Optimized negative-staining electron microscopy for lipoprotein studies

Background

Negative-staining (NS), a rapid, simple and conventional technique of electron microscopy (EM), has been commonly used to initially study the morphology and structure of proteins for half a century. Certain NS protocols however can cause artifacts, especially for structurally flexible or lipid-related proteins, such as lipoproteins. Lipoproteins were often observed in the form of rouleau as lipoprotein particles appeared to be stacked together by conventional NS protocols. The flexible components of lipoproteins, i.e. lipids and amphipathic apolipoproteins, resulted in the lipoprotein structure being sensitive to the NS sample preparation parameters, such as operational procedures, salt concentrations, and the staining reagents.

Scope of review

The most popular NS protocols that have been used to examine lipoprotein morphology and structure were reviewed.

Major conclusions

The comparisons show that an optimized NS (OpNS) protocol can eliminate the rouleau artifacts of lipoproteins, and that the lipoproteins are similar in size and shape as statistically measured from two EM methods, OpNS and cryo-electron microscopy (cryo-EM). OpNS is a high-throughput, high-contrast and high-resolution (near 1 nm, but rarely better than 1 nm) method which has been used to discover the mechanics of a small protein, 53 kDa cholesterol ester transfer protein (CETP), and the structure of an individual particle of a single protein by individual-particle electron tomography (IPET), i.e. a 14 Å-resolution IgG antibody three-dimensional map.

General significance

It is suggested that OpNS can be used as a general protocol to study the structure of proteins, especially highly dynamic proteins with equilibrium-fluctuating structures.     

Synthesis, structure and optic properties of 2-methylimidazolium and 2-phenylimidazolium uranyl acetates

Two new salts based on heterocyclic organic cations and uranyl triacetate anion were obtained via reaction of zinc uranyl acetate with 2-substituted imidazoles in presence of an excess of acetic acid. Uranyl triacetate anion in [2-MeImH]⁺ [UO₂(CH₃COO)₃]⁻ and [2-PhImH]⁺ [UO₂(CH₃COO)₃]⁻ H₂O has an expected bipyramidal structure with linear uranyl group and three acetate groups laying in equatorial plane. [2-MeImH]⁺ [UO₂(CH₃COO)₃]⁻ structure analysis reveals H-bonded 1D chains connected through N-H···O hydrogen bonds. 2-phenylimidazolium in [2-PhImH]⁺ [UO₂(CH₃COO)₃]⁻ H₂O demonstrate planar geometry without any rotation of its rings, which was not registered before. H-bonds and π-π interactions of phenyl groups in this system lead to complicate 2D “sandwich” layer formation. The main features of IR- and luminescence spectrum of both compounds are also discussed.     

Predicting the disruption by of a protein-ligand interaction

The uranyl cation (UO₂²⁺) can be suspected to interfere with the binding of essential metal cations to proteins, underlying some mechanisms of toxicity. A dedicated computational screen was used to identify UO₂²⁺ binding sites within a set of nonredundant protein structures. The list of potential targets was compared to data from a small molecules interaction database to pinpoint specific examples where UO₂²⁺ should be able to bind in the vicinity of an essential cation, and would be likely to affect the function of the corresponding protein. The C‐reactive protein appeared as an interesting hit since its structure involves critical calcium ions in the binding of phosphorylcholine. Biochemical experiments confirmed the predicted binding site for UO₂²⁺ and it was demonstrated by surface plasmon resonance assays that UO₂²⁺ binding to CRP prevents the calcium‐mediated binding of phosphorylcholine. Strikingly, the apparent affinity of UO₂²⁺ for native CRP was almost 100‐fold higher than that of Ca²⁺. This result exemplifies in the case of CRP the capability of our computational tool to predict effective binding sites for UO₂²⁺ in proteins and is a first evidence of calcium substitution by the uranyl cation in a native protein.     

Nephrotoxicity of simultaneous exposure to mercury and uranium in comparison to individual effects of these metals in rats

Both inorganic mercury and uranium are known nephrotoxicants in mammals. In this study, the renal toxicity of a concurrent exposure to inorganic mercury and uranium was compared with the nephrotoxic effects of the individual metals in a rat model. Eight groups of rats, 10 animals per group, were subcutaneously given a single administration of mercuric chloride (HgCl₂, 0.34 mg/kg and 0.68 mg/kg), uranyl acetate dihydrate (UAD, 2.5 mg/kg and 5 mg/kg), or combinations of both compounds at the same doses. A ninth group of rats received sc injections of 0.9% saline and was designated as the control group. Necrosis of proximal tubules, which was observed in all experimental groups, was the most relevant morphologic abnormality. Marked changes, which were remarkably greater than those induced by the individual elements, were noted in some urinary parameters in the groups concurrently exposed to HgCl₂ and UAD. It could be an indicator of a synergistic interaction between mercury and uranium. In contrast, compared with the urinary levels found after individual administration of the highest doses of mercury and uranium, significant reductions in the urinary concentrations of these elements were noted following simultaneous exposure to both metals. At these doses, the reduction in the urinary metal excretion was also accompanied by significant decreases in the renal content of mercury and uranium. Whereas the results of some parameters pointed out a possible synergistic interaction between mercury and uranium, other measures hinted that an antagonistic interaction between these elements is also present.     

Luminescent probing of the simplest chiral α‐amino acid–alanine in an enantiopure and racemic state

Luminescent spectroscopy combined with the technique of luminescent probing with rare earth ions (europium, gadolinium, terbium) and an actinide ion (uranyl) was used to differentiate enantiopure and racemic alanine, the simplest chiral proteinogenic amino acid. Using the achiral luminescent probes, small differences between pure L and DL alanine in the solid state were strongly amplified. Based on the observed electronic transitions of the probes, the position of the triplet level of the coordinated alanine was estimated. Formation of homo‐ and heterochiral complexes between enantiomers of alanine and the metal ions is discussed as a possible mechanism of chiral self‐discrimination.     

Yeast Inner-Subunit PA–NZ-1 Labeling Strategy for Accurate Subunit Identification in a Macromolecular Complex through Cryo-EM Analysis

Cryo-electron microscopy (cryo-EM) has been established as one of the central tools in the structural study of macromolecular complexes. Although intermediate- or low-resolution structural information through negative staining or cryo-EM analysis remains highly valuable, we lack general and efficient ways to achieve unambiguous subunit identification in these applications. Here, we took advantage of the extremely high affinity between a dodecapeptide “PA” tag and the NZ-1 antibody Fab fragment to develop an efficient “yeast inner-subunit PA–NZ-1 labeling” strategy that when combined with cryo-EM could precisely identify subunits in macromolecular complexes. Using this strategy combined with cryo-EM 3D reconstruction, we were able to visualize the characteristic NZ-1 Fab density attached to the PA tag inserted into a surface-exposed loop in the middle of the sequence of CCT6 subunit present in the Saccharomyces cerevisiae group II chaperonin TRiC/CCT. This procedure facilitated the unambiguous localization of CCT6 in the TRiC complex. The PA tag was designed to contain only 12 amino acids and a tight turn configuration; when inserted into a loop, it usually has a high chance of maintaining the epitope structure and low likelihood of perturbing the native structure and function of the target protein compared to other tagging systems. We also found that the association between PA and NZ-1 can sustain the cryo freezing conditions, resulting in very high occupancy of the Fab in the final cryo-EM images. Our study demonstrated the robustness of this strategy combined with cryo-EM in efficient and accurate subunit identification in challenging multi-component complexes.     

Accumulation of uranium at low concentration by the green alga Scenedesmus obliquus 34

Accumulation of UO ₂ ^{2 +} by Scenedesmus obliquus 34 was rapid and energy-independent and the biosorption of UO ₂ ^{2 +} could be described by the Freundlich adsorption isotherm below the maximum adsorption capacity (75 mg g-¹ dry wt). The optimum pH for uranium uptake was between 5.0_8.5.0.1_2.0 M NaCl enhanced uranyl, while Cu²⁺, Ni²⁺, Zn²⁺, Cd²⁺ and Mn²⁺ competed slightly with uranyl. Pretreatment had an unexpected effect on biosorption. After being killed by 0.1 M HCl, S. Obliquus 34 showed 45% of the uptake capacity of the control in which fresh cells were suspended directly in uranyl solution, while the pretreatment of cells by 0.1 M NaOH, 2.0 M NaCl, ethanol or heating decreased uptake slightly. Fresh S. obliquus 34 at 1.2_2.4 mg dry wt mL-1 was able to decrease U from 5.0 to 0.05 mg L-1 after 4_6 equilibrium stages with batch adsorption. Deposited U could be desorbed by pH 4.0 buffer. It is suggested that U was captured by effective groups or by capillary action in the cell wall in the form of [UO2OH]+. This revised version was published online in August 2006 with corrections to the Cover Date.     

Sequence/structure selective thermal and photochemical cleavage of yeast-tRNAPhe by UO

The uranyl(VI) ion, UO, cleaves yeast tRNA^Phe both thermally and photochemically. Photochemical cleavage takes place at all positions but exhibits maxima at G₁₀, G₁₈, G₃₀, A₃₈, C₄₉ and A₆₂. Furthermore, in the presence of stoichiometric concentrations of citrate, the cleavage is generally suppressed except that strong cleavage at positions G₁₀ and C₄₈–U₅₀ persists, indicating the presence of a high-affinity metal-ion binding site. It is proposed that these photocleavage sites reflect the tertiary structure of the yeast tRNA^Phe molecule in terms of D-loop/T-loop interaction and anticodon loop conformation and that uranyl-mediated photocleavage of RNA may be used as a probe of RNA tertiary structure, and in particular for identifying binding sites for divalent metal ions. Thus a high-affinity metal-ion binding site is inferred in the Rcentral pocket' formed by the D-loop, the T-loop and the acceptor stem.     

Enhanced uranyl photocleavage across the minor groove of all (A/T)4 sequences indicates a similar narrow minor groove conformation

The uranyl(VI)-mediated photocleavage of a Drew–Dickerson sequence oligonucleotide (5′-dGATCACGCGAATTCGCGT) either as the (self-complementary) duplex or cloned into the BamH1 site of pUC19 has been studied. At pH 6.5 in acetate buffer relatively enhanced photocleavage is observed at the 3′-end of the AATT sequence corresponding to maximum cleavage across the minor groove in the A/T tract. Thus maximum cleavage correlates with minimum minor groove width in the crystal structure and also with the largest electronegative potential according to computations. Using plasmid constructs with cloned inserts of the type [CGCG(A/T₄)]_n, we also analysed all possible sequence combinations of the (A/T)₄ tract and in all cases we observed maximum uranyl-mediated photocleavage across the minor groove in the (A/T)₄ tract without any significant differences between the various sequences. From these results we infer that DNA double helices of all (A/T)₄ sequences share the same narrow minor groove helix conformation.     

Selective recognition of acetate ion based on fluorescence enhancement chemosensor

Fluorescence study of the complexation between uranyl salophen (L) and some common anions in acetonitrile–water (90:10, v/v) solution showed a tendency of L toward acetate ion (AcO^?). The fluorescence enhancement of L is attributed to a 1:1 complex formation between L and acetate ion which was utilized as the basis for the selective detection of AcO^?. The association constant of the 1:1 complex formation of L–AcO^? was calculated as 6.60 × 10⁶. The linear response range of the fluorescent chemosensor covers a AcO^? concentration range of 1.6 × 10^?7 to 2.5 × 10^?5 mol/L, with a detection limit of 2.5 × 10^?8 mol/L. L showed a selective and sensitive fluorescence enhancement response toward acetate ion over I₃^?, NO₃^?, CN^?, CO₃^2?, Br^?, Cl^?, F^?, H₂PO4^? and SO₄^2?, which was attributed to the higher stability of inorganic complex between acetate and L. Copyright © 2012 John Wiley & Sons, Ltd.