Separative techniques for metalloproteomics require balance between separation and perturbation

Recent Advances in Metalloproteomics

Interactions between proteins and metal ions and their complexes are important in many areas of the life sciences, including physiology, medicine, and toxicology. Despite the involvement of essential elements in all major processes necessary for sustaining life, metalloproteomes remain ill-defined. This is not only owing to the complexity of metalloproteomes, but also to the non-covalent character of the complexes that most essential metals form, which complicates analysis. Similar issues may also be encountered for some toxic metals. The review discusses recently developed approaches and current challenges for the study of interactions involving entire (sub-)proteomes with such labile metal ions. In the second part, transition metals from the fourth and fifth periods are examined, most of which are xenobiotic and also tend to form more stable and/or inert complexes. A large research area in this respect concerns metallodrug-protein interactions. Particular attention is paid to separation approaches, as these need to be adapted to the reactivity of the metal under consideration.

Fasten the analysis of metal-binding proteins with GE-ICP-MS via increasing the electrolyte concentration of the running buffer

The coupled system of column gel electrophoresis and inductively coupled plasma mass spectrometry (GE-ICP-MS) is a highly effective technique for detecting metal-binding proteins. However, it takes a long time for this method to test a single sample, which greatly limits its application. In this study, GE-ICP-MS system was optimized by adjusting the analytical conditions, including the concentration and pH of running buffer and the proportion of polyacrylamide gel. The results of the experiment showed that the migration speed of proteins in GE was enhanced by increasing the electrolyte concentration in the running buffer solution. Additionally, the ICP-MS response, which was dramatically decreased because of the change in running buffer solution, can be stabilized by adjusting pH of running buffer. Meanwhile, the optimization of polyacrylamide gel ratio allows GE-ICP-MS to maintain high resolution for proteins of similar molecular weight with increased detection speed. After increasing the concentration of running buffer by 10 times, four iodine labeled proteins were successfully separated at baseline by the GE-ICP-MS system at pH 8.0 in 40 min using a resolving gel (8%, 7 cm) and a stacking gel (4%, 1 cm), which was three times faster than the original one. Finally, the optimized method was proved by detecting a silver-binding protein in rat plasma samples. The above method provided an effective and rapid detection for metal-binding proteins in organism.

Determination of the affinity of biomimetic peptides for uranium through the simultaneous coupling of HILIC to ESI-MS and ICP-MS

Several proteins have been identified in the past decades as targets of uranyl (UO₂²⁺) in vivo. However, the molecular interactions responsible for this affinity are still poorly known which requires the identification of the UO₂²⁺ coordination sites in these proteins. Biomimetic peptides are efficient chemical tools to characterize these sites. In this work, we developed a dedicated analytical method to determine the affinity of biomimetic, synthetic, multi-phosphorylated peptides for UO₂²⁺ and evaluate the effect of several structural parameters of these peptides on this affinity at physiological pH. The analytical strategy was based on the implementation of the simultaneous coupling of hydrophilic interaction chromatography (HILIC) with electrospray ionization mass spectrometry (ESI-MS) and inductively coupled plasma mass spectrometry (ICP-MS). An essential step had been devoted to the definition of the best separation conditions of UO₂²⁺ complexes formed with di-phosphorylated peptide isomers and also with peptides of different structure and degrees of phosphorylation. We performed the first separations of several sets of UO₂²⁺ complexes by HILIC ever reported in the literature. A dedicated method had then been developed for identifying the separated peptide complexes online by ESI-MS and simultaneously quantifying them by ICP-MS, based on uranium quantification using external calibration. Thus, the affinity of the peptides for UO₂²⁺ was determined and made it possible to demonstrate that (i) the increasing number of phosphorylated residues (pSer) promotes the affinity of the peptides for UO₂²⁺, (ii) the position of the pSer in the peptide backbone has very low impact on this affinity (iii) and finally the cyclic structure of the peptide favors the UO₂²⁺ complexation in comparison with the linear structure. These results are in agreement with those previously obtained by spectroscopic techniques, which allowed to validate the method. Through this approach, we obtained essential information to better understand the mechanisms of toxicity of UO₂²⁺ at the molecular level and to further develop selective decorporating agents by chelation.

Simultaneous Quantification and Speciation of Trace Metals in Paired Serum and CSF Samples by Size Exclusion Chromatography-Inductively Coupled Plasma-Dynamic Reaction Cell-Mass Spectrometry (SEC-DRC-ICP-MS)

BACKGROUND

Transition metals play a crucial role in brain metabolism: since they exist in different oxidation states they are involved in ROS generation, but they are also co-factors of enzymes in cellular energy metabolism or oxidative defense.

METHODS

Paired serum and cerebrospinal fluid (CSF) samples were analyzed for iron, zinc, copper and manganese as well as for speciation using SEC-ICP-DRC-MS. Brain extracts from Mn-exposed rats were additionally analyzed with SEC-ICP-DRC-MS.

RESULTS

The concentration patterns of transition metal size fractions were correlated between serum and CSF: Total element concentrations were significantly lower in CSF. Fe-ferritin was decreased in CSF whereas a LMW Fe fraction was relatively increased. The 400-600 kDa Zn fraction and the Cu-ceruloplasmin fraction were decreased in CSF, by contrast the 40-80 kDa fraction, containing Cu- and Zn-albumin, relatively increased. For manganese, the α-2-macroglobulin fraction showed significantly lower concentration in CSF, whereas the citrate Mn fraction was enriched. Results from the rat brain extracts supported the findings from human paired serum and CSF samples.

CONCLUSIONS

Transition metals are strictly controlled at neural barriers (NB) of neurologic healthy patients. High molecular weight species are down-concentrated along NB, however, the Mn-citrate fraction seems to be less controlled, which may be problematic under environmental load.

Development of a metalloproteomic approach to analyse the response of Arabidopsis cells to uranium stress

Elaboration of a top-down proteomic, biochemical and ionoproteomic toolbox to gain insights into the impact of uranyl (U) on Arabidopsis cells.

Regional iron distribution and soluble ferroprotein profiles in the healthy human brain

Iron is essential for brain development and health where its redox properties are used for a number of neurological processes. However, iron is also a major driver of oxidative stress if not properly controlled. Brain iron distribution is highly compartmentalised and regulated by a number of proteins and small biomolecules. Here, we examine heterogeneity in regional iron levels in 10 anatomical structures from seven post-mortem human brains with no apparent neuropathology. Putamen contained the highest levels, and most case-to-case variability, of iron compared with the other regions examined. Partitioning of iron between cytosolic and membrane-bound iron was generally consistent in each region, with a slightly higher proportion (55 %) in the 'insoluble' phase. We expand on this using the Allen Human Brain Atlas to examine patterns between iron levels and transcriptomic expression of iron regulatory proteins and using quantitative size exclusion chromatography-inductively coupled plasma-mass spectrometry to assess regional differences in the molecular masses to which cytosolic iron predominantly binds. Approximately 60 % was associated with ferritin, equating to approximately 25 % of total tissue iron essentially in storage. This study is the first of its kind in human brain tissue, providing a valuable resource and new insight for iron biologists and neuroscientists, alike.

Analysis of silver-associated proteins in pathogen via combination of native SDS-PAGE, fluorescent staining, and inductively coupled plasma mass spectrometry

Characterization of silver-associated proteins is important to elucidate underlined mechanisms of silver-containing materials against microbes. Gel electrophoresis based methods are the most popular and basic strategy for the analysis of biomolecules, i.e., proteins and nucleic acids. It solely provides molecular weights of analytes. Extending the method from molecular weight to elemental composition is highly desired when investigating metal-containing molecules. Herein, a gel electrophoresis based method combining native sodium dodecyl sulfate-polyacrylamide gel electrophoresis (native SDS-PAGE), fluorescent staining, and inductively coupled plasma mass spectrometry (ICP-MS) strategy was developed for separation and detection of silver-associated proteins. Two home-made silver-labeled proteins, carbonic anhydrase and ovalbumin, were used for validation of the strategy performance. Silver-associated proteins in Pseudomonas aeruginosa and Staphylococcus aureus treated with silver nanoparticles were further characterized by this method. Some well-known and new proteins were identified to associate to silver in both P. aeruginosa and S. aureus, demonstrating the feasibility of the developed strategy. In conclusion, the current study provides a convenient method for readily identification of silver-associated proteins in biological samples.

3D printed gel electrophoresis device coupling with ICP-MS for online separation and detection of metalloproteins

We successfully developed a strategy to combine a customized gel electrophoresis device with ICP-MS for online separation and detection of metalloproteins. The self-designed horizontal column gel electrophoresis device was rapidly and easily fabricated in the laboratory via 3D printing with a low cost. The feasibility of 3D printing to fabricate this device was investigated by offline separation of commercial protein standards. And a better separation efficiency was found when using gel tubes printed with higher printing precision. As a proof-of-concept, the performance of the whole system is demonstrated by online separation and detection of both iodinated protein standards and proteins in rat blood plasma samples. Benefits from 3D printing, customized modification or further optimization can be readily achieved for a better protein separation and detection efficiency.

Cadmium specific proteomic responses of a highly resistantPseudomonas aeruginosasan ai

Pseudomonas aeruginosa san ai is a promising candidate for bioremediation of cadmium pollution, as it resists a high concentration of up to 7.2 mM of cadmium. Leaving biomass of P. aeruginosa san ai exposed to cadmium has a large biosorption potential, implying its capacity to extract heavy metal from contaminated medium. In the present study, we investigated tolerance and accumulation of cadmium on protein level by shotgun proteomics approach based on liquid chromatography and tandem mass spectrometry coupled with bioinformatics to identify proteins. Size exclusion chromatography was used for protein prefractionation to preserve native forms of metalloproteins and protein complexes. Using this approach a total of 60 proteins were observed as up-regulated in cadmium-amended culture. Almost a third of the total numbers of up-regulated were metalloproteins. Particularly interesting are denitrification proteins which are over expressed but not active, suggesting their protective role in conditions of heavy metal exposure. P. aeruginosa san ai developed a complex mechanism to adapt to cadmium, based on: extracellular biosorption, bioaccumulation, the formation of biofilm, controlled siderophore production, enhanced respiration and modified protein profile. An increased abundance of proteins involved in: cell energy metabolism, including denitrification proteins; amino acid metabolism; cell motility and posttranslational modifications, primarily based on thiol-disulfide exchange, were observed. Enhanced oxygen consumption of biomass in cadmium-amended culture versus control was found. Our results signify that P. aeruginosa san ai is naturally well equipped to overcome and survive high doses of cadmium and, as such, has a great potential for application in bioremediation of cadmium polluted sites.

When exposed to cadmium a highly resistant strain P. aeruginosa san ai responds by an increased metalloprotein expression (particularly denitrification proteins), an enhanced respiration, and a pronounced thiol-disulfide protein modifications.

Relative association of Rubisco with manganese and magnesium as a regulatory mechanism in plants

Rubisco, the enzyme that constitutes as much as half of the protein in a leaf, initiates either the photorespiratory pathway that supplies reductant for the assimilation of nitrate into amino acids or the C3 carbon fixation pathway that generates carbohydrates. The relative rates of these two pathways depend both on the relative extent to which O2 and CO2 occupies the active site of Rubisco and on whether manganese or magnesium is bound to the enzyme. This study quantified the activities of manganese and magnesium in isolated tobacco chloroplasts and the thermodynamics of binding of these metals to Rubisco purified from tobacco or a bacterium. In tobacco chloroplasts, manganese was less active than magnesium, but Rubisco purified from tobacco had a higher affinity for manganese. The activity of each metal in the chloroplast was similar in magnitude to the affinity of tobacco Rubisco for each. This indicates that, in tobacco chloroplasts, Rubisco associates almost equally with both metals and rapidly exchanges one metal for the other. Binding of magnesium was similar in Rubisco from tobacco and a bacterium, whereas binding of manganese differed greatly between the Rubisco from these species. Moreover, the ratio of leaf manganese to magnesium in C3 plants increased as atmospheric CO2 increased. These results suggest that Rubisco has evolved to improve the energy transfers between photorespiration and nitrate assimilation and that plants regulate manganese and magnesium activities in the chloroplast to mitigate detrimental changes in their nitrogen/carbon balance as atmospheric CO2 varies.

Investigation of uranium interactions with calcium phosphate-binding proteins using ICP/MS and CE-ICP/MS

During long-term exposure, uranium accumulates in bone. Since uranium in U(vi) complexes shares similar coordination properties to calcium, this toxicant is assumed to be exchanged with calcium ions at the surfaces of bone mineral crystals. Recently, two proteins involved in bone turnover, fetuin A and osteopontin, were shown to exhibit a high affinity for U(vi). A common biochemical feature of both fetuin A and osteopontin is their inhibiting role in calcium phosphate precipitation. Therefore it is conceivable that complexation of U(vi) with these proteins may alter their interaction with calcium and/or calcium phosphate. Quantitative analyses of calcium, phosphorus and uranium performed using inductively coupled plasma/mass spectrometry (ICP/MS) demonstrated the inhibition of the precipitation of calcium phosphate by fetuin A and osteopontin for 2 h. In addition, the presence of U(vi) did not seem to alter the duration of this process. However, dynamic light scattering studies revealed that the size of the colloidal particles formed with osteopontin was altered by the presence of U(vi) in a concentration-dependent manner. Finally, using hyphenated capillary electrophoresis-ICP/MS (CE-ICP/MS), we showed that in these systems, at a low concentration of U(vi) (protein : U(vi) 8 : 1), U(vi) might remain in solution by forming a complex with proteins and not by sequestration of a precipitate of either autunite or uranyl orthophosphate.

Investigation of an optimal cell lysis method for the study of the zinc metalloproteome of Histoplasma capsulatum

This work sought to assess optimal extraction conditions in the study of the metalloproteome of the dimorphic fungus Histoplasma capsulatum. One of the body's responses to H. capsulatum infection is sequestration of zinc within host macrophage (MØ), as reported by Vignesh et al. (Immunity 39:697-710, 2013) and Vignesh et al. (PLOS Pathog 9:E1003815, 2013). Thus, metalloproteins containing zinc were of greatest interest as it plays a critical role in survival of the fungus. One challenge in metalloproteomics is the preservation of the native structure of proteins to retain non-covalently bound metals. Many of the conventional cell lysis, separation, and identification techniques in proteomics are carried out under conditions that could lead to protein denaturation. Various cell lysis techniques were investigated in an effort to both maintain the metalloproteins during lysis and subsequent analysis while, at the same time, serving to be strong enough to break the cell wall, allowing access to cytosolic metalloproteins. The addition of 1% Triton x-100, a non-ionic detergent, to the lysis buffer was also studied. Seven lysis methods were considered and these included: Glass Homogenizer (H), Bead Beater (BB), Sonication Probe (SP), Vortex with 1% Triton x-100 (V, T), Vortex with no Triton x-100 (V, NT), Sonication Bath, Vortex, and 1% Triton x-100 (SB, V, T) and Sonication Bath, Vortex, and no Triton x-100 (SB, V, NT). A Qubit® Assay was used to compare total protein concentration and inductively coupled plasma-mass spectrometry (ICP-MS) was utilized for total metal analysis of cell lysates. Size exclusion chromatography coupled to ICP-MS (SEC-HPLC-ICP-MS) was used for separation of the metalloproteins in the cell lysate and the concentration of Zn over a wide molecular weight range was examined. Additional factors such as potential contamination sources were also considered. A cell lysis method involving vortexing H. capsulatum yeast cells with 500 μm glass beads in a 1% Triton x-100 lysis buffer (V, T) was found to be most advantageous to extract intact zinc metalloproteins as demonstrated by the highest Zn to protein ratio, 1.030 ng Zn/μg protein, and Zn distribution among high, mid, and low molecular weights suggesting the least amount of protein denaturation. Graphical abstract In this work, several cell lysis techniques and two lysis buffers were investigated to evaluate the preservation of the zinc metalloproteome of H. capsulatum while maintaining compatibility with the analytical techniques employed.

ICPMS analysis of proteins separated by Native-PAGE: Evaluation of metaloprotein profiles in human synovial fluid with acute and chronic arthritis

The role of trace elements bound to proteins in the etiology and pathogenesis of rheumatoid arthritis (RA) remains unclear. In this sense, the identification and detection of metalloproteins has a strong and growing interest. Metalloprotein studies are currently carried out by polyacrylamide gel electrophoresis (PAGE) associated to inductively coupled plasma mass spectrometry (ICPMS), and despite that complete information can be obtained for metals such as Fe, Cu and Zn, difficulties due to poor sensitivity for other trace elements such as Sn, As, etc, are currently faced. In the present work, a simple and fast method for the determination of trace metals bound to synovial fluid (SF) proteins was optimized. Proteins from SF (long and short-term RA) were separated in ten fractions by native PAGE, then dissolved in nitric acid and peroxide hydrogen, and analyzed by ICPMS. Fifteen metals were determined in each separated protein fraction (band). Adequate calibration of proteins molecular weight allowed stablishing which protein type were bound to different metals.

Assessment of CE-ICP/MS hyphenation for the study of uranyl/protein interactions

Identification of uranyl transport proteins is key to develop efficient detoxification approaches. Therefore, analytical approaches have to be developed to cope with the complexity of biological media and allow the analysis of metal speciation. CE-ICP/MS was used to combine the less-intrusive character and high separation efficiency of CE with the sensitive detection of ICP/MS. The method was based on the incubation of samples with uranyl prior to the separation. Electrophoretic buffers were compared to select a 10 mM Tris to 15 mM NaCl buffer, which enabled analyses at pH 7.4 and limited dissociation. This method was applied to the analysis of a serum. Two main fractions were observed. By comparison with synthetic mixtures of proteins, the first one was attributed to fetuin and in a lesser extent to HSA, and the second one to uranyl unbound to proteins. The analysis showed that fetuin was likely to be the main target of uranyl. CE-ICP/MS was also used to investigate the behavior of the fetuin-uranyl complex, in the presence of carbonate, an abundant complexing agent of uranyl in blood. This method enabled association constants determination, suggesting the occurrence of both FETUA(UO2(2+)) and FETUA(UO2(2+))(CO3(2-)) complexes, depending on the carbonate concentration.