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.

Laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS)-based strategies applied for the analysis of metal-binding protein in biological samples: an update on recent advances

New analytical strategies for metal-binding protein facilitate researchers learning about how metals play a significant role in life. Laser ablation-inductively coupled plasma mass spectrometry (LA-ICP-MS) offers many advantages for the metal analysis of biological samples and shows a promising future in protein analysis, but recent advances in LA-ICP-MS-based strategies for identifying metal-binding proteins via endogenous metals remain less updated yet. To present the current status in this field, the main analytical strategies for metal-binding proteins with LA-ICP-MS are reviewed here, including in situ analysis of biospecimens and ex situ analysis with gel electrophoresis. A critical discussion of challenges and future perspectives is also given. Multifarious laser ablation-inductively coupled plasma mass spectrometry (LA-ICP-MS)-based strategies have been developed and applied to investigate the metal-binding proteins in biospecimens in situ or through gel electrophoresis ex situ over the past decades, facilitating researchers disclosing how essential metals are implicated in life or what proteins toxic metals will target.

Speciomics as a concept involving chemical speciation and omics

The study of chemical speciation and the refinement and expansion of omics-based methods are both consolidated and highly active research fields. Although well established, such fields are extremely dynamic and are driven by the emergence of new strategies and improvements in instrumentation. In the case of omics-based studies, subareas including lipidomics, proteomics, metallomics, metabolomics and foodomics have emerged. Here, speciomics is being proposed as an "umbrella" term, that incorporates all of these subareas, to capture studies where the evaluation of chemical species is carried out using omics approaches. This paper contextualizes both speciomics and the speciome, and reviews omics applications used for species identification through examination of proteins, metalloproteins, metabolites, and nucleic acids. In addition, some implications from such studies and a perspective for future development of this area are provided. SIGNIFICANCE: The synergic effect between chemical speciation and omics is highlighted in this work, demonstrating an emerging area of research with a multitude of possibilities in terms of applications and further developments. This work not only defines and contextualizes speciomics and individual speciomes, but also demonstrates with some examples the great potential of this new interdisciplinary area of research.

Quantification of human plasma metalloproteins in multiple sclerosis, ischemic stroke and healthy controls reveals an association of haptoglobin-hemoglobin complexes with age

Advanced analytical methods play an important role in quantifying serum disease biomarkers. The problem of separating thousands of proteins can be reduced by analyzing for a ‘sub-proteome’, such as the ‘metalloproteome’, defined as all proteins that contain bound metals. We employed size exclusion chromatography (SEC) coupled to an inductively coupled plasma atomic emission spectrometer (ICP-AES) to analyze plasma from multiple sclerosis (MS) participants (n = 21), acute ischemic stroke (AIS) participants (n = 17) and healthy controls (n = 21) for Fe, Cu and Zn-metalloproteins. Using ANOVA analysis to compare the mean peak areas among the groups revealed no statistically significant differences for ceruloplasmin (p = 0.31), α2macroglobulin (p = 0.51) and transferrin (p = 0.31). However, a statistically significant difference was observed for the haptoglobin-hemoglobin (Hp-Hb) complex (p = 0.04), being driven by the difference between the control group and AIS (p = 0.012), but not with the MS group (p = 0.13), based on Dunnes test. A linear regression model for Hp-Hb complex with the groups now adjusted for age found no statistically significant differences between the groups (p = 0.95), but was suggestive for age (p = 0.057). To measure the strength of association between the Hp-Hb complex and age without possible modifications due to disease, we calculated the Spearman rank correlation in the healthy controls. The latter revealed a positive association (r = 0.39, 95% Confidence Interval = (-0.05, 0.83), which suggests that either the removal of Hp-Hb complexes from the blood circulation slows with age or that the release of Hb from red blood cells increases with age. We also observed that the Fe-peak corresponding to the Hp-Hb complex eluted ~100 s later in ~14% of all study samples, which was not correlated with age or disease diagnosis, but is consistent with the presence of the smaller Hp (1–1) isoform in 15% of the population.

Toxic Metal Species and 'Endogenous' Metalloproteins at the Blood-Organ Interface: Analytical and Bioinorganic Aspects

Globally, human exposure to environmental pollutants causes an estimated 9 million deaths per year and it could also be implicated in the etiology of diseases that do not appear to have a genetic origin. Accordingly, there is a need to gain information about the biomolecular mechanisms that causally link exposure to inorganic environmental pollutants with distinct adverse health effects. Although the analysis of blood plasma and red blood cell (RBC) cytosol can provide important biochemical information about these mechanisms, the inherent complexity of these biological matrices can make this a difficult task. In this perspective, we will examine the use of metalloentities that are present in plasma and RBC cytosol as potential exposure biomarkers to assess human exposure to inorganic pollutants. Our primary objective is to explore the principal bioinorganic processes that contribute to increased or decreased metalloprotein concentrations in plasma and/or RBC cytosol. Furthermore, we will also identify metabolites which can form in the bloodstream and contain essential as well as toxic metals for use as exposure biomarkers. While the latter metal species represent useful biomarkers for short-term exposure, endogenous plasma metalloproteins represent indicators to assess the long-term exposure of an individual to inorganic pollutants. Based on these considerations, the quantification of metalloentities in blood plasma and/or RBC cytosol is identified as a feasible research avenue to better understand the adverse health effects that are associated with chronic exposure of various human populations to inorganic pollutants. Exposure to these pollutants will likely increase as a consequence of technological advances, including the fast-growing applications of metal-based engineering nanomaterials.

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.

Identification of a haptoglobin-hemoglobin complex in human blood plasma

Blood plasma metalloproteins that contain copper (Cu), iron (Fe), zinc (Zn) and/or other metals/metalloids are potential disease biomarkers because the bloodstream is in permanent contact with organs. Their quantification and/or the presence of additional metal-entities or the absence of certain metalloproteins in blood plasma (e.g. in Wilson's disease) may provide insight into the dyshomeostasis of the corresponding metal (s) to gain insight into disease processes. The first step in investigating if the determination of plasma metalloproteins is useful for the diagnosis of diseases is their definitive qualitative identification. To this end, we have added individual highly pure Cu, Fe or Zn-containing metalloproteins to plasma (healthy volunteer) and analyzed this mixture by size-exclusion chromatography (SEC) coupled to an inductively coupled plasma atomic spectrometer (ICP-AES), simultaneously monitoring the emission lines of Cu, Fe and Zn. The results clearly identified ceruloplasmin (Cp), holo-transferrin (hTf), and α₂-macroglobulin (α₂M), which verifies our previous assignments. Interestingly, another major Fe-peak in plasma was identified as a haptoglobin (Hp)-hemoglobin (Hb) complex. This Hp-Hb complex is formed after Hb, which is released during the hemolysis of erythrocytes, binds to the plasma protein Hp. The Hp-Hb complex formation is known to be one of the strongest interactions in biochemistry (K_d≈1pmol/L) and is critical because it prevents kidney toxicity of free Hb. Hence, the simultaneous determination of Cp, hTf, α₂M and the Hp-Hb complex in plasma in <25min has the potential to provide new insight into disease processes associated with the bioinorganic chemistry of Cu, Fe and Zn.

Hybrid model for efficient prediction of poly(A) signals in human genomic DNA

Polyadenylation signals (PAS) are found in most protein-coding and some non-coding genes in eukaryotes. Their accurate recognition improves understanding gene regulation mechanisms and recognition of the 3'-end of transcribed gene regions where premature or alternate transcription ends may lead to various diseases. Although different methods and tools for in-silico prediction of genomic signals have been proposed, the correct identification of PAS in genomic DNA remains challenging due to a vast number of non-relevant hexamers identical to PAS hexamers. In this study, we developed a novel method for PAS recognition. The method is implemented in a hybrid PAS recognition model (HybPAS), which is based on deep neural networks (DNNs) and logistic regression models (LRMs). One of such models is developed for each of the 12 most frequent human PAS hexamers. DNN models appeared the best for eight PAS types (including the two most frequent PAS hexamers), while LRM appeared best for the remaining four PAS types. The new models use different combinations of signal processing-based, statistical, and sequence-based features as input. The results obtained on human genomic data show that HybPAS outperforms the well-tuned state-of-the-art Omni-PolyA models, reducing the classification error for different PAS hexamers by up to 57.35% for 10 out of 12 PAS types, with Omni-PolyA models being better for two PAS types. For the most frequent PAS types, 'AATAAA' and 'ATTAAA', HybPAS reduced the error rate by 35.14% and 34.48%, respectively. On average, HybPAS reduces the error by 30.29%. HybPAS is implemented partly in Python and in MATLAB available at https://github.com/EMANG-KAUST/PolyA_Prediction_LRM_DNN.

Sample Preparation Focusing on Plant Omics

Because of strong impact of omics in many fields, and the complexity of the samples when focusing on areas such as genomics, (metallo)proteomics, metabolomics, among others, it is easy to rationalize the great importance that sample preparation has for achieving reliable results, mainly considering plant science. Then, this chapter points out applications of the sample preparation focusing on such areas, and a diversity of strategies, techniques, and procedures is highlighted and commented.

Chemical Speciation and Metallomics

Chemical speciation approaches is an inherent part of metallomics, once metals/metalloids and organic structures need to be currently evaluated for attaining metallomics studies. Then, this chapter focuses on the applications of the chemical speciation applied to the human health risk, food and human diet, drugs, forensic, nanoscience, and geological metallomics, also pointing out the advances in such area. Some aspects regarding sample preparation is commented along this chapter, and some strategies for maintaining the integrity of the metallomics information are also emphasized.

Laser ablation ICP-MS: Application in biomedical research

In the last decade, the development of diverse bioanalytical methodologies based on mass spectrometry imaging has increased, as has their application in biomedical questions. The distribution analysis of elements (metals, semimetals, and non-metals) in biological samples is a point of interest in life sciences, especially within the context of metallomics, which is the scientific field that encompasses the global analysis of the entirety of elemental species inside a cell or tissue. Laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) has been efficiently employed to generate qualitative and quantitative maps of elemental distribution in thin tissue sections of a variety of biological samples, for example, brain, cartilage, spinal cord, etc. The combination of elemental with molecular mass spectrometry allows obtaining information about the elements bound to proteins, when they are previously separated by gel electrophoresis (metalloproteomics), and also adding a new dimension to molecular mass spectrometry imaging by the correlation of molecular and elemental distribution maps in definite regions in a biological tissue. In the present review, recent biomedical applications in LA-ICP-MS imaging as a stand-alone technique and in combination with molecular mass spectrometry imaging techniques are discussed. Applications of LA-ICP-MS in the study of neurodegenerative diseases, distribution of contrast agents and metallodrugs, and metalloproteomics will be focused in this review. © 2015 Wiley Periodicals, Inc. Mass Spec Rev 36:47-57, 2017.

Metalloproteomics: focus on metabolic issues relating to metals

PURPOSE OF REVIEW

By determining metalloproteomes via high-throughput methodology, metalloproteomics provides a research strategy for investigating nutritional and metabolic issues relating to metals. In this review, we examine recent developments in metalloproteomics since its early days approximately 12 years ago, when we utilized metalloproteomics to investigate copper disposition in hepatocytes in relation to Wilson disease.

RECENT FINDINGS

A metalloproteome is the set of proteins that have metal-binding capacity by being metalloproteins or manifesting metal-binding sites. Like all proteomes, a metalloproteome is determined within the context of a well defined system. It can be ascertained for a single metal or multiple metals in that system. Apart from major technological advances in analytical techniques, recent work has examined metalloproteomes for metals other than copper, notably nickel, zinc and manganese. Given the importance of microbiomes to metabolism, microbial metalloproteomics is a rapidly expanding and promising new field.

SUMMARY

Metals play key roles in metabolic processes. Sufficient technological progress has taken place in the past decade to make metalloproteomics an exciting and innovative type of research in nutrition and metabolism. It elucidates how metals contribute to metabolic physiology across the phyla, including in microbes. For humans, it may clarify mechanisms as well as identify informative diagnostic or prognostic biomarkers.

Identification of major zinc-binding proteins from a marine cyanobacterium: insight into metal uptake in oligotrophic environments

The open ocean cyanobacteriumSynechococcussp. WH8102 thrives at extremely low zinc concentrations. Metalloproteomics experiments have identified an outer-membrane bound porin with zinc-binding ability that is upregulated at low zinc levels, suggesting a role for porins in highly efficient zinc uptake.

Metal Species in Biology: Bottom-Up and Top-Down LC Approaches in Applied Toxicological Research

Since the inception of liquid chromatography (LC) more than 100 years ago this separation technique has been developed into a powerful analytical tool that is frequently applied in life science research. To this end, unique insights into the interaction of metal species (throughout this manuscript “metal species” refers to “toxic metals, metalloid compounds, and metal-based drugs” and “toxic metals” to “toxic metals and metalloid compounds”) with endogenous ligands can be obtained by using LC approaches that involve their hyphenation with inductively coupled plasma-based element specific detectors. This review aims to provide a synopsis of the different LC approaches which may be employed to advance our understanding of these interactions either in a “bottom-up” or a “top-down” manner. In the “bottom-up” LC-configuration, endogenous ligands are introduced into a physiologically relevant mobile phase buffer, and the metal species of interest is injected. Subsequent “interrogation” of the on-column formed complex(es) by employing a suitable separation mechanism (e.g., size exclusion chromatography or reversed-phase LC) while changing the ligand concentration(s), the column temperature or the pH can provide valuable insight into the formation of complexes under near physiological conditions. This approach allows to establish the relative stability and hydrophobicity of metal-ligand complexes as well as the dynamic coordination of a metal species (injected) to two ligands (dissolved in the mobile phase). Conversely, the “top-down” analysis of a biological fluid (e.g., blood plasma) by LC (e.g., using size exclusion chromatography) can be used to determine the size distribution of endogenous metalloproteins which are collectively referred to as the “metalloproteome”. This approach can provide unique insight into the metabolism and the plasma protein binding of metal species, and can simultaneously visualize the dose-dependent perturbation of the metalloproteome by a particular metal species. The concerted application of these LC approaches is destined to provide new insight into biochemical processes which represent an important starting point to advance human health in the 21st century.

Liquid chromatography-inductively coupled plasma-based metallomic approaches to probe health-relevant interactions between xenobiotics and mammalian organisms

In mammals, the transport of essential elements from the gastrointestinal tract to organs is orchestrated by biochemical mechanisms which have evolved over millions of years. The subsequent organ-based assembly of sufficient amounts of metalloproteins is a prerequisite to maintain mammalian health and well-being. The chronic exposure of various human populations to environmentally abundant toxic metals/metalloid compounds and/or the deliberate administration of medicinal drugs, however, can adversely affect these processes which may eventually result in disease. A better understanding of the perturbation of these processes has the potential to advance human health, but their visualization poses a major problem. Nonetheless, liquid chromatography-inductively coupled plasma-based 'metallomics' methods, however, can provide much needed insight. Size-exclusion chromatography-inductively coupled plasma atomic emission spectrometry, for example, can be used to visualize changes that toxic metals/medicinal drugs exert at the metalloprotein level when they are added to plasma in vitro. In addition, size-exclusion chromatography-inductively coupled plasma mass spectrometry can be employed to analyze organs from toxic metal/medicinal drug-exposed organisms for metalloproteins to gain insight into the biochemical changes that are associated with their acute or chronic toxicity. The execution of such studies-from the selection of an appropriate model organism to the generation of accurate analytical data-is littered with potential pitfalls that may result in artifacts. Drawing on recent lessons that were learned by two research groups, this tutorial review is intended to provide relevant information with regard to the experimental design and the practical application of these aforementioned metallomics tools in applied health research.