1
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Kim J. Systematic approach to characterize the dynamics of protein adsorption on the surface of biomaterials using proteomics. Colloids Surf B Biointerfaces 2020; 188:110756. [DOI: 10.1016/j.colsurfb.2019.110756] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Revised: 12/03/2019] [Accepted: 12/23/2019] [Indexed: 01/08/2023]
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2
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Optimization of MALDI-TOF mass spectrometry imaging for the visualization and comparison of peptide distributions in dry-cured ham muscle fibers. Food Chem 2019; 283:275-286. [DOI: 10.1016/j.foodchem.2018.12.126] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 12/29/2018] [Accepted: 12/29/2018] [Indexed: 01/02/2023]
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3
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Machálková M, Schejbal J, Glatz Z, Preisler J. A label-free MALDI TOF MS-based method for studying the kinetics and inhibitor screening of the Alzheimer’s disease drug target β-secretase. Anal Bioanal Chem 2018; 410:7441-7448. [DOI: 10.1007/s00216-018-1354-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 08/21/2018] [Accepted: 08/30/2018] [Indexed: 01/19/2023]
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4
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Banerjee S, Coussens NP, Gallat FX, Sathyanarayanan N, Srikanth J, Yagi KJ, Gray JSS, Tobe SS, Stay B, Chavas LMG, Ramaswamy S. Structure of a heterogeneous, glycosylated, lipid-bound, in vivo-grown protein crystal at atomic resolution from the viviparous cockroach Diploptera punctata. IUCRJ 2016; 3:282-93. [PMID: 27437115 PMCID: PMC4937783 DOI: 10.1107/s2052252516008903] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 06/02/2016] [Indexed: 05/20/2023]
Abstract
Macromolecular crystals for X-ray diffraction studies are typically grown in vitro from pure and homogeneous samples; however, there are examples of protein crystals that have been identified in vivo. Recent developments in micro-crystallography techniques and the advent of X-ray free-electron lasers have allowed the determination of several protein structures from crystals grown in cellulo. Here, an atomic resolution (1.2 Å) crystal structure is reported of heterogeneous milk proteins grown inside a living organism in their functional niche. These in vivo-grown crystals were isolated from the midgut of an embryo within the only known viviparous cockroach, Diploptera punctata. The milk proteins crystallized in space group P1, and a structure was determined by anomalous dispersion from the native S atoms. The data revealed glycosylated proteins that adopt a lipocalin fold, bind lipids and organize to form a tightly packed crystalline lattice. A single crystal is estimated to contain more than three times the energy of an equivalent mass of dairy milk. This unique storage form of nourishment for developing embryos allows access to a constant supply of complete nutrients. Notably, the crystalline cockroach-milk proteins are highly heterogeneous with respect to amino-acid sequence, glycosylation and bound fatty-acid composition. These data present a unique example of protein heterogeneity within a single in vivo-grown crystal of a natural protein in its native environment at atomic resolution.
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Affiliation(s)
- Sanchari Banerjee
- Institute of Stem Cell Biology and Regenerative Medicine, Bellary Road, GKVK Campus, Bangalore, Karnataka 560 065, India
| | - Nathan P. Coussens
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - François-Xavier Gallat
- Structural Biology Research Centre, High Energy Accelerator Research Organization, Tsukuba, Ibaraki 305-0801, Japan
| | - Nitish Sathyanarayanan
- Institute of Stem Cell Biology and Regenerative Medicine, Bellary Road, GKVK Campus, Bangalore, Karnataka 560 065, India
| | - Jandhyam Srikanth
- Centre for Cellular and Molecular Platforms, Bellary Road, GKVK Campus, Bangalore, Karnataka 560 065, India
| | - Koichiro J. Yagi
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON M5S 3G5, Canada
| | - James S. S. Gray
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
- Bio-Research Products Inc., Cherry Street, North Liberty, IA 52317, USA
| | - Stephen S. Tobe
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON M5S 3G5, Canada
| | - Barbara Stay
- Department of Biology, University of Iowa, Iowa City, IA 52242, USA
| | - Leonard M. G. Chavas
- Structural Biology Research Centre, High Energy Accelerator Research Organization, Tsukuba, Ibaraki 305-0801, Japan
- Experimental Division, Synchrotron SOLEIL, BP 48, L’Orme des Merisiers, 91192 Gif-sur-Yvette, France
| | - Subramanian Ramaswamy
- Institute of Stem Cell Biology and Regenerative Medicine, Bellary Road, GKVK Campus, Bangalore, Karnataka 560 065, India
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
- Centre for Cellular and Molecular Platforms, Bellary Road, GKVK Campus, Bangalore, Karnataka 560 065, India
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5
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Rešetar D, Marchetti-Deschmann M, Allmaier G, Katalinić JP, Kraljević Pavelić S. Matrix assisted laser desorption ionization mass spectrometry linear time-of-flight method for white wine fingerprinting and classification. Food Control 2016. [DOI: 10.1016/j.foodcont.2015.12.035] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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6
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Kim J. Study of the conformational change of adsorbed proteins on biomaterial surfaces using hydrogen-deuterium exchange with mass spectroscopy. Colloids Surf B Biointerfaces 2016; 141:513-518. [DOI: 10.1016/j.colsurfb.2016.02.023] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Revised: 02/06/2016] [Accepted: 02/08/2016] [Indexed: 10/22/2022]
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7
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Gopal J, Muthu M, Chun SC, Wu HF. State-of-the-art nanoplatform-integrated MALDI-MS impacting resolutions in urinary proteomics. Proteomics Clin Appl 2015; 9:469-81. [PMID: 25736343 DOI: 10.1002/prca.201400182] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Revised: 12/26/2014] [Accepted: 02/26/2015] [Indexed: 12/17/2022]
Abstract
Urine proteomics has become a subject of interest, since it has led to a number of breakthroughs in disease diagnostics. Urine contains information not only from the kidney and the urinary tract but also from other organs, thus urinary proteome analysis allows for identification of biomarkers for both urogenital and systemic diseases. The following review gives a brief overview of the analytical techniques that have been in practice for urinary proteomics. MALDI-MS technique and its current application status in this area of clinical research have been discussed. The review comments on the challenges facing the conventional MALDI-MS technique and the upgradation of this technique with the introduction of nanotechnology. This review projects nano-based techniques such as nano-MALDI-MS, surface-assisted laser desorption/ionization, and nanostructure-initiator MS as the platforms that have the potential in trafficking MALDI-MS from the lab to the bedside.
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Affiliation(s)
- Judy Gopal
- Department of Molecular Biotechnology, Konkuk University, Seoul, Korea
| | - Manikandan Muthu
- Department of Molecular Biotechnology, Konkuk University, Seoul, Korea
| | - Se-Chul Chun
- Department of Molecular Biotechnology, Konkuk University, Seoul, Korea
| | - Hui-Fen Wu
- Department of Chemistry, National Sun Yat-Sen University, Kaohsiung, Taiwan.,School of Pharmacy, College of Pharmacy, Kaohsiung Medical University, Kaohsiung, Taiwan.,Institute of Medical Science and Technology, National Sun Yat-Sen University, Kaohsiung, Taiwan.,Doctoral Degree Program in Marine Biotechnology, National Sun Yat-Sen University and Academia Sinica, Kaohsiung, Taiwan.,Center for Nanosciences and Nanotechnology, National Sun Yat-Sen University, Kaohsiung, Taiwan
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8
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Zhang G, Annan RS, Carr SA, Neubert TA. Overview of peptide and protein analysis by mass spectrometry. ACTA ACUST UNITED AC 2014; 108:10.21.1-10.21.30. [PMID: 25271712 DOI: 10.1002/0471142727.mb1021s108] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Mass spectrometry is an indispensable tool for peptide and protein analysis owing to its speed, sensitivity, and versatility. It can be used to determine amino acid sequences of peptides, and to characterize a wide variety of post-translational modifications such as phosphorylation and glycosylation. Mass spectrometry can also be used to determine absolute and relative protein quantities, and can identify and quantify thousands of proteins from complex samples, which makes it an extremely powerful tool for systems biology studies. The main goals of this unit are to familiarize peptide and protein chemists and biologists with the types of mass spectrometers that are appropriate for the majority of their analytical needs, to describe the kinds of experiments that can be performed with these instruments on a routine basis, and to discuss the kinds of information that these experiments provide.
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Affiliation(s)
- Guoan Zhang
- Kimmel Center for Biology and Medicine, Skirball Institute and Department of Pharmacology, New York University School of Medicine, New York, New York
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9
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Schulz S, Gerhardt D, Meyer B, Seegel M, Schubach B, Hopf C, Matheis K. DMSO-enhanced MALDI MS imaging with normalization against a deuterated standard for relative quantification of dasatinib in serial mouse pharmacology studies. Anal Bioanal Chem 2014; 405:9467-76. [PMID: 24121470 DOI: 10.1007/s00216-013-7393-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Revised: 09/23/2013] [Accepted: 09/23/2013] [Indexed: 10/26/2022]
Abstract
Matrix-assisted laser desorption/ionization mass spectrometry imaging is an emerging powerful technique in drug metabolism and pharmacokinetics research. Despite recent progress in mass-spectrometry-based localization and relative quantification of small-molecule drugs and their metabolites in tissue, improved methods for drug extraction/ionization are required. Furthermore, relative quantification of drugs by mass spectrometry imaging in larger rodent cohorts is a necessary proof-of-concept study to demonstrate the utility of such a workflow in an industrial setting. Using as an example the tyrosine kinase inhibitor dasatinib, a leukemia drug, we demonstrate that inclusion of dimethyl sulfoxide in standard matrix solutions significantly improves ion intensity in mass spectrometry images and reveals enrichment of the drug in mouse kidney medulla. We furthermore show in a time-course study in multiple mice that normalization against a deuterated internal standard, dasatinib-D8, which is applied together with the matrix, makes possible relative quantification of the drug that correlates well with canonical liquid chromatography–tandem mass spectrometry based drug quantification.
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10
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Diggle MA, Clarke SC. Molecular methods for the detection and characterization ofNeisseria meningitidis. Expert Rev Mol Diagn 2014; 6:79-87. [PMID: 16359269 DOI: 10.1586/14737159.6.1.79] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Neisseria meningitidis remains a common global cause of morbidity and mortality. The laboratory confirmation of meningococcal disease is, therefore, very important for individual patient management and for public health management. Through surveillance schemes, it provides long-term epidemiologic data that can be used to inform vaccine policy. Traditional methods, such as latex agglutination and the enzyme-linked immunosorbent assay, are still used, but molecular methods are now also established. In this review, molecular methods for the laboratory confirmation and characterization of meningococci are described. PCR is an invaluable tool in modern biology and can be used to predict the group, type and subtype of meningococci. It is now also used in a fluorescence-based format for increased sensitivity and specificity. The method also provides the amplified DNA for other techniques, such as multilocus sequence typing. Other methods for the discrimination of meningococci have also played and continue to play an important part in epidemiology. For example, pulsed-field gel electrophoresis is highly discriminatory, whilst multilocus enzyme electrophoresis provided the basis for the description of global meningococcal clones and formed the foundation for multilocus sequence typing. Other less commonly used methods, such as matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and pyrosequencing, may increasingly find their way into microbiology reference laboratories. Nevertheless, nucleotide sequencing and laboratory automation have aided the introduction of many methods and provide data that are digitally based and, therefore, highly accurate and portable.
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Affiliation(s)
- Mathew A Diggle
- Stobhill Hospital, Scottish Meningococcus & Pneumococcus Reference Laboratory, Glasgow, UK
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11
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Classical MALDI-MS versus CE-based ESI-MS proteomic profiling in urine for clinical applications. Bioanalysis 2014; 6:247-66. [DOI: 10.4155/bio.13.313] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Human urine is an attractive and informative biofluid for medical diagnosis, which has been shown to reflect the (patho)-physiology of not only the urogenital system, but also others such as the cardiovascular system. For this reason, many studies have concentrated on the study of the urine proteome, aiming to find relevant biomarkers that could be applied in a clinical setting. However, this goal can only be achieved after reliable quantitative and qualitative analysis of the urinary proteome. In the last two decades, MS-based platforms have evolved to become indispensable tools for biomarker research. In this review, we will present and compare two of the most clinically relevant analytical platforms that have been used for the study of the urinary proteome, namely CE-based ESI-MS and classical MALDI-MS. These platforms, although not directly comparable, have been extensively used in proteomic profiling and therefore their comparison is fundamentally relevant to this field.
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12
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Signor L, Boeri Erba E. Matrix-assisted laser desorption/ionization time of flight (MALDI-TOF) mass spectrometric analysis of intact proteins larger than 100 kDa. J Vis Exp 2013. [PMID: 24056304 PMCID: PMC3857990 DOI: 10.3791/50635] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Effectively determining masses of proteins is critical to many biological studies (e.g. for structural biology investigations). Accurate mass determination allows one to evaluate the correctness of protein primary sequences, the presence of mutations and/or post-translational modifications, the possible protein degradation, the sample homogeneity, and the degree of isotope incorporation in case of labelling (e.g.13C labelling). Electrospray ionisation (ESI) mass spectrometry (MS) is widely used for mass determination of denatured proteins, but its efficiency is affected by the composition of the sample buffer. In particular, the presence of salts, detergents, and contaminants severely undermines the effectiveness of protein analysis by ESI-MS. Matrix-assisted laser desorption/ionization (MALDI) MS is an attractive alternative, due to its salt tolerance and the simplicity of data acquisition and interpretation. Moreover, the mass determination of large heterogeneous proteins (bigger than 100 kDa) is easier by MALDI-MS due to the absence of overlapping high charge state distributions which are present in ESI spectra. Here we present an accessible approach for analysing proteins larger than 100 kDa by MALDI-time of flight (TOF). We illustrate the advantages of using a mixture of two matrices (i.e. 2,5-dihydroxybenzoic acid and α-cyano-4-hydroxycinnamic acid) and the utility of the thin layer method as approach for sample deposition. We also discuss the critical role of the matrix and solvent purity, of the standards used for calibration, of the laser energy, and of the acquisition time. Overall, we provide information necessary to a novice for analysing intact proteins larger than 100 kDa by MALDI-MS.
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Affiliation(s)
- Luca Signor
- Institute of Structural Biology "J.P. Ebel", UMR5075, Commissariat à L'Energie Atomique et aux Energies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Université J. Fourier
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13
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Norris JL, Caprioli RM. Analysis of tissue specimens by matrix-assisted laser desorption/ionization imaging mass spectrometry in biological and clinical research. Chem Rev 2013; 113:2309-42. [PMID: 23394164 PMCID: PMC3624074 DOI: 10.1021/cr3004295] [Citation(s) in RCA: 509] [Impact Index Per Article: 46.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Jeremy L. Norris
- National Research Resource for Imaging Mass Spectrometry, Mass Spectrometry Research Center, and Department of Biochemistry, Vanderbilt University School of Medicine, 9160 Medical Research Building III, 465 21st Avenue South, Nashville, TN 37232-8575
| | - Richard M. Caprioli
- National Research Resource for Imaging Mass Spectrometry, Mass Spectrometry Research Center, and Department of Biochemistry, Vanderbilt University School of Medicine, 9160 Medical Research Building III, 465 21st Avenue South, Nashville, TN 37232-8575
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14
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Bllaci L, Kjellström S, Eliasson L, Friend JR, Yeo LY, Nilsson S. Fast surface acoustic wave-matrix-assisted laser desorption ionization mass spectrometry of cell response from islets of Langerhans. Anal Chem 2013; 85:2623-9. [PMID: 23384197 DOI: 10.1021/ac3019125] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A desire for higher speed and performance in molecular profiling analysis at a reduced cost is driving a trend in miniaturization and simplification of procedures. Here we report the use of a surface acoustic wave (SAW) atomizer for fast sample handling in matrix-assisted laser desorption ionization mass spectrometry (MALDI MS) peptide and protein profiling of Islets of Langerhans, for future type 2 diabetes (T2D) studies. Here the SAW atomizer was used for ultrasound (acoustic) extraction of insulin and other peptide hormones released from freshly prepared islets, stimulated directly on a membrane. A high energy propagating SAW atomizes the membrane-bound liquid into approximately 2 μm diameter droplets, rich in cell-released molecules. Besides acting as a sample carrier, the membrane provides a purification step by entrapping cell clusters and other impurities within its fibers. A new SAW-based sample-matrix deposition method for MALDI MS was developed and characterized by a strong insulin signal, and a limit of detection (LOD) lower than 100 amol was achieved. Our results support previous work reporting the SAW atomizer as a fast and inexpensive tool for ultrasound, membrane-based sample extraction. When interfaced with MALDI MS, the SAW atomizer constitutes a valuable tool for rapid cell studies. Other biomedical applications of SAW-MALDI MS are currently being developed, aiming at fast profiling of biofluids. The membrane sampling is a simplistic and noninvasive collection method of limited volume biofluids such as the gingival fluid and the tearfilm.
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Affiliation(s)
- Loreta Bllaci
- Lund University, Center for Chemistry and Chemical Engineering, Pure and Applied Biochemistry, Box 124, 221 00 Lund, Sweden
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15
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Special issue in quantitative mass spectrometric proteomics. Amino Acids 2012; 43:1005-7. [PMID: 22821271 DOI: 10.1007/s00726-012-1350-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Accepted: 06/22/2012] [Indexed: 10/28/2022]
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16
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Lee J, Jayathilaka LP, Gupta S, Huang JS, Lee BS. Gold ion-angiotensin peptide interaction by mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:942-951. [PMID: 22351290 DOI: 10.1007/s13361-011-0328-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2011] [Revised: 12/21/2011] [Accepted: 12/22/2011] [Indexed: 05/31/2023]
Abstract
Stimulated by the interest in developing gold compounds for treating cancer, gold ion-angiotensin peptide interactions are investigated by mass spectrometry. Under the experimental conditions used, the majority of gold ion-angiotensin peptide complexes contain gold in the oxidation states I and III. Both ESI-MS and MALDI-TOF MS detect singly/multiply charged ions for mononuclear/multinuclear gold-attached peptides, which are represented as [peptide + a Au(I) + b Au(III) + (e - a -3b) H](e+), where a,b ≥ 0 and e is charge. ESI-MS data shows singly/multiply charged ions of Au(I)-peptide and Au(III)-peptide complexes. This study reveals that MALDI-TOF MS mainly detects singly charged Au(I)-peptide complexes, presumably due to the ionization process. The electrons in the MALDI plume seem to efficiently reduce Au(III) to Au(I). MALDI also tends to enhance the higher polymeric forms of gold-peptide complexes regardless of the laser power used. Collision-induced dissociation experiments of the mononuclear and dinuclear gold-attached peptide ions for angiotensin peptides show that the gold ion (a soft acid) binding sites are in the vicinity of Cys (a soft ligand), His (a major anchor of peptide for metal ion chelation), and the basic residue Arg. Data also suggests that the abundance of gold-attached peptides increases with higher gold concentration until saturation, after which an increase in gold ion concentration leads to the aggregation and/or precipitation of gold-bound peptides.
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Affiliation(s)
- Jenny Lee
- Illinois Mathematics and Science Academy, 1500 Sullivan Rd, Aurora, IL 60506-1000, USA
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17
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Rivera-Tirado E, Wesdemiotis C. Fragmentation characteristics of b(n) (n=2-15) ions from protonated peptides. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2011; 25:2283-2290. [PMID: 21755549 DOI: 10.1002/rcm.5115] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The fragmentation reactions of protonated oligoalanines (trialanine, tetraalanine and pentaalanine) and the fragments present in the electrospray ionization (ESI) mass spectrum of polyalanine have been studied by collisionally activated dissociation (CAD) mass spectrometry (MS(2) and MS(3) experiments). The MS(n) experiments provided strong evidence that the m/z 71n+1 ion series in the ESI mass spectrum of polyalanine is a b(n) series. These ions are formed via the b(n) -y(m) pathway of amide bond cleavage, which results in the formation of a proton-bound complex of an oxazolone and a peptide/amino acid. Also, the MS(2) spectra of the b(n) series from polyalanine revealed that the chain length of b(n) ions influences significantly the dissociations taking place. For example, b(n) ions start losing H(2)O at n ≥5 and the losses of CO and CO+NH(3) decrease in intensity from b(2) to b(15). The elimination of H(2)O+NH(3) and the elimination of 61 mass (HN=C=O+H(2)O) commence with b(6); their abundances initially increase up to ~ b(8)-b(9) and then gradually decrease until b(15) (largest fragment studied). The tandem mass spectrometry experiments help to elucidate the dissociation mechanisms of the observed structures of biopolymer fragments.
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Zhang G, Annan RS, Carr SA, Neubert TA. Overview of peptide and protein analysis by mass spectrometry. ACTA ACUST UNITED AC 2011; Chapter 16:Unit16.1. [PMID: 21104985 DOI: 10.1002/0471140864.ps1601s62] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Mass spectrometry is an indispensable tool for peptide and protein analysis owing to its speed, sensitivity, and versatility. It can be used to determine amino acid sequences of peptides, and to characterize a wide variety of post-translational modifications such as phosphorylation and glycosylation. Mass spectrometry can also be used to determine absolute and relative protein quantities, and can identify and quantify thousands of proteins from complex samples, which makes it an extremely powerful tool for systems biology studies. The main goals of this unit are to familiarize peptide and protein chemists and biologists with the types of mass spectrometers that are appropriate for the majority of their analytical needs, to describe the kinds of experiments that can be performed with these instruments on a routine basis, and to discuss the kinds of information that these experiments provide.
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Affiliation(s)
- Guoan Zhang
- Kimmel Center for Biology and Medicine, Skirball Institute and Department of Pharmacology, New York University School of Medicine, New York, New York, USA
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19
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Knapp-Mohammady M, Young AB, Paizs B, Harrison AG. Fragmentation of doubly-protonated Pro-His-Xaa tripeptides: formation of b(2)(2+) ions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2009; 20:2135-2143. [PMID: 19683937 DOI: 10.1016/j.jasms.2009.07.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2009] [Revised: 06/29/2009] [Accepted: 07/01/2009] [Indexed: 05/28/2023]
Abstract
When ionized by electrospray from acidic solutions, the tripeptides Pro-His-Xaa (Xaa = Gly, Ala, Leu) form abundant doubly-protonated ions, [M + 2H]2+. Collision-induced dissociation (CID) of these doubly-protonated species results, in part, in formation of b(2)(2+) ions, which fragment further by loss of CO to form a(2)(2+) ions; the latter fragment by loss of CO to form the Pro and His iminium [immonium is commonly used in peptide MS work] ions. Although larger doubly-charged b ions are known, this represents the first detailed study of b(2)(2+) ions in CID of small doubly protonated peptides. The most abundant CID products of the studied doubly-protonated peptides arise mainly in charge separation involving two primary fragmentation channels, formation of the b2/y1 pair and formation of the a1/y2 pair. Combined molecular dynamics and density functional theory calculations are used to gain insight into the structures and fragmentation pathways of doubly-protonated Pro-His-Gly including the energetics of potential protonation sites, backbone cleavages, post-cleavage charge-separation reactions and the isomeric structures of b(2)(2+) ions. Three possible structures are considered for the b(2)(2+) ions: the oxazolone, diketopiperazine, and fused ring isomers. The last is formed by cleavage of the His-Gly amide bond on a pathway that is initiated by nucleophilic attack of one of the His side-chain imidazole nitrogens. Our calculations indicate the b(2)(2+) ion population is dominated by the oxazolone and/or fused ring isomers.
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20
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Intoh A, Kurisaki A, Fukuda H, Asashima M. Separation with zwitterionic hydrophilic interaction liquid chromatography improves protein identification by matrix-assisted laser desorption/ionization-based proteomic analysis. Biomed Chromatogr 2009; 23:607-14. [PMID: 19280682 DOI: 10.1002/bmc.1159] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Comprehensive proteomic analyses necessitate efficient separation of peptide mixtures for the subsequent identification of proteins by mass spectrometry (MS). However, digestion of proteins extracted from cells and tissues often yields complex peptide mixtures that confound direct comprehensive MS analysis. This study investigated a zwitterionic hydrophilic interaction liquid chromatography (ZIC-HILIC) technique for the peptide separation step, which was verified by subsequent MS analysis. Human serum albumin (HSA) was the model protein used for this analysis. HSA was digested with trypsin and resolved by ZIC-HILIC or conventional strong cation exchange (SCX) prior to MS analysis for peptide identification. Separation with ZIC-HILIC significantly improved the identification of HSA peptides over SCX chromatography. Detailed analyses of the identified peptides revealed that the ZIC-HILIC has better peptide fractionation ability. We further demonstrated that ZIC-HILIC is useful for quantitatively surveying cell surface markers specifically expressed in undifferentiated embryonic stem cells. These results suggested the value of ZIC-HILIC as a novel and efficient separation method for comprehensive and quantitative proteomic analyses.
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Affiliation(s)
- Atsushi Intoh
- Department of Life Sciences Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
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Abboud N, De Jesus M, Nakouzi A, Cordero RJB, Pujato M, Fiser A, Rivera J, Casadevall A. Identification of linear epitopes in Bacillus anthracis protective antigen bound by neutralizing antibodies. J Biol Chem 2009; 284:25077-86. [PMID: 19617628 DOI: 10.1074/jbc.m109.022061] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Protective antigen (PA), the binding subunit of anthrax toxin, is the major component in the current anthrax vaccine, but the fine antigenic structure of PA is not well defined. To identify linear neutralizing epitopes of PA, 145 overlapping peptides covering the entire sequence of the protein were synthesized. Six monoclonal antibodies (mAbs) and antisera from mice specific for PA were tested for their reactivity to the peptides by enzyme-linked immunosorbent assays. Three major linear immunodominant B-cell epitopes were mapped to residues Leu(156) to Ser(170), Val(196) to Ile(210), and Ser(312) to Asn(326) of the PA protein. Two mAbs with toxin-neutralizing activity recognized two different epitopes in close proximity to the furin cleavage site in domain 1. The three-dimensional complex structure of PA and its neutralizing mAbs 7.5G and 19D9 were modeled using the molecular docking method providing models for the interacting epitope and paratope residues. For both mAbs, LeTx neutralization was associated with interference with furin cleavage, but they differed in effectiveness depending on whether they bound on the N- or C-terminal aspect of the cleaved products. The two peptides containing these epitopes that include amino acids Leu(156)-Ser(170) and Val(196)-Ile(210) were immunogenic and elicited neutralizing antibody responses to PA. These results identify the first linear neutralizing epitopes of PA and show that peptides containing epitope sequences can elicit neutralizing antibody responses, a finding that could be exploited for vaccine design.
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Affiliation(s)
- Nareen Abboud
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
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22
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Harrison AG. Fragmentation reactions of some peptide b3 ions: an energy-resolved study. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2009; 23:1298-1302. [PMID: 19306282 DOI: 10.1002/rcm.4003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The fragmentation reactions of b3 ions of nominal structure AAAoxa, YAAoxa, AYAoxa and AAYoxa have been studied as a function of collision energy, allowing the construction of breakdown graphs expressing in a qualitative way the energy dependence of the fragmentation reactions. The primary fragmentation reactions of the AAAoxa b3 ion involve formation of the a3* (a3-NH3) ion and the b2 ion, with the latter becoming the dominant product at higher internal energies. For both YAAoxa and AYAoxa b3 ions the pathway to a3* is relatively minor with formation of b2 the dominant primary fragmentation reaction. For the AAYoxa b3 ion, in addition to a3*, abundant formation of the tyrosine (Y) iminium ion is observed with only minor formation of the b2 ion. The results support and expand upon the detailed mechanism of fragmentation of b3 ions proposed by Cooper et al. (J. Am. Soc. Mass Spectrom. 2006; 17: 1654).
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Affiliation(s)
- Alex G Harrison
- Department of Chemistry, University of Toronto, Toronto, Canada.
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23
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Abstract
There is accumulating evidence of the importance of linear polysaccharides in modulating biological phenomena in both the normal and the diseased states. This layer of regulation results from interactions between polysaccharides and other biomolecules, such as proteins, at the cell-extracellular matrix interface. The specific sequence of chemical modifications within the polymer backbone imparts a potential for interaction with other molecular species, and thus there exists important information within the various sulfation, acetylation, and epimerization states of such complex carbohydrates. A variety of factors have made the deciphering of this chemical code elusive. To this end, this report describes several techniques to elucidate the structural information inherent in glycosaminoglycan species. First, the use of depolymerizing enzymes that cleave polysaccharides at specific sites is described. Then, capillary electrophoretic (CE) techniques are employed to characterize the disaccharide species present in an enzymatically-cleaved polysaccharide sample. Mass spectrometry (MS) procedures can further be used to establish the length of an oligosaccharide chain and the presence of specific functional groups.
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Affiliation(s)
- Vikas Prabhakar
- Division of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
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24
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Wang CY, Staniforth V, Chiao MT, Hou CC, Wu HM, Yeh KC, Chen CH, Hwang PI, Wen TN, Shyur LF, Yang NS. Genomics and proteomics of immune modulatory effects of a butanol fraction of echinacea purpurea in human dendritic cells. BMC Genomics 2008; 9:479. [PMID: 18847511 PMCID: PMC2571112 DOI: 10.1186/1471-2164-9-479] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2008] [Accepted: 10/13/2008] [Indexed: 11/10/2022] Open
Abstract
Background Echinacea spp. extracts and the derived phytocompounds have been shown to induce specific immune cell activities and are popularly used as food supplements or nutraceuticals for immuno-modulatory functions. Dendritic cells (DCs), the most potent antigen presenting cells, play an important role in both innate and adaptive immunities. In this study, we investigated the specific and differential gene expression in human immature DCs (iDCs) in response to treatment with a butanol fraction containing defined bioactive phytocompounds extracted from stems and leaves of Echinacea purpurea, that we denoted [BF/S+L/Ep]. Results Affymetrix DNA microarray results showed significant up regulation of specific genes for cytokines (IL-8, IL-1β, and IL-18) and chemokines (CXCL 2, CCL 5, and CCL 2) within 4 h after [BF/S+L/Ep] treatment of iDCs. Bioinformatics analysis of genes expressed in [BF/S+L/Ep]-treated DCs revealed a key-signaling network involving a number of immune-modulatory molecules leading to the activation of a downstream molecule, adenylate cyclase 8. Proteomic analysis showed increased expression of antioxidant and cytoskeletal proteins after treatment with [BF/S+L/Ep] and cichoric acid. Conclusion This study provides information on candidate target molecules and molecular signaling mechanisms for future systematic research into the immune-modulatory activities of an important traditional medicinal herb and its derived phytocompounds.
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Affiliation(s)
- Chien-Yu Wang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan.
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25
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Seibert C, Veldkamp CT, Peterson FC, Chait BT, Volkman BF, Sakmar TP. Sequential tyrosine sulfation of CXCR4 by tyrosylprotein sulfotransferases. Biochemistry 2008; 47:11251-62. [PMID: 18834145 DOI: 10.1021/bi800965m] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
CXC-chemokine receptor 4 (CXCR4) is a G protein-coupled receptor for stromal cell-derived factor-1 (SDF-1/CXCL12). SDF-1-induced CXCR4 signaling is indispensable for embryonic development and crucial for immune cell homing and has been implicated in metastasis of numerous types of cancer. CXCR4 also serves as the major coreceptor for cellular entry of T-cell line-tropic (X4) HIV-1 strains. Tyrosine residues in the N-terminal tail of CXCR4, which are post-translationally sulfated, are implicated in the high-affinity binding of SDF-1 to CXCR4. However, the specific roles of three potential tyrosine sulfation sites are not well understood. We investigated the pattern and sequence of CXCR4 sulfation by using recombinant human tyrosylprotein sulfotransferases TPST-1 and TPST-2 to modify a peptide that corresponds to amino acids 1-38 of the receptor (CXCR4 1-38). We analyzed the reaction products with a combination of reversed-phase HPLC, proteolytic cleavage, and mass spectrometry. We found that CXCR4 1-38 is sulfated efficiently by both TPST enzymes, leading to a final product with three sulfotyrosine residues. Sulfates were added stepwise to the peptide, producing specific intermediates with one or two sulfotyrosines. The pattern of sulfation in these intermediates indicates that with both enzymes Tyr-21 is sulfated first, followed by Tyr-12 or Tyr-7. Using heteronuclear NMR spectroscopy, we demonstrated that the SDF-1 binding affinity of CXCR4 1-38 increases with the number of sulfotyrosines present, which suggests a potential physiological role for sulfation of all three sites in the N-terminus of CXCR4. These results provide a structural basis for understanding the role of post-translational tyrosine sulfation in SDF-1-induced CXCR4 signaling.
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Affiliation(s)
- Christoph Seibert
- Laboratory of Molecular Biology and Biochemistry, The Rockefeller University, New York, New York 10065, USA.
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26
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Mass spectrometry of full-length integral membrane proteins to define functionally relevant structural features. Methods 2008; 46:54-61. [DOI: 10.1016/j.ymeth.2008.10.021] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2008] [Revised: 07/30/2008] [Accepted: 10/20/2008] [Indexed: 10/21/2022] Open
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Aggregation and catabolism of disease-associated intra-Abeta mutations: reduced proteolysis of AbetaA21G by neprilysin. Neurobiol Dis 2008; 31:442-50. [PMID: 18602473 DOI: 10.1016/j.nbd.2008.06.001] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2008] [Revised: 06/04/2008] [Accepted: 06/05/2008] [Indexed: 01/23/2023] Open
Abstract
Five point mutations within the amyloid beta-protein (Abeta) sequence of the APP gene are associated with hereditary diseases which are similar or identical to Alzheimer's disease and encode: the A21G (Flemish), E22G (Arctic), E22K (Italian), E22Q (Dutch) and the D23N (Iowa) amino acid substitutions. Although a substantial body of data exists on the effects of these mutations on Abeta production, whether or not intra-Abeta mutations alter degradation and how this relates to their aggregation state remain unclear. Here we report that the E22G, E22Q and the D23N substitutions significantly increase fibril nucleation and extension, whereas the E22K substitution exhibits only an increased rate of extension and the A21G substitution actually causes a decrease in the extension rate. These substantial differences in aggregation together with our observation that aggregated wild type Abeta(1-40) was much less well degraded than monomeric wild type Abeta(1-40), prompted us to assess whether or not disease-associated intra-Abeta mutations alter proteolysis independent of their effects on aggregation. Neprilysin (NEP), insulin degrading enzyme (IDE) and plasmin play a major role in Abeta catabolism, therefore we compared the ability of these enzymes to degrade wild type and mutant monomeric Abeta peptides. Experiments investigating proteolysis revealed that all monomeric peptides are degraded similarly by IDE and plasmin, but that the Flemish peptide was degraded significantly more slowly by NEP than wild type Abeta or any of the other mutant peptides. This finding suggests that resistance to NEP-mediated proteolysis may underlie the pathogenicity associated with the A21G mutation.
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28
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Begg GE, Harper SL, Speicher DW. Characterizing recombinant proteins using HPLC gel filtration and mass spectrometry. ACTA ACUST UNITED AC 2008; Chapter 7:Unit 7.10. [PMID: 18429196 DOI: 10.1002/0471140864.ps0710s16] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Recombinant proteins are subject to many forms of heterogeneity, including aggregation, proteolytic degradation, chemical modification, mutation, and incorrect translation. This unit describes methods for the detection and identification of these problems using analytical HPLC gel filtration and MALDI-MS. Preliminary characterization of recombinants is necessary before the structure or function of the protein can be investigated.
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Affiliation(s)
- G E Begg
- The Wistar Institute, Philadelphia, Pennsylvania, USA
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29
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Avdoshenko SM, Ioffe IN, Kozlov AA, Markov VY, Nikolaev EN, Sidorov LN. Novel possibilities in the study of isolated carbon nanotubes. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2008; 22:1372-1376. [PMID: 18381622 DOI: 10.1002/rcm.3508] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
We report the first detection of carbon nanotubes in the gas phase in a matrix-assisted laser desorption/ionization (MALDI) mass spectrometric experiment. These observations open the possibility of studying isolated nanotubes in the gas phase by means of various spectroscopic methods and a possible way to separate them.
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30
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ERRA-BALSELLS R, NONAMI H. UV-MALDI-TOF MS Analysis of Carbohydrates. Reviewing Comparative Studies Performed Using nor-Harmane and Classical UV-MALDI Matrices. ACTA ACUST UNITED AC 2008. [DOI: 10.2525/ecb.46.65] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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31
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Wong CCL, Xu T, Rai R, Bailey AO, Yates JR, Wolf YI, Zebroski H, Kashina A. Global analysis of posttranslational protein arginylation. PLoS Biol 2007; 5:e258. [PMID: 17896865 PMCID: PMC1988855 DOI: 10.1371/journal.pbio.0050258] [Citation(s) in RCA: 115] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2007] [Accepted: 07/30/2007] [Indexed: 11/27/2022] Open
Abstract
Posttranslational arginylation is critical for embryogenesis, cardiovascular development, and angiogenesis, but its molecular effects and the identity of proteins arginylated in vivo are largely unknown. Here we report a global analysis of this modification on the protein level and identification of 43 proteins arginylated in vivo on highly specific sites. Our data demonstrate that unlike previously believed, arginylation can occur on any N-terminally exposed residue likely defined by a structural recognition motif on the protein surface, and that it preferentially affects a number of physiological systems, including cytoskeleton and primary metabolic pathways. The results of our study suggest that protein arginylation is a general mechanism for regulation of protein structure and function and outline the potential role of protein arginylation in cell metabolism and embryonic development. A common cellular mechanism for the regulation of proteins, once they have been translated from mRNA, is the addition and removal of chemical groups via enzymatic reactions. The posttranslational addition of arginyl groups is critical for the embryonic development and survival of an organism, but the molecular effects and the identity of proteins arginylated in vivo are largely unknown. We developed a technique to screen large numbers of proteins for this modification and identified 43 proteins arginylated in vivo on highly specific sites. Arginylation can occur on any exposed residue at the N-terminus of a protein and appears to require a specific structural recognition motif on the protein surface. It preferentially affects a number of physiological systems, including cytoskeleton and primary metabolic pathways and seems to be a general mechanism for regulation of protein structure and function. Our data provide insights into the previously unknown arginylation-dependent mechanisms of the regulation of embryonic development. A comprehensive study indicates that protein arginylation may be a general mechanism for regulation of protein structure and function, similar to other major posttranslational modifications.
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Affiliation(s)
- Catherine C. L Wong
- The Scripps Research Institute, LaJolla, California, United States of America
| | - Tao Xu
- The Scripps Research Institute, LaJolla, California, United States of America
| | - Reena Rai
- Department of Animal Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Aaron O Bailey
- The Scripps Research Institute, LaJolla, California, United States of America
| | - John R Yates
- The Scripps Research Institute, LaJolla, California, United States of America
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Henry Zebroski
- Rockefeller University, New York, NewYork, United States of America
| | - Anna Kashina
- Department of Animal Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- * To whom correspondence should be addressed. E-mail:
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32
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Forbes MW, Jockusch RA, Young AB, Harrison AG. Fragmentation of protonated dipeptides containing arginine. Effect of activation method. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2007; 18:1959-66. [PMID: 17869129 DOI: 10.1016/j.jasms.2007.08.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2007] [Revised: 08/07/2007] [Accepted: 08/07/2007] [Indexed: 05/17/2023]
Abstract
The fragmentation reactions of the protonated dipeptides Gly-Arg and Arg-Gly have been studied using collision-induced dissociation (CID) in a quadrupole ion trap, by in-source CID in a single-quadrupole mass spectrometer and by CID in the quadrupole cell of a QqTOF mass spectrometer. In agreement with earlier quadrupole ion trap studies (Farrugia, J. M.; O'Hair, R. A. J., Int. J. Mass Spectrom., 2003, 222, 229), the CID mass spectra obtained with the ion trap for the MH(+) ions and major fragment ions are very similar for the two isomers indicating rearrangement to a common structure before fragmentation. In contrast, in-source CID of the MH(+) ions and QqTOF CID of the MH(+), [MH - NH(3)](+) and [MH <23 HN = C(NH(2))(2)](+) ions provide distinctly different spectra for the isomeric dipeptides, indicating that rearrangement to a common structure has not occurred to a significant extent under these conditions even near the threshold for fragmentation in the QqTOF instrument. Clearly, under normal operating conditions significantly different fragmentation behavior is observed in the ion trap and beam-type experiments. This different behavior probably can be attributed to the shorter observation times and concomitant higher excitation energies in the in-source and QqTOF experiments compared to the long observation times and lower excitation energies relevant to the ion trap experiments. Based largely on elemental compositions derived from accurate mass measurements in QqTOF studies fragmentation schemes are proposed for the MH(+), [MH - NH(3)](+), and [MH - (HN = C(NH(2))(2))](+) ions.
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Affiliation(s)
- Matthew W Forbes
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
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33
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Manning LR, Russell JE, Padovan JC, Chait BT, Popowicz A, Manning RS, Manning JM. Human embryonic, fetal, and adult hemoglobins have different subunit interface strengths. Correlation with lifespan in the red cell. Protein Sci 2007; 16:1641-58. [PMID: 17656582 PMCID: PMC2203358 DOI: 10.1110/ps.072891007] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The different types of naturally occurring, normal human hemoglobins vary in their tetramer-dimer subunit interface strengths (stabilities) by three orders of magnitude in the liganded (CO or oxy) state. The presence of embryonic zeta-subunits leads to an average 20-fold weakening of tetramer-dimer interfaces compared to corresponding hemoglobins containing adult alpha-subunits. The dimer-monomer interfaces of these hemoglobins differ by at least 500-fold in their strengths; such interfaces are weak if they contain zeta-subunits and exchange with added beta-subunits in the form of beta(4) (HbH) significantly faster than do those with alpha-subunits. Subunit exchange occurs at the level of the dimer, although tetramer formation reciprocally influences the amount of dimer available for exchange. Competition between subunit types occurs so that pairs of weak embryonic hemoglobins can exchange subunits to form the stronger fetal and adult hemoglobins. The dimer strengths increase in the order Hb Portland-2 (zeta(2)beta(2)) < Hb Portland-1 (zeta(2)gamma(2)) approximately equal Hb Gower-1 (zeta(2)epsilon(2)) < Hb Gower-2 (alpha(2)epsilon(2)) < HbF(1) < HbF (alpha(2)gamma(2)) < HbA(2) (alpha(2)delta(2)), i.e., from embryonic to fetal to adult types, representing maturation from weaker to stronger monomer-monomer subunit contacts. This increasing order recapitulates the developmental order in which globins are expressed (embryonic --> fetal --> adult), suggesting that the intrinsic binding properties of the subunits themselves regarding the strengths of interfaces they form with competing subunits play an important role in the dynamics of protein assemblies and networks.
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Affiliation(s)
- Lois R Manning
- Department of Biology, Northeastern University, Boston, Massachusetts 02115, USA
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34
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Singh AK, Gupta S. Analysis of recombinant human erythropoietin and darbepoietin in spiked plasma. Proteomics Clin Appl 2007; 1:626-39. [DOI: 10.1002/prca.200600972] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2006] [Indexed: 11/10/2022]
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35
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Poon TCW. Opportunities and limitations of SELDI-TOF-MS in biomedical research: practical advices. Expert Rev Proteomics 2007; 4:51-65. [PMID: 17288515 DOI: 10.1586/14789450.4.1.51] [Citation(s) in RCA: 111] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Surface-enhanced laser desorption/ionization time-of-flight mass spectrometry, or surface-enhanced laser desorption/ionization ProteinChip technology, has been widely used in obtaining the quantitative profiles of tissue proteomes, particularly plasma proteomes. Its high-throughput nature and simplicity in its experimental procedures have allowed this technology to become a popular research tool for biomarker discovery in the past 5 years. After accumulating more research experiences, researchers now have a better understanding of the characteristics and limitations of this technology, as well as the pitfalls in biomarker research, by undertaking a comparative proteomic approach. This review provides an overview of the surface-enhanced laser desorption/ionization time-of-flight mass spectrometry, discusses its limitations and provides some possible solutions to help apply this technology to biomarker research.
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Affiliation(s)
- Terence C W Poon
- Li Ka Shing Institute of Health Sciences, Department of Medicine & Therapeutics, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong Special Administrative Region, China.
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36
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Sugiura N, Shimokata S, Watanabe H, Kimata K. MS analysis of chondroitin polymerization: effects of Mn2+ ions on the stability of UDP-sugars and chondroitin synthesis. Anal Biochem 2007; 365:62-73. [PMID: 17395146 DOI: 10.1016/j.ab.2007.02.023] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2007] [Revised: 02/12/2007] [Accepted: 02/19/2007] [Indexed: 12/01/2022]
Abstract
Chondroitin polymerase from Escherichia coli strain K4 (K4CP) synthesizes chondroitin (CH) polysaccharides by the alternate addition of N-acetyl-D-galactosamine (GalNAc) and D-glucuronic acid (GlcA) to acceptor CH oligosaccharides in the presence of Mn(2+) ions. In this study, we applied matrix-assisted laser desorption ionization and time-of-flight mass spectrometry (MALDI-TOF MS) for the further characterization of the products synthesized by K4CP from CH hexasaccharide as an initial acceptor and UDP-GalNAc and UDP-GlcA as donors. The analysis identified individual CH chains of various lengths and enabled the calculation of their average molecular weights. The ion peaks of the CH chains synthesized in the short-time reactions demonstrated not only the alternate addition of GlcA and GalNAc but also the more frequent transfer of GlcA and GalNAc, consistent with our previous kinetic data. In contrast, the MS spectra of the chains synthesized in the long-time reaction showed that CH chains containing GalNAc at the nonreducing ends were more abundant than those containing GlcA. We found that this inconsistency was due to the preferential decomposition of UDP-GlcA by Mn(2+) ions. We defined the optimal conditions to yield further elongation of the CH chains that have nearly equal numbers of GlcA and GalNAc residues at the nonreducing ends.
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Affiliation(s)
- Nobuo Sugiura
- Institute for Molecular Science of Medicine, Aichi Medical University, Yazako, Nagakute, Aichi 480-1195, Japan
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37
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Qian W, Yu C, Qin H, Liu X, Zhang A, Johansen IE, Wang D. Molecular and functional analysis of phosphomannomutase (PMM) from higher plants and genetic evidence for the involvement of PMM in ascorbic acid biosynthesis in Arabidopsis and Nicotiana benthamiana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2007; 49:399-413. [PMID: 17217471 DOI: 10.1111/j.1365-313x.2006.02967.x] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Phosphomannomutase (PMM) catalyzes the interconversion of mannose-6-phosphate and mannose-1-phosphate. However, systematic molecular and functional investigations on PMM from higher plants have hitherto not been reported. In this work, PMM cDNAs were isolated from Arabidopsis, Nicotiana benthamiana, soybean, tomato, rice and wheat. Amino acid sequence comparisons indicated that plant PMM proteins exhibited significant identity to their fungal and mammalian orthologs. In line with the similarity in primary structure, plant PMM complemented the sec53-6 temperature sensitive mutant of Saccharomyces cerevisiae. Histidine-tagged Arabidopsis PMM (AtPMM) purified from Escherichia coli converted mannose-1-phosphate into mannose-6-phosphate and glucose-1-phosphate into glucose-6-phosphate, with the former reaction being more efficient than the latter one. In Arabidopsis and N. benthamiana, PMM was constitutively expressed in both vegetative and reproductive organs. Reducing the PMM expression level through virus-induced gene silencing caused a substantial decrease in ascorbic acid (AsA) content in N. benthamiana leaves. Conversely, raising the PMM expression level in N. benthamiana using viral-vector-mediated ectopic expression led to a 20-50% increase in AsA content. Consistent with this finding, transgenic expression of an AtPMM-GFP fusion protein in Arabidopsis also increased AsA content by 25-33%. Collectively, this study improves our understanding on the molecular and functional properties of plant PMM and provides genetic evidence on the involvement of PMM in the biosynthesis of AsA in Arabidopsis and N. benthamiana plants.
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Affiliation(s)
- Weiqiang Qian
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
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38
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Kao WY, Qin J, Fushitani K, Smith SS, Gorr TA, Riggs CK, Knapp JE, Chait BT, Riggs AF. Linker chains of the gigantic hemoglobin of the earthworm Lumbricus terrestris: primary structures of linkers L2, L3, and L4 and analysis of the connectivity of the disulfide bonds in linker L1. Proteins 2006; 63:174-87. [PMID: 16425180 DOI: 10.1002/prot.20852] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The extracellular hemoglobin (Hb) of the earthworm, Lumbricus terrestris, has four major kinds of globin chains: a, b, c, and d, present in equimolar proportions, and additional non-heme, non-globin scaffolding chains called linkers that are required for the calcium-dependent assembly of the full-sized molecule. The amino acid sequences of all four of the globin chains and one of the linkers (L1) have previously been determined. The amino acid sequences via cDNA of each of the three remaining linkers, L2, L3, and L4, have been determined so that the sequences of all constituent polypeptides of the hemoglobin are now known. Each linker has a highly conserved cysteine-rich segment of approximately 40 residues that is homologous with the seven ligand-binding repeats of the human low-density lipoprotein receptor (LDLR). Analysis of linker L1 shows that the connectivity of the three disulfide bonds is exactly the same as in the LDLR ligand-binding repeats. The presence of a calcium-binding site comprising one glutamyl and three aspartyl residues in both the LDLR repeats and in the linkers supports the suggestion that calcium is required for the folding and disulfide connectivity of the linkers as in the LDLR repeats. Linker L2 is markedly heterogeneous and contains unusual glycine-rich sequences near the NH2-terminus and a polar zipper-like sequence with imperfect repeats of Asp-Asp-His at the carboxyl terminus. Similar Asp-Asp-His repeats have been found in a protein homologous to superoxide dismutase in the hemolymph of certain mussels. These repeats may function as metal-binding sites.
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MESH Headings
- Amino Acid Sequence
- Animals
- Aspartic Acid/chemistry
- Base Sequence
- Binding Sites
- Calcium/chemistry
- Calcium/metabolism
- Chromatography, High Pressure Liquid
- Cysteine/chemistry
- DNA, Complementary/metabolism
- Disulfides/chemistry
- Dithiothreitol/pharmacology
- Glutamic Acid/chemistry
- Heme/chemistry
- Hemoglobins/chemistry
- Histidine/chemistry
- Humans
- Ligands
- Mass Spectrometry
- Models, Molecular
- Molecular Sequence Data
- Oligochaeta
- Protein Binding
- Protein Processing, Post-Translational
- Protein Structure, Tertiary
- RNA, Messenger/metabolism
- Receptors, LDL/chemistry
- Sequence Homology, Amino Acid
- Sodium Dodecyl Sulfate/chemistry
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
- Superoxide Dismutase/chemistry
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Affiliation(s)
- Wen-Yen Kao
- Institute of Cellular and Molecular Biology, Section of Neurobiology, School of Biological Sciences, University of Texas, Austin, Texas, USA
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39
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Talkington MWT, Siuzdak G, Williamson JR. An assembly landscape for the 30S ribosomal subunit. Nature 2005; 438:628-32. [PMID: 16319883 PMCID: PMC1444899 DOI: 10.1038/nature04261] [Citation(s) in RCA: 207] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2005] [Accepted: 09/22/2005] [Indexed: 11/09/2022]
Abstract
Self-assembling macromolecular machines drive fundamental cellular processes, including transcription, messenger RNA processing, translation, DNA replication and cellular transport. The ribosome, which carries out protein synthesis, is one such machine, and the 30S subunit of the bacterial ribosome is the preeminent model system for biophysical analysis of large RNA-protein complexes. Our understanding of 30S assembly is incomplete, owing to the challenges of monitoring the association of many components simultaneously. Here we have developed a method involving pulse-chase monitored by quantitative mass spectrometry (PC/QMS) to follow the assembly of the 20 ribosomal proteins with 16S ribosomal RNA during formation of the functional particle. These data represent a detailed and quantitative kinetic characterization of the assembly of a large multicomponent macromolecular complex. By measuring the protein binding rates at a range of temperatures, we find that local transformations throughout the assembling subunit have similar but distinct activation energies. Thus, the prevailing view of 30S assembly as a pathway proceeding through a global rate-limiting conformational change must give way to one in which the assembly of the complex traverses a landscape dotted with various local conformational transitions.
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Affiliation(s)
- Megan W T Talkington
- Department of Molecular Biology, and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, USA
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40
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Harrison AG. Structural and sequence effects in the fragmentation of protonated tripeptides containing tyrosine. CAN J CHEM 2005. [DOI: 10.1139/v05-206] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The fragmentation reactions of a variety of protonated tripeptides containing tyrosine in the three possible positions have been studied by energy-resolved collision-induced dissociation mass spectrometry. The primary fragmentation reactions involve cleavage of the N-terminal and (or) C-terminal amide bond with the relative importance of the two cleavages depending strongly on the identity and position of the amino acid residues in the tripeptide. The results are interpreted in terms of the a1y mechanism for cleavage of the N-terminal amide bond and the bxyz mechanism for cleavage of the C-terminal amide bond and, indeed, provide support for these mechanisms. However, it appears likely that, for protonated H-Val-Tyr-Pro-OH, the neutral accompanying formation of the y1 (protonated proline) ion is a cyclic dipeptide (cyclo-Val-Tyr) rather than the oxazolone predicted by the bxyz mechanism.Key words: tyrosine-containing peptides, fragmentation mechanisms, tandem mass spectrometry.
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41
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Ashiuchi M, Yagami T, Willey RJ, Padovan JC, Chait BT, Popowicz A, Manning LR, Manning JM. N-terminal acetylation and protonation of individual hemoglobin subunits: position-dependent effects on tetramer strength and cooperativity. Protein Sci 2005; 14:1458-71. [PMID: 15929996 PMCID: PMC2253374 DOI: 10.1110/ps.041267405] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The presence of alanine (Ala) or acetyl serine (AcSer) instead of the normal Val residues at the N-terminals of either the alpha- or the beta-subunits of human adult hemoglobin confers some novel and unexpected features on the protein. Mass spectrometric analysis confirmed that these substitutions were correct and that they were the only ones. Circular dichroism studies indicated no global protein conformational changes, and isoelectric focusing showed the absence of impurities. The presence of Ala at the N-terminals of the alpha-subunits of liganded hemoglobin results in a significantly increased basicity (increased pK(a) values) and a reduction in the strength of subunit interactions at the allosteric tetramer-dimer interface. Cooperativity in O(2) binding is also decreased. Substitution of Ala at the N-terminals of the beta-subunits gives neither of these effects. The substitution of Ser at the N terminus of either subunit leads to its complete acetylation (during expression) and a large decrease in the strength of the tetramer-dimer allosteric interface. When either Ala or AcSer is present at the N terminus of the alpha-subunit, the slope of the plot of the tetramer-dimer association/dissociation constant as a function of pH is decreased by 60%. It is suggested that since the network of interactions involving the N and C termini of the alpha-subunits is less extensive than that of the beta-subunits in liganded human hemoglobin disruptions there are likely to have a profound effect on hemoglobin function such as the increased basicity, the effects on tetramer strength, and on cooperativity.
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Affiliation(s)
- Makoto Ashiuchi
- Department of Biology, Mugar Life Sciences Building, Room 134, Northeastern University, 360 Huntington Avenue, Boston, MA 02115, USA
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42
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Jagannadham MV, Nagaraj R. Detection of peptides covalently modified with multiple fatty acids by MALDI-TOF mass spectrometry. ACTA ACUST UNITED AC 2005; 66:94-100. [PMID: 16000123 DOI: 10.1111/j.1399-3011.2005.00277.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Analysis and characterization of membrane proteins and hydrophobic peptides by matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) is a considerable challenge because of their lower ionization efficiency. Detergents are used to solubilize hydrophobic peptides and proteins. However, in MALDI-MS, the presence of detergents can cause considerable loss of signal intensity. The extent of interference depends on the matrix/sample preparation method and experimental conditions. In the present study, we have analyzed the MALDI response of multiple fatty acylated peptides in the presence of the matrices alpha-cyano-4-hydroxy cinnamic acid (HCCA) and 2,5-dihydroxy benzoic acid (DHB). The effect of adding the nonionic detergent n-octylglucoside (OG) was also examined. The presence of OG facilitated detection of tetrapalmitoylated peptide, particularly when HCCA was used as the matrix. When DHB was used as the matrix, good signal intensity was observed in the absence of OG. Lower laser pulse rate in the linear mode of analysis resulted in good signal intensity for the tetrapalmitoylated peptide. Conditions for obtaining good signal intensities for dipalmitoylated and N-myristoyl peptides with both HCCA and DHB as matrices were also investigated.
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Affiliation(s)
- M V Jagannadham
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500 007, India
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43
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Kumarathasan P, Mohottalage S, Goegan P, Vincent R. An optimized protein in-gel digest method for reliable proteome characterization by MALDI-TOF-MS analysis. Anal Biochem 2005; 346:85-9. [PMID: 16168381 DOI: 10.1016/j.ab.2005.06.004] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2005] [Accepted: 06/01/2005] [Indexed: 11/21/2022]
Abstract
Human lung epithelial cells (A549) were used as a model to develop a reliable proteome characterization method by peptide mass fingerprinting (PMF). Lung cell lysate proteins and protein standards were separated by 2D-gel electrophoresis, stained with Coomassie blue, gel plugs were subjected to commonly adapted as well as optimized in-gel digestion/sample preparation methods. Samples were analyzed by MALDI-TOF-MS. Optimization parameters included, use of NH(4)OAc in destaining and in-gel digestion buffers, detergent/salt removal prior to in-gel digestion, use of solvents of varying polarities (0%, 30%, 60% ACN containing 0.1% TFA) to improve peptide recoveries, matrix composition (alpha-cyano-4-hydroxycinamic acid-organic solvent combinations) and on-target salt removal. This led to enhanced mass spectral information and a sensitivity gain in the order of 6-10 fold compared to that of common procedures, yielding reliable, unambiguous protein identification with femtomol protein sensitivity by Autoflex MALDI-TOF-MS. Triplicate analyses by two analysts revealed consistent, wide range m/z values including in < 1200Da region by relieving matrix-exerted signal suppression, requiring one trial to obtain a unique protein identification with superior PMF results for the optimized method. Analyses of ten A549 proteins in replicates using the optimized method yielded fast, reliable characterization, suggesting the potential application of this method in high-throughput protein identification by PMF.
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Affiliation(s)
- P Kumarathasan
- Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ont., Canada K1A 0L2
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44
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Peters J, Minuth T, Schröder W. Implementation of a crystallization step into the purification process of a recombinant protein. Protein Expr Purif 2005; 39:43-53. [PMID: 15596359 DOI: 10.1016/j.pep.2004.09.011] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2004] [Revised: 09/06/2004] [Indexed: 11/28/2022]
Abstract
Identification of crystallization conditions of new proteins is still regarded as a tedious trial-and-error work, especially when the crystallization step has to meet the requirements of a given purification process. The traditional screening kit method and a multifactorial approach were compared against each other with regard to their ability to find new crystallization conditions that are compatible to the purification process of a recombinant aprotinin variant. Overall, the multifactorial approach turned out to be 10-fold more efficient. The new crystallization conditions were scaled up and implemented into the purification process as a bulk storage step. The aprotinin variant derived from this process was fully characterized biochemically.
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Affiliation(s)
- Jörg Peters
- Bayer HealthCare AG, Friedrich-Ebert-Str. 217, D-42096 Wuppertal, Germany.
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45
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Callesen AK, Mohammed S, Bunkenborg J, Kruse TA, Cold S, Mogensen O, Christensen RD, Vach W, Jørgensen PE, Jensen ON. Serum protein profiling by miniaturized solid-phase extraction and matrix-assisted laser desorption/ionization mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2005; 19:1578-86. [PMID: 15915448 DOI: 10.1002/rcm.1960] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Serum profiling by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) holds promise as a clinical tool for early diagnosis of cancer and other human diseases. Sample preparation is key to achieving reproducible and well-resolved signals in MALDI-MS; a prerequisite for translation of MALDI-MS based diagnostic methods to clinical applications. We have investigated a number of MALDI matrices and several miniaturized solid-phase extraction (SPE) methods for serum protein concentration and desalting with the aim of generating reproducible, high-quality protein profiles by MALDI-MS. We developed a simple protocol for serum profiling that combines a matrix mixture of 2,5-dihydroxybenzoic acid and alpha-cyano-4-hydroxycinnamic acid with miniaturized SPE and MALDI-MS. Functionalized membrane discs with hydrophobic, ion-exchange or chelating properties allowed reproducible MALDI mass spectra (m/z 1000-12,000) to be obtained from serum. In a proof-of-principle application, SPE with chelating material and MALDI-MS identified protein peaks in serum that had been previously reported for distinguishing a person diagnosed with breast cancer from a control. These preliminary results indicate that this simple SPE/MALDI-MS method for serum profiling provides a versatile and scalable platform for clinical proteomics.
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Affiliation(s)
- Anne K Callesen
- Protein Research Group, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
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46
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Harrison AG, Young AB. Fragmentation of protonated oligoalanines: amide bond cleavage and beyond. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2004; 15:1810-1819. [PMID: 15589757 DOI: 10.1016/j.jasms.2004.08.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2004] [Revised: 08/26/2004] [Accepted: 08/26/2004] [Indexed: 05/24/2023]
Abstract
The fragmentation reactions of the singly-protonated oligoalanines trialanine to hexaalanine have been studied using energy-resolved mass spectrometry in MS(2) and MS(3) experiments. The primary fragmentation reactions are rationalized in terms of the b(x)-y(z) pathway of amide bond cleavage which results in formation of a proton-bound complex of an oxazolone and a peptide/amino acid; on decomposition of this complex the species of higher proton affinity preferentially retains the proton. For protonated pentaalanine and protonated hexaalanine the major primary fragmentation reaction involves cleavage of the C-terminal amide bond to form the appropriate b ion. The lower mass b ions originate largely, if not completely, by further fragmentation of the initially formed b ion. MS(3) energy-resolved experiments clearly show the fragmentation sequence b(n) --> b(n-1) --> b(n-2). A more minor pathway for the alanines involves the sequence b(n) --> a(n) --> b(n-1) --> b(n-2). The a(5) ion formed from hexaalanine loses, in part, NH(3) to begin the sequence of fragmentation reactions a(5) --> a(5)* --> a(4)* --> a(3)* where a(n)* = a(n) - NH(3). The a(3)* ion also is formed from the b(3) ion by the sequence b(3) --> a(3) --> a(3)* with the final step being sufficiently facile that the a(3) ion is not observed with significant intensity in CID mass spectra. A cyclic structure is proposed for the a(3)* ion.
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Affiliation(s)
- Alex G Harrison
- Department of Chemistry, University of Toronto, 80 George Street, Toronto, Ontario M5S 3H6, Canada.
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47
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Abstract
YiiP is a 32.9-kDa metal transporter found in the plasma membrane of Escherichia coli (Chao, Y., and Fu, D. (2004) J. Biol. Chem. 279, 17173-17180). Here we report the determination of the YiiP oligomeric state in detergent-lipid micelles and in membranes. Molecular masses of YiiP solubilized with dodecyl-, undecyl-, decyl-, or nonyl-beta-d-maltoside were measured directly using size-exclusion chromatography coupled with laser light-scattering photometry, yielding a mass distribution of YiiP homo-oligomers within a narrow range (68.0-68.8 kDa) that equals the predicted mass of a YiiP dimer within experimental error. The detergent-lipid masses associated with YiiP in the mixed micelles were found to increase from 135.5 to 232.6 kDa, with an apparent correlation with the alkyl chain length of the maltoside detergents. Cross-linking the detergent-solubilized YiiP with 1-ethyl-3-[3-dimethylaminopropyl] carbodiimide hydrochloride (EDC) resulted in a dimeric cross-linked product in an EDC concentration-dependent manner. The oligomeric state of the purified YiiP in reconstituted membranes was determined by electron microscopic analysis of two-dimensional YiiP crystals in negative stain. A projection structure calculated from measurable optical diffractions to 25 A revealed a pseudo-2-fold symmetry within a molecular boundary of approximately 75 x 40 A, indicative of the presence of YiiP dimers in membranes. These data provide direct structural evidence for a dimeric association of YiiP both in detergent-lipid micelles and in the reconstituted lipid bilayer. The functional relevance of the dimeric association in YiiP is discussed.
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Affiliation(s)
- Yinan Wei
- Department of Biology, Brookhaven National Laboratory, Upton, New York 11973, USA
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48
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Pang RTK, Johnson PJ, Chan CML, Kong EKC, Chan ATC, Sung JJY, Poon TCW. Technical evaluation of MALDI-TOF mass spectrometry for quantitative proteomic profiling matrix formulation and application. Clin Proteomics 2004. [DOI: 10.1385/cp:1:3-4:259] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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49
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Hirsch J, Hansen KC, Burlingame AL, Matthay MA. Proteomics: current techniques and potential applications to lung disease. Am J Physiol Lung Cell Mol Physiol 2004; 287:L1-23. [PMID: 15187006 DOI: 10.1152/ajplung.00301.2003] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Proteomics aims to study the whole protein content of a biological sample in one set of experiments. Such an approach has the potential value to acquire an understanding of the complex responses of an organism to a stimulus. The large vascular and air space surface area of the lung expose it to a multitude of stimuli that can trigger a variety of responses by many different cell types. This complexity makes the lung a promising, but also challenging, target for proteomics. Important steps made in the last decade have increased the potential value of the results of proteomics studies for the clinical scientist. Advances in protein separation and staining techniques have improved protein identification to include the least abundant proteins. The evolution in mass spectrometry has led to the identification of a large part of the proteins of interest rather than just describing changes in patterns of protein spots. Protein profiling techniques allow the rapid comparison of complex samples and the direct investigation of tissue specimens. In addition, proteomics has been complemented by the analysis of posttranslational modifications and techniques for the quantitative comparison of different proteomes. These methodologies have made the application of proteomics on the study of specific diseases or biological processes under clinically relevant conditions possible. The quantity of data that is acquired with these new techniques places new challenges on data processing and analysis. This article provides a brief review of the most promising proteomics methods and some of their applications to pulmonary research.
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Affiliation(s)
- Jan Hirsch
- Cardiovascular Research Institute, University of California, San Francisco, 505 Parnassus Ave. HSW 825, San Francisco, CA 94143-0130, USA.
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50
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Jock CA, Paulauskis JD, Baker D, Olle E, Bleavins MR, Johnson KJ, Heard PL. Influence of matrix application timing on spectral reproducibility and quality in SELDI-TOF-MS. Biotechniques 2004; 37:30-2, 34. [PMID: 15283196 DOI: 10.2144/04371bm01] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Affiliation(s)
- Carissa A Jock
- Pfizer Global Research and Development, Ann Arbor, MI 48105, USA
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