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Abstract
Mass spectrometry, a technology to determine the mass of ionized molecules and biomolecules, is increasingly applied for the global identification and quantification of proteins. Proteomics applies mass spectrometry in many applications, and each application requires consideration of analytical choices, instrumental limitations and data processing steps. These depend on the aim of the study and means of conducting it. Choosing the right combination of sample preparation, MS instrumentation, and data processing allows exploration of different aspects of the proteome. This chapter gives an outline for some of these commonly used setups and some of the key concepts, many of which later chapters discuss in greater depth. Understanding and handling mass spectrometry data is a multifaceted task that requires many user decisions to obtain the most comprehensive information from an MS experiment. Later chapters in this book deal in-depth with various aspects of the process and how different tools addresses the many analytical challenges. This chapter revises the basic concept in mass spectrometry (MS)-based proteomics.
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Affiliation(s)
- Rune Matthiesen
- Computational and Experimental Biology Group, CEDOC, Chronic Diseases Research Centre, NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Lisboa, Portugal.
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2
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Hyun JS, Park SJ. Dynamic Profile of the Copper Chaperone CopP from Helicobacter Pylori Depending on the Bound Metals. JOURNAL OF THE KOREAN MAGNETIC RESONANCE SOCIETY 2016. [DOI: 10.6564/jkmrs.2016.20.3.076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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3
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Kay KL, Hamilton CJ, Le Brun NE. Mass spectrometry of B. subtilis CopZ: Cu(i)-binding and interactions with bacillithiol. Metallomics 2016; 8:709-19. [DOI: 10.1039/c6mt00036c] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Mass spectrometry reveals a high resolution overview of species formed by CopZ and Cu(i), and the effects of the physiological low molecular weight thiol bacillithiol.
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Affiliation(s)
- Kristine L. Kay
- Centre for Molecular and Structural Biochemistry
- School of Chemistry
- University of East Anglia
- Norwich, UK
| | | | - Nick E. Le Brun
- Centre for Molecular and Structural Biochemistry
- School of Chemistry
- University of East Anglia
- Norwich, UK
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4
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Abstract
Mass spectrometry has been widely applied to study biomolecules and one rapidly developing field is the global analysis of proteins, proteomics. Understanding and handling mass spectrometry data is a multifaceted task that requires many decisions to be made to get the most comprehensive information from an experiment. Later chapters in this book deal in-depth with various aspects of the process and how different tools can be applied to the many analytical challenges. This introductory chapter is intended as a basic introduction to mass spectrometry (MS)-based proteomics to set the scene for newcomers and give pointers to reference material. There are many applications of mass spectrometry in proteomics and each application is associated with some analytical choices, instrumental limitations and data processing steps that depend on the aim of the study and means of conducting it. Different aspects of the proteome can be explored by choosing the right combination of sample preparation, MS instrumentation and data processing. This chapter gives an outline for some of these commonly used setups and some of the key concepts, many of which are explored in greater depth in later chapters.
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Affiliation(s)
- Rune Matthiesen
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
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5
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Schmidt AC, Steier S. Some critical aspects in the determination of binding constants by electrospray ionisation mass spectrometry at the example of arsenic bindings to sulphur-containing biomolecules. JOURNAL OF MASS SPECTROMETRY : JMS 2010; 45:870-879. [PMID: 20648690 DOI: 10.1002/jms.1774] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The influences of reactant concentrations, solvent type, acid strength, pH conditions and ionic strength on the determination of apparent gas-phase equilibrium constants K using electrospray ionisation mass spectrometry (ESI-MS) were elucidated. As example serves the interaction of the tripeptide glutathione (GSH) with phenylarsine oxide (PAO). It was shown that rising initial concentrations of both reactants were not adequately compensated by increasing signal intensities of the reaction products in the mass spectra. The equilibrium constant for the formation of the phenylarsenic-substituted peptide species decreased from 1.42 x 10(5) +/- 1.81 x 10(4) l micromol(-1) to 1.54 x 10(4) +/- 1.5 x 10(3) l micromol(-1) with rising initial GSH concentrations from 1 to 10 microM at fixed PAO molarity of 50 microM. K values resulting from a series with a fixed GSH molarity of 5 microM and a PAO molarity varied from 10 to 100 microM remained in a narrower range between 4.59 x 10(4) +/- 2.15 x 10(4) l micromol(-1) and 1.07 x 10(4) +/- 4.0 x 10(3) l micromol(-1). In contrast, consumption numbers calculated from the ion intensity ratios of reaction products to the unreacted peptide were not influenced by the initial reactant concentrations. In a water-acetonitrile-acetic acid mixture (48:50:2, v:v), the consumption of 5 micro M GSH increased from 8.3 +/- 1.4% to 39.6 +/- 1.6% with increased molar excess of PAO from 2 to 20, respectively. The GSH consumption was considerably enhanced in a changed solvent system consisting of 25% acetonitrile and 75% 10 mM ammonium formate, pH 5.0 (v:v) up to 80% of the original peptide amount at an only threefold molar arsenic excess.
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Affiliation(s)
- Anne-Christine Schmidt
- Technical University Bergakademie Freiberg, Institute of Analytical Chemistry, Freiberg, Germany.
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6
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Wu CL, Zhang WB, Mai KS, Liang XF, Xu W, Wang J, Ma HM. Molecular cloning, characterization and mRNA expression of selenium-binding protein in abalone (Haliotis discus hannai Ino): Response to dietary selenium, iron and zinc. FISH & SHELLFISH IMMUNOLOGY 2010; 29:117-125. [PMID: 20211737 DOI: 10.1016/j.fsi.2010.02.028] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2009] [Revised: 02/23/2010] [Accepted: 02/26/2010] [Indexed: 05/28/2023]
Abstract
Selenium-binding protein (SEBP) is believed to play crucial role in controlling the oxidation/reduction in the physiological processes. In this study, the cDNA of selenium-binding protein from abalone Haliotis discus hannai Ino (HdhSEBP) was cloned by homology cloning and rapid amplification of cDNA ends (RACE) technique. The full length of HdhSEBP cDNA was 2071 bp, consisting of a 5' untranslated region (UTR) of 55 bp, a 3' UTR of 522 bp, and an open reading frame (ORF) of 1494 bp. The deduced protein has 497 amino acid residues with a calculated molecular mass of 55.6 kDa and a predicted isoelectric point of 5.47. BLAST analysis reveals that HdhSEBP shares high identities with other known SEBPs from mammal, bird, fish and mollusk, etc. The mRNA expression patterns of HdhSEBP in hepatopancreas and haemocytes were measured by real-time PCR in abalone fed with nine different diets containing graded levels of selenium (0, 1 and 50 mg kg(-1)), iron (0, 65 and 1300 mg kg(-1)) and zinc (0, 35 and 700 mg kg(-1)) for 20 weeks, respectively. The results showed that the expression of the HdhSEBP mRNA increased and reached the maximum at optimal dietary selenium (1 mg kg(-1)), iron (65 mg kg(-1)) and zinc (35 mg kg(-1)), respectively. Deficient or excessive level of dietary selenium, iron or zinc, respectively, leaded to significant depression of HdhSEBP mRNA. It is concluded that the expression levels of HdhSEBP are affected by dietary selenium, iron or zinc.
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Affiliation(s)
- Cheng-Long Wu
- The Key Laboratory of Mariculture (Education Ministry of China), Ocean University of China, 5 Yushan Road, Qingdao 266003, PR China
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7
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Bonnaire N, Dannoux A, Pernelle C, Amekraz B, Moulin C. On the use of electrospray ionization and desorption electrospray ionization mass spectrometry for bulk and surface polymer analysis. APPLIED SPECTROSCOPY 2010; 64:810-818. [PMID: 20615295 DOI: 10.1366/000370210791666318] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Electrospray ionization (ESI) and desorption electrospray ionization (DESI) mass spectrometry were for the first time compared to investigate degradation products resulting from radiolysis of polyurethane (PUR) irradiated using accelerated electrons. First, DESI optimization was performed to obtain the best results in terms of sensitivity for surface polymer analysis. Then, a comparison was performed between DESI-MS and ESI-MS characterization of the degradation products of irradiated PUR with different doses up to 10 MGy. Similar results were obtained despite a lower sensitivity of DESI. Finally, DESI results obtained by direct surface analysis of irradiated PUR films as a function of depth were compared to bulk analysis results obtained by ESI. This comparison shows that degradation products of PUR are very comparable at the surface or within the polymer, confirming the radio-oxidation homogeneity.
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Affiliation(s)
- Nicolas Bonnaire
- CNAM-Génie analytique, 292 rue Saint-Martin, 75141 Paris, France
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8
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Abstract
A key property of metallo-proteins and -enzymes is the affinity of metal ion M for protein ligand P as defined by the dissociation constant KD = [M][P]/[MP]. Its accurate determination is essential for a quantitative understanding of metal selection and speciation. However, the surfaces of proteins are defined by the sidechains of amino acids and so abound in good metal ligands (e.g., imidazole of histidine,thiol of cysteine, carboxylate of aspartic and glutamic acids, etc.). Consequently, adventitious binding of metal ions to protein surfaces is common with KD values > or = 10(-6) M. On the other hand, transport proteins responsible for 'chaperoning' essential metals to their cellular destinations appear to bind the metal ions selectively (KD < 10(-7) M, both for speciation and to minimise the toxic effects of 'free' metal ions. These ions are normally bound with still higher affinities at their ultimate destinations (the active sites of metallo-proteins and -enzymes). This review surveys possible approaches to estimation of these dissociation constants and pinpoints the various problems associated with each approach.
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Affiliation(s)
- Zhiguang Xiao
- University of Melbourne, Parkville, Victoria, Australia.
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9
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Bersch B, Favier A, Schanda P, van Aelst S, Vallaeys T, Covès J, Mergeay M, Wattiez R. Molecular Structure and Metal-binding Properties of the Periplasmic CopK Protein Expressed in Cupriavidus metallidurans CH34 During Copper Challenge. J Mol Biol 2008; 380:386-403. [DOI: 10.1016/j.jmb.2008.05.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2008] [Revised: 05/06/2008] [Accepted: 05/08/2008] [Indexed: 11/16/2022]
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10
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Park SJ, Jung YS, Kim JS, Seo MD, Lee BJ. Structural insight into the distinct properties of copper transport by the Helicobacter pylori CopP protein. Proteins 2008; 71:1007-19. [PMID: 18214986 DOI: 10.1002/prot.21957] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Helicobacter pylori CopP (HpCopP) is a putative copper binding regulatory protein composed of 66 amino acid residues. The small HpCopP protein is homologous to CopZ, encoded by the E. hirae and B. subtilis cop operons. To clarify the role of HpCopP in copper metabolism in H. pylori, we studied the structural and copper binding characteristics by NMR spectroscopy. Based on the resonance assignments, the tertiary structure of HpCopP was determined. Unlike the betaalphabetabetaalphabeta fold of the homologous CopZ, HpCopP adopts the betaalphabetabetaalpha fold. The superposition with structures of other bacterial copper binding proteins showed that the global structure of HpCopP follows the general topology of the family, regardless of absence of the C-terminal beta-strand. The Cu(I) binding property of HpCopP was well conserved like CopZs: the structural changes due to Cu(I) and Ag(I) bindings were primarily restricted to the metal binding motif (CXXC motif). On the other hand, the Cu(II) binding property of CopP was different with that of CopZ: in the absence of reducing agent, Cu(II) ion oxidized a mutant HpCopP, resulting in disulfide bond formation in the CXXC motif. The Cu(II) ion binding property was evaluated using the mutant HpCopP, in which two amino acids were artificially introduced at the C-terminus, since the reduced state of the CXXC motif was more stabile in the mutant HpCopP without a reducing agent. Here, the structure and copper binding property of HpCopP are discussed in detail.
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Affiliation(s)
- Sung Jean Park
- National Laboratory of Membrane Protein Structure, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, San 56-1, Shillim-Dong, Kwanak-Gu, Seoul 151-742, Korea
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11
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Hussain F, Wittung-Stafshede P. Impact of cofactor on stability of bacterial (CopZ) and human (Atox1) copper chaperones. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2007; 1774:1316-22. [PMID: 17881304 DOI: 10.1016/j.bbapap.2007.07.020] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2007] [Revised: 07/30/2007] [Accepted: 07/31/2007] [Indexed: 11/18/2022]
Abstract
Here, we present the first characterization of in vitro unfolding and thermodynamic stability of two copper chaperone proteins: Bacillus subtilis CopZ and Homo sapiens Atox1. We find that the unfolding reactions for apo- and Cu(I)-forms of CopZ and Atox1, induced by the chemical denaturant, guanidine hydrochloride (GuHCl), and by thermal perturbation are reversible two-state reactions. For both proteins, the unfolding midpoints shift to higher GuHCl concentrations and the thermodynamic stability is increased in the presence of Cu(I). Despite the same overall fold, apo-CopZ exhibits much lower thermal stability than apo-Atox1. Although the thermal stability of both proteins is increased in the presence of copper, the stabilizing effect is largest for the less stable variant. Divergent energetic properties of the apo- and holo-forms may be linked to conformational changes that facilitate copper transfer to the target.
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Affiliation(s)
- Faiza Hussain
- Department of Biochemistry and Cell Biology, Rice University, 6100 Main Street, Houston, TX 77251, USA
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12
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Hong J, Kharenko OA, Ogawa MY. Incorporating electron-transfer functionality into synthetic metalloproteins from the bottom-up. Inorg Chem 2007; 45:9974-84. [PMID: 17140193 PMCID: PMC2566827 DOI: 10.1021/ic060222j] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The alpha-helical coiled-coil motif serves as a robust scaffold for incorporating electron-transfer (ET) functionality into synthetic metalloproteins. These structures consist of a supercoiling of two or more aplha helices that are formed by the self-assembly of individual polypeptide chains whose sequences contain a repeating pattern of hydrophobic and hydrophilic residues. Early work from our group attached abiotic Ru-based redox sites to the most surface-exposed positions of two stranded coiled-coils and used electron-pulse radiolysis to study both intra- and intermolecular ET reactions in these systems. Later work used smaller metallopeptides to investigate the effects of conformational gating within electrostatic peptide-protein complexes. We have recently designed the C16C19-GGY peptide, which contains Cys residues located at both the "a" and "d" positions of its third heptad repeat in order to construct a nativelike metal-binding domain within its hydrophobic core. It was shown that the binding of both Cd(II) and Cu(I) ions induces the peptide to undergo a conformational change from a disordered random coil to a metal-bridged coiled-coil. However, whereas the Cd(II)-protein exists as a two-stranded coiled-coil, the Cu(I) derivative exists as a four-stranded coiled-coil. Upon the incorporation of other metal ions, metal-bridged peptide dimers, tetramers, and hexamers are formed. The Cu(I)-protein is of particular interest because it exhibits a long-lived (microsecond) room-temperature luminescence at 600 nm. The luminophore in this protein is thought to be a multinuclear CuI4Cys4(N/O)4 cage complex, which can be quenched by exogenous electron acceptors in solution, as shown by emission-lifetime and transient-absorption experiments. It is anticipated that further investigation into these systems will contribute to the expanding effort of bioinorganic chemists to prepare new kinds of functionally active synthetic metalloproteins.
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13
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Schmidt AC, Koppelt J, Neustadt M, Otto M. Mass spectrometric evidence for different complexes of peptides and proteins with arsenic(III), arsenic(V), copper(II), and zinc(II) species. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2007; 21:153-63. [PMID: 17154358 DOI: 10.1002/rcm.2823] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Trivalent and pentavalent arsenic were incubated with sulfur-containing amino acid, peptide and protein solutions both as organic compounds (phenylarsine oxide, phenylarsonic acid, dimethylarsinic acid, monomethylarsonic acid) and as inorganic compounds (arsenite, As(III), and arsenate, As(V)). After incubation of phenylarsine oxide solutions with cysteine and glutathione the mass spectra showed a covalent bond between arsenic and sulfur, which was stable at both acidic and neutral pH values. The mass spectra were dominated by monovalent ions at m/z 272 for cysteine samples and at m/z 458 for glutathione samples. Based on these masses the ionic structures could be ascribed to either fragment ions of the covalent arsenic-sulfur complexes or to other arsenic-bonding sites presumably at the amino group. Interestingly, under the same conditions no interactions of inorganic arsenite or arsenate could be measured. In the presence of added Cu(2+) ions all mass signals caused by a reaction of phenylarsine oxide with glutathione disappeared. In these mass spectra only the oxidised form of glutathione (GSSG) was found because of the redox activity of Cu(II). For the model protein lysozyme, no interactions with arsenic could be detected, whereas definite Cu- and Zn-lysozyme complexes with a stoichiometry of 1:1 and 2:1 for Zn(2+) ions and Cu(2+) ions, respectively, were observed. In contrast, for thioredoxin a bonding of As that depended on the concentration of the disulfide-reducing agent tris(2-carboxyethyl) phosphine was demonstrated. For three different phenylarsonic acids and for dimethylarsinic acid that all contain pentavalent arsenic, complexes with glutathione appeared in the mass spectra, which can be attributed to non-covalent interactions or to a covalent bond caused by an additive reaction. The optimisation of the experimental conditions necessary for the mass spectrometric analysis of the interactions of the arsenic species with peptides and proteins is described and the obtained mass spectra that provide information on the kinds of bonds are discussed.
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Affiliation(s)
- Anne-Christine Schmidt
- TU Bergakademie Freiberg, Faculty of Chemistry and Physics, Institute of Analytical Chemistry, Leipziger Strasse 29, D-09596 Freiberg, Germany.
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14
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Boutin M, Bich C, Afonso C, Fournier F, Tabet JC. Negative-charge driven fragmentations for evidencing zwitterionic forms from doubly charged coppered peptides. JOURNAL OF MASS SPECTROMETRY : JMS 2007; 42:25-35. [PMID: 17149792 DOI: 10.1002/jms.1127] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
In aqueous solution, amino acids (AA) and peptides are known to exist as zwitterions over a large pH range. However, in the gas phase, i.e. in electrospray (ESI), the zwitterionic form becomes unfavorable owing to the absence of stabilizing effects from intermolecular solvation. Nevertheless, during mass spectrometry experiments, the presence of a metallic cation can reinforce the zwitterionic character of the molecule and thus influence its fragmentation under low energy collision-induced dissociation (CID) conditions. The [M + Cu(II)](2+) complexes of six pentapeptides (YGGFL, YGGFL(NH(2)), YGGFK, YGGFQ, KYGGF and QYGGF) were analyzed by collision to highlight the presence of zwitterions. The experiments were performed on a 3D-ion trap equipped with an orthogonal ESI source. For each peptides studied, negative-charge driven fragmentations on globally positively charged ions were observed. These fragmentation mechanisms, generally observed in the negative mode, suggest the competitive deprotonation of the C-terminal carboxylic acid or of the tyrosine side-chain residue for each peptide studied and thus a zwitterionic form to preserve the charge balance. Moreover, the specific loss of (CH(3)--C(6)H(4)--O)(*) characterizes YGGFK compared to YGGFQ and the specific loss of styrene characterizes KYGGF compared to QYGGF. These results allow the differentiation of the two couples of isobaric pentapeptides. An unusual loss of NH(4) (+), which occurred from the N-terminus, was also observed for YGGFL, YGGFL(NH(2)), YGGFK and YGGFQ. Finally, the reduction of Cu(II) to Cu(I), concomitant with the (CH(3)--C(6)H(4)--O)(*) release, was pointed out for YGGFK.
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Affiliation(s)
- Michel Boutin
- Université Pierre et Marie Curie-Paris 6, UMR7613, Synthèse, Structure et Fonction de Molécules Bioactives, Paris, F-75005 France
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15
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Liu LL, Franz KJ. Phosphorylation-dependent metal binding by alpha-synuclein peptide fragments. J Biol Inorg Chem 2006; 12:234-47. [PMID: 17082919 DOI: 10.1007/s00775-006-0181-y] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2006] [Accepted: 10/04/2006] [Indexed: 10/24/2022]
Abstract
Alpha-synuclein (alpha-syn) is the major protein component of the insoluble fibrils that make up Lewy bodies, the hallmark lesions of Parkinson's disease. Its C-terminal region contains motifs of charged amino acids that potentially bind metal ions, as well as several identified phosphorylation sites. We have investigated the metal-binding properties of synthetic model peptides and phosphopeptides that correspond to residues 119-132 of the C-terminal, polyacidic stretch of human alpha-syn, with the sequence Ac-Asp-Pro-Asp-Asn-Glu-Ala-Tyr-Glu-Met-Pro-Ser-Glu-Glu-Gly (alpha-syn119-132). The peptide pY125 replaces tyrosine with phosphotyrosine, whereas pS129 replaces serine with phosphoserine. By using Tb(3+) as a luminescent probe of metal binding, we find a marked selectivity of pY125 for Tb(3+) compared with pS129 and alpha-syn119-132, a result confirmed by isothermal titration calorimetry. Truncated or alanine-substituted peptides show that the phosphoester group on tyrosine provides a metal-binding anchor that is supplemented by carboxylic acid groups at positions 119, 121, and 126 to establish a multidentate ligand, while two glutamic acid residues at positions 130 and 131 contribute to binding additional Tb(3+) ions. The interaction of other metal ions was investigated by electrospray ionization mass spectrometry, which confirmed that pY125 is selective for trivalent metal ions over divalent metal ions, and revealed that Fe(3+) and Al(3+) induce peptide dimerization through metal ion cross-links. Circular dichroism showed that Fe(3+) can induce a partially folded structure for pY125, whereas no change was observed for pS129 or the unphosphorylated analog. The results of this study show that the type and location of a phosphorylated amino acid influence a peptide's metal-binding specificity and affinity as well as its overall conformation.
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Affiliation(s)
- Lucy L Liu
- Department of Chemistry, Duke University, P.O. Box 90346, Durham, NC 27708, USA
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16
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Lobinski R, Moulin C, Ortega R. Imaging and speciation of trace elements in biological environment. Biochimie 2006; 88:1591-604. [PMID: 17064836 DOI: 10.1016/j.biochi.2006.10.003] [Citation(s) in RCA: 134] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2006] [Accepted: 10/03/2006] [Indexed: 11/24/2022]
Abstract
Mineral elements, often at the trace level, play a considerable role in physiology and pathology of biological systems. Metallogenomics, metalloproteomics, and metallomics are among the emerging disciplines which are critically dependent on spatially resolved concentration maps of trace elements in a cell or tissue, on information on chemical speciation, and on that on metal-binding coordination sites. The mini-review discusses recent progress in analytical techniques for element profiling on the genome scale, biological trace element imaging, and probing, identification and quantification of chemical species in the biological environment. Imaging of the element distribution in cells and tissue sections is becoming possible with sub-micrometer spatial resolution and picogram-level sensitivity owing to advances in laser ablation MS, ion beam and synchrotron radiation X-ray fluorescence microprobes. Progress in nanoflow chromatography and capillary electrophoresis coupled with element specific ICP MS and molecule-specific electrospray MS/MS and MALDI enables speciation of elements in microsamples in a complex biological environment. Laser ablation ICP MS, micro-SXRF, and micro-PIXE allow mapping of trace element distribution in 1D and 2D proteomics gels. The increasing sensitivity of EXAFS and XANES owing to the use of more intense synchrotron beams and efficient focusing optics provide information about oxidation state, fingerprint speciation of metal sites and metal-site structures.
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Affiliation(s)
- R Lobinski
- Equipe de chimie analytique bio-inorganique, CNRS UMR5034, Hélioparc, 2, avenue Professeur-Angot, 64053 Pau, France
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17
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Agalou A, Spaink HP, Roussis A. Novel interaction of selenium-binding protein with glyceraldehyde-3-phosphate dehydrogenase and fructose-bisphosphate aldolase of Arabidopsis thaliana. FUNCTIONAL PLANT BIOLOGY : FPB 2006; 33:847-856. [PMID: 32689295 DOI: 10.1071/fp05312] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2005] [Accepted: 05/16/2006] [Indexed: 06/11/2023]
Abstract
The metabolic role and regulation of selenium, particularly in plants, is poorly understood. One of the proteins probably involved in the metabolic regulation of this element is the selenium-binding protein (SBP) with homologues present across prokaryotic and eukaryotic species. The high degree of conservation of SBP in different organisms suggests that this protein may play a role in fundamental biological processes. In order to gain insight into the biochemical function of SBP in plants we used the yeast two-hybrid system to identify proteins that potentially interact with an Arabidopsis thaliana (L.) Heynh. homologue. Among the putative binding partners of SBP, a NADP-dependent glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and a fructose-bisphosphate aldolase (FBA) were found as reliable positive candidates. The interaction of these proteins with SBP was confirmed by in vitro binding assays. Previous findings in Escherichia coli, demonstrated the direct binding of selenium to both GAPDH and aldolase. Therefore our results reveal the interaction, at least in pairs, of three proteins that are possibly linked to selenium and suggest the existence of a protein network consisting of at least SBP, GAPDH and FBA, triggered by or regulating selenium metabolism in plant cells.
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Affiliation(s)
- Adamantia Agalou
- Institute of Biology, Clusius Laboratory, Leiden University, Wassenaarseweg 64, 2333AL Leiden, The Netherlands
| | - Herman P Spaink
- Institute of Biology, Clusius Laboratory, Leiden University, Wassenaarseweg 64, 2333AL Leiden, The Netherlands
| | - Andreas Roussis
- Center for Human and Clinical Genetics, Leiden University Medical Center, Wassenaarseweg 72, 2333AL Leiden, The Netherlands. Current address: Agricultural University of Athens, Department of Agricultural Biotechnology, Iera odos 75, 118 55 Athens, Greece
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18
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Di Marco VB, Bombi GG. Electrospray mass spectrometry (ESI-MS) in the study of metal-ligand solution equilibria. MASS SPECTROMETRY REVIEWS 2006; 25:347-79. [PMID: 16369936 DOI: 10.1002/mas.20070] [Citation(s) in RCA: 215] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
In the 20 years, since the introduction of electrospray mass spectrometry (ESI-MS), the use of this technique in various fields of inorganic, organometallic, and analytical chemistry has been steadily increasing. In this study, the application of ESI-MS to the study of metal-ligand solution equilibria is reviewed (till 2004 included). In a first section, advantages and drawbacks of ESI-MS in this type of application are described. Subsequently, a list of ca. 300 studies is reported, in which ESI-MS was used to give number and stoichiometry of the species at equilibrium, or also to estimate their stability constants. All studies are classified according to the metal ions under examination. Other related applications, such as host-guest interactions and metal ion-protein binding studies, are briefly reviewed as well.
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Kulkarni PP, She YM, Smith SD, Roberts EA, Sarkar B. Proteomics of Metal Transport and Metal-Associated Diseases. Chemistry 2006; 12:2410-22. [PMID: 16134204 DOI: 10.1002/chem.200500664] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Proteomics technology has the potential to identify groups of proteins that have similar biological function. However, few attempts have been made to identify and characterize metal-binding proteins by using proteomics strategies. Many transition metals are essential to sustain life. Copper, iron, and zinc are the most abundant transition metals relevant to biological systems. In addition to their important biological functions, metals can also catalyze the formation of damaging free radical species. Hence, their intracellular transport is tightly regulated. Despite recent insights into the intracellular transport of copper and other metals, our overall understanding of intracellular metal metabolism remains incomplete and it is likely that many metal-binding proteins remain undiscovered. Furthermore, the protein targets for metals during metal-associated disease states or during exposure to toxic levels of environmental metals are yet to be unravelled. A proteomics strategy for the analysis of metal-transporting or metal-binding proteins has the potential to uncover how a large number of proteins function in normal or metal-associated diseased states. Here we discuss the principal aspects of metal metabolism, and the recent developments in the area of the proteomics of metal transport.
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Affiliation(s)
- Prasad P Kulkarni
- Department of Biochemistry, University of Toronto, Medical Sciences Building, Toronto, ON, M5S 1A8, Canada
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20
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Lobiński R, Schaumlöffel D, Szpunar J. Mass spectrometry in bioinorganic analytical chemistry. MASS SPECTROMETRY REVIEWS 2006; 25:255-89. [PMID: 16273552 DOI: 10.1002/mas.20069] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
A considerable momentum has recently been gained by in vitro and in vivo studies of interactions of trace elements in biomolecules due to advances in inductively coupled plasma mass spectrometry (ICP MS) used as a detector in chromatography and capillary and planar electrophoresis. The multi-isotopic (including non-metals such as S, P, or Se) detection capability, high sensitivity, tolerance to matrix, and large linearity range regardless of the chemical environment of an analyte make ICP MS a valuable complementary technique to electrospray MS and MALDI MS. This review covers different facets of the recent progress in metal speciation in biochemistry, including probing in vitro interactions between metals and biomolecules, detection, determination, and structural characterization of heteroatom-containing molecules in biological tissues, and protein monitoring and quantification via a heteroelement (S, Se, or P) signal. The application areas include environmental chemistry, plant and animal biochemistry, nutrition, and medicine.
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Affiliation(s)
- Ryszard Lobiński
- Equipe de Chimie Analytique Bio-Inorganique, CNRS UMR 5034, Hélioparc, 2, av. du Pr. Angot, F-64053 Pau, France.
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Lelais G, Seebach D, Jaun B, Mathad R, Flögel O, Rossi F, Campo M, Wortmann A. β-Peptidic Secondary Structures Fortified and Enforced by Zn2+ Complexation – On the Way toβ-Peptidic Zinc Fingers? Helv Chim Acta 2006. [DOI: 10.1002/hlca.339] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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22
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Lelais G, Seebach D, Jaun B, Mathad R, Flögel O, Rossi F, Campo M, Wortmann A. β-Peptidic Secondary Structures Fortified and Enforced by Zn2+ Complexation – On the Way toβ-Peptidic Zinc Fingers? Helv Chim Acta 2006. [DOI: 10.1002/hlca.200690040] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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23
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De Vriendt K, Van Driessche G, Devreese B, Bebrone C, Anne C, Frère JM, Galleni M, Van Beeumen J. Monitoring the zinc affinity of the metallo-beta-lactamase CphA by automated nanoESI-MS. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2006; 17:180-8. [PMID: 16406807 DOI: 10.1016/j.jasms.2005.10.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2005] [Revised: 10/05/2005] [Accepted: 10/14/2005] [Indexed: 05/06/2023]
Abstract
Metallo-beta-lactamases are zinc containing enzymes that are able to hydrolyze and inactivate beta-lactam antibiotics. The subclass B2 enzyme CphA of Aeromonas hydrophila is a unique metallo-beta-lactamase because it degrades only carbapenems efficiently and is only active when it has one zinc ion bound. A zinc titration experiment was used to study the zinc affinity of the wild-type and of several mutant CphA enzymes. It shows that a second Zn(2+) is also bound at high ion concentrations. All samples were analyzed using mass spectrometry in combination with an automated nanoESI source. The metal-free enzyme has a bimodal charge distribution indicative of two conformational states. A completely folded enzyme is detected when the apo-enzyme has bound the first zinc. Intensity ratios of the different enzyme forms were used to deduce the zinc affinities. CphA enzymes mutated in metal ligands show decreased zinc affinity compared to wild-type, especially D120 mutants.
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Affiliation(s)
- Kris De Vriendt
- Laboratory of Protein Biochemistry and Protein Engineering, Ghent University, Ghent, Belgium
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24
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Szpunar J. Advances in analytical methodology for bioinorganic speciation analysis: metallomics, metalloproteomics and heteroatom-tagged proteomics and metabolomics. Analyst 2005; 130:442-65. [PMID: 15776152 DOI: 10.1039/b418265k] [Citation(s) in RCA: 248] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The recent developments in analytical techniques capable of providing information on the identity and quantity of heteroatom-containing biomolecules are critically discussed. Particular attention is paid to the emerging areas of bioinorganic analysis including: (i) a comprehensive analysis of the entirety of metal and metalloid species within a cell or tissue type (metallomics), (ii) the study of the part of the metallome involving the protein ligands (metalloproteomics), and (iii) the use of a heteroelement, naturally present in a protein or introduced in a tag added by means of derivatisation, for the spotting and quantification of proteins (heteroatom-tagged proteomics). Inductively coupled plasma mass spectrometry (ICP MS), used as detector in chromatography and electrophoresis, and supported by electrospray and MALDI MS, appears as the linchpin analytical technique for these emerging areas. This review focuses on the recent advances in ICP MS in biological speciation analysis including sensitive detection of non-metals, especially of sulfur and phosphorus, couplings to capillary and nanoflow HPLC and capillary electrophoresis, laser ablation ICP MS detection of proteins in gel electrophoresis, and isotope dilution quantification of biomolecules. The paper can be considered as a followup of a previous review by the author on a similar topic (J. Szpunar, Analyst, 2000, 125, 963).
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Affiliation(s)
- Joanna Szpunar
- Equipe de Chimie Analytique Bio-inorganique, CNRS UMR 5034, Helioparc, 2, av. Pr. Angot, F-64053 Pau, France.
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Delobel A, Graciet E, Andreescu S, Gontero B, Halgand F, Laprévote O. Mass spectrometric analysis of the interactions between CP12, a chloroplast protein, and metal ions: a possible regulatory role within a PRK/GAPDH/CP12 complex. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2005; 19:3379-88. [PMID: 16259044 DOI: 10.1002/rcm.2192] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The small chloroplast protein CP12 plays the role of a protein linker in the assembly process of a PRK/GAPDH/CP12 complex that is involved in CO2 assimilation in photosynthetic organisms. The redox state of CP12 regulates its role as a protein linker. Only the oxidized protein, with two disulfide bonds, is active in complex formation. Several observations indicating that CP12 might bind a metal ion led us to screen the binding of different metal ions on oxidized or reduced CP12 using non-covalent electrospray ionization mass spectrometry (ESI-MS) experiments. The oxidized protein bound specifically Cu2+ and Ni2+ (Kd of 26+/-1 microM and 11+/-1 microM, respectively); other cations such as Fe2+ and Zn2+ did not bind, while cations such as Cd2+ formed non-specific adducts to CP12. Similar results were obtained for metal ions on screening with the reduced CP12. Interestingly, the present results suggest that Cu2+ catalyzes the re-formation of the disulfide bonds of the reduced CP12, leading to recovery of the fully oxidized CP12 that is then able to bind a Cu2+ ion. Finally the high similarity between CP12 and copper chaperones from Arabidopsis thaliana, as judged by hydrophobic cluster analysis, provides additional evidence for the relevance of metal binding for the in vivo situation. The findings that CP12 is able to bind a metal ion, and that Cu2+ catalyzes the oxidation of the thiol groups of CP12, are new characteristics of this protein that may prove to be important in the regulation of the assembly process of the PRK/GAPDH/CP12 complex.
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Affiliation(s)
- Arnaud Delobel
- Institut de Chimie des Substances Naturelles, CNRS, 1 avenue de la terrasse, 91198 Gif/Yvette, France
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Urvoas A, Moutiez M, Estienne C, Couprie J, Mintz E, Le Clainche L. Metal-binding stoichiometry and selectivity of the copper chaperone CopZ from Enterococcus hirae. ACTA ACUST UNITED AC 2004; 271:993-1003. [PMID: 15009211 DOI: 10.1111/j.1432-1033.2004.04001.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
We studied the interaction of several metal ions with the copper chaperone from Enterococcus hirae (EhCopZ). We show that the stoichiometry of the protein-metal complex varies with the experimental conditions used. At high concentration of the protein in a noncoordinating buffer, a dimer, (EhCopZ)2-metal, was formed. The presence of a potentially coordinating molecule L in the solution leads to the formation of a monomeric ternary complex, EhCopZ-Cu-L, where L can be a buffer or a coordinating molecule (glutathione, tris(2-carboxyethyl)phosphine). This was demonstrated in the presence of glutathione by electrospray ionization MS. The presence of a tyrosine close to the metal-binding site allowed us to follow the binding of cadmium to EhCopZ by fluorescence spectroscopy and to determine the corresponding dissociation constant (Kd = 30 nm). Competition experiments were performed with mercury, copper and cobalt, and the corresponding dissociation constants were calculated. A high preference for copper was found, with an upper limit for the dissociation constant of 10-12 m. These results confirm the capacity of EhCopZ to bind copper at very low concentrations in living cells and may provide new clues in the determination of the mechanism of the uptake and transport of copper by the chaperone EhCopZ.
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Affiliation(s)
- Agathe Urvoas
- Département d'Ingénierie et d'Etudes des Protéines, Direction des Sciences du Vivant, CEA Saclay, Gif sur Yvette, France
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Arnesano F, Banci L, Bertini I, Ciofi‐Baffoni S. Perspectives in Inorganic Structural Genomics: A Trafficking Route for Copper. Eur J Inorg Chem 2004. [DOI: 10.1002/ejic.200300841] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Fabio Arnesano
- Magnetic Resonance Center CERM and Department of Chemistry, University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Florence, Italy, Fax: (internat.) + 39‐055‐4574271
| | - Lucia Banci
- Magnetic Resonance Center CERM and Department of Chemistry, University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Florence, Italy, Fax: (internat.) + 39‐055‐4574271
| | - Ivano Bertini
- Magnetic Resonance Center CERM and Department of Chemistry, University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Florence, Italy, Fax: (internat.) + 39‐055‐4574271
| | - Simone Ciofi‐Baffoni
- Magnetic Resonance Center CERM and Department of Chemistry, University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Florence, Italy, Fax: (internat.) + 39‐055‐4574271
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28
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Current literature in mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2003; 38:1290-1301. [PMID: 14696212 DOI: 10.1002/jms.415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
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She YM, Narindrasorasak S, Yang S, Spitale N, Roberts EA, Sarkar B. Identification of Metal-binding Proteins in Human Hepatoma Lines by Immobilized Metal Affinity Chromatography and Mass Spectrometry. Mol Cell Proteomics 2003; 2:1306-18. [PMID: 14534351 DOI: 10.1074/mcp.m300080-mcp200] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The metalloproteome is defined as the set of proteins that have metal-binding capacity by being metalloproteins or having metal-binding sites. A different metalloproteome may exist for each metal. Mass spectrometric characterization of metalloproteomes provides valuable information relating to cellular disposition of metals physiologically and in metal-associated diseases. We examined the Cu and Zn metalloproteomes in three human hepatoma lines: Hep G2 and Mz-Hep-1, which retain many functional characteristics of normal human hepatocytes, and SK-Hep-1, which is poorly differentiated. Additionally we studied a single specimen of normal human liver and Hep G2 cells depleted in vitro of cellular copper. We used matrix-assisted laser desorption ionization and electrospray ionization quadrupole time-of-flight mass spectrometry to analyze peptide sequences of tryptic digests obtained by either in-gel digestion of metal-binding proteins or peptides on an immobilized metal affinity chromatography column loaded with either Cu or Zn. Mainly high abundance proteins were identified. Cu-binding proteins identified included enolase, albumin, transferrin, and alcohol dehydrogenase as well as certain intracellular chaperone proteins. The Cu metalloproteome was not identical to the Zn metalloproteome. Peptide binding experiments demonstrated that Cu coordination prefers the order of residues histidine > methionine > cysteine. Although the Cu metalloproteome was similar from line to line, subtle differences were apparent. Gel profiling showed more extensive variation in expression of annexin II in SK-Hep-1 and Mz-Hep-1 than in Hep G2 and normal liver tissue. Glycerylphosphorylethanolamine was identified as a post-translational modification at residue Glu-301 of elongation factor 1-alpha in Hep G2. Intracellular copper depletion was associated with loss of the glycerylphosphoryl side group. These findings suggest that post-translational modification could be affected by intracellular actions of copper. Comparison of the Cu and Zn metalloproteomes in Hep G2 with a published general proteome of Hep G2 disclosed little overlap (Seow, T. K., et al. (2001) Proteomics 1, 1249-1263). Proteins in the metalloproteomes of human hepatocytes can be identified by these methods. Variations in these metalloproteomes may have important physiological relevance.
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Affiliation(s)
- Yi-Min She
- Program in Structural Biology and Biochemistry, The Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada
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30
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Current literature in mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2003; 38:1215-1224. [PMID: 14648831 DOI: 10.1002/jms.414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
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