scholarly journals Production of Human Norovirus Protruding Domains in E. coli for X-ray Crystallography

Author(s):  
Mila M. Leuthold ◽  
Anna D. Koromyslova ◽  
Bishal K. Singh ◽  
Grant S. Hansman
mSphere ◽  
2016 ◽  
Vol 1 (5) ◽  
Author(s):  
Sylvie Y. Doerflinger ◽  
Julia Tabatabai ◽  
Paul Schnitzler ◽  
Carlo Farah ◽  
Steffen Rameil ◽  
...  

ABSTRACT We previously identified a Nanobody (termed Nano-85) that bound to a highly conserved region on the norovirus capsid. In this study, the Nanobody was biotinylated and gold conjugated for a lateral flow immunoassay (termed Nano-IC). We showed that the Nano-IC assay was capable of detecting at least four antigenically distinct GII genotypes, including the newly emerging GII.17. In the clinical setting, the Nano-IC assay had sensitivities equivalent to other commercially available lateral flow systems. The Nano-IC method was capable of producing results in ~5 min, which makes this method useful in settings that require rapid diagnosis, such as cruise ship outbreaks and elder care facilities. The Nano-IC assay has several advantages over antibody-based IC methods: for example, Nanobodies can be readily produced in large quantities, they are generally more stable than conventional antibodies, and the Nanobody binding sites can be easily obtained by X-ray crystallography. Human noroviruses are the dominant cause of outbreaks of acute gastroenteritis. These viruses are usually detected by molecular methods, including reverse transcriptase PCR (RT-PCR) and enzyme-linked immunosorbent assay (ELISA). Human noroviruses are genetically and antigenically diverse, with two main genogroups that are further subdivided into over 40 different genotypes. During the past decade, genogroup 2 genotype 4 (GII.4) has dominated in most countries, but recently, viruses belonging to GII.17 have increased in prevalence in a number of countries. A number of commercially available ELISAs and lateral flow immunoassays were found to have lower sensitivities to the GII.17 viruses, indicating that the antibodies used in these methods may not have a high level of cross-reactivity. In this study, we developed a rapid Nanobody-based lateral flow immunoassay (Nano-immunochromatography [Nano-IC]) for the detection of human norovirus in clinical specimens. The Nano-IC assay detected virions from two GII.4 norovirus clusters, which included the current dominant strain and a novel variant strain. The Nano-IC method had a sensitivity of 80% and specificity of 86% for outbreak specimens. Norovirus virus-like particles (VLPs) representing four genotypes (GII.4, GII.10, GII.12, and GII.17) could be detected by this method, demonstrating the potential in clinical screening. However, further modifications to the Nano-IC method are needed in order to improve this sensitivity, which may be achieved by the addition of other broadly reactive Nanobodies to the system. IMPORTANCE We previously identified a Nanobody (termed Nano-85) that bound to a highly conserved region on the norovirus capsid. In this study, the Nanobody was biotinylated and gold conjugated for a lateral flow immunoassay (termed Nano-IC). We showed that the Nano-IC assay was capable of detecting at least four antigenically distinct GII genotypes, including the newly emerging GII.17. In the clinical setting, the Nano-IC assay had sensitivities equivalent to other commercially available lateral flow systems. The Nano-IC method was capable of producing results in ~5 min, which makes this method useful in settings that require rapid diagnosis, such as cruise ship outbreaks and elder care facilities. The Nano-IC assay has several advantages over antibody-based IC methods: for example, Nanobodies can be readily produced in large quantities, they are generally more stable than conventional antibodies, and the Nanobody binding sites can be easily obtained by X-ray crystallography.


Antibiotics ◽  
2019 ◽  
Vol 8 (4) ◽  
pp. 213 ◽  
Author(s):  
V.A. Karetsi ◽  
C.N. Banti ◽  
N. Kourkoumelis ◽  
C. Papachristodoulou ◽  
C.D. Stalikas ◽  
...  

The [Zn3(CitH)2] (1) (CitH4= citric acid), was dispersed in sodium lauryl sulphate (SLS) to form the micelle of SLS@[Zn3(CitH)2] (2). This material 2 was incorporated in hydrogel made by hydroxyethyl-methacrylate (HEMA), an ingredient of contact lenses, toward the formation of pHEMA@(SLS@[Zn3(CitH)2]) (3). Samples of 1 and 2 were characterized by UV-Vis, 1H-NMR, FT-IR, FT-Raman, single crystal X-ray crystallography, X-ray fluorescence analysis, atomic absorption and TG/DTA/DSC. The antibacterial activity of 1–3 as well as of SLS against Gram-positive (Staphylococcus epidermidis (St. epidermidis) and Staphylococcus aureus (St. aureus)) and Gram-negative (Pseudomonas aeruginosa (PAO1), and Escherichia coli (E. coli)) bacteria was evaluated by the means of minimum inhibitory concentration (MIC), minimum bactericidal concentration (MBC) and inhibitory zone (IZ). 2 showed 10 to 20-fold higher activity than 1 against the bacteria tested. Moreover the 3 decreases the abundance of Gram-positive microbes up to 30% (St. aureus) and up to 20% (PAO1) the Gram-negative ones. The noteworthy antimicrobial activity of the obtained composite 3 suggests an effective antimicrobial additive for infection-free contact lenses.


2015 ◽  
Vol 17 (16) ◽  
pp. 10899-10909 ◽  
Author(s):  
Robert W. Wheatley ◽  
Douglas H. Juers ◽  
Bogdan B. Lev ◽  
Reuben E. Huber ◽  
Sergei Yu. Noskov

X-ray crystallography and computational simulations reveal novel mechanisms important for Na+/K+selectivity in enzymes.


2010 ◽  
Vol 19 (12) ◽  
pp. 2430-2439 ◽  
Author(s):  
Louise J. Gourlay ◽  
Silvia Sommaruga ◽  
Marco Nardini ◽  
Paola Sperandeo ◽  
Gianni Dehò ◽  
...  

mSphere ◽  
2016 ◽  
Vol 1 (2) ◽  
Author(s):  
Bishal K. Singh ◽  
Mila M. Leuthold ◽  
Grant S. Hansman

ABSTRACT Human norovirus interacts with the polymorphic human histo-blood group antigens (HBGAs), and this interaction is thought to be important for infection. The genogroup II genotype 4 (GII.4) noroviruses are the dominant cluster, evolve every other year, and are thought to modify their binding interactions with different HBGA types. Most human noroviruses bind HBGAs, while some strains were found to have minimal or no HBGA interactions. Here, we explain some possible structural constraints for several noroviruses that were found to bind poorly to HBGAs by using X-ray crystallography. We showed that one aspartic acid was flexible or positioned away from the fucose moiety of the HBGAs and this likely hindered binding, although other fucose-interacting residues were perfectly oriented. Interestingly, a neighboring loop also appeared to influence the loop hosting the aspartic acid. These new findings might explain why some human noroviruses bound HBGAs poorly, although further studies are required.


2018 ◽  
Author(s):  
Sabine Wenzel ◽  
Tsuyoshi Imasaki ◽  
Yuichiro Takagi

AbstractThe use of Selenomethionine (SeMet) incorporated protein crystals for single or multiwavelength anomalous diffraction (SAD or MAD) to facilitate phasing has become almost synonymous with modern X-ray crystallography. The anomalous signals from SeMets can be used for phasing as well as sequence markers for subsequent model building. The production of large quantities of SeMet incorporated recombinant proteins is relatively straightforward when expressed in E. coli. In contrast, production of SeMet substituted recombinant proteins expressed in the insect cells is not as robust due to the toxicity of SeMet in eukaryotic systems. Previous protocols for SeMet-incorporation in the insect cells are laborious, and more suited for secreted proteins. In addition, these protocols have generally not addressed the SeMet toxicity issue, and typically result in low recovery of the labeled proteins. Here we report that SeMet toxicity can be circumvented by fully infecting insect cells with baculovirus. Quantitatively controlling infection levels using our Titer Estimation of Quality Control (TEQC) method allows for incorporation of substantial amounts of SeMet, resulting in an efficient and optimal production of labeled recombinant protein complexes. With the method described here, we were able to consistently reach incorporation levels of about 75% and protein yield of 60-90% compared to native protein expression.


2010 ◽  
Vol 66 (7) ◽  
pp. 806-812 ◽  
Author(s):  
Samuel Lara-González ◽  
Jens J. Birktoft ◽  
Catherine L. Lawson

The α subunit C-terminal domain (αCTD) of RNA polymerase (RNAP) is a key element in transcription activation inEscherichia coli, possessing determinants responsible for the interaction of RNAP with DNA and with transcription factors. Here, the crystal structure ofE. coliαCTD (α subunit residues 245–329) determined to 2.0 Å resolution is reported. Crystals were obtained after reductive methylation of the recombinantly expressed domain. The crystals belonged to space groupP21and possessed both pseudo-translational symmetry and pseudo-merohedral twinning. The refined coordinate model (Rfactor = 0.193,Rfree= 0.236) has improved geometry compared with prior lower resolution determinations of the αCTD structure [Jeonet al.(1995),Science,270, 1495–1497; Benoffet al.(2002),Science,297, 1562–1566]. An extensive dimerization interface formed primarily by N- and C-terminal residues is also observed. The new coordinates will facilitate the improved modeling of αCTD-containing multi-component complexes visualized at lower resolution using X-ray crystallography and electron-microscopy reconstruction.


2014 ◽  
Vol 70 (a1) ◽  
pp. C1680-C1680
Author(s):  
Haytham Wahba ◽  
Ahmed Mansour ◽  
Julien Vanasse ◽  
Laurent Cappadocia ◽  
Jurgen Sygusch ◽  
...  

Select bacterial strains survive in mercury-contaminated environments due to acquisition of a transferable genetic element known as the mer operon. The mer operon typically encodes for a series of proteins that includes two enzymes, MerA and MerB. The organomercurial lyase (MerB) cleaves carbon-mercury bonds of organomercurial compounds yielding ionic mercury Hg (II) and a reduced-carbon compound. The Hg (II) ion product remains bounds until it is shuttled directly to the mercuric ion reductase (MerA) to be reduced. Based on NMR spectroscopy and X-ray crystallography studies1, we have determined that Cys96, Asp99 and Cys159 of E. Coli MerB form a catalytic triad required for cleavage of the carbon-Hg bond and binding of the Hg (II) ion product. The three catalytic residues are conserved in 61 of 65 known variants of MerB and the four remaining variants retain both cysteine residues, but contain a serine in place of Asp99. Given its unique activity, we have examined the role of serine as a catalytic residue and the ability of MerB to cleave other organometals such as organotin (known substrates or inhibitors) and organolead compounds. Soaking MerB crystals with either dimethyltindibromide or trimethylleadchloride compound indicates that MerB crystals have the capacity to cleave both carbon-Sn and carbon-Pb bonds, and we have determined crystal structures of a MerB-Sn and a MerB-Pb complex. Furthermore, substitution of Ser for Asp99 (MerB D99S) in E. coli MerB alters the metal-binding specificity, as MerB D99S chelated an unknown metal during its purification. X-ray crystallography, ICP-MS and electron paramagnetic resonance (EPR) studies were performed to identify the unknown metal and the results of these studies will be presented. Given that mercury contaminated sites are often contaminated with other heavy metals, these studies indicate that other heavy metals may have important implications when using MerA and MerB in bioremediation of organomercurial compounds.


2016 ◽  
Author(s):  
James M. Wagstaff ◽  
Matthew Tsim ◽  
María A. Oliva ◽  
Alba García-Sanchez ◽  
Danguole Kureisaite-Ciziene ◽  
...  

AbstractBacterial cell division in many organisms involves a constricting cytokinetic ring that is orchestrated by the tubulin-like protein FtsZ. FtsZ forms dynamic filaments close to the membrane at the site of division that have recently been shown to treadmill around the division ring, guiding septal wall synthesis.Here, using X-ray crystallography ofStaphylococcus aureusSaFtsZ we reveal how an FtsZ can adopt two functionally distinct conformations, open and closed. The open form is found in SaFtsZ filaments formed in crystals and also in soluble filaments ofE. coliFtsZ as deduced by cryoEM. The closed form is found within several crystal forms of two non-polymerising SaFtsZ mutants and corresponds to many previous FtsZ structures from other organisms.We argue that FtsZ undergoes a polymerisation-associated conformational switch. We show that such a switch provides explanations for both how treadmilling may occur within a single-stranded filament, and why filament assembly is cooperative.


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