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Ekanayake RSK, Streltsov VA, Best SP, Chantler CT. Nanostructure and dynamics of N-truncated copper amyloid-β peptides from advanced X-ray absorption fine structure. IUCrJ 2024; 11:325-346. [PMID: 38602752 PMCID: PMC11067746 DOI: 10.1107/s2052252524001830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 02/26/2024] [Indexed: 04/12/2024]
Abstract
An X-ray absorption spectroscopy (XAS) electrochemical cell was used to collect high-quality XAS measurements of N-truncated Cu:amyloid-β (Cu:Aβ) samples under near-physiological conditions. N-truncated Cu:Aβ peptide complexes contribute to oxidative stress and neurotoxicity in Alzheimer's patients' brains. However, the redox properties of copper in different Aβ peptide sequences are inconsistent. Therefore, the geometry of binding sites for the copper binding in Aβ4-8/12/16 was determined using novel advanced extended X-ray absorption fine structure (EXAFS) analysis. This enables these peptides to perform redox cycles in a manner that might produce toxicity in human brains. Fluorescence XAS measurements were corrected for systematic errors including defective-pixel data, monochromator glitches and dispersion of pixel spectra. Experimental uncertainties at each data point were measured explicitly from the point-wise variance of corrected pixel measurements. The copper-binding environments of Aβ4-8/12/16 were precisely determined by fitting XAS measurements with propagated experimental uncertainties, advanced analysis and hypothesis testing, providing a mechanism to pursue many similarly complex questions in bioscience. The low-temperature XAS measurements here determine that CuII is bound to the first amino acids in the high-affinity amino-terminal copper and nickel (ATCUN) binding motif with an oxygen in a tetragonal pyramid geometry in the Aβ4-8/12/16 peptides. Room-temperature XAS electrochemical-cell measurements observe metal reduction in the Aβ4-16 peptide. Robust investigations of XAS provide structural details of CuII binding with a very different bis-His motif and a water oxygen in a quasi-tetrahedral geometry. Oxidized XAS measurements of Aβ4-12/16 imply that both CuII and CuIII are accommodated in an ATCUN-like binding site. Hypotheses for these CuI, CuII and CuIII geometries were proven and disproven using the novel data and statistical analysis including F tests. Structural parameters were determined with an accuracy some tenfold better than literature claims of past work. A new protocol was also developed using EXAFS data analysis for monitoring radiation damage. This gives a template for advanced analysis of complex biosystems.
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Affiliation(s)
| | - Victor A. Streltsov
- School of Physics, University of Melbourne, Australia
- The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Australia
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Ekanayake RSK, Streltsov VA, Best SP, Chantler CT. Using XAS to monitor radiation damage in real time and post-analysis, and investigation of systematic errors of fluorescence XAS for Cu-bound amyloid-β. J Appl Crystallogr 2024; 57:125-139. [PMID: 38322727 PMCID: PMC10840304 DOI: 10.1107/s1600576723010890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 12/20/2023] [Indexed: 02/08/2024] Open
Abstract
X-ray absorption spectroscopy (XAS) is a promising technique for determining structural information from sensitive biological samples, but high-accuracy X-ray absorption fine structure (XAFS) requires corrections of systematic errors in experimental data. Low-temperature XAS and room-temperature X-ray absorption spectro-electrochemical (XAS-EC) measurements of N-truncated amyloid-β samples were collected and corrected for systematic effects such as dead time, detector efficiencies, monochromator glitches, self-absorption, radiation damage and noise at higher wavenumber (k). A new protocol was developed using extended X-ray absorption fine structure (EXAFS) data analysis for monitoring radiation damage in real time and post-analysis. The reliability of the structural determinations and consistency were validated using the XAS measurement experimental uncertainty. The correction of detector pixel efficiencies improved the fitting χ2 by 12%. An improvement of about 2.5% of the structural fitting was obtained after dead-time corrections. Normalization allowed the elimination of 90% of the monochromator glitches. The remaining glitches were manually removed. The dispersion of spectra due to self-absorption was corrected. Standard errors of experimental measurements were propagated from pointwise variance of the spectra after systematic corrections. Calculated uncertainties were used in structural refinements for obtaining precise and reliable values of structural parameters including atomic bond lengths and thermal parameters. This has permitted hypothesis testing.
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Affiliation(s)
| | - Victor A. Streltsov
- School of Physics, University of Melbourne, Australia
- The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Australia
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3
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Mukherjee S, Dubois C, Perez K, Varghese S, Birchall IE, Leckey M, Davydova N, McLean C, Nisbet RM, Roberts BR, Li QX, Masters CL, Streltsov VA. Quantitative proteomics of tau and Aβ in detergent fractions from Alzheimer's disease brains. J Neurochem 2023; 164:529-552. [PMID: 36271678 DOI: 10.1111/jnc.15713] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 09/16/2022] [Accepted: 10/17/2022] [Indexed: 11/27/2022]
Abstract
The two hallmarks of Alzheimer's disease (AD) are amyloid-β (Aβ) plaques and neurofibrillary tangles marked by phosphorylated tau. Increasing evidence suggests that aggregating Aβ drives tau accumulation, a process that involves synaptic degeneration leading to cognitive impairment. Conversely, there is a realization that non-fibrillar (oligomeric) forms of Aβ mediate toxicity in AD. Fibrillar (filamentous) aggregates of proteins across the spectrum of the primary and secondary tauopathies were the focus of recent structural studies with a filament structure-based nosologic classification, but less emphasis was given to non-filamentous co-aggregates of insoluble proteins in the fractions derived from post-mortem human brains. Here, we revisited sarkosyl-soluble and -insoluble extracts to characterize tau and Aβ species by quantitative targeted mass spectrometric proteomics, biochemical assays, and electron microscopy. AD brain sarkosyl-insoluble pellets were greatly enriched with Aβ42 at almost equimolar levels to N-terminal truncated microtubule-binding region (MTBR) isoforms of tau with multiple site-specific post-translational modifications (PTMs). MTBR R3 and R4 tau peptides were most abundant in the sarkosyl-insoluble materials with a 10-fold higher concentration than N-terminal tau peptides. This indicates that the major proportion of the enriched tau was the aggregation-prone N-terminal and proline-rich region (PRR) of truncated mixed 4R and 3R tau with more 4R than 3R isoforms. High concentration and occupancies of site-specific phosphorylation pT181 (~22%) and pT217 (~16%) (key biomarkers of AD) along with other PTMs in the PRR and MTBR indicated a regional susceptibility of PTMs in aggregated tau. Immunogold labelling revealed that tau may exist in globular non-filamentous form (N-terminal intact tau) co-localized with Aβ in the sarkosyl-insoluble pellets along with tau filaments (N-truncated MTBR tau). Our results suggest a model that Aβ and tau interact forming globular aggregates, from which filamentous tau and Aβ emerge. These characterizations contribute towards unravelling the sequence of events which lead to end-stage AD changes.
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Affiliation(s)
- Soumya Mukherjee
- The Florey Institute, The University of Melbourne, Parkville, Victoria, Australia
| | - Celine Dubois
- The Florey Institute, The University of Melbourne, Parkville, Victoria, Australia
| | - Keyla Perez
- The Florey Institute, The University of Melbourne, Parkville, Victoria, Australia
| | - Shiji Varghese
- The Florey Institute, The University of Melbourne, Parkville, Victoria, Australia
| | - Ian E Birchall
- The Florey Institute, The University of Melbourne, Parkville, Victoria, Australia
| | - Miranda Leckey
- The Florey Institute, The University of Melbourne, Parkville, Victoria, Australia
| | - Natalia Davydova
- National Deuteration Facility, Australian Nuclear Science and Technology Organization, Lucas Heights, New South Wales, Australia
| | - Catriona McLean
- The Florey Institute, The University of Melbourne, Parkville, Victoria, Australia.,Department of Anatomical Pathology, Alfred Hospital, Prahran, Victoria, Australia
| | - Rebecca M Nisbet
- The Florey Institute, The University of Melbourne, Parkville, Victoria, Australia
| | - Blaine R Roberts
- The Florey Institute, The University of Melbourne, Parkville, Victoria, Australia
| | - Qiao-Xin Li
- The Florey Institute, The University of Melbourne, Parkville, Victoria, Australia
| | - Colin L Masters
- The Florey Institute, The University of Melbourne, Parkville, Victoria, Australia
| | - Victor A Streltsov
- The Florey Institute, The University of Melbourne, Parkville, Victoria, Australia
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Mukherjee S, Perez KA, Dubois C, Nisbet RM, Li QX, Varghese S, Jin L, Birchall I, Streltsov VA, Vella LJ, McLean C, Barham KJ, Roberts BR, Masters CL. Citrullination of Amyloid-β Peptides in Alzheimer's Disease. ACS Chem Neurosci 2021; 12:3719-3732. [PMID: 34519476 DOI: 10.1021/acschemneuro.1c00474] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Protein citrullination (deimination of arginine residue) is a well-known biomarker of inflammation. Elevated protein citrullination has been shown to colocalize with extracellular amyloid plaques in postmortem AD patient brains. Amyloid-β (Aβ) peptides which aggregate and accumulate in the plaques of Alzheimer's disease (AD) have sequential N-terminal truncations and multiple post-translational modifications (PTM) such as isomerization, pyroglutamate formation, phosphorylation, nitration, and dityrosine cross-linking. However, no conclusive biochemical evidence exists whether citrullinated Aβ is present in AD brains. In this study, using high-resolution mass spectrometry, we have identified citrullination of Aβ in sporadic and familial AD brains by characterizing the tandem mass spectra of endogenous N-truncated citrullinated Aβ peptides. Our quantitative estimations demonstrate that ∼ 35% of pyroglutamate3-Aβ pool was citrullinated in plaques in the sporadic AD temporal cortex and ∼ 22% in the detergent-insoluble frontal cortex fractions. Similarly, hypercitrullinated pyroglutamate3-Aβ (∼ 30%) was observed in both the detergent-soluble as well as insoluble Aβ pool in familial AD cases. Our results indicate that a common mechanism for citrullination of Aβ exists in both the sporadic and familial AD. We establish that citrullination of Aβ is a remarkably common PTM, closely associated with pyroglutamate3-Aβ formation and its accumulation in AD. This may have implications for Aβ toxicity, autoantigenicity of Aβ, and may be relevant for the design of diagnostic assays and therapeutic targeting.
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Affiliation(s)
- Soumya Mukherjee
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Keyla A. Perez
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Celine Dubois
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Rebecca M. Nisbet
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Melbourne, Victoria 3010, Australia
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
| | - Qiao-Xin Li
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Shiji Varghese
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Liang Jin
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Ian Birchall
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Victor A. Streltsov
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Laura J. Vella
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Melbourne, Victoria 3010, Australia
- Department of Surgery, The University of Melbourne, The Royal Melbourne Hospital, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Catriona McLean
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Melbourne, Victoria 3010, Australia
- Department of Anatomical Pathology, Alfred Hospital, Prahran, Victoria 3004, Australia
| | - Kevin J. Barham
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Blaine R. Roberts
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322, United States
- Department of Neurology, Emory University School of Medicine, Atlanta, Georgia 30322, United States
| | - Colin L. Masters
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Melbourne, Victoria 3010, Australia
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Best SP, Streltsov VA, Chantler CT, Li W, Ash PA, Hayama S, Diaz-Moreno S. Redox state and photoreduction control using X-ray spectroelectrochemical techniques - advances in design and fabrication through additive engineering. J Synchrotron Radiat 2021; 28:472-479. [PMID: 33650559 DOI: 10.1107/s1600577520016021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 12/08/2020] [Indexed: 06/12/2023]
Abstract
The design and performance of an electrochemical cell and solution flow system optimized for the collection of X-ray absorption spectra from solutions of species sensitive to photodamage is described. A combination of 3D CAD and 3D printing techniques facilitates highly optimized design with low unit cost and short production time. Precise control of the solution flow is critical to both minimizing the volume of solution needed and minimizing the photodamage that occurs during data acquisition. The details of an integrated four-syringe stepper-motor-driven pump and associated software are described. It is shown that combined electrochemical and flow control can allow repeated measurement of a defined volume of solution, 100 µl, of samples sensitive to photoreduction without significant change to the X-ray absorption near-edge structure and is demonstrated by measurements of copper(II) complexes. The flow in situ electrochemical cell allows the collection of high-quality X-ray spectral measurements both in the near-edge region and over an extended energy region as is needed for structural analysis from solution samples. This approach provides control over photodamage at a level at least comparable with that achieved using cryogenic techniques and at the same time eliminates problems associated with interference due to Bragg peaks.
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Affiliation(s)
- Stephen Peter Best
- School of Chemistry, The University of Melbourne, Parkville, Melbourne, Victoria 3010, Australia
| | - Victor A Streltsov
- Florey Department of Neuroscience and Mental Health, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | | | - Wangzhe Li
- Department of Chemistry, University of Oxford, Oxford OX1 3QR, United Kingdom
| | - Philip A Ash
- Department of Chemistry, University of Leicester, Leicester LE1 7RH, United Kingdom
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Mohr PG, Williams J, Tashiro M, Streltsov VA, McKimm-Breschkin JL. Substitutions at H134 and in the 430-loop region in influenza B neuraminidases can confer reduced susceptibility to multiple neuraminidase inhibitors. Antiviral Res 2020; 182:104895. [PMID: 32750469 DOI: 10.1016/j.antiviral.2020.104895] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 07/15/2020] [Accepted: 07/20/2020] [Indexed: 11/26/2022]
Abstract
With the introduction of the influenza specific neuraminidase inhibitors (NAIs) in 1999, there were concerns about the emergence and spread of resistant viruses in the community setting. Surveillance and testing of community isolates for their susceptibility to the NAIs was initially carried out by the Neuraminidase Inhibitor Susceptibility Network (NISN) and has subsequently been taken on by the global WHO influenza network laboratories. During the NISN surveillance, we identified two Yamagata lineage influenza B viruses with amino acid substitutions of H134Y (B/Auckland/2/2001) or W438R (B/Yokohama/12/2005) which had slightly elevated IC50 values for zanamivir and/or oseltamivir, but not sufficiently to be characterized as mild outliers at the time. As it has now been well demonstrated that mixed populations can mask the true magnitude of resistance of a mutant, we re-examined both of these isolates by plaque purification to see if the true susceptibilities were being masked due to mixed populations. Results confirmed that the B/Auckland isolate contained both wild type and H134Y mutant populations, with mutant IC50 values > 250 nM for both oseltamivir and peramivir in the enzyme inhibition assay. The B/Yokohama isolate also contained both wild type and W438R mutant populations, the latter now demonstrating IC50 values > 400 nM for zanamivir, oseltamivir and peramivir. In addition, plaque purification of the B/Yokohama isolate identified viruses with other single neuraminidase substitutions H134Y, H134R, H431R, or T436P. H134R and H431R viruses had IC50 values > 400 nM and >250 nM respectively against all three NAIs. All changes conferred much greater resistance to peramivir than to zanamivir, and less to oseltamivir, and affected the kinetics of binding and dissociation of the NAIs. Most affected affinity (Km) for the MUNANA substrate, but some had decreased while others had increased affinity. Despite resistance in the enzyme assay, no reduced susceptibility was seen in plaque reduction assays in MDCK cells for any of the mutant viruses. None of these substitutions was in the active site. Modelling suggests that these substitutions affect the 150 and 430-loop regions described for influenza A NAs, suggesting they may also be important for substrate and inhibitor binding for influenza B NAs.
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Affiliation(s)
- Peter G Mohr
- CSIRO Australian Centre for Disease Preparedness, 5 Portarlington Rd., East Geelong, 3219, Australia.
| | - Janelle Williams
- CSIRO Manufacturing, 343 Royal Parade, Parkville, 3052, Australia.
| | - Masato Tashiro
- Influenza Virus Research Center, National Institute of Infectious Diseases, Tokyo, 208-0011, Japan.
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McKimm-Breschkin JL, Barrett S, McKenzie-Kludas C, McAuley J, Streltsov VA, Withers SG. Passaging of an influenza A(H1N1)pdm09 virus in a difluoro sialic acid inhibitor selects for a novel, but unfit I106M neuraminidase mutant. Antiviral Res 2019; 169:104542. [PMID: 31233807 DOI: 10.1016/j.antiviral.2019.104542] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 06/18/2019] [Accepted: 06/19/2019] [Indexed: 01/17/2023]
Abstract
An influenza A(H1N1)pdm09 and an influenza B virus were passaged in 3-fluoro(eq)-4-guanidino difluoro sialic acid (3Feq4Gu DFSA), an inhibitor of the influenza neuraminidase (NA) to determine whether resistant variants could be selected. 3Feq4Gu DFSA is a mechanism-based inhibitor, forming a covalent link to Y406 in the NA active site. Given its similarity to the natural substrate, sialic acid, we predicted resistant variants would be difficult to select. Yields of both viruses decreased with passaging, so that after 12 passages both viruses were only growing to low titers. Drug concentrations were decreased for another three passages. There was no difference in NA sensitivity in the MUNANA fluorescence-based assay, nor in plaque assays for the passaged virus stocks. All influenza B plaques were still wild type in all assays. There were isolated small diffuse plaques in the P15 pdm09 stock, which after purification had barely detectable NA or hemagglutinin (HA) activity. These had a novel non-active site I106M substitution in the NA gene, but unexpectedly no HA changes. The I106M may impact NA function through steric effects on the movement of the 150 and 430-loops. The I106M viruses had similar replication kinetics in MDCK cells as wild type viruses, but their ability to bind to and infect CHO-K1 cells expressing high levels of cell-bound mucin was compromised. The I106M substitution was unstable, with progeny rapidly reverting to wild type by three different mechanisms. Some had reverted to I106, some had V106, both with wild type NA and HA properties. A third group retained the I106M, but had a compensating R363K substitution, which regained almost wild type NA properties. These viruses now agglutinated chicken red blood cells (CRBCs) but unlike the I/V106, they rebound after elution at 37 °C. There were no mutations in the HA, but each phenotype correlated with the NA sequence. We propose that the activity in the I106M mutant is insufficient to remove carbohydrates from the virion HA and NA, sterically limiting HA access to CRBC receptors, thus resulting in poor HA binding.
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Affiliation(s)
- Jennifer L McKimm-Breschkin
- CSIRO Manufacturing, 343 Royal Parade, Parkville, 3052, Australia; Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, 792 Elizabeth Street, Melbourne, 3000, Australia.
| | - Susan Barrett
- CSIRO Manufacturing, 343 Royal Parade, Parkville, 3052, Australia.
| | - Charley McKenzie-Kludas
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, 792 Elizabeth Street, Melbourne, 3000, Australia.
| | - Julie McAuley
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, 792 Elizabeth Street, Melbourne, 3000, Australia.
| | - Victor A Streltsov
- CSIRO Manufacturing, 343 Royal Parade, Parkville, 3052, Australia; The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, 30 Royal Parade, Parkville, 3052, Australia.
| | - Stephen G Withers
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia, V6T 1Z1, Canada.
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Streltsov VA, Schmidt PM, McKimm-Breschkin JL. Structure of an Influenza A virus N9 neuraminidase with a tetrabrachion-domain stalk. Acta Crystallogr F Struct Biol Commun 2019; 75:89-97. [PMID: 30713159 PMCID: PMC6360442 DOI: 10.1107/s2053230x18017892] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 12/18/2018] [Indexed: 12/26/2022] Open
Abstract
The influenza neuraminidase (NA) is a homotetramer with head, stalk, transmembrane and cytoplasmic regions. The structure of the NA head with a stalk has never been determined. The NA head from an N9 subtype influenza A virus, A/tern/Australia/G70C/1975 (H1N9), was expressed with an artificial stalk derived from the tetrabrachion (TB) tetramerization domain from Staphylothermus marinus. The NA was successfully crystallized both with and without the TB stalk, and the structures were determined to 2.6 and 2.3 Å resolution, respectively. Comparisons of the two NAs with the native N9 NA structure from egg-grown virus showed that the artificial TB stalk maintained the native NA head structure, supporting previous biological observations.
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Affiliation(s)
- Victor A. Streltsov
- CSIRO Manufacturing, 343 Royal Parade, Parkville, Victoria 3052, Australia
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, 30 Royal Parade, Parkville, Victoria 3052, Australia
| | - Peter M. Schmidt
- CSIRO Manufacturing, 343 Royal Parade, Parkville, Victoria 3052, Australia
- R&D, CSL Behring GmbH, Emil-von-Behring Strasse 76, 35041 Marburg, Germany
| | - Jennifer L. McKimm-Breschkin
- CSIRO Manufacturing, 343 Royal Parade, Parkville, Victoria 3052, Australia
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, 792 Elizabeth Street, Melbourne, Victoria 3000, Australia
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Streltsov VA, Ekanayake RSK, Drew SC, Chantler CT, Best SP. Structural Insight into Redox Dynamics of Copper Bound N-Truncated Amyloid-β Peptides from in Situ X-ray Absorption Spectroscopy. Inorg Chem 2018; 57:11422-11435. [PMID: 30169035 DOI: 10.1021/acs.inorgchem.8b01255] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
X-ray absorption spectroscopy of CuII amyloid-β peptide (Aβ) under in situ electrochemical control (XAS-EC) has allowed elucidation of the redox properties of CuII bound to truncated peptide forms. The Cu binding environment is significantly different for the Aβ1-16 and the N-truncated Aβ4-9, Aβ4-12, and Aβ4-16 (Aβ4-9/12/16) peptides, where the N-truncated sequence (F4R5H6) provides the high-affinity amino-terminal copper nickel (ATCUN) binding motif. Low temperature (ca. 10 K) XAS measurements show the adoption of identical CuII ATCUN-type binding sites (CuIIATCUN) by the first three amino acids (FRH) and a longer-range interaction modeled as an oxygen donor ligand, most likely water, to give a tetragonal pyramid geometry in the Aβ4-9/12/16 peptides not previously reported. Both XAS-EC and EPR measurements show that CuII:Aβ4-16 can be reduced at mildly reducing potentials, similar to that of CuII:Aβ1-16. Reduction of peptides lacking the H13H14 residues, CuII:Aβ4-9/12, require far more forcing conditions, with metallic copper the only metal-based reduction product. The observations suggest that reduction of CuIIATCUN species at mild potentials is possible, although the rate of reduction is significantly enhanced by involvement of H13H14. XAS-EC analysis reveals that, following reduction, the peptide acts as a terdentate ligand to CuI (H13, H14 together with the linking amide oxygen atom). Modeling of the EXAFS is most consistent with coordination of an additional water oxygen atom to give a quasi-tetrahedral geometry. XAS-EC analysis of oxidized CuII:Aβ4-12/16 gives structural parameters consistent with crystallographic data for a five-coordinate CuIII complex and the CuIIATCUN complex. The structural results suggest that CuII and the oxidation product are both accommodated in an ATCUN-like binding site.
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Affiliation(s)
- Victor A Streltsov
- Florey Department of Neuroscience and Mental Health , The University of Melbourne , Melbourne , Australia.,School of Physics , The University of Melbourne , Melbourne , Australia
| | | | - Simon C Drew
- Department of Medicine (Royal Melbourne Hospital) , The University of Melbourne , Melbourne , Australia
| | | | - Stephen P Best
- School of Chemistry , The University of Melbourne , Melbourne , Australia
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McKimm-Breschkin JL, Barrett S, Pilling PA, Hader S, Watts AG, Streltsov VA. Structural and Functional Analysis of Anti-Influenza Activity of 4-, 7-, 8- and 9-Deoxygenated 2,3-Difluoro- N-acetylneuraminic Acid Derivatives. J Med Chem 2018; 61:1921-1933. [PMID: 29397718 DOI: 10.1021/acs.jmedchem.7b01467] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Competitive inhibitors of the influenza neuraminidase (NA) were discovered almost 20 years ago, with zanamivir and oseltamivir licensed globally. These compounds are based on a transition state analogue of the sialic acid substrate. We recently showed that 5- N-(acetylamino)-2,3,5-trideoxy-2,3-difluoro-d-erythro-β-l-manno-2-nonulopyranosonic acid (DFSA) and its derivatives are also potent inhibitors of the influenza NA. They are mechanism based inhibitors, forming a covalent bond between the C2 of the sugar ring and Y406 in the NA active site, thus inactivating the enzyme. We have now synthesized a series of deoxygenated DFSA derivatives in order to understand the contribution of each hydroxyl in DFSA to binding and inhibition of the influenza NA. We have investigated their relative efficacy in enzyme assays in vitro, in cell culture, and by X-ray crystallography. We found loss of the 8- and 9-OH had the biggest impact on the affinity of binding and antiviral potency.
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Affiliation(s)
| | - Susan Barrett
- CSIRO Manufacturing , 343 Royal Parade , Parkville , Victoria 3052 , Australia
| | - Patricia A Pilling
- CSIRO Manufacturing , 343 Royal Parade , Parkville , Victoria 3052 , Australia
| | - Stefan Hader
- Department of Pharmacy and Pharmacology , University of Bath , Claverton Down, Bath BA2 7AY , United Kingdom
| | - Andrew G Watts
- Department of Pharmacy and Pharmacology , University of Bath , Claverton Down, Bath BA2 7AY , United Kingdom
| | - Victor A Streltsov
- The Florey Institute of Neuroscience and Mental Health , 30 Royal Parade , Parkville , Victoria 3052 , Australia
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11
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Ryan RA, Williams S, Martin AV, Dilanian RA, Darmanin C, Putkunz CT, Wood D, Streltsov VA, Jones MWM, Gaffney N, Hofmann F, Williams GJ, Boutet S, Messerschmidt M, Seibert MM, Curwood EK, Balaur E, Peele AG, Nugent KA, Quiney HM, Abbey B. Measurements of Long-range Electronic Correlations During Femtosecond Diffraction Experiments Performed on Nanocrystals of Buckminsterfullerene. J Vis Exp 2017. [PMID: 28872125 PMCID: PMC5614354 DOI: 10.3791/56296] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The precise details of the interaction of intense X-ray pulses with matter are a topic of intense interest to researchers attempting to interpret the results of femtosecond X-ray free electron laser (XFEL) experiments. An increasing number of experimental observations have shown that although nuclear motion can be negligible, given a short enough incident pulse duration, electronic motion cannot be ignored. The current and widely accepted models assume that although electrons undergo dynamics driven by interaction with the pulse, their motion could largely be considered 'random'. This would then allow the supposedly incoherent contribution from the electronic motion to be treated as a continuous background signal and thus ignored. The original aim of our experiment was to precisely measure the change in intensity of individual Bragg peaks, due to X-ray induced electronic damage in a model system, crystalline C60. Contrary to this expectation, we observed that at the highest X-ray intensities, the electron dynamics in C60 were in fact highly correlated, and over sufficiently long distances that the positions of the Bragg reflections are significantly altered. This paper describes in detail the methods and protocols used for these experiments, which were conducted both at the Linac Coherent Light Source (LCLS) and the Australian Synchrotron (AS) as well as the crystallographic approaches used to analyse the data.
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Affiliation(s)
- Rebecca A Ryan
- ARC Centre of Excellence in Advanced Molecular Imaging, School of Physics, University of Melbourne
| | - Sophie Williams
- ARC Centre of Excellence in Advanced Molecular Imaging, School of Physics, University of Melbourne
| | - Andrew V Martin
- ARC Centre of Excellence in Advanced Molecular Imaging, School of Physics, University of Melbourne
| | - Ruben A Dilanian
- ARC Centre of Excellence in Advanced Molecular Imaging, School of Physics, University of Melbourne
| | - Connie Darmanin
- Australian Research Council (ARC) Centre of Excellence in Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe Institute for Molecular Sciences, La Trobe University
| | - Corey T Putkunz
- ARC Centre of Excellence in Advanced Molecular Imaging, School of Physics, University of Melbourne
| | - David Wood
- Department of Physics, Imperial College London
| | | | - Michael W M Jones
- Science and Engineering Faculty, Queensland University of Technology
| | | | - Felix Hofmann
- Department of Engineering Science, University of Oxford
| | | | - Sebastien Boutet
- Linac Coherent Light Source, SLAC National Accelerator Laboratory
| | | | - M Marvin Seibert
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University
| | - Evan K Curwood
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University
| | - Eugeniu Balaur
- Australian Research Council (ARC) Centre of Excellence in Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe Institute for Molecular Sciences, La Trobe University
| | - Andrew G Peele
- Science and Engineering Faculty, Queensland University of Technology
| | - Keith A Nugent
- Australian Research Council (ARC) Centre of Excellence in Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe Institute for Molecular Sciences, La Trobe University
| | - Harry M Quiney
- ARC Centre of Excellence in Advanced Molecular Imaging, School of Physics, University of Melbourne;
| | - Brian Abbey
- Australian Research Council (ARC) Centre of Excellence in Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe Institute for Molecular Sciences, La Trobe University;
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12
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Davydova N, Harris NC, Roufail S, Paquet-Fifield S, Ishaq M, Streltsov VA, Williams SP, Karnezis T, Stacker SA, Achen MG. Differential Receptor Binding and Regulatory Mechanisms for the Lymphangiogenic Growth Factors Vascular Endothelial Growth Factor (VEGF)-C and -D. J Biol Chem 2016; 291:27265-27278. [PMID: 27852824 PMCID: PMC5207153 DOI: 10.1074/jbc.m116.736801] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 11/14/2016] [Indexed: 12/31/2022] Open
Abstract
VEGF-C and VEGF-D are secreted glycoproteins that induce angiogenesis and lymphangiogenesis in cancer, thereby promoting tumor growth and spread. They exhibit structural homology and activate VEGFR-2 and VEGFR-3, receptors on endothelial cells that signal for growth of blood vessels and lymphatics. VEGF-C and VEGF-D were thought to exhibit similar bioactivities, yet recent studies indicated distinct signaling mechanisms (e.g. tumor-derived VEGF-C promoted expression of the prostaglandin biosynthetic enzyme COX-2 in lymphatics, a response thought to facilitate metastasis via the lymphatic vasculature, whereas VEGF-D did not). Here we explore the basis of the distinct bioactivities of VEGF-D using a neutralizing antibody, peptide mapping, and mutagenesis to demonstrate that the N-terminal α-helix of mature VEGF-D (Phe93–Arg108) is critical for binding VEGFR-2 and VEGFR-3. Importantly, the N-terminal part of this α-helix, from Phe93 to Thr98, is required for binding VEGFR-3 but not VEGFR-2. Surprisingly, the corresponding part of the α-helix in mature VEGF-C did not influence binding to either VEGFR-2 or VEGFR-3, indicating distinct determinants of receptor binding by these growth factors. A variant of mature VEGF-D harboring a mutation in the N-terminal α-helix, D103A, exhibited enhanced potency for activating VEGFR-3, was able to promote increased COX-2 mRNA levels in lymphatic endothelial cells, and had enhanced capacity to induce lymphatic sprouting in vivo. This mutant may be useful for developing protein-based therapeutics to drive lymphangiogenesis in clinical settings, such as lymphedema. Our studies shed light on the VEGF-D structure/function relationship and provide a basis for understanding functional differences compared with VEGF-C.
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Affiliation(s)
- Natalia Davydova
- From the Tumour Angiogenesis and Microenvironment Program, Peter MacCallum Cancer Centre, Melbourne, Victoria 3000
| | - Nicole C Harris
- From the Tumour Angiogenesis and Microenvironment Program, Peter MacCallum Cancer Centre, Melbourne, Victoria 3000
| | - Sally Roufail
- From the Tumour Angiogenesis and Microenvironment Program, Peter MacCallum Cancer Centre, Melbourne, Victoria 3000
| | - Sophie Paquet-Fifield
- From the Tumour Angiogenesis and Microenvironment Program, Peter MacCallum Cancer Centre, Melbourne, Victoria 3000
| | - Musarat Ishaq
- From the Tumour Angiogenesis and Microenvironment Program, Peter MacCallum Cancer Centre, Melbourne, Victoria 3000
| | - Victor A Streltsov
- the Florey Institute of Neuroscience and Mental Health, 30 Royal Parade, Parkville, Victoria 3052, and
| | - Steven P Williams
- From the Tumour Angiogenesis and Microenvironment Program, Peter MacCallum Cancer Centre, Melbourne, Victoria 3000
| | - Tara Karnezis
- From the Tumour Angiogenesis and Microenvironment Program, Peter MacCallum Cancer Centre, Melbourne, Victoria 3000
| | - Steven A Stacker
- From the Tumour Angiogenesis and Microenvironment Program, Peter MacCallum Cancer Centre, Melbourne, Victoria 3000.,the Sir Peter MacCallum Department of Oncology, University of Melbourne, Victoria 3010, Australia
| | - Marc G Achen
- From the Tumour Angiogenesis and Microenvironment Program, Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, .,the Sir Peter MacCallum Department of Oncology, University of Melbourne, Victoria 3010, Australia
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13
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Dilanian RA, Williams SR, Martin AV, Streltsov VA, Quiney HM. Whole-pattern fitting technique in serial femtosecond nanocrystallography. IUCrJ 2016; 3:127-38. [PMID: 27006776 PMCID: PMC4775161 DOI: 10.1107/s2052252516001238] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 01/19/2016] [Indexed: 05/31/2023]
Abstract
Serial femtosecond X-ray crystallography (SFX) has created new opportunities in the field of structural analysis of protein nanocrystals. The intensity and timescale characteristics of the X-ray free-electron laser sources used in SFX experiments necessitate the analysis of a large collection of individual crystals of variable shape and quality to ultimately solve a single, average crystal structure. Ensembles of crystals are commonly encountered in powder diffraction, but serial crystallography is different because each crystal is measured individually and can be oriented via indexing and merged into a three-dimensional data set, as is done for conventional crystallography data. In this way, serial femtosecond crystallography data lie in between conventional crystallography data and powder diffraction data, sharing features of both. The extremely small sizes of nanocrystals, as well as the possible imperfections of their crystallite structure, significantly affect the diffraction pattern and raise the question of how best to extract accurate structure-factor moduli from serial crystallography data. Here it is demonstrated that whole-pattern fitting techniques established for one-dimensional powder diffraction analysis can be feasibly extended to higher dimensions for the analysis of merged SFX diffraction data. It is shown that for very small crystals, whole-pattern fitting methods are more accurate than Monte Carlo integration methods that are currently used.
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Affiliation(s)
- Ruben A. Dilanian
- ARC Centre of Excellence for Advanced Molecular Imaging, School of Physics, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Sophie R. Williams
- ARC Centre of Excellence for Advanced Molecular Imaging, School of Physics, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Andrew V. Martin
- ARC Centre of Excellence for Advanced Molecular Imaging, School of Physics, University of Melbourne, Parkville, Victoria 3010, Australia
| | | | - Harry M. Quiney
- ARC Centre of Excellence for Advanced Molecular Imaging, School of Physics, University of Melbourne, Parkville, Victoria 3010, Australia
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14
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Luan B, Friedrich T, Zhai J, Streltsov VA, Lindsey BW, Kaslin J, de Jonge MD, Zhu J, Hughes TC, Hao X. A library of AuNPs modified by RAFT polymers of different charge and chain length: high throughput synthesis and synchrotron XFM imaging using a zebrafish larvae model. RSC Adv 2016. [DOI: 10.1039/c6ra02801b] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A PAuNPs library was constructed via high throughput methods and PAuNPs were visualized in PAuNPs injected zebrafish larvae by synchrotron XFM.
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Affiliation(s)
- Bao Luan
- Chengdu Institute of Organic Chemistry
- Chinese Academy of Sciences
- Chengdu 610041
- China
- Graduate University of Chinese Academy of Sciences
| | - Timo Friedrich
- Australian Regenerative Medicine Institute
- Monash University
- Clayton
- Australia
| | | | | | | | - Jan Kaslin
- Australian Regenerative Medicine Institute
- Monash University
- Clayton
- Australia
| | | | - Jin Zhu
- Chengdu Institute of Organic Chemistry
- Chinese Academy of Sciences
- Chengdu 610041
- China
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15
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Gildenhuys J, Sammy CJ, Müller R, Streltsov VA, le Roex T, Kuter D, de Villiers KA. Alkoxide coordination of iron(III) protoporphyrin IX by antimalarial quinoline methanols: a key interaction observed in the solid-state and solution. Dalton Trans 2015; 44:16767-77. [PMID: 26335948 DOI: 10.1039/c5dt02671g] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The quinoline methanol antimalarial drug mefloquine is a structural analogue of the Cinchona alkaloids, quinine and quinidine. We have elucidated the single crystal X-ray diffraction structure of the complexes formed between racemic erythro mefloquine and ferriprotoporphyrin IX (Fe(iii)PPIX) and show that alkoxide coordination is a key interaction in the solid-state. Mass spectrometry confirms the existence of coordination complexes of quinine, quinidine and mefloquine to Fe(iii)PPIX in acetonitrile. The length of the iron(iii)-O bond in the quinine and quinidine complexes as determined by Extended X-ray Absorption Fine Structure (EXAFS) spectroscopy unequivocally confirms that coordination of the quinoline methanol compounds to Fe(iii)PPIX occurs in non-aqueous aprotic solution via their benzylic alkoxide functional group. UV-visible spectrophotometric titrations of the low-spin bis-pyridyl-Fe(iii)PPIX complex with each of the quinoline methanol compounds results in the displacement of a single pyridine molecule and subsequent formation of a six-coordinate pyridine-Fe(iii)PPIX-drug complex. We propose that formation of the drug-Fe(iii)PPIX coordination complexes is favoured in a non-aqueous environment, such as that found in lipid bodies or membranes in the malaria parasite, and that their existence may contribute to the mechanism of haemozoin inhibition or other toxicity effects that lead ultimately to parasite death. In either case, coordination is a key interaction to be considered in the design of novel antimalarial drug candidates.
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Affiliation(s)
- Johandie Gildenhuys
- Stellenbosch University, Department of Chemistry and Polymer Science, Private Bag X1, Matieland, 7602, Stellenbosch, South Africa.
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16
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Lomas KF, Bird MK, Suryadinata R, Williams C, Nuttall SD, Streltsov VA. IC‐P‐226: INSIGHT INTO THE ALZHEIMER'S DISEASE BRAIN FINE STRUCTURE AFTER LIPID REMOVAL USING THE CLARITY METHOD. Alzheimers Dement 2014. [DOI: 10.1016/j.jalz.2014.05.234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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17
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Ren B, Peat TS, Streltsov VA, Pollard M, Fernley R, Grusovin J, Seabrook S, Pilling P, Phan T, Lu L, Lovrecz GO, Graham LD, Hill RJ. Unprecedented conformational flexibility revealed in the ligand-binding domains of theBovicola ovisecdysone receptor (EcR) and ultraspiracle (USP) subunits. ACTA ACUST UNITED AC 2014; 70:1954-64. [DOI: 10.1107/s1399004714009626] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 04/28/2014] [Indexed: 11/10/2022]
Abstract
The heterodimeric ligand-binding region of theBovicola ovisecdysone receptor has been crystallized either in the presence of an ecdysteroid or a synthetic methylene lactam insecticide. Two X-ray crystallographic structures, determined at 2.7 Å resolution, show that the ligand-binding domains of both subunits of this receptor, like those of other nuclear receptors, can display significant conformational flexibility. Thermal melt experiments show that while ponasterone A stabilizes the higher order structure of the heterodimer in solution, the methylene lactam destabilizes it. The conformations of the EcR and USP subunits observed in the structure crystallized in the presence of the methylene lactam have not been seen previously in any ecdysone receptor structure and represent a new level of conformational flexibility for these important receptors. Interestingly, the new USP conformation presents an open, unoccupied ligand-binding pocket.
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18
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Streltsov VA, Chandana Epa V, James SA, Churches QI, Caine JM, Kenche VB, Barnham KJ. Structural insights into the interaction of platinum-based inhibitors with the Alzheimer's disease amyloid-β peptide. Chem Commun (Camb) 2014; 49:11364-6. [PMID: 24161993 DOI: 10.1039/c3cc47326k] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Extended X-ray absorption fine structure spectroscopy, mass spectrometry, dynamic light scattering and density functional theory are combined to derive structural models for the interaction of neurotoxicity-ablating platinum-based compounds with the amyloid-β peptide.
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Affiliation(s)
- Victor A Streltsov
- CSIRO Materials Science & Engineering and Preventative-Health Flagship, Parkville, Victoria 3052, Australia.
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19
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Nisbet RM, Nuttall SD, Robert R, Caine JM, Dolezal O, Hattarki M, Pearce LA, Davydova N, Masters CL, Varghese JN, Streltsov VA. Structural studies of the tethered N-terminus of the Alzheimer's disease amyloid-β peptide. Proteins 2013; 81:1748-58. [PMID: 23609990 DOI: 10.1002/prot.24312] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Revised: 03/28/2013] [Accepted: 04/03/2013] [Indexed: 01/13/2023]
Abstract
Alzheimer's disease is the most common form of dementia in humans and is related to the accumulation of the amyloid-β (Aβ) peptide and its interaction with metals (Cu, Fe, and Zn) in the brain. Crystallographic structural information about Aβ peptide deposits and the details of the metal-binding site is limited owing to the heterogeneous nature of aggregation states formed by the peptide. Here, we present a crystal structure of Aβ residues 1-16 fused to the N-terminus of the Escherichia coli immunity protein Im7, and stabilized with the fragment antigen binding fragment of the anti-Aβ N-terminal antibody WO2. The structure demonstrates that Aβ residues 10-16, which are not in complex with the antibody, adopt a mixture of local polyproline II-helix and turn type conformations, enhancing cooperativity between the two adjacent histidine residues His13 and His14. Furthermore, this relatively rigid region of Aβ (residues, 10-16) appear as an almost independent unit available for trapping metal ions and provides a rationale for the His13-metal-His14 coordination in the Aβ1-16 fragment implicated in Aβ metal binding. This novel structure, therefore, has the potential to provide a foundation for investigating the effect of metal ion binding to Aβ and illustrates a potential target for the development of future Alzheimer's disease therapeutics aimed at stabilizing the N-terminal monomer structure, in particular residues His13 and His14, and preventing Aβ metal-binding-induced neurotoxicity.
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Affiliation(s)
- Rebecca M Nisbet
- Materials Science and Engineering & Preventative Health Flagship, CSIRO, Parkville, Victoria, 3052, Australia
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20
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Peters C, Fernandez-Perez EJ, Burgos CF, Espinoza MP, Castillo C, Urrutia JC, Streltsov VA, Opazo C, Aguayo LG. Inhibition of amyloid beta-induced synaptotoxicity by a pentapeptide derived from the glycine zipper region of the neurotoxic peptide. Neurobiol Aging 2013; 34:2805-14. [PMID: 23855983 DOI: 10.1016/j.neurobiolaging.2013.06.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2013] [Revised: 05/29/2013] [Accepted: 06/04/2013] [Indexed: 10/26/2022]
Abstract
A major characteristic of Alzheimer's disease is the presence of amyloid beta (Aβ) oligomers and aggregates in the brain. Aβ oligomers interact with the neuronal membrane inducing perforations, causing an influx of calcium ions and increasing the release of synaptic vesicles that leads to a delayed synaptic failure by vesicle depletion. Here, we identified a neuroprotective pentapeptide anti-Aβ compound having the sequence of the glycine zipper region of the C-terminal of Aβ (G33LMVG37). Docking and Förster resonance energy transfer experiments showed that G33LMVG37 interacts with Aβ at the C-terminal region, which is important for Aβ association and insertion into the lipid membrane. Furthermore, this pentapeptide interfered with Aβ aggregation, association, and perforation of the plasma membrane. The synaptotoxicity induced by Aβ after acute and chronic applications were abolished by G33LMVG37. These results provide a novel rationale for drug development against Alzheimer's disease.
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Affiliation(s)
- Christian Peters
- Laboratory of Neurophysiology, Department of Physiology, University of Concepción, Concepción, Chile; Laboratory of Neurobiometals, Department of Physiology, University of Concepción, Concepción, Chile
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21
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Ryan TM, Caine J, Mertens HDT, Kirby N, Nigro J, Breheney K, Waddington LJ, Streltsov VA, Curtain C, Masters CL, Roberts BR. Ammonium hydroxide treatment of Aβ produces an aggregate free solution suitable for biophysical and cell culture characterization. PeerJ 2013; 1:e73. [PMID: 23678397 PMCID: PMC3646356 DOI: 10.7717/peerj.73] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2012] [Accepted: 04/22/2013] [Indexed: 11/20/2022] Open
Abstract
Alzheimer's disease is the leading cause of dementia in the elderly. Pathologically it is characterized by the presence of amyloid plaques and neuronal loss within the brain tissue of affected individuals. It is now widely hypothesised that fibrillar structures represent an inert structure. Biophysical and toxicity assays attempting to characterize the formation of both the fibrillar and the intermediate oligomeric structures of Aβ typically involves preparing samples which are largely monomeric; the most common method by which this is achieved is to use the fluorinated organic solvent 1,1,1,3,3,3-hexafluoro-2-propanol (HFIP). Recent evidence has suggested that this method is not 100% effective in producing an aggregate free solution. We show, using dynamic light scattering, size exclusion chromatography and small angle X-ray scattering that this is indeed the case, with HFIP pretreated Aβ peptide solutions displaying an increased proportion of oligomeric and aggregated material and an increased propensity to aggregate. Furthermore we show that an alternative technique, involving treatment with strong alkali results in a much more homogenous solution that is largely monomeric. These techniques for solubilising and controlling the oligomeric state of Aβ are valuable starting points for future biophysical and toxicity assays.
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Affiliation(s)
- Timothy M Ryan
- The Florey Institute of Neuroscience and Mental Health, University of Melbourne , Parkville, Victoria , Australia
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22
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Kim JH, Resende R, Wennekes T, Chen HM, Bance N, Buchini S, Watts AG, Pilling P, Streltsov VA, Petric M, Liggins R, Barrett S, McKimm-Breschkin JL, Niikura M, Withers SG. Mechanism-based covalent neuraminidase inhibitors with broad-spectrum influenza antiviral activity. Science 2013; 340:71-5. [PMID: 23429702 DOI: 10.1126/science.1232552] [Citation(s) in RCA: 151] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Influenza antiviral agents play important roles in modulating disease severity and in controlling pandemics while vaccines are prepared, but the development of resistance to agents like the commonly used neuraminidase inhibitor oseltamivir may limit their future utility. We report here on a new class of specific, mechanism-based anti-influenza drugs that function through the formation of a stabilized covalent intermediate in the influenza neuraminidase enzyme, and we confirm this mode of action with structural and mechanistic studies. These compounds function in cell-based assays and in animal models, with efficacies comparable to that of the neuraminidase inhibitor zanamivir and with broad-spectrum activity against drug-resistant strains in vitro. The similarity of their structure to that of the natural substrate and their mechanism-based design make these attractive antiviral candidates.
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Affiliation(s)
- Jin-Hyo Kim
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
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23
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Dilanian RA, Streltsov VA, Quiney HM, Nugent KA. Continuous X-ray diffractive field in protein nanocrystallography. Acta Crystallogr A 2012; 69:108-18. [PMID: 23250067 DOI: 10.1107/s0108767312042535] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2012] [Accepted: 10/11/2012] [Indexed: 11/11/2022] Open
Abstract
The recent development of X-ray free-electron laser sources has created new opportunities for the structural analysis of protein nanocrystals. The extremely small sizes of the crystals, as well as imperfections of the crystal structure, result in an interference phenomenon in the diffraction pattern. With decreasing crystallite size the structural imperfections play a role in the formation of the diffraction pattern that is comparable in importance to the size effects and should be taken into account during the data analysis and structure reconstruction processes. There now exists a need to develop new methods of protein structure determination that do not depend on the availability of good-quality crystals and that can treat proteins under conditions close to the active form. This paper demonstrates an approach that is specifically tailored to nanocrystalline samples and offers a unique crystallographic solution.
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Affiliation(s)
- Ruben A Dilanian
- ARC Centre of Excellence for Coherent X-ray Science, School of Physics, The University of Melbourne, Victoria, Australia.
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24
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Davydova N, Roufail S, Streltsov VA, Stacker SA, Achen MG. The VD1 neutralizing antibody to vascular endothelial growth factor-D: binding epitope and relationship to receptor binding. J Mol Biol 2011; 407:581-93. [PMID: 21315726 DOI: 10.1016/j.jmb.2011.02.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2010] [Revised: 02/02/2011] [Accepted: 02/03/2011] [Indexed: 11/28/2022]
Abstract
Vascular endothelial growth factor-D (VEGF-D) is a secreted protein that promotes tumor growth and metastatic spread in animal models of cancer. Expression of VEGF-D in prevalent human cancers was reported to correlate with lymph node metastasis and patient outcome-hence, this protein is a potential target for novel anticancer therapeutics designed to restrict tumor growth and spread. Here, we define the binding site in VEGF-D of a neutralizing antibody, designated VD1, which blocks the interaction of VEGF-D with its cell surface receptors vascular endothelial growth factor receptor (VEGFR)-2 and VEGFR-3 and is being used for the development of therapeutic antibodies. We show by peptide-based mapping and site-directed mutagenesis that the VD1 binding site includes the five residues (147)NEESL(151) and that immunization with a synthetic peptide containing this motif generates antibodies that neutralize VEGF-D. The tertiary structure of VEGF-D indicates that the (147)NEESL(151) epitope is located in the L2 loop of the growth factor, which is important for receptor binding. Mutation of any of these five residues influences receptor binding; for example, mutations to E148, which abolished binding to VD1, impaired the interaction with VEGFR-2 but enhanced binding to VEGFR-3. This structure/function study indicates that the VD1 binding epitope is part of the receptor binding site of VEGF-D, identifies a region of VEGF-D critical for binding of receptors and explains why VD1 does not bind other members of the VEGF family of growth factors.
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Affiliation(s)
- Natalia Davydova
- Ludwig Institute for Cancer Research, Post Office Box 2008, Royal Melbourne Hospital, Victoria 3050, Australia
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25
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Nuttall SD, Wilkins ML, Streltsov VA, Pontes-Braz L, Dolezal O, Tran H, Liu CQ. Isolation, kinetic analysis, and structural characterization of an antibody targeting the Bacillus anthracis major spore surface protein BclA. Proteins 2011; 79:1306-17. [PMID: 21322055 DOI: 10.1002/prot.22971] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2010] [Accepted: 11/10/2010] [Indexed: 11/11/2022]
Abstract
One method of laboratory- or field-based testing for anthrax is detection of Bacillus anthracis spores by high-affinity, high specificity binding reagents. From a pool of monoclonal antibodies, we selected one such candidate (A4D11) with high affinity for tBclA, a truncated version of the B. anthracis exosporium protein BclA. Kinetic analysis utilising both standard and kinetic titration on a Biacore biosensor indicated antibody affinities in the 300 pM range for recombinant tBclA, and the A4D11 antibody was also re-formatted into scFv configuration with no loss of affinity. However, assays against B. anthracis and related Bacilli species showed limited binding of intact spores as well as significant cross-reactivity between species. These results were rationalized by determination of the three-dimensional crystallographic structure of the scFv-tBclA complex. A4D11 binds the side of the tBclA trimer, contacting a face of the antigen normally packed against adjacent trimers within the exosporium structure; this inter-spore interface is highly conserved between Bacilli species. Our results indicate the difficulty of generating a high-affinity antibody to differentiate between the highly conserved spore structures of closely related species, but suggest the possibility of future structure-based antibody design for this difficult target.
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Affiliation(s)
- Stewart D Nuttall
- CSIRO Division of Materials Science and Engineering, Parkville, Victoria, 3052, Australia.
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Oakley AJ, Barrett S, Peat TS, Newman J, Streltsov VA, Waddington L, Saito T, Tashiro M, McKimm-Breschkin JL. Structural and functional basis of resistance to neuraminidase inhibitors of influenza B viruses. J Med Chem 2010; 53:6421-31. [PMID: 20695427 PMCID: PMC2932999 DOI: 10.1021/jm100621s] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
We have identified a virus, B/Perth/211/2001, with a spontaneous mutation, D197E in the neuraminidase (NA), which confers cross-resistance to all NA inhibitors. We analyzed enzyme properties of the D197 and E197 NAs and compared these to a D197N NA, known to arise after oseltamivir treatment. Zanamivir and peramivir bound slowly to the wild type NA, but binding of oseltamivir was more rapid. The D197E/N mutations resulted in faster binding of all three inhibitors. Analysis of the crystal structures of D197 and E197 NAs with and without inhibitors showed that the D197E mutation compromised the interaction of neighboring R150 with the N-acetyl group, common to the substrate sialic acid and all NA inhibitors. Although rotation of the E275 in the NA active site occurs upon binding peramivir in both the D197 and E197 NAs, this does not occur upon binding oseltamivir in the E197 NA. Lack of the E275 rotation would also account for the loss of slow binding and the partial resistance of influenza B wild type NAs to oseltamivir.
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Affiliation(s)
- Aaron J Oakley
- CSIRO Materials Science and Engineering, Parkville, 343 Royal Parade, Parkville, Victoria, 3052, Australia
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27
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Luang S, Ketudat Cairns JR, Streltsov VA, Hrmova M. Crystallisation of wild-type and variant forms of a recombinant plant enzyme β-D-glucan glucohydrolase from barley (Hordeum vulgare L.) and preliminary X-ray analysis. Int J Mol Sci 2010; 11:2759-69. [PMID: 20717535 PMCID: PMC2920565 DOI: 10.3390/ijms11072759] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2010] [Revised: 07/16/2010] [Accepted: 07/16/2010] [Indexed: 11/17/2022] Open
Abstract
Wild-type and variant crystals of a recombinant enzyme beta-d-glucan glucohydrolase from barley (Hordeum vulgare L.) were obtained by macroseeding and cross-seeding with microcrystals obtained from native plant protein. Crystals grew to dimensions of up to 500 x 250 x 375 mum at 277 K in the hanging-drops by vapour-diffusion. Further, the conditions are described that yielded the wild-type crystals with dimensions of 80 x 40 x 60 mum by self-nucleation vapour-diffusion in sitting-drops at 281 K. The wild-type and recombinant crystals prepared by seeding techniques achived full size within 5-14 days, while the wild-type crystals grown by self-nucleation appeared after 30 days and reached their maximum size after another two months. Both the wild-type and recombinant variant crystals, the latter altered in the key catalytic and substrate-binding residues Glu220, Trp434 and Arg158/Glu161 belonged to the P4(3)2(1)2 tetragonal space group, i.e., the space group of the native microcrystals was retained in the newly grown recombinant crystals. The crystals diffracted beyond 1.57-1.95 A and the cell dimensions were between a = b = 99.2-100.8 A and c = 183.2-183.6 A. With one molecule in the asymmetric unit, the calculated Matthews coefficients were between 3.4-3.5 A(3).Da(-1) and the solvent contents varied between 63.4% and 64.5%. The macroseeding and cross-seeding techniques are advantageous, where a limited amount of variant proteins precludes screening of crystallisation conditions, or where variant proteins could not be crystallized.
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Affiliation(s)
- Sukanya Luang
- School of Biochemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand; E-Mail: (S.L.); (J.R.K.C.)
| | - James R. Ketudat Cairns
- School of Biochemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand; E-Mail: (S.L.); (J.R.K.C.)
| | - Victor A. Streltsov
- Molecular and Health Technologies, CSIRO-Commonwealth Scientific Research Organization, Victoria 3052, Australia; E-Mail:
| | - Maria Hrmova
- Australian Centre for Plant Functional Genomics, University of Adelaide, Waite Campus, Glen Osmond, South Australia 5064, Australia
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Robert R, Streltsov VA, Newman J, Pearce LA, Wark KL, Dolezal O. Germline humanization of a murine Abeta antibody and crystal structure of the humanized recombinant Fab fragment. Protein Sci 2010; 19:299-308. [PMID: 20014445 DOI: 10.1002/pro.312] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Alzheimer's disease is the most common form of dementia, affecting 26 million people worldwide. The Abeta peptide (39-43 amino acids) derived from the proteolytic cleavage of the amyloid precursor protein is one of the main constituents of amyloid plaques associated with disease pathogenesis and therefore a validated target for therapy. Recently, we characterized antibody fragments (Fab and scFvs) derived from the murine monoclonal antibody WO-2, which bind the immunodominant epitope ((3)EFRH(6)) in the Abeta peptide at the N-terminus. In vitro, these fragments are able to inhibit fibril formation, disaggregate preformed amyloid fibrils, and protect neuroblastoma cells against oligomer-mediated toxicity. In this study, we describe the humanization of WO-2 using complementary determining region loop grafting onto the human germline gene and the determination of the three-dimensional structure by X-ray crystallography. This humanized version retains a high affinity for the Abeta peptide and therefore is a potential candidate for passive immunotherapy of Alzheimer's disease.
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Affiliation(s)
- Remy Robert
- CSIRO Molecular and Health Technologies, 343 Royal Parade, Parkville, Victoria 3052, Australia.
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29
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Abstract
Oxidative modification due to reactive oxygen species generated by Cu2+ bound to the amyloid-β peptide may be one of the sources of neurodegeneration observed in Alzheimer’s disease. Understanding the structure and function of the copper binding site can assist in the design of effective therapeutics. This paper highlights some of the most significant recent developments in computational modelling studies of the structure of the binding site and reaction mechanisms of reactive oxygen species generation.
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30
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Abstract
X-Ray absorption near-edge spectroscopy (XANES) has been used to probe the substrate mediated reduction of Cu(2+) in Abeta-Cu(2+) complexes by ascorbate and the neurotoxin 6-hydroxydopamine (6-OHDA), however dopamine and, in particular, cholesterol are incapable of reducing soluble monomeric Abeta-Cu(2+) complexes.
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Affiliation(s)
- Victor A Streltsov
- CSIRO Molecular and Health Technologies and P-Health Flagship, Parkville, VIC 3052, Australia.
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Simmons DP, Streltsov VA, Dolezal O, Hudson PJ, Coley AM, Foley M, Proll DF, Nuttall SD. Shark IgNAR antibody mimotopes target a murine immunoglobulin through extended CDR3 loop structures. Proteins 2008; 71:119-30. [PMID: 17932913 DOI: 10.1002/prot.21663] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Mimotopes mimic the three-dimensional topology of an antigen epitope, and are frequently recognized by antibodies with affinities comparable to those obtained for the original antibody-antigen interaction. Peptides and anti-idiotypic antibodies are two classes of protein mimotopes that mimic the topology (but not necessarily the sequence) of the parental antigen. In this study, we combine these two classes by selecting mimotopes based on single domain IgNAR antibodies, which display exceptionally long CDR3 loop regions (analogous to a constrained peptide library) presented in the context of an immunoglobulin framework with adjacent and supporting CDR1 loops. By screening an in vitro phage-display library of IgNAR variable domains (V(NAR)s) against the target antigen monoclonal antibody MAb5G8, we obtained four potential mimotopes. MAb5G8 targets a linear tripeptide epitope (AYP) in the flexible signal sequence of the Plasmodium falciparum Apical Membrane Antigen-1 (AMA1), and this or similar motifs were detected in the CDR loops of all four V(NAR)s. The V(NAR)s, 1-A-2, -7, -11, and -14, were demonstrated to bind specifically to this paratope by competition studies with an artificial peptide and all showed enhanced affinities (3-46 nM) compared to the parental antigen (175 nM). Crystallographic studies of recombinant proteins 1-A-7 and 1-A-11 showed that the SYP motifs on these V(NAR)s presented at the tip of the exposed CDR3 loops, ideally positioned within bulge-like structures to make contact with the MAb5G8 antibody. These loops, in particular in 1-A-11, were further stabilized by inter- and intra- loop disulphide bridges, hydrogen bonds, electrostatic interactions, and aromatic residue packing. We rationalize the higher affinity of the V(NAR)s compared to the parental antigen by suggesting that adjacent CDR1 and framework residues contribute to binding affinity, through interactions with other CDR regions on the antibody, though of course definitive support of this hypothesis will rely on co-crystallographic studies. Alternatively, the selection of mimotopes from a large (<4 x 10(8)) constrained library may have allowed selection of variants with even more favorable epitope topologies than present in the original antigenic structure, illustrating the power of in vivo selection of mimotopes from phage-displayed molecular libraries.
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Affiliation(s)
- David P Simmons
- CSIRO Division of Molecular and Health Technologies, Parkville, Victoria 3052, Australia
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32
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Henderson KA, Streltsov VA, Coley AM, Dolezal O, Hudson PJ, Batchelor AH, Gupta A, Bai T, Murphy VJ, Anders RF, Foley M, Nuttall SD. Structure of an IgNAR-AMA1 complex: targeting a conserved hydrophobic cleft broadens malarial strain recognition. Structure 2008; 15:1452-66. [PMID: 17997971 DOI: 10.1016/j.str.2007.09.011] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2007] [Revised: 08/13/2007] [Accepted: 09/10/2007] [Indexed: 11/18/2022]
Abstract
Apical membrane antigen 1 (AMA1) is essential for invasion of erythrocytes and hepatocytes by Plasmodium parasites and is a leading malarial vaccine candidate. Although conventional antibodies to AMA1 can prevent such invasion, extensive polymorphisms within surface-exposed loops may limit the ability of these AMA1-induced antibodies to protect against all parasite genotypes. Using an AMA1-specific IgNAR single-variable-domain antibody, we performed targeted mutagenesis and selection against AMA1 from three P. falciparum strains. We present cocrystal structures of two antibody-AMA1 complexes which reveal extended IgNAR CDR3 loops penetrating deep into a hydrophobic cleft on the antigen surface and contacting residues conserved across parasite species. Comparison of a series of affinity-enhancing mutations allowed dissection of their relative contributions to binding kinetics and correlation with inhibition of erythrocyte invasion. These findings provide insights into mechanisms of single-domain antibody binding, and may enable design of reagents targeting otherwise cryptic epitopes in pathogen antigens.
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Affiliation(s)
- Kylie A Henderson
- CSIRO Molecular and Health Technologies, 343 Royal Parade, Parkville 3052, Australia
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33
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Liu CQ, Nuttall SD, Tran H, Wilkins M, Streltsov VA, Alderton MR. Construction, crystal structure and application of a recombinant protein that lacks the collagen-like region of BclA fromBacillus anthracis spores. Biotechnol Bioeng 2008; 99:774-82. [PMID: 17879302 DOI: 10.1002/bit.21637] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Spores of Bacillus anthracis, the causative agent of anthrax, are enclosed by an exosporium, which consists of a basal layer surrounded by a nap of hair-like filaments. The major structural component of the filaments is called BclA, which comprises a central collagen-like region (CLR) and a globular C-terminal domain. Here, the entire CLR coding sequence of BclA was removed, and the resulting protein (tBclA) produced in Escherichia coli. The crystallographic structure of tBclA was determined to 1.35 A resolution, and consists of an all-beta structure with a TNF-like jelly fold topology (12 beta-strands which form 2 beta-sheets of five strands each) consistent with previous studies on wild-type BclA. These globular domains are tightly packed into trimeric structures (surface shape complementarity; S (c) = 0.83), demonstrating that formation of the core structure of BclA is independent of the anchoring collagen-like region. A polyclonal antibody raised against tBclA recognized B. anthracis spores directly, and showed little cross-reactivity (<10%) with the spores of the closely related species Bacillus cereus and Bacillus thuringiensis, when compared to two other polyclonal antibodies raised against B. anthracis spore extracts and inactivated spores. The tBclA protein was used to purify a pool of specific antibodies from bovine colostrum whey samples from cows inoculated with the Sterne strain anthrax vaccine, which also showed reactivity with B. anthracis spores. Together, these results demonstrate that tBclA provides a safer and more effective way to the production and purification of antibodies with high binding affinity for B. anthracis spores. Biotechnol. Bioeng. 2008;99: 774-782. (c) 2007 Wiley Periodicals, Inc.
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Affiliation(s)
- Chun-Qiang Liu
- DSTO Human Protection & Performance Division, 506 Lorimer Street, Fishermans Bend, Melbourne, Victoria 3207, Australia.
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34
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Ward CW, Lawrence MC, Streltsov VA, Adams TE, McKern NM. The insulin and EGF receptor structures: new insights into ligand-induced receptor activation. Trends Biochem Sci 2007; 32:129-37. [PMID: 17280834 DOI: 10.1016/j.tibs.2007.01.001] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2006] [Revised: 12/15/2006] [Accepted: 01/26/2007] [Indexed: 10/23/2022]
Abstract
The insulin receptor (IR) and epidermal growth factor receptor (EGFR; also known as ErbB) families exhibit similarities in the composition of their ectodomains. The past five years have seen structures determined for all members of the EGFR family including some complexes with ligand or monoclonal antibody fragments. These structures have led to a clearer understanding of their mechanism of activation and inhibition. By contrast, obtaining equivalent understanding of the IR family has lagged behind. However, within the past year, structures of partial and complete ectodomains of the IR have been published that show that the extracellular region of the receptor adopts an unexpected 'inverted V' conformation relative to the cell membrane. This is very different from the folded-over (tethered) conformation of the unactivated EGFR and provides insight into the potential mechanism of activation of the IR.
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Affiliation(s)
- Colin W Ward
- Australian Commonwealth Scientific and Research Organization Molecular and Health Technologies, 343 Royal Parade, Parkville, Victoria 3052, Australia.
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35
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Kopsidas G, Roberts AS, Coia G, Streltsov VA, Nuttall SD. In vitro improvement of a shark IgNAR antibody by Qbeta replicase mutation and ribosome display mimics in vivo affinity maturation. Immunol Lett 2006; 107:163-8. [PMID: 17069896 DOI: 10.1016/j.imlet.2006.09.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2006] [Revised: 09/23/2006] [Accepted: 09/23/2006] [Indexed: 01/28/2023]
Abstract
We have employed a novel mutagenesis system, which utilizes an error-prone RNA dependent RNA polymerase from Qbeta bacteriophage, to create a diverse library of single domain antibody fragments based on the shark IgNAR antibody isotype. Coupling of these randomly mutated mRNA templates directly to the translating ribosome allowed in vitro selection of affinity matured variants showing enhanced binding to target, the apical membrane antigen 1 (AMA1) from Plasmodium falciparum. One mutation mapping to the IgNAR CDR1 loop was not readily additive to other changes, a result explained by structural analysis of aromatic interactions linking the CDR1, CDR3, and Ig framework regions. This combination appeared also to be counter-selected in experiments, suggesting that in vitro affinity maturation is additionally capable of discriminating against incorrectly produced protein variants. Interestingly, a further mutation was directed to a position in the IgNAR heavy loop 4 which is also specifically targeted during the in vivo shark response to antigen, providing a correlation between natural processes and laboratory-based affinity maturation systems.
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Affiliation(s)
- George Kopsidas
- EvoGenix Limited, 343 Royal Parade, Parkville, Vic. 3052, Australia
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36
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McKern NM, Lawrence MC, Streltsov VA, Lou MZ, Adams TE, Lovrecz GO, Elleman TC, Richards KM, Bentley JD, Pilling PA, Hoyne PA, Cartledge KA, Pham TM, Lewis JL, Sankovich SE, Stoichevska V, Da Silva E, Robinson CP, Frenkel MJ, Sparrow LG, Fernley RT, Epa VC, Ward CW. Structure of the insulin receptor ectodomain reveals a folded-over conformation. Nature 2006; 443:218-21. [PMID: 16957736 DOI: 10.1038/nature05106] [Citation(s) in RCA: 238] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2006] [Accepted: 07/21/2006] [Indexed: 11/08/2022]
Abstract
The insulin receptor is a phylogenetically ancient tyrosine kinase receptor found in organisms as primitive as cnidarians and insects. In higher organisms it is essential for glucose homeostasis, whereas the closely related insulin-like growth factor receptor (IGF-1R) is involved in normal growth and development. The insulin receptor is expressed in two isoforms, IR-A and IR-B; the former also functions as a high-affinity receptor for IGF-II and is implicated, along with IGF-1R, in malignant transformation. Here we present the crystal structure at 3.8 A resolution of the IR-A ectodomain dimer, complexed with four Fabs from the monoclonal antibodies 83-7 and 83-14 (ref. 4), grown in the presence of a fragment of an insulin mimetic peptide. The structure reveals the domain arrangement in the disulphide-linked ectodomain dimer, showing that the insulin receptor adopts a folded-over conformation that places the ligand-binding regions in juxtaposition. This arrangement is very different from previous models. It shows that the two L1 domains are on opposite sides of the dimer, too far apart to allow insulin to bind both L1 domains simultaneously as previously proposed. Instead, the structure implicates the carboxy-terminal surface of the first fibronectin type III domain as the second binding site involved in high-affinity binding.
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Affiliation(s)
- Neil M McKern
- CSIRO Molecular & Health Technologies, 343 Royal Parade, Parkville, Victoria 3052, Australia
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37
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Simmons DP, Abregu FA, Krishnan UV, Proll DF, Streltsov VA, Doughty L, Hattarki MK, Nuttall SD. Dimerisation strategies for shark IgNAR single domain antibody fragments. J Immunol Methods 2006; 315:171-84. [PMID: 16962608 DOI: 10.1016/j.jim.2006.07.019] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2006] [Revised: 07/07/2006] [Accepted: 07/25/2006] [Indexed: 11/23/2022]
Abstract
Immunoglobulin new antigen receptors (IgNARs) are unique single domain antibodies found in the serum of sharks. The individual variable (VNAR) domains bind antigen independently and are candidates for the smallest antibody-based immune recognition units (approximately 13 kDa). Here, we first isolated and sequenced the cDNA of a mature IgNAR antibody from the spotted wobbegong shark (Orectolobus maculatus) and confirmed the independent nature of the VNAR domains by dynamic light scattering. Second, we asked which of the reported antibody fragment dimerisation strategies could be applied to VNAR domains to produce small bivalent proteins with high functional affinity (avidity). In contrast to single chain Fv (scFv) fragments, separate IgNARs could not be linked into a tandem single chain format, with the resulting proteins exhibited only monovalent binding due solely to interaction of the N-terminal domain with antigen. Similarly, incorporation of C-terminal helix-turn-helix (dhlx) motifs, while resulting in efficiently dimerised protein, resulted in only a modest enhancement of affinity, probably due to an insufficiently long hinge region linking the antibody to the dhlx motif. Finally, generation of mutants containing half-cystine residues at the VNAR C-terminus produced dimeric recombinant proteins exhibiting high functional affinity for the target antigens, but at the cost of 50-fold decreased protein expression levels. This study demonstrates the potential for construction of bivalent or bispecific IgNAR-based binding reagents of relatively small size (approximately 26 kDa), equivalent to a monovalent antibody Fv fragment, for formulation into future diagnostic and therapeutic formats.
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Hrmova M, Streltsov VA, Smith BJ, Vasella A, Varghese JN, Fincher GB. Structural Rationale for Low-Nanomolar Binding of Transition State Mimics to a Family GH3 β-d-Glucan Glucohydrolase from Barley†,‡. Biochemistry 2005; 44:16529-39. [PMID: 16342944 DOI: 10.1021/bi0514818] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The interactions of a transition state mimic anilinomethyl glucoimidazole (AmGlcIm), with a K(i) constant of 0.6 x 10(-)(9) M and a Gibbs free energy value of -53.5 kJ/mol, with a family GH3 beta-d-glucan glucohydrolase from barley have been analyzed crystallographically and by ab initio quantum mechanical modeling. AmGlcIm binds 3 times more tightly to the beta-d-glucan glucohydrolase than a previously investigated phenyl glucoimidazole. In the enzyme-AmGlcIm complex, an additional residue, Tyr253, and a water molecule positioned between subsites -1 and +1 are recruited for binding. Analyses of the two binary complexes reveal the following. (i) An intricate network exists in which hydrogen bonds between the enzyme's catalytic pocket residues Lys206, His207, Tyr253, Asp285, and Glu491 and the glucoimidazoles are shorter by 0.15-0.53 A, compared with distances of hydrogen bonds in the Michaelis complex. (ii) The "glucose" moiety of the glucoimidazoles adopts a (4)E conformation that is vital for the low-nanomolar binding. (iii) The N1 atoms of the glucoimidazoles are positioned nearly optimally for in-line protonation by the Oepsilon1 atom of the catalytic acid/base Glu491. (iv) The enzyme derives binding energies from both glycone and aglycone components of the glucoimidazoles. (iv) The prevalent libration motion of the two domains of the enzyme could play a significant role during induced fit closure in the active site. (v) Modeling based on the structural data predicts that protons could be positioned on the N1 atoms of the glucoimidazoles, and the catalytic acid/base Glu491 could carry an overall negative charge. (vi) The enzyme-AmGlcIm complex reveals the likely structure of an early transition state during hydrolysis. Finally, the high-resolution structures enabled us to define minimal structures of oligosaccharides attached to Asn221, Asn498, and Asn600 N-glycosylation sites.
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Affiliation(s)
- Maria Hrmova
- School of Agriculture and Wine and Australian Centre for Plant Functional Genomics, University of Adelaide, Waite Campus, Glen Osmond, SA 5064, Australia.
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Abstract
The new antigen receptor (IgNAR) antibodies from sharks are disulphide bonded dimers of two protein chains, each containing one variable and five constant domains. Three types of IgNAR variable domains have been discovered, with Type 3 appearing early in shark development and being overtaken by the antigen-driven affinity-matured Type 1 and 2 response. Here, we have determined the first structure of a naturally occurring Type 2 IgNAR variable domain, and identified the disulphide bond that links and stabilizes the CDR1 and CDR3 loops. This disulphide bridge locks the CDR3 loop in an "upright" conformation in contrast to other shark antibody structures, where a more lateral configuration is observed. Further, we sought to model the Type 3 isotype based on the crystallographic structure reported here. This modeling indicates (1) that internal Type 3-specific residues combine to pack into a compact immunoglobulin core that supports the CDR loop regions, and (2) that despite apparent low-sequence variability, there is sufficient plasticity in the CDR3 loop to form a conformationally diverse antigen-binding surface.
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Affiliation(s)
- Victor A Streltsov
- CSIRO Molecular and Health Technologies, 343 Royal Parade, Parkville, Victoria 3052, Australia.
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40
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Streltsov VA, Nakashima PNH, Sobolev AN, Ozerov RP. Crystal structure study of a β′-copper vanadium bronze, Cu
x
V2O5 (x = 0.63), by X-ray and convergent beam electron diffraction. Acta Crystallogr B Struct Sci 2005; 61:17-24. [PMID: 15659853 DOI: 10.1107/s0108768104027739] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2004] [Accepted: 10/29/2004] [Indexed: 11/10/2022]
Abstract
The single-crystal structure of a β′-copper vanadium bronze, Cu0.63V2O5, has been studied at room temperature and 9.6 K, and compared with that of the β-sodium vanadium bronze, Na0.33V2O5, structure. No convincing evidence to oppose an assignment of centrosymmetric C2/m symmetry to the structure was identified using the X-ray data. A subsequent convergent beam electron diffraction (CBED) experiment was performed and confirmed the C2/m space group. The oxygen–vanadium atom framework of Cu0.63V2O5 is close to that of Na0.33V2O5. However, in the copper compound the Cu atoms are located in two positions: Cu1 in the 4(i) position with x = 0.541, y = 0 and z = 0.345, and Cu2 in the 8(j) position with x = 0.529, y = 0.038 and z = 0.357. The crystal structure changes little with temperature. Disorder of the Cu ion over two sites is seen at 9.6 K. This suggests that distribution of the Cu atoms over two sites is of a more static than dynamic nature.
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Streltsov VA, Varghese JN, Carmichael JA, Irving RA, Hudson PJ, Nuttall SD. Structural evidence for evolution of shark Ig new antigen receptor variable domain antibodies from a cell-surface receptor. Proc Natl Acad Sci U S A 2004; 101:12444-9. [PMID: 15304650 PMCID: PMC515081 DOI: 10.1073/pnas.0403509101] [Citation(s) in RCA: 101] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2004] [Indexed: 11/18/2022] Open
Abstract
The Ig new antigen receptors (IgNARs) are single-domain antibodies found in the serum of sharks. Here, we report 2.2- and 2.8-A structures of the type 2 IgNAR variable domains 12Y-1 and 12Y-2. Structural features include, first, an Ig superfamily topology transitional between cell adhesion molecules, antibodies, and T cell receptors; and, second, a vestigial complementarity-determining region 2 at the "bottom" of the molecule, apparently discontinuous from the antigen-binding paratope and similar to that observed in cell adhesion molecules. Thus, we suggest that IgNARs originated as cell-surface adhesion molecules coopted to the immune repertoire and represent an evolutionary lineage independent of variable heavy chain/variable light chain type antibodies. Additionally, both 12Y-1 and 12Y-2 form unique crystallographic dimers, predominantly mediated by main-chain framework interactions, which represent a possible model for primordial cell-based interactions. Unusually, the 12Y-2 complementarity-determining region 3 also adopts an extended beta-hairpin structure, suggesting a distinct selective advantage in accessing cryptic antigenic epitopes.
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Affiliation(s)
- V A Streltsov
- Division of Health Sciences and Nutrition, Commonwealth Scientific and Industrial Research Organization, and Cooperative Research Centre for Diagnostics, 343 Royal Parade, Parkville 3052, Australia
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Lawrence MC, Borg NA, Streltsov VA, Pilling PA, Epa VC, Varghese JN, McKimm-Breschkin JL, Colman PM. Structure of the haemagglutinin-neuraminidase from human parainfluenza virus type III. J Mol Biol 2004; 335:1343-57. [PMID: 14729348 DOI: 10.1016/j.jmb.2003.11.032] [Citation(s) in RCA: 175] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The three-dimensional structure of the haemagglutinin-neuraminidase (HN) from a human parainfluenza virus is described at ca 2.0 A resolution, both in native form and in complex with three substrate analogues. In support of earlier work on the structure of the homologous protein from the avian pathogen Newcastle disease virus (NDV), we observe a dimer of beta-propellers and find no evidence for spatially separated sites performing the receptor-binding and neuraminidase functions of the protein. As with the NDV HN, the active site of the HN of parainfluenza viruses is structurally flexible, suggesting that it may be able to switch between a receptor-binding state and a catalytic state. However, in contrast to the NDV structures, we observe no ligand-induced structural changes that extend beyond the active site and modify the dimer interface.
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Affiliation(s)
- Michael C Lawrence
- CSIRO Health Sciences and Nutrition, 343 Royal Parade, Parkville, Vic 3052, Australia.
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Streltsov VA, Prokop Z, Damborský J, Nagata Y, Oakley A, Wilce MCJ. Haloalkane Dehalogenase LinB from Sphingomonas paucimobilis UT26: X-ray Crystallographic Studies of Dehalogenation of Brominated Substrates. Biochemistry 2003. [DOI: 10.1021/bi0330141] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Streltsov VA, Nakashima PNH, Johnson AWS. A combination method of charge density measurement in hard materials using accurate, quantitative electron and X-ray diffraction: the alpha-Al2O3 case. Microsc Microanal 2003; 9:419-427. [PMID: 19771698 DOI: 10.1017/s1431927603030356] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Current X-ray diffraction techniques intended for "ideally imperfect" specimens provide structure factors only on a relative scale and ever-present multiple scattering in strong low-angle Bragg reflections is difficult to correct. Multiple scattering is implicit in the quantitative convergent beam electron diffraction (QCBED) method, which provides absolutely scaled structure factors. Conventional single crystal X-ray diffraction has proved adequate in softer materials where crystal perfection is limited. In hard materials, the highly perfect nature of the crystals is often a difficulty, due to the inadequacy of the conventional corrections for multiple scattering (extinction corrections). The present study on alpha-Al2O3 exploits the complementarity of synchrotron X-ray measurements for weak and medium intensities and QCBED measurement of the strong low-angle reflections. Two-dimensional near zone axis QCBED data from different crystals at various accelerating voltages, thicknesses, and orientations have been matched using Bloch-wave and multislice methods. The reproducibility of QCBED data is better than 0.5%. The low-angle strong QCBED structure factors were combined with middle and high-angle extinction-free data from synchrotron X-ray diffraction measurements. Static deformation charge density maps for alpha-Al2O3 have been calculated from a multipole expansion model refined using the combined QCBED and X-ray data.
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Affiliation(s)
- Victor A Streltsov
- Crystallography Centre, Department of Physics, University of Western Australia, Nedlands 6907, Australia.
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Streltsov VA, Prokop Z, Damborský J, Nagata Y, Oakley A, Wilce MCJ. Haloalkane dehalogenase LinB from Sphingomonas paucimobilis UT26: X-ray crystallographic studies of dehalogenation of brominated substrates. Biochemistry 2003; 42:10104-12. [PMID: 12939138 DOI: 10.1021/bi027280a] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The haloalkane dehalogenases are detoxifying enzymes that convert a broad range of halogenated substrates to the corresponding alcohols. Complete crystal structures of haloalkane dehalogenase from Sphingomonas paucimobilis UT26 (LinB), and complexes of LinB with 1,2-propanediol/1-bromopropane-2-ol and 2-bromo-2-propene-1-ol, products of debromination of 1,2-dibromopropane and 2,3-dibromopropene, respectively, were determined from 1.8 A resolution X-ray diffraction data. Published structures of native LinB and its complex with 1,3-propanediol [Marek et al. (2000) Biochemistry 39, 14082-14086] were reexamined. The full and partial debromination of 1,2-dibromopropane and 2,3-dibromopropene, respectively, conformed to the observed general trend that the sp(3)-hybridized carbon is the predominant electrophilic site for the S(N)2 bimolecular nucleophilic substitution in dehalogenation reaction. The 2-bromo-2-propene-1-ol product of 2,3-dibromopropene dehalogenation in crystal was positively identified by the gas chromatography-mass spectroscopy (GC-MS) technique. The 1,2-propanediol and 1-bromopropane-2-ol products of 1,2-dibromopropane dehalogenation in crystal were also supported by the GC-MS identification. Comparison of native LinB with its complexes showed high flexibility of residues 136-157, in particular, Asp146 and Glu147, from the cap domain helices alpha(4) and alpha(5)('). Those residues were shifted mainly in direction toward the ligand molecules in the complex structures. It seems the cap domain moves nearer to the core squeezing substrate into the active center closer to the catalytic triad. This also leads to slight contraction of the whole complex structures. The flexibility detected by crystallographic analysis is in remarkable agreement with flexibility observed by molecular dynamic simulations.
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Affiliation(s)
- Victor A Streltsov
- Crystallography Centre, School of Biomedical and Chemical Sciences, University of Western Australia, 35 Stirling Highway, Crawley 6009, Western Australia, Australia.
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Norberg ST, Sobolev AN, Streltsov VA. Cation movement and phase transitions in KTP isostructures; X-ray study of sodium-doped KTP at 10.5 K. Acta Crystallogr B 2003; 59:353-60. [PMID: 12761405 DOI: 10.1107/s0108768103008450] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2003] [Accepted: 04/14/2003] [Indexed: 11/10/2022]
Abstract
An accurate structure model of sodium-doped potassium titanyl phosphate, (Na(0.114)K(0.886))K(TiO)(2)(PO(4))(2), has been determined at 10.5 K by single-crystal X-ray diffraction. In addition to the low-temperature data, X-ray intensities have been collected at room temperature. When the temperature was decreased from room temperature to 10.5 K, both potassium cations moved 0.033 (2) A along the c-axis, i.e. in the polar direction within the rigid Ti-O-P network. This alkaline metal ion displacement can be related to the Abrahams-Jamieson-Kurtz T(C) criteria for oxygen framework ferroelectrics. Potassium titanyl phosphate (KTP) is a well known material for second harmonic generation (SHG), and the influence of sodium dopant on the TiO(6) octahedral geometry and SHG is discussed. The material studied crystallizes in the space group Pna2(1) with Z = 4, a = 12.7919 (5), b = 6.3798 (4), c = 10.5880 (7) A, V = 864.08 (9) A(3), T = 10.5 (3) K and R = 0.023.
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Affiliation(s)
- Stefan T Norberg
- Materials and Surface Chemistry, Chalmers University of Technology, SE-412 96 Göteborg, Sweden.
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Ozerov RP, Streltsov VA, Sobolev AN, Figgis BN, Volkov VL. Electron density in the sodium vanadium oxide bronze β-Na
x
V2O5 at 9 K. Acta Crystallogr B Struct Sci 2001; 57:244-50. [PMID: 11373381 DOI: 10.1107/s0108768101002038] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2000] [Accepted: 01/30/2001] [Indexed: 11/10/2022]
Abstract
The crystal structure and electron density in sodium vanadium oxide bronze, β-Na
x
V2O5 [x = 0.282 (3)], have been studied by accurate Mo Kα X-ray diffraction measurements at 9.6 (3) K. No noticeable difference in the crystal structures at room temperature and 9.6 K has been observed. No superstructure reflections, previously found by Kanai, Kagoshima & Nagasawa [(1982), J. Phys. Soc. Jpn, 51, 697–698], have been detected at low temperature. Analysis of the deformation electron density has revealed the presence of the quasi-two-dimensional sheets of the —V—O—V—O— bonds in the structure. The electron density in the different chemical bonds within each of the three crystallographically independent VO6 polyhedra noticeably varies, although there is no clear evidence that the three crystallographically independent V atoms have different valence states.
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Affiliation(s)
- R P Ozerov
- Mendeleev University of Chemical Technology of Russia, 125047 Moscow, Russia.
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O'Toole NJ, Streltsov VA. Synchrotron X-ray analysis of the electron density in CoF2 and ZnF2. Acta Crystallogr B 2001; 57:128-35. [PMID: 11262426 DOI: 10.1107/s0108768100017353] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2000] [Accepted: 10/13/2000] [Indexed: 11/10/2022]
Abstract
Accurate structure factors for small crystals of the rutile-type structures CoF(2), cobalt difluoride, and ZnF(2), zinc difluoride, have been measured with focused lambda = 0.8400 (2) A synchrotron X-radiation at room temperature. Phenomenological structural trends across the full series of rutile-type transition metal difluorides are analysed, showing the importance of the metal atom in the degree of distortion of the metal-F(6) octahedra in these structures. Multipole models reveal strong asphericities in the electron density surrounding the transition metals, which are consistent with expectations from crystal field theory and the structural trends in these compounds. Transition metal 3d-orbital populations were computed from the multipole refinement parameters, showing significant repopulation of orbitals compared with the free atom, particularly for CoF(2).
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Affiliation(s)
- N J O'Toole
- Crystallography Centre, The University of Western Australia, Nedlands 6907, Austalia
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Streltsov VA, Nordborg J, Albertsson J. Synchrotron X-ray analysis of RbTiOAsO4. Acta Crystallogr B 2000; 56 ( Pt 5):785-92. [PMID: 11006554 DOI: 10.1107/s0108768100006285] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/1999] [Accepted: 04/25/2000] [Indexed: 11/10/2022]
Abstract
Structure factors for rubidium oxotitanium arsenate, RbTiOAsO(4), were measured at 293 K with focused synchrotron X-radiation [lambda = 0.7500 (9) A] using a fast avalanche photodiode counter. The accurate synchrotron single-crystal data are of sufficient quality and resolution to detect the splitting positions of the Rb cations at room temperature. Strong accumulation of the Deltarho difference charge density near the Rb atoms at a distance of approximately 0.5 A in the -c direction can be attributed to the partial occupancy of additional sites related by pseudosymmetry. This type of static and/or dynamic disorder is temperature-dependent and seems to be universal for the KTiOPO(4) family of compounds. The best modelling of the experimental data was obtained with the Rb atom in split positions described within the harmonic approximation and the multipole functions for the other atoms. The Deltarho density features in the Ti-O and As-O covalent bonds can be related to the linear and non-linear susceptibility using bond-polarization theory. The charge-density maps reflect the anisotropy of non-linear susceptibility, which is larger for directions where locally antisymmetric components of Deltarho are strong.
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Affiliation(s)
- V A Streltsov
- Crystallography Centre, University of Western Australia, Nedlands 6907, Australia.
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Streltsov VA, Ishizawa N, Kishimoto S. Synchrotron X-ray imaging of the electron density in RFeO3 (R = Y, Ho) using an APD detector. J Synchrotron Radiat 1998; 5:1309-16. [PMID: 16687839 DOI: 10.1107/s0909049598001447] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/1997] [Accepted: 01/21/1998] [Indexed: 05/09/2023]
Abstract
Structure factors for small hydrothermally grown yttrium and holmium orthoferrites, RFeO(3) (R = Y, Ho), were measured with focused synchrotron radiation at wavelengths of 0.70 and 0.84 A using both scintillation and high-speed avalanche photodiode (APD) detectors. Resulting APD Deltarho images showed striking correlations between aspherical electron densities around Fe and rare-earth metals. Approximate high symmetry in the Deltarho images indicates that cations deform the electron density far more strongly than the O atoms. The Ho-Fe magnetic interactions appear to affect the electron density distribution of the Fe atoms and the magnetic phase transitions. Space group Pnma, orthorhombic, YFeO3 (APD): Mr = 192.76, a = 5.5931 (3), b = 7.6102 (4), c = 5.2806 (3) A, V = 224.77 (2) A(3), Z = 4, Dx = 5.695 Mg m(-3), mu(0.84) = 15.56 mm(-1), F(000) = 356, T = 293 K, R = 0.045, wR = 0.073, S = 4.83 (9) for 1282 unique reflections; HoFeO3 (APD): Mr = 268.78, a = 5.5922 (3), b = 7.6157 (5), c = 5.2798 (3) A, V = 224.86 (2) A(3), Z = 4, D(x) = 7.939 Mg m(-3), mu(0.84) = 61.98 mm(-1), F(000) = 356, T = 293 K, R = 0.036, wR = 0.037, S = 3.07 (6) for 1284 unique reflections.
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Affiliation(s)
- V A Streltsov
- Crystallography Centre, The University of Western Australia, Nedlands 6907, Australia
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