) receptor family and their Slit ligands. Despite their great importance, the molecular mechanism by which Robos' switch from "off" to "on" states remains unclear. Here, we report a 3.6 Å crystal structure of the intact human Robo2 ectodomain (domains D1-8). We demonstrate that Robo cis dimerization via D4 is conserved through hRobo1, 2, and 3 and the C. elegans homolog SAX-3 and is essential for SAX-3 function in vivo. The structure reveals two levels of auto-inhibition that prevent premature activation: (1) cis blocking of the D4 dimerization interface and (2) trans interactions between opposing Robo receptors that fasten the D4-blocked conformation. Complementary experiments in mouse primary neurons and C. elegans support the auto-inhibition model. These results suggest that Slit stimulation primarily drives the release of Robo auto-inhibition required for dimerization and activation.
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Affiliation(s)
- Reut Barak
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Israel
| | - Galit Yom-Tov
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Israel
| | - Julia Guez-Haddad
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Israel
| | | | - Roy Maimon
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Israel
| | - Moran Cohen-Berkman
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Israel
| | | | - Eran Perlson
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Israel
| | | | | | - Yarden Opatowsky
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Israel.
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39
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Qiu C, Yuan Y, Zajicek J, Liang Z, Balsara RD, Brito-Robionson T, Lee SW, Ploplis VA, Castellino FJ. Contributions of different modules of the plasminogen-binding Streptococcus pyogenes M-protein that mediate its functional dimerization. J Struct Biol 2018; 204:151-164. [PMID: 30071314 PMCID: PMC6544907 DOI: 10.1016/j.jsb.2018.07.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 07/26/2018] [Accepted: 07/28/2018] [Indexed: 10/28/2022]
Abstract
Group A Streptococcus pyogenes (GAS) is a causative agent of pharyngeal and dermal infections in humans. A major virulence determinant of GAS is its dimeric signature fibrillar M-protein (M-Prt), which is evolutionarily designed in modules, ranging from a hypervariable extracellular N-terminal region to a progressively more highly conserved C-terminus that is covalently anchored to the cell wall. Of the >250 GAS isolates classified, only the subset of skin-trophic Pattern D strains expresses a specific serotype of M-Prt, PAM, that directly binds to host human plasminogen (hPg) via its extracellular NH2-terminal variable A-domain region. This interaction allows these GAS strains to accumulate components of the host fibrinolytic system on their surfaces to serve extracellular functions. While structure-function studies have been accomplished on M-Prts from Pattern A-C GAS isolates with different direct ligand binding properties compared to PAM, much less is known regarding the structure-function relationships of PAM-type M-Prts, particularly their dimerization determinants. To examine these questions, PAMs from seven GAS strains with sequence variations in the NH2-terminal ligand binding domains, as well as truncated versions of PAM, were designed and studied. The results from bioinformatic and biophysical analyses show that the different domains of PAM are disparately engaged in dimerization. From these data, we propose an experimentally-based model for PAM secondary and quaternary structures that is highly dependent on the conserved helical C-terminal C-D-domains. In addition, while the N-terminal regions of PAMs are variable in sequence, the binding properties of hPg and its activated product, plasmin, to the A-domain, remain intact.
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Affiliation(s)
- Cunjia Qiu
- W.M. Keck Center for Transgene Research, University of Notre Dame, Notre Dame, IN 46556, United States; Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, United States
| | - Yue Yuan
- W.M. Keck Center for Transgene Research, University of Notre Dame, Notre Dame, IN 46556, United States
| | - Jaroslav Zajicek
- W.M. Keck Center for Transgene Research, University of Notre Dame, Notre Dame, IN 46556, United States; Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, United States
| | - Zhong Liang
- W.M. Keck Center for Transgene Research, University of Notre Dame, Notre Dame, IN 46556, United States; Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, United States
| | - Rashna D Balsara
- W.M. Keck Center for Transgene Research, University of Notre Dame, Notre Dame, IN 46556, United States; Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, United States
| | - Teresa Brito-Robionson
- W.M. Keck Center for Transgene Research, University of Notre Dame, Notre Dame, IN 46556, United States
| | - Shaun W Lee
- W.M. Keck Center for Transgene Research, University of Notre Dame, Notre Dame, IN 46556, United States; Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, United States
| | - Victoria A Ploplis
- W.M. Keck Center for Transgene Research, University of Notre Dame, Notre Dame, IN 46556, United States; Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, United States
| | - Francis J Castellino
- W.M. Keck Center for Transgene Research, University of Notre Dame, Notre Dame, IN 46556, United States; Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, United States.
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40
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Channell GA, Adams GG, Lu Y, Gillis RB, Dinu V, Grundy MML, Bajka B, Butterworth PJ, Ellis PR, Mackie A, Ballance S, Harding SE. Use of the Extended Fujita method for representing the molecular weight and molecular weight distributions of native and processed oat beta-glucans. Sci Rep 2018; 8:11809. [PMID: 30087367 PMCID: PMC6081461 DOI: 10.1038/s41598-018-29997-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 07/18/2018] [Indexed: 11/08/2022] Open
Abstract
Beta 1-3, 1-4 glucans ("beta-glucans") are one of the key components of the cell wall of cereals, complementing the main structural component cellulose. Beta-glucans are also an important source of soluble fibre in foods containing oats with claims of other beneficial nutritional properties such as plasma cholesterol lowering in humans. Key to the function of beta-glucans is their molecular weight and because of their high polydispersity - molecular weight distribution. Analytical ultracentrifugation provides a matrix-free approach (not requiring separation columns or media) to polymer molecular weight distribution determination. The sedimentation coefficient distribution is converted to a molecular weight distribution via a power law relation using an established procedure known as the Extended Fujita approach. We establish and apply the power law relation and Extended Fujita method for the first time to a series of native and processed oat beta-glucans. The application of this approach to beta-glucans from other sources is considered.
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Affiliation(s)
- Guy A Channell
- National Centre for Macromolecular Hydrodynamics, The University of Nottingham, Sutton Bonington, LE12 5RD, UK
| | - Gary G Adams
- National Centre for Macromolecular Hydrodynamics, The University of Nottingham, Sutton Bonington, LE12 5RD, UK
- Faculty of Medicine and Health Sciences, Queens Medical Centre, University of Nottingham, Nottingham, NG7 2HA, UK
| | - YuDong Lu
- National Centre for Macromolecular Hydrodynamics, The University of Nottingham, Sutton Bonington, LE12 5RD, UK
| | - Richard B Gillis
- National Centre for Macromolecular Hydrodynamics, The University of Nottingham, Sutton Bonington, LE12 5RD, UK
- Faculty of Medicine and Health Sciences, Queens Medical Centre, University of Nottingham, Nottingham, NG7 2HA, UK
| | - Vlad Dinu
- National Centre for Macromolecular Hydrodynamics, The University of Nottingham, Sutton Bonington, LE12 5RD, UK
| | - Myriam M-L Grundy
- School of Agriculture, The Sustainable Agricultural and Food Systems Research Division, Reading, RG6 6AR, UK
| | - Balazs Bajka
- Biopolymers Group, Department Nutritional Sciences, Kings College London, London, SE1 9NH, UK
| | - Peter J Butterworth
- Biopolymers Group, Department Nutritional Sciences, Kings College London, London, SE1 9NH, UK
| | - Peter R Ellis
- Biopolymers Group, Department Nutritional Sciences, Kings College London, London, SE1 9NH, UK
| | - Alan Mackie
- School of Food Science & Nutrition, University of Leeds, Leeds, LS2 9JT, UK
| | - Simon Ballance
- Nofima AS, Norwegian Institute of Food, Fisheries and Aquaculture Research, Ås, Norway
| | - Stephen E Harding
- National Centre for Macromolecular Hydrodynamics, The University of Nottingham, Sutton Bonington, LE12 5RD, UK.
- Kulturhistorisk Museum, Universitetet i Oslo, Postboks 6762, St. Olavs plass, 0130, Oslo, Norway.
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41
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The Svedberg Lecture 2017. From nano to micro: the huge dynamic range of the analytical ultracentrifuge for characterising the sizes, shapes and interactions of molecules and assemblies in Biochemistry and Polymer Science. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2018; 47:697-707. [PMID: 30056489 PMCID: PMC6182603 DOI: 10.1007/s00249-018-1321-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 04/25/2018] [Accepted: 07/06/2018] [Indexed: 12/19/2022]
Abstract
The analytical ultracentrifuge (AUC) invented by T. Svedberg has now become an extremely versatile and diverse tool in Biochemistry and Polymer Science for the characterisation of the sizes, shapes and interactions of particles ranging in size from a few nanometres to tens of microns, or in molecular weight, M (molar mass) terms from a few hundred daltons to hundreds of megadaltons. We illustrate this diversity by reviewing recent work on (1) small lignin-like isoeugenols of M ~ 0.4–0.9 kDa for archaeological wood conservation, (2) protein-like association of a functional amino-cellulose M = 3.25 kDa, (3) a small glycopeptide antibiotic (M ~ 1.5 kDa) and its association with a protein involved in antibiotic resistance (M ~ 47 kDa), (4) tetanus toxoid protein TTP (M ~ 150 kDa) and (5) the incorporation of TTP into two huge glycoconjugates considered in glycovaccine development with molecular weight species in a broad distribution appearing to reach 100 MDa. In illustrating the diversity, we will highlight developments in hydrodynamic analysis which have made the AUC such an exciting and important instrument, and point to a potential future development for extending its capability to highly concentrated systems.
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42
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Adams GG, Meal A, Morgan PS, Alzahrani QE, Zobel H, Lithgo R, Kok MS, Besong DTM, Jiwani SI, Ballance S, Harding SE, Chayen N, Gillis RB. Characterisation of insulin analogues therapeutically available to patients. PLoS One 2018; 13:e0195010. [PMID: 29596514 PMCID: PMC5875863 DOI: 10.1371/journal.pone.0195010] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 03/14/2018] [Indexed: 11/29/2022] Open
Abstract
The structure and function of clinical dosage insulin and its analogues were assessed. This included ‘native insulins’ (human recombinant, bovine, porcine), ‘fast-acting analogues’ (aspart, glulisine, lispro) and ‘slow-acting analogues’ (glargine, detemir, degludec). Analytical ultracentrifugation, both sedimentation velocity and equilibrium experiments, were employed to yield distributions of both molar mass and sedimentation coefficient of all nine insulins. Size exclusion chromatography, coupled to multi-angle light scattering, was also used to explore the function of these analogues. On ultracentrifugation analysis, the insulins under investigation were found to be in numerous conformational states, however the majority of insulins were present in a primarily hexameric conformation. This was true for all native insulins and two fast-acting analogues. However, glargine was present as a dimer, detemir was a multi-hexameric system, degludec was a dodecamer (di-hexamer) and glulisine was present as a dimer-hexamer-dihexamer system. However, size-exclusion chromatography showed that the two hexameric fast-acting analogues (aspart and lispro) dissociated into monomers and dimers due to the lack of zinc in the mobile phase. This comprehensive study is the first time all nine insulins have been characterised in this way, the first time that insulin detemir have been studied using analytical ultracentrifugation and the first time that insulins aspart and glulisine have been studied using sedimentation equilibrium. The structure and function of these clinically administered insulins is of critical importance and this research adds novel data to an otherwise complex functional physiological protein.
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Affiliation(s)
- Gary G. Adams
- Faculty of Medicine and Health Sciences, University of Nottingham, Queens Medical Centre, Nottingham, NG7 2UH, United Kingdom
- National Centre for Macromolecular Hydrodynamics, University of Nottingham, School of Biosciences, Sutton Bonington, LE12 5RD, United Kingdom
- * E-mail: (GGA); (RBG)
| | - Andrew Meal
- Faculty of Medicine and Health Sciences, University of Nottingham, Queens Medical Centre, Nottingham, NG7 2UH, United Kingdom
| | - Paul S. Morgan
- Faculty of Medicine and Health Sciences, University of Nottingham, Queens Medical Centre, Nottingham, NG7 2UH, United Kingdom
| | - Qushmua E. Alzahrani
- Faculty of Medicine and Health Sciences, University of Nottingham, Queens Medical Centre, Nottingham, NG7 2UH, United Kingdom
- National Centre for Macromolecular Hydrodynamics, University of Nottingham, School of Biosciences, Sutton Bonington, LE12 5RD, United Kingdom
- Taif University, Faculty of Science, Taif, Saudi Arabia
| | | | - Ryan Lithgo
- National Centre for Macromolecular Hydrodynamics, University of Nottingham, School of Biosciences, Sutton Bonington, LE12 5RD, United Kingdom
| | - M. Samil Kok
- Faculty of Medicine and Health Sciences, University of Nottingham, Queens Medical Centre, Nottingham, NG7 2UH, United Kingdom
- Department of Food Engineering, Abant Izzet Baysal University, Bolu, Turkey
| | - David T. M. Besong
- Functional Nanomaterials Lab, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Shahwar I. Jiwani
- Faculty of Medicine and Health Sciences, University of Nottingham, Queens Medical Centre, Nottingham, NG7 2UH, United Kingdom
- National Centre for Macromolecular Hydrodynamics, University of Nottingham, School of Biosciences, Sutton Bonington, LE12 5RD, United Kingdom
| | | | - Stephen E. Harding
- National Centre for Macromolecular Hydrodynamics, University of Nottingham, School of Biosciences, Sutton Bonington, LE12 5RD, United Kingdom
| | - Naomi Chayen
- Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, SW7 2AZ, United Kingdom
| | - Richard B. Gillis
- Faculty of Medicine and Health Sciences, University of Nottingham, Queens Medical Centre, Nottingham, NG7 2UH, United Kingdom
- National Centre for Macromolecular Hydrodynamics, University of Nottingham, School of Biosciences, Sutton Bonington, LE12 5RD, United Kingdom
- * E-mail: (GGA); (RBG)
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43
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Controlled depolymerisation assessed by analytical ultracentrifugation of low molecular weight chitosan for use in archaeological conservation. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2018; 47:769-775. [PMID: 29550902 PMCID: PMC6182601 DOI: 10.1007/s00249-018-1290-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 02/12/2018] [Accepted: 02/19/2018] [Indexed: 11/06/2022]
Abstract
The heterogeneity and molecular weight of a chitosan of low molecular weight (molar mass) and low degree of acetylation (0.1) for potential use as a consolidant for decayed archaeological wood were examined by sedimentation velocity and sedimentation equilibrium in the analytical ultracentrifuge before and after depolymerisation. Sedimentation velocity before depolymerisation revealed a uniform distribution of sedimentation coefficient with little concentration dependence. SEDFIT-MSTAR analysis revealed a weight average molecular weight Mw of (14.2 ± 1.2) kDa, and polydispersity index of ~ 1.2. Further analysis using MULTISIG revealed a distribution of material between 2 and 20 kDa and consistent with the weight average Mw. Controlled depolymerisation using hydrogen peroxide and ultra-violet radiation in an acetic acid medium reduced this to (4.9 ± 0.7) kDa, with a similar polydispersity. The depolymerised material appears to be within the range that has been predicted to fully penetrate into archaeological wood. The consequences for this finding and the use of the analytical ultracentrifuge in wood conservation strategies are considered.
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Yom-Tov G, Barak R, Matalon O, Barda-Saad M, Guez-Haddad J, Opatowsky Y. Robo Ig4 Is a Dimerization Domain. J Mol Biol 2017; 429:3606-3616. [PMID: 29017837 DOI: 10.1016/j.jmb.2017.10.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 10/02/2017] [Accepted: 10/02/2017] [Indexed: 01/06/2023]
Abstract
Robo receptors play pivotal roles in axonal guidance as well as in neurogenesis, angiogenesis, cell migration, and cancer progression and invasiveness. They are considered to be attractive drug targets for the treatment of cancer, ocular neovascular disorders, chronic kidney diseases, and more. Despite their great importance, the mechanisms by which Robo receptors switch from their "off" to "on" states remain obscure. One possibility involves a monomer-to-dimer or dimer-to-monomer transition that facilitates the recruitment and activation of enzymatic effectors to instigate intracellular signaling. However, it is not known which domains mediate Robo dimerization, or the structural properties of the dimeric interactions. Here, we identify the extracellular Ig4 (D4) as a Robo dimerization domain. We have determined the crystal structure of the tandem Ig4-5 domains (D4-5) of human Robo2 and found that a hydrophobic surface on D4 mediates close homotypic contacts with a reciprocal D4. Analytical ultracentrifugation measurements of intact and mutated D4-5 shows that dimerization through the D4 interface is specific and has a dimerization dissociation constant of 16.9μM in solution. Direct fluorescence resonance energy transfer dimerization measurements in HEK293 cells corroborate the dimerization of transmembrane hRobo2 through D4, and a functional COS-7 cell collapse assay links D4-mediated dimerization with Robo intracellular signaling. The high level of conservation in the D4 dimerization interface throughout all Robo orthologs and paralogs implies that D4-mediated dimerization is a central hallmark in Robo activation and signaling.
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Affiliation(s)
- Galit Yom-Tov
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Reut Barak
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Omri Matalon
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Mira Barda-Saad
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Julia Guez-Haddad
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Yarden Opatowsky
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel.
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45
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Phillips-Jones MK, Lithgo R, Dinu V, Gillis RB, Harding JE, Adams GG, Harding SE. Full hydrodynamic reversibility of the weak dimerization of vancomycin and elucidation of its interaction with VanS monomers at clinical concentration. Sci Rep 2017; 7:12697. [PMID: 28983082 PMCID: PMC5629194 DOI: 10.1038/s41598-017-12620-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 08/29/2017] [Indexed: 12/16/2022] Open
Abstract
The reversibility and strength of the previously established dimerization of the important glycopeptide antibiotic vancomycin in four different aqueous solvents (including a medically-used formulation) have been studied using short-column sedimentation equilibrium in the analytical ultracentrifuge and model-independent SEDFIT-MSTAR analysis across a range of loading concentrations. The change in the weight average molar mass M w with loading concentration was consistent with a monomer-dimer equilibrium. Overlap of data sets of point weight average molar masses M w(r) versus local concentration c(r) for different loading concentrations demonstrated a completely reversible equilibrium process. At the clinical infusion concentration of 5 mg.mL-1 all glycopeptide is dimerized whilst at 19 µg.mL-1 (a clinical target trough serum concentration), vancomycin was mainly monomeric (<20% dimerized). Analysis of the variation of M w with loading concentration revealed dissociation constants in the range 25-75 μM, commensurate with a relatively weak association. The effect of two-fold vancomycin (19 µg.mL-1) appears to have no effect on the monomeric enterococcal VanS kinase involved in glycopeptide resistance regulation. Therefore, the 30% increase in sedimentation coefficient of VanS on adding vancomycin observed previously is more likely to be due to a ligand-induced conformational change of VanS to a more compact form rather than a ligand-induced dimerization.
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Affiliation(s)
- Mary K Phillips-Jones
- AMR Biophysics Group, School of Pharmacy & Biomedical Sciences, University of Central Lancashire, Preston, PR1 2HE, United Kingdom.
| | - Ryan Lithgo
- National Centre for Macromolecular Hydrodynamics, School of Biosciences, University of Nottingham, Sutton Bonington, LE12 5RD, United Kingdom
| | - Vlad Dinu
- National Centre for Macromolecular Hydrodynamics, School of Biosciences, University of Nottingham, Sutton Bonington, LE12 5RD, United Kingdom
| | - Richard B Gillis
- National Centre for Macromolecular Hydrodynamics, School of Biosciences, University of Nottingham, Sutton Bonington, LE12 5RD, United Kingdom
- School of Health Sciences, University of Nottingham, Nottingham, NG7 2HA, United Kingdom
| | - John E Harding
- Department of Architecture and the Built Environment, The University of the West of England, Bristol, BS16 1QY, United Kingdom
| | - Gary G Adams
- National Centre for Macromolecular Hydrodynamics, School of Biosciences, University of Nottingham, Sutton Bonington, LE12 5RD, United Kingdom
- School of Health Sciences, University of Nottingham, Nottingham, NG7 2HA, United Kingdom
| | - Stephen E Harding
- National Centre for Macromolecular Hydrodynamics, School of Biosciences, University of Nottingham, Sutton Bonington, LE12 5RD, United Kingdom.
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46
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A composite polynomial approach for analyzing the indefinite self-association of macromolecules studied by sedimentation equilibrium. Biophys Chem 2017. [PMID: 28628895 DOI: 10.1016/j.bpc.2017.06.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A different approach is described for analyzing sedimentation equilibrium experiments of indefinitely self-associating systems. The procedure involves application of conservation of mass criteria, along with local evaluation of the weight average molar mass, to generate a polynomial based on a composite pseudo-independent variable. The outlined method does not depend upon non-linear regression to generate a solution, but instead requires evaluation of the roots of a high-order polynomial.
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47
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Purification of bacterial membrane sensor kinases and biophysical methods for determination of their ligand and inhibitor interactions. Biochem Soc Trans 2017; 44:810-23. [PMID: 27284046 PMCID: PMC4900758 DOI: 10.1042/bst20160023] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Indexed: 01/20/2023]
Abstract
This article reviews current methods for the reliable heterologous overexpression in Escherichia coli and purification of milligram quantities of bacterial membrane sensor kinase (MSK) proteins belonging to the two-component signal transduction family of integral membrane proteins. Many of these methods were developed at Leeds alongside Professor Steve Baldwin to whom this review is dedicated. It also reviews two biophysical methods that we have adapted successfully for studies of purified MSKs and other membrane proteins–synchrotron radiation circular dichroism (SRCD) spectroscopy and analytical ultracentrifugation (AUC), both of which are non-immobilization and matrix-free methods that require no labelling strategies. Other techniques such as isothermal titration calorimetry (ITC) also share these features but generally require high concentrations of material. In common with many other biophysical techniques, both of these biophysical methods provide information regarding membrane protein conformation, oligomerization state and ligand binding, but they possess the additional advantage of providing direct assessments of whether ligand binding interactions are accompanied by conformational changes. Therefore, both methods provide a powerful means by which to identify and characterize inhibitor binding and any associated protein conformational changes, thereby contributing valuable information for future drug intervention strategies directed towards bacterial MSKs.
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48
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McHale E, Steindal CC, Kutzke H, Benneche T, Harding SE. In situ polymerisation of isoeugenol as a green consolidation method for waterlogged archaeological wood. Sci Rep 2017; 7:46481. [PMID: 28447666 PMCID: PMC5406834 DOI: 10.1038/srep46481] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 03/17/2017] [Indexed: 12/05/2022] Open
Abstract
Waterlogged archaeological wood is often in need of consolidation prior to drying to prevent shrinkage and cracking of the object. There is a need for new greener materials (than for example polyethylene glycol) and methods for consolidation to be developed. The use of wood-based components could provide good interaction between the consolidant and the remaining wood structure and would also support a shift away from fossil fuel-based materials to those with more sustainable sources. Based on this, lignin-like structures have been investigated for their ability to consolidate waterlogged archaeological wood. The in situ formation of a lignin-like material has been carried out using isoeugenol polymerised by horse radish peroxidase in aqueous solution. The formation of the oligomeric/polymeric materials within the wood following this reaction has been determined by Attenuated Total Reflectance Fourier Transform Infra Red (ATR-FTIR) spectroscopy. The oligomers remaining in solution have been characterised by ATR-FTIR and nuclear magnetic resonance (NMR) spectroscopy as well as analytical ultracentrifugation, showing that they have a weight average Mw of 0.4–0.9 kDa and a lignin-like structure rich in the β-5′ moiety. Therefore, this approach is proposed as a basis to further develop a green consolidation method for waterlogged archaeological wood.
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Affiliation(s)
- Emily McHale
- Museum of Cultural History, University of Oslo, Postbox 6762 St. Olavs plass, 0130 Oslo, Norway.,Department of Chemistry, University of Oslo, Postbox 1033 Blindern, 0315 Oslo, Norway
| | - Calin C Steindal
- Museum of Cultural History, University of Oslo, Postbox 6762 St. Olavs plass, 0130 Oslo, Norway
| | - Hartmut Kutzke
- Museum of Cultural History, University of Oslo, Postbox 6762 St. Olavs plass, 0130 Oslo, Norway
| | - Tore Benneche
- Department of Chemistry, University of Oslo, Postbox 1033 Blindern, 0315 Oslo, Norway
| | - Stephen E Harding
- National Centre for Macromolecular Hydrodynamics, University of Nottingham, Sutton Bonington, LE12 5RD, United Kingdom
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49
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Phillips-Jones MK, Channell G, Kelsall CJ, Hughes CS, Ashcroft AE, Patching SG, Dinu V, Gillis RB, Adams GG, Harding SE. Hydrodynamics of the VanA-type VanS histidine kinase: an extended solution conformation and first evidence for interactions with vancomycin. Sci Rep 2017; 7:46180. [PMID: 28397853 PMCID: PMC5387412 DOI: 10.1038/srep46180] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 03/10/2017] [Indexed: 11/08/2022] Open
Abstract
VanA-type resistance to glycopeptide antibiotics in clinical enterococci is regulated by the VanSARA two-component signal transduction system. The nature of the molecular ligand that is recognised by the VanSA sensory component has not hitherto been identified. Here we employ purified, intact and active VanSA membrane protein (henceforth referred to as VanS) in analytical ultracentrifugation experiments to study VanS oligomeric state and conformation in the absence and presence of vancomycin. A combination of sedimentation velocity and sedimentation equilibrium in the analytical ultracentrifuge (SEDFIT, SEDFIT-MSTAR and MULTISIG analysis) showed that VanS in the absence of the ligand is almost entirely monomeric (molar mass M = 45.7 kDa) in dilute aqueous solution with a trace amount of high molar mass material (M ~ 200 kDa). The sedimentation coefficient s suggests the monomer adopts an extended conformation in aqueous solution with an equivalent aspect ratio of ~(12 ± 2). In the presence of vancomycin over a 33% increase in the sedimentation coefficient is observed with the appearance of additional higher s components, demonstrating an interaction, an observation consistent with our circular dichroism measurements. The two possible causes of this increase in s - either a ligand induced dimerization and/or compaction of the monomer are considered.
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Affiliation(s)
- Mary K. Phillips-Jones
- School of Pharmacy & Biomedical Sciences, Membranes, Membrane Proteins & Peptides Research Group, University of Central Lancashire, Preston, PR1 2HE, United Kingdom
| | - Guy Channell
- National Centre for Macromolecular Hydrodynamics, School of Biosciences, University of Nottingham, Sutton Bonington, LE12 5RD United Kingdom
| | - Claire J. Kelsall
- School of Pharmacy & Biomedical Sciences, Membranes, Membrane Proteins & Peptides Research Group, University of Central Lancashire, Preston, PR1 2HE, United Kingdom
| | - Charlotte S. Hughes
- School of Pharmacy & Biomedical Sciences, Membranes, Membrane Proteins & Peptides Research Group, University of Central Lancashire, Preston, PR1 2HE, United Kingdom
- Diamond Light Source Ltd., Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0FA, United Kingdom
| | - Alison E. Ashcroft
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, United Kingdom
| | - Simon G. Patching
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, United Kingdom
| | - Vlad Dinu
- National Centre for Macromolecular Hydrodynamics, School of Biosciences, University of Nottingham, Sutton Bonington, LE12 5RD United Kingdom
| | - Richard B. Gillis
- National Centre for Macromolecular Hydrodynamics, School of Biosciences, University of Nottingham, Sutton Bonington, LE12 5RD United Kingdom
- School of Health Sciences, University of Nottingham, Nottingham, NG7 2HA United Kingdom
| | - Gary G. Adams
- National Centre for Macromolecular Hydrodynamics, School of Biosciences, University of Nottingham, Sutton Bonington, LE12 5RD United Kingdom
- School of Health Sciences, University of Nottingham, Nottingham, NG7 2HA United Kingdom
| | - Stephen E. Harding
- National Centre for Macromolecular Hydrodynamics, School of Biosciences, University of Nottingham, Sutton Bonington, LE12 5RD United Kingdom
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50
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LaMattina JW, Delrossi M, Uy KG, Keul ND, Nix DB, Neelam AR, Lanzilotta WN. Anaerobic Heme Degradation: ChuY Is an Anaerobilin Reductase That Exhibits Kinetic Cooperativity. Biochemistry 2017; 56:845-855. [PMID: 28045510 DOI: 10.1021/acs.biochem.6b01099] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Heme catabolism is an important biochemical process that many bacterial pathogens utilize to acquire iron. However, tetrapyrrole catabolites can be reactive and often require further processing for transport out of the cell or conversion to another useful cofactor. In previous work, we presented in vitro evidence of an anaerobic heme degradation pathway in Escherichia coli O157:H7. Consistent with reactions that have been reported for other radical S-adenosyl-l-methionine methyltransferases, ChuW transfers a methyl group to heme by a radical-mediated mechanism and catalyzes the β-scission of the porphyrin macrocycle. This facilitates iron release and the production of a new linear tetrapyrrole termed "anaerobilin". In this work, we describe the structure and function of ChuY, an enzyme expressed downstream from chuW within the same heme utilization operon. ChuY is structurally similar to biliverdin reductase and forms a dimeric complex in solution that reduces anaerobilin to the product we have termed anaerorubin. Steady state analysis of ChuY exhibits kinetic cooperativity that is best explained by a random addition mechanism with a kinetically preferred path for initial reduced nicotinamide adenine dinucleotide phosphate binding.
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Affiliation(s)
- Joseph W LaMattina
- Department of Biochemistry and Molecular Biology and ‡The Complex Carbohydrate Research Center, University of Georgia , Athens, Georgia 30602, United States
| | - Michael Delrossi
- Department of Biochemistry and Molecular Biology and ‡The Complex Carbohydrate Research Center, University of Georgia , Athens, Georgia 30602, United States
| | - Katherine G Uy
- Department of Biochemistry and Molecular Biology and ‡The Complex Carbohydrate Research Center, University of Georgia , Athens, Georgia 30602, United States
| | - Nicholas D Keul
- Department of Biochemistry and Molecular Biology and ‡The Complex Carbohydrate Research Center, University of Georgia , Athens, Georgia 30602, United States
| | - David B Nix
- Department of Biochemistry and Molecular Biology and ‡The Complex Carbohydrate Research Center, University of Georgia , Athens, Georgia 30602, United States
| | - Anudeep R Neelam
- Department of Biochemistry and Molecular Biology and ‡The Complex Carbohydrate Research Center, University of Georgia , Athens, Georgia 30602, United States
| | - William N Lanzilotta
- Department of Biochemistry and Molecular Biology and ‡The Complex Carbohydrate Research Center, University of Georgia , Athens, Georgia 30602, United States
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