1
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Shepherd SO, Green AW, Resendiz ES, Newton KR, Kurulugama RT, Prell JS. Effects of Nano-Electrospray Ionization Emitter Position on Unintentional In-Source Activation of Peptide and Protein Ions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:498-507. [PMID: 38374644 PMCID: PMC11315166 DOI: 10.1021/jasms.3c00371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/21/2024]
Abstract
Native ion mobility-mass spectrometry (IM-MS) typically introduces protein ions into the gas phase through nano-electrospray ionization (nESI). Many nESI setups have mobile stages for tuning the ion signal and extent of co-solute and salt adduction. However, tuning the position of the emitter capillary in nESI can have unintended downstream consequences for collision-induced unfolding or collision-induced dissociation (CIU/D) experiments. Here, we show that relatively small variations in the nESI emitter position can shift the midpoint (commonly called the "CID50" or "CIU50") potential of CID breakdown curves and CIU transitions by as much as 8 V on commercial instruments. A spatial "map" of the shift in CID50 for the loss of heme from holomyoglobin onto the emitter position on a Waters Synapt G2-Si mass spectrometer shows that emitter positions closer to the instrument inlet can result in significantly greater in-source activation, whereas different effects are found on an Agilent 6545XT instrument for the ions studied. A similar effect is observed for CID of the singly protonated leucine enkephalin peptide and Shiga toxin 1 subunit B homopentamer on the Waters Synapt G2-Si instrument. In-source activation effects on a Waters Synapt G2-Si are also investigated by examining the RMSD between CIU fingerprints acquired at different emitter positions and the shifts in CIU50 for structural transitions of bovine serum albumin and NIST monoclonal antibody.
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Affiliation(s)
- Samantha O. Shepherd
- Department of Chemistry and Biochemistry, 1253 University of Oregon, Eugene, OR, USA, 97403-1253
| | - Austin W. Green
- Department of Chemistry and Biochemistry, 1253 University of Oregon, Eugene, OR, USA, 97403-1253
| | - Elizabeth S. Resendiz
- Department of Chemistry and Biochemistry, 1253 University of Oregon, Eugene, OR, USA, 97403-1253
| | - Kenneth R. Newton
- Department of Chemistry and Biochemistry, 1253 University of Oregon, Eugene, OR, USA, 97403-1253
- 5301 Stevens Creek Blvd, Agilent Technologies, Santa Clara, 95051, CA, USA
| | | | - James S. Prell
- Department of Chemistry and Biochemistry, 1253 University of Oregon, Eugene, OR, USA, 97403-1253
- Materials Science Institute, 1252 University of Oregon, Eugene, OR, USA, 97403-1252
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2
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Illes-Toth E, Stubbs CJ, Sisley EK, Bellamy-Carter J, Simmonds AL, Mize TH, Styles IB, Goodwin RJA, Cooper HJ. Quantitative Characterization of Three Carbonic Anhydrase Inhibitors by LESA Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:1168-1175. [PMID: 35675480 PMCID: PMC9264382 DOI: 10.1021/jasms.2c00024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Liquid extraction surface analysis (LESA) coupled to native mass spectrometry (MS) presents unique analytical opportunities due to its sensitivity, speed, and automation. Here, we examine whether this tool can be used to quantitatively probe protein-ligand interactions through calculation of equilibrium dissociation constants (Kd values). We performed native LESA MS analyses for a well-characterized system comprising bovine carbonic anhydrase II and the ligands chlorothiazide, dansylamide, and sulfanilamide, and compared the results with those obtained from direct infusion mass spectrometry and surface plasmon resonance measurements. Two LESA approaches were considered: In one approach, the protein and ligand were premixed in solution before being deposited and dried onto a solid substrate for LESA sampling, and in the second, the protein alone was dried onto the substrate and the ligand was included in the LESA sampling solvent. Good agreement was found between the Kd values derived from direct infusion MS and LESA MS when the protein and ligand were premixed; however, Kd values determined from LESA MS measurements where the ligand was in the sampling solvent were inconsistent. Our results suggest that LESA MS is a suitable tool for quantitative analysis of protein-ligand interactions when the dried sample comprises both protein and ligand.
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Affiliation(s)
- Eva Illes-Toth
- School
of Biosciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Christopher J. Stubbs
- Mechanistic
and Structural Biology, Discovery Sciences,
R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Emma K. Sisley
- School
of Biosciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | | | - Anna L. Simmonds
- School
of Biosciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Todd H. Mize
- School
of Biosciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Iain B. Styles
- School
of Computer Science and Centre of Membrane Proteins and Receptors
(COMPARE), University of Birmingham, Birmingham B15 2TT, United Kingdom
- The Alan Turing Institute, London NW1 2DB, United Kingdom
- University of Nottingham, Midlands NG7 2RD, United Kingdom
| | - Richard J. A. Goodwin
- Imaging and
Data Analytics, Clinical Pharmacology & Safety Sciences, BioPharmaceuticals
R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Helen J. Cooper
- School
of Biosciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
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3
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Abstract
Native mass spectrometry (nMS) has emerged as an important tool in studying the structure and function of macromolecules and their complexes in the gas phase. In this review, we cover recent advances in nMS and related techniques including sample preparation, instrumentation, activation methods, and data analysis software. These advances have enabled nMS-based techniques to address a variety of challenging questions in structural biology. The second half of this review highlights recent applications of these technologies and surveys the classes of complexes that can be studied with nMS. Complementarity of nMS to existing structural biology techniques and current challenges in nMS are also addressed.
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Affiliation(s)
- Kelly R Karch
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA;
- Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, Ohio, USA
| | - Dalton T Snyder
- Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, Ohio, USA
| | - Sophie R Harvey
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA;
- Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, Ohio, USA
| | - Vicki H Wysocki
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA;
- Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, Ohio, USA
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4
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Blevins MS, Walker JN, Schaub JM, Finkelstein IJ, Brodbelt JS. Characterization of the T4 gp32-ssDNA complex by native, cross-linking, and ultraviolet photodissociation mass spectrometry. Chem Sci 2021; 12:13764-13776. [PMID: 34760161 PMCID: PMC8549804 DOI: 10.1039/d1sc02861h] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 09/23/2021] [Indexed: 12/28/2022] Open
Abstract
Protein-DNA interactions play crucial roles in DNA replication across all living organisms. Here, we apply a suite of mass spectrometry (MS) tools to characterize a protein-ssDNA complex, T4 gp32·ssDNA, with results that both support previous studies and simultaneously uncover novel insight into this non-covalent biological complex. Native mass spectrometry of the protein reveals the co-occurrence of Zn-bound monomers and homodimers, while addition of differing lengths of ssDNA generates a variety of protein:ssDNA complex stoichiometries (1 : 1, 2 : 1, 3 : 1), indicating sequential association of gp32 monomers with ssDNA. Ultraviolet photodissociation (UVPD) mass spectrometry allows characterization of the binding site of the ssDNA within the protein monomer via analysis of holo ions, i.e. ssDNA-containing protein fragments, enabling interrogation of disordered regions of the protein which are inaccessible via traditional crystallographic techniques. Finally, two complementary cross-linking (XL) approaches, bottom-up analysis of the crosslinked complexes as well as MS1 analysis of the intact complexes, are used to showcase the absence of ssDNA binding with the intact cross-linked homodimer and to generate two homodimer gp32 model structures which highlight that the homodimer interface overlaps with the monomer ssDNA-binding site. These models suggest that the homodimer may function in a regulatory capacity by controlling the extent of ssDNA binding of the protein monomer. In sum, this work underscores the utility of a multi-faceted mass spectrometry approach for detailed investigation of non-covalent protein-DNA complexes.
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Affiliation(s)
- Molly S Blevins
- Department of Chemistry, University of Texas at Austin Austin TX 78712 USA
| | - Jada N Walker
- Department of Chemistry, University of Texas at Austin Austin TX 78712 USA
| | - Jeffrey M Schaub
- Department of Molecular Biosciences, University of Texas at Austin Austin TX 78712 USA
| | - Ilya J Finkelstein
- Department of Molecular Biosciences, University of Texas at Austin Austin TX 78712 USA
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5
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Largy E, König A, Ghosh A, Ghosh D, Benabou S, Rosu F, Gabelica V. Mass Spectrometry of Nucleic Acid Noncovalent Complexes. Chem Rev 2021; 122:7720-7839. [PMID: 34587741 DOI: 10.1021/acs.chemrev.1c00386] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Nucleic acids have been among the first targets for antitumor drugs and antibiotics. With the unveiling of new biological roles in regulation of gene expression, specific DNA and RNA structures have become very attractive targets, especially when the corresponding proteins are undruggable. Biophysical assays to assess target structure as well as ligand binding stoichiometry, affinity, specificity, and binding modes are part of the drug development process. Mass spectrometry offers unique advantages as a biophysical method owing to its ability to distinguish each stoichiometry present in a mixture. In addition, advanced mass spectrometry approaches (reactive probing, fragmentation techniques, ion mobility spectrometry, ion spectroscopy) provide more detailed information on the complexes. Here, we review the fundamentals of mass spectrometry and all its particularities when studying noncovalent nucleic acid structures, and then review what has been learned thanks to mass spectrometry on nucleic acid structures, self-assemblies (e.g., duplexes or G-quadruplexes), and their complexes with ligands.
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Affiliation(s)
- Eric Largy
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Alexander König
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Anirban Ghosh
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Debasmita Ghosh
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Sanae Benabou
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Frédéric Rosu
- Univ. Bordeaux, CNRS, INSERM, IECB, UMS 3033, F-33600 Pessac, France
| | - Valérie Gabelica
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
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6
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Hou S, Liu D, Huang S, Luo D, Liu Z, Xiang Q, Wang P, Mu R, Han Z, Chen S, Chai J, Shan L, He P. The Arabidopsis MIK2 receptor elicits immunity by sensing a conserved signature from phytocytokines and microbes. Nat Commun 2021; 12:5494. [PMID: 34535661 PMCID: PMC8448819 DOI: 10.1038/s41467-021-25580-w] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 08/17/2021] [Indexed: 11/09/2022] Open
Abstract
Sessile plants encode a large number of small peptides and cell surface-resident receptor kinases, most of which have unknown functions. Here, we report that the Arabidopsis receptor kinase MALE DISCOVERER 1-INTERACTING RECEPTOR-LIKE KINASE 2 (MIK2) recognizes the conserved signature motif of SERINE-RICH ENDOGENOUS PEPTIDEs (SCOOPs) from Brassicaceae plants as well as proteins present in fungal Fusarium spp. and bacterial Comamonadaceae, and elicits various immune responses. SCOOP signature peptides trigger immune responses and altered root development in a MIK2-dependent manner with a sub-nanomolar sensitivity. SCOOP12 directly binds to the extracellular leucine-rich repeat domain of MIK2 in vivo and in vitro, indicating that MIK2 is the receptor of SCOOP peptides. Perception of SCOOP peptides induces the association of MIK2 and the coreceptors SOMATIC EMBRYOGENESIS RECEPTOR KINASE 3 (SERK3) and SERK4 and relays the signaling through the cytosolic receptor-like kinases BOTRYTIS-INDUCED KINASE 1 (BIK1) and AVRPPHB SUSCEPTIBLE1 (PBS1)-LIKE 1 (PBL1). Our study identifies a plant receptor that bears a dual role in sensing the conserved peptide motif from phytocytokines and microbial proteins via a convergent signaling relay to ensure a robust immune response. Peptide signals generated during plant microbe interactions can trigger immune responses in plants. Here the authors show that SCOOP12, a member of a family of peptides present in Brassicaceae plants, and SCOOP12-like motifs in Fusarium fungi, can trigger immune responses following perception by the MIK2 receptor kinase.
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Affiliation(s)
- Shuguo Hou
- School of Municipal and Environmental Engineering, Shandong Jianzhu University, Jinan, China.
| | - Derui Liu
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
| | - Shijia Huang
- Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Dexian Luo
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
| | - Zunyong Liu
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
| | - Qingyuan Xiang
- Department of Biology, Genetics Institute, Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL, USA
| | - Ping Wang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
| | - Ruimin Mu
- School of Municipal and Environmental Engineering, Shandong Jianzhu University, Jinan, China
| | - Zhifu Han
- Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Sixue Chen
- Department of Biology, Genetics Institute, Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL, USA
| | - Jijie Chai
- Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China.,Max-Planck Institute for Plant Breeding Research, Institute of Biochemistry, University of Cologne, Cologne, Germany
| | - Libo Shan
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA.
| | - Ping He
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA.
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7
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Yu Y, Liu H, Yu Z, Witkowska HE, Cheng Y. Stoichiometry of Nucleotide Binding to Proteasome AAA+ ATPase Hexamer Established by Native Mass Spectrometry. Mol Cell Proteomics 2020; 19:1997-2015. [PMID: 32883800 PMCID: PMC7710143 DOI: 10.1074/mcp.ra120.002067] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 08/04/2020] [Indexed: 11/06/2022] Open
Abstract
AAA+ ATPases constitute a large family of proteins that are involved in a plethora of cellular processes including DNA disassembly, protein degradation and protein complex disassembly. They typically form a hexametric ring-shaped structure with six subunits in a (pseudo) 6-fold symmetry. In a subset of AAA+ ATPases that facilitate protein unfolding and degradation, six subunits cooperate to translocate protein substrates through a central pore in the ring. The number and type of nucleotides in an AAA+ ATPase hexamer is inherently linked to the mechanism that underlies cooperation among subunits and couples ATP hydrolysis with substrate translocation. We conducted a native MS study of a monodispersed form of PAN, an archaeal proteasome AAA+ ATPase, to determine the number of nucleotides bound to each hexamer of the WT protein. We utilized ADP and its analogs (TNP-ADP and mant-ADP), and a nonhydrolyzable ATP analog (AMP-PNP) to study nucleotide site occupancy within the PAN hexamer in ADP- and ATP-binding states, respectively. Throughout all experiments we used a Walker A mutant (PANK217A) that is impaired in nucleotide binding as an internal standard to mitigate the effects of residual solvation on mass measurement accuracy and to serve as a reference protein to control for nonspecific nucleotide binding. This approach led to the unambiguous finding that a WT PAN hexamer carried - from expression host - six tightly bound ADP molecules that could be exchanged for ADP and ATP analogs. Although the Walker A mutant did not bind ADP analogs, it did bind AMP-PNP, albeit at multiple stoichiometries. We observed variable levels of hexamer dissociation and an appearance of multimeric species with the over-charged molecular ion distributions across repeated experiments. We posit that these phenomena originated during ESI process at the final stages of ESI droplet evolution.
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Affiliation(s)
- Yadong Yu
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA
| | - Haichuan Liu
- Department of OBGYN & Reproductive Sci, Sandler-Moore MS Core Facility, University of California San Francisco, San Francisco, California, USA
| | - Zanlin Yu
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA
| | - H Ewa Witkowska
- Department of OBGYN & Reproductive Sci, Sandler-Moore MS Core Facility, University of California San Francisco, San Francisco, California, USA.
| | - Yifan Cheng
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA; Howard Hughes Medical Institute, University of California San Francisco, San Francisco, California, USA.
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8
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Abstract
Retinoic acid receptors (RARs) heterodimerize with retinoid X receptors (RXRs) to regulate gene expression. The heterodimer recognizes the genome via a large and diverse repertoire of DNA response elements. Assessing the binding mode of RAR and RXR with various DNA response elements is important for understanding how they select their binding site and how DNA sequence and topology allosterically regulate RAR function. A number of complementary assays are often employed for analysis of the binding mode. To biochemically and structurally characterize RAR and RXR-DNA complexes, we describe how to express and purify RAR and RXR-DNA binding domains (DBDs) and multidomain constructs. We also describe the use of electrospray ionization mass spectrometry (ESI MS) and isothermal titration calorimetry (ITC) that give information about stoichiometry and binding affinity, as well as our approaches for co-crystallization of RAR and RXR DBDs with DNA.
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Affiliation(s)
- Carole Peluso-Iltis
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France; Centre National de la Recherche Scientifique, Illkirch, France; Institut National de la Santé et de la Recherche Médicale, Illkirch, France; Université de Strasbourg, Illkirch, France
| | - Judit Osz
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France; Centre National de la Recherche Scientifique, Illkirch, France; Institut National de la Santé et de la Recherche Médicale, Illkirch, France; Université de Strasbourg, Illkirch, France
| | - Natacha Rochel
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France; Centre National de la Recherche Scientifique, Illkirch, France; Institut National de la Santé et de la Recherche Médicale, Illkirch, France; Université de Strasbourg, Illkirch, France.
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9
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Schmidt MA, Herman EM. Characterization and functional biology of the soybean aleurone layer. BMC PLANT BIOLOGY 2018; 18:354. [PMID: 30545296 PMCID: PMC6293662 DOI: 10.1186/s12870-018-1579-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 11/29/2018] [Indexed: 06/09/2023]
Abstract
BACKGROUND Soybean is a globally important oil seed crop. Both the high protein and oil content of soybean seeds make this crop a lucrative commodity. As in higher eukaryotic species with available genomes, the functional annotation of most of soybean's genes still remains to be investigated. A major hurdle in the functional genomics of soybean is a rapid method to test gene constructs before embarking on stable transformation experiments. RESULTS In this paper we describe the morphology and composition of the persistent single-cell aleurone layer that derives from the endosperm of developing soybean seeds. Its composition compared to cotyledonary tissue indicates the aleurone layer plays a role in both abiotic and biotic stress. The potential utility as the aleurone layer as a transient expression system in soybean was shown. As a near transparent single-cell layer it can be used as a transient expression system to study transgene expression and inter- and intra-cellular targeting as it is amenable to microscopic techniques. CONCLUSION The transparent single cell aleurone layer was shown to be compositionally comparable to cotyledonary tissue in soybean with an enrichment in oxidative response proteins and shown to be a potential transient expression platform.
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Affiliation(s)
- Monica A. Schmidt
- School of Plant Sciences/BIO5 Institute/University of Arizona, 1657 E. Helen St, Tucson, AZ 85721 USA
| | - Eliot M. Herman
- School of Plant Sciences/BIO5 Institute/University of Arizona, 1657 E. Helen St, Tucson, AZ 85721 USA
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10
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Shiu-Hin Chan D, Seetoh WG, McConnell BN, Matak-Vinković D, Thomas SE, Mendes V, Blaszczyk M, Coyne AG, Blundell TL, Abell C. Structural insights into the EthR-DNA interaction using native mass spectrometry. Chem Commun (Camb) 2018; 53:3527-3530. [PMID: 28287239 DOI: 10.1039/c7cc00804j] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
EthR is a transcriptional repressor that increases Mycobacterium tuberculosis resistance to ethionamide. In this study, the EthR-DNA interaction has been investigated by native electrospray-ionization mass spectrometry for the first time. The results show that up to six subunits of EthR are able to bind to its operator.
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Affiliation(s)
- Daniel Shiu-Hin Chan
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB21EW, UK.
| | - Wei-Guang Seetoh
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB21EW, UK.
| | - Brendan N McConnell
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB21EW, UK.
| | - Dijana Matak-Vinković
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB21EW, UK.
| | - Sherine E Thomas
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, CB2 1GA Cambridge, UK
| | - Vitor Mendes
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, CB2 1GA Cambridge, UK
| | - Michal Blaszczyk
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, CB2 1GA Cambridge, UK
| | - Anthony G Coyne
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB21EW, UK.
| | - Tom L Blundell
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, CB2 1GA Cambridge, UK
| | - Chris Abell
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB21EW, UK.
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11
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Michelucci E, Pieraccini G, Moneti G, Gabbiani C, Pratesi A, Messori L. Mass spectrometry and metallomics: A general protocol to assess stability of metallodrug-protein adducts in bottom-up MS experiments. Talanta 2017; 167:30-38. [PMID: 28340724 DOI: 10.1016/j.talanta.2017.01.074] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 01/23/2017] [Accepted: 01/25/2017] [Indexed: 10/20/2022]
Abstract
The bottom-up mass spectrometry approach is today one of the best tools of Metallomics to characterize the binding of metal-based drugs to proteins. Yet, the stability of metal-protein coordination bonds along the whole process may be a critical issue. This led us to build up a general protocol to test metallodrug-protein adduct stability under the typical conditions of the filter-aided sample preparation (FASP)/bottom-up procedure, ranging from the analysis of solutions containing metal-protein adducts to tandem mass spectrometry experiments. More in detail, we identified nine critical situations, either during the sample manipulations or instrumental, as a potential source of metal-protein bond impairment when using FASP operative conditions and a nano high performance liquid chromatography-nanoelectrospray ionization-LTQ-Orbitrap (nanoLC-nanoESI-LTQ-Orbitrap) mass spectrometer system, equipped with a preconcentration/purification device. These are: 1) sample permanence in the ammonium bicarbonate buffer; 2) denaturation with urea; 3) reduction with dithiothreitol; 4) alkylation with iodoacetamide; 5) sample permanence in the loading mobile phase; 6) sample permanence in the elution mobile phase; 7) the nanoESI process; 8) the transfer of the adduct through ion transfer tube and tube lens; 9) collision induced dissociation in the ion trap. Accordingly, an ad hoc experimental protocol was developed and applied to the adducts formed between cytochrome c (Cyt c) and two different metallodrugs, i.e. cisplatin (cis-diamminedichloridoplatinum(II), CDDP) and RAPTA-C, a well-known ruthenium(II)-arene compound [Ru(η6-p-cymene)Cl2(pta)] (pta=1,3,5-triaza-7-phosphaadamantane), used here as models. Notably, Cyt c-CDDP adducts were stable through all the above conditions while Cyt c-RAPTA-C adducts turned out unstable in the ammonium bicarbonate buffer. This latter finding supports the need to perform a test-protocol of this kind when starting any extensive bottom-up MS investigation of protein-metallodrug systems.
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Affiliation(s)
- Elena Michelucci
- Mass Spectrometry Center (CISM), University of Florence, via Ugo Schiff 6, 50019 Sesto Fiorentino, FI, Italy.
| | - Giuseppe Pieraccini
- Mass Spectrometry Center (CISM), University of Florence, via Ugo Schiff 6, 50019 Sesto Fiorentino, FI, Italy
| | - Gloriano Moneti
- Mass Spectrometry Center (CISM), University of Florence, via Ugo Schiff 6, 50019 Sesto Fiorentino, FI, Italy
| | - Chiara Gabbiani
- Department of Chemistry and Industrial Chemistry, University of Pisa, via Moruzzi 13, 56124 Pisa, Italy
| | - Alessandro Pratesi
- MetMed, Department of Chemistry, University of Florence, via della Lastruccia 3, 50019 Sesto Fiorentino, FI, Italy
| | - Luigi Messori
- MetMed, Department of Chemistry, University of Florence, via della Lastruccia 3, 50019 Sesto Fiorentino, FI, Italy
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12
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Iqbal MJ, Majeed M, Humayun M, Lightfoot DA, Afzal AJ. Proteomic Profiling and the Predicted Interactome of Host Proteins in Compatible and Incompatible Interactions Between Soybean and Fusarium virguliforme. Appl Biochem Biotechnol 2016; 180:1657-1674. [PMID: 27491306 DOI: 10.1007/s12010-016-2194-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 07/13/2016] [Indexed: 12/27/2022]
Abstract
Sudden death syndrome (SDS) is a complex of two diseases of soybean (Glycine max), caused by the soil borne pathogenic fungus Fusarium virguliforme. The root rot and leaf scorch diseases both result in significant yield losses worldwide. Partial SDS resistance has been demonstrated in multiple soybean cultivars. This study aimed to highlight proteomic changes in soybean roots by identifying proteins which are differentially expressed in near isogenic lines (NILs) contrasting at the Rhg1/Rfs2 locus for partial resistance or susceptibility to SDS. Two-dimensional gel electrophoresis resolved approximately 1000 spots on each gel; 12 spots with a significant (P < 0.05) difference in abundance of 1.5-fold or more were picked, trypsin-digested, and analyzed using quadruple time-of-flight tandem mass spectrometry. Several spots contained more than one protein, so that 18 distinct proteins were identified overall. A functional analysis performed to categorize the proteins depicted that the major pathways altered by fungal infection include disease resistance, stress tolerance, and metabolism. This is the first report which identifies proteins whose abundances are altered in response to fungal infection leading to SDS. The results provide valuable information about SDS resistance in soybean plants, and plant partial resistance responses in general. More importantly, several of the identified proteins could be good candidates for the development of SDS-resistant soybean plants.
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Affiliation(s)
- M Javed Iqbal
- Department of Plant Sciences, University of California, Davis, California, 95616, USA
| | - Maryam Majeed
- Department of Biology, SBA School of Science and Engineering, Lahore University of Management Sciences, Lahore, 54792, Pakistan
- Department of Biological Sciences, Columbia University, New York, NY, 10027, USA
| | - Maheen Humayun
- Department of Biology, SBA School of Science and Engineering, Lahore University of Management Sciences, Lahore, 54792, Pakistan
| | - David A Lightfoot
- Department of Molecular Biology, Microbiology, and Biochemistry, Genomics Core Facility and Center for Excellence in Soybean Research, Teaching, and Outreach, and Department of Plant Biology, Southern Illinois University, Carbondale, Illinois, 62901, USA
| | - Ahmed J Afzal
- Department of Biology, SBA School of Science and Engineering, Lahore University of Management Sciences, Lahore, 54792, Pakistan.
- Department of Molecular Biology, Microbiology, and Biochemistry, Genomics Core Facility and Center for Excellence in Soybean Research, Teaching, and Outreach, and Department of Plant Biology, Southern Illinois University, Carbondale, Illinois, 62901, USA.
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13
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Sun Y, Vahidi S, Sowole MA, Konermann L. Protein Structural Studies by Traveling Wave Ion Mobility Spectrometry: A Critical Look at Electrospray Sources and Calibration Issues. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:31-40. [PMID: 26369778 DOI: 10.1007/s13361-015-1244-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Revised: 07/27/2015] [Accepted: 07/29/2015] [Indexed: 06/05/2023]
Abstract
The question whether electrosprayed protein ions retain solution-like conformations continues to be a matter of debate. One way to address this issue involves comparisons of collision cross sections (Ω) measured by ion mobility spectrometry (IMS) with Ω values calculated for candidate structures. Many investigations in this area employ traveling wave IMS (TWIMS). It is often implied that nanoESI is more conducive for the retention of solution structure than regular ESI. Focusing on ubiquitin, cytochrome c, myoglobin, and hemoglobin, we demonstrate that Ω values and collisional unfolding profiles are virtually indistinguishable under both conditions. These findings suggest that gas-phase structures and ion internal energies are independent of the type of electrospray source. We also note that TWIMS calibration can be challenging because differences in the extent of collisional activation relative to drift tube reference data may lead to ambiguous peak assignments. It is demonstrated that this problem can be circumvented by employing collisionally heated calibrant ions. Overall, our data are consistent with the view that exposure of native proteins to electrospray conditions can generate kinetically trapped ions that retain solution-like structures on the millisecond time scale of TWIMS experiments. ᅟ
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Affiliation(s)
- Yu Sun
- Department of Chemistry, The University of Western Ontario, London, ON, N6A 5B7, Canada
| | - Siavash Vahidi
- Department of Chemistry, The University of Western Ontario, London, ON, N6A 5B7, Canada
| | - Modupeola A Sowole
- Department of Chemistry, The University of Western Ontario, London, ON, N6A 5B7, Canada
| | - Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, ON, N6A 5B7, Canada.
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14
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Laughlin S, Wilson WD. May the Best Molecule Win: Competition ESI Mass Spectrometry. Int J Mol Sci 2015; 16:24506-31. [PMID: 26501262 PMCID: PMC4632762 DOI: 10.3390/ijms161024506] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Revised: 09/18/2015] [Accepted: 10/09/2015] [Indexed: 02/07/2023] Open
Abstract
Electrospray ionization mass spectrometry has become invaluable in the characterization of macromolecular biological systems such as nucleic acids and proteins. Recent advances in the field of mass spectrometry and the soft conditions characteristic of electrospray ionization allow for the investigation of non-covalent interactions among large biomolecules and ligands. Modulation of genetic processes through the use of small molecule inhibitors with the DNA minor groove is gaining attention as a potential therapeutic approach. In this review, we discuss the development of a competition method using electrospray ionization mass spectrometry to probe the interactions of multiple DNA sequences with libraries of minor groove binding molecules. Such an approach acts as a high-throughput screening method to determine important information including the stoichiometry, binding mode, cooperativity, and relative binding affinity. In addition to small molecule-DNA complexes, we highlight other applications in which competition mass spectrometry has been used. A competitive approach to simultaneously investigate complex interactions promises to be a powerful tool in the discovery of small molecule inhibitors with high specificity and for specific, important DNA sequences.
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Affiliation(s)
- Sarah Laughlin
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA.
| | - W David Wilson
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA.
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15
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Phelps M, Hamilton J, Verbeck GF. Nanomanipulation-coupled nanospray mass spectrometry as an approach for single cell analysis. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2014; 85:124101. [PMID: 25554307 DOI: 10.1063/1.4902322] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Electrospray mass spectrometry is now a widely used technique for observing cell content of various biological tissues. However, electrospray techniques (liquid chromatography and direct infusion) often involve lysing a group of cells and extracting the biomolecules of interest, rather than a sensitive, individual cell method to observe local chemistry. Presented here is an approach of combining a nanomanipulator workstation with nanospray mass spectrometry, which allows for extraction of a single cell, followed by rapid mass analysis that can provide a detailed metabolic profile. Triacylglycerol content was profiled with this tool coupled to mass spectrometry to investigate heterogeneity between healthy and tumorous tissues as well as lipid droplet containing adipocytes in vitro as proof of concept. This selective approach provides cellular resolution and complements existing bioanalytical techniques with minimal invasion to samples. In addition, the coupling of nanomanipulation and mass spectrometry holds the potential to be used in a great number of applications for individual organelles, diseased tissues, and in vitro cell cultures for observing heterogeneity even amongst cells and organelles of the same tissue.
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Affiliation(s)
- Mandy Phelps
- Department of Chemistry, University of North Texas, Denton, Texas 76203, USA
| | - Jason Hamilton
- Department of Chemistry, University of North Texas, Denton, Texas 76203, USA
| | - Guido F Verbeck
- Department of Chemistry, University of North Texas, Denton, Texas 76203, USA
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16
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Ogorzalek Loo RR, Lakshmanan R, Loo JA. What protein charging (and supercharging) reveal about the mechanism of electrospray ionization. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:1675-93. [PMID: 25135609 PMCID: PMC4163133 DOI: 10.1007/s13361-014-0965-1] [Citation(s) in RCA: 111] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Revised: 06/13/2014] [Accepted: 07/08/2014] [Indexed: 05/11/2023]
Abstract
Understanding the charging mechanism of electrospray ionization is central to overcoming shortcomings such as ion suppression or limited dynamic range, and explaining phenomena such as supercharging. Towards that end, we explore what accumulated observations reveal about the mechanism of electrospray. We introduce the idea of an intermediate region for electrospray ionization (and other ionization methods) to account for the facts that solution charge state distributions (CSDs) do not correlate with those observed by ESI-MS (the latter bear more charge) and that gas phase reactions can reduce, but not increase, the extent of charging. This region incorporates properties (e.g., basicities) intermediate between solution and gas phase. Assuming that droplet species polarize within the high electric field leads to equations describing ion emission resembling those from the equilibrium partitioning model. The equations predict many trends successfully, including CSD shifts to higher m/z for concentrated analytes and shifts to lower m/z for sprays employing smaller emitter opening diameters. From this view, a single mechanism can be formulated to explain how reagents that promote analyte charging ("supercharging") such as m-NBA, sulfolane, and 3-nitrobenzonitrile increase analyte charge from "denaturing" and "native" solvent systems. It is suggested that additives' Brønsted basicities are inversely correlated to their ability to shift CSDs to lower m/z in positive ESI, as are Brønsted acidities for negative ESI. Because supercharging agents reduce an analyte's solution ionization, excess spray charge is bestowed on evaporating ions carrying fewer opposing charges. Brønsted basicity (or acidity) determines how much ESI charge is lost to the agent (unavailable to evaporating analyte).
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Affiliation(s)
- Rachel R Ogorzalek Loo
- Department of Biological Chemistry, David Geffen School of Medicine at UCLA, University of California-Los Angeles, Los Angeles, CA, 90095, USA,
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17
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Zhang S, Van Pelt CK. Chip-based nanoelectrospray mass spectrometry for protein characterization. Expert Rev Proteomics 2014; 1:449-68. [PMID: 15966841 DOI: 10.1586/14789450.1.4.449] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
In the last several years, significant progress has been made in the development of microfluidic-based analytical technologies for proteomic and drug discovery applications. Chip-based nanoelectrospray coupled to a mass spectrometer detector is one of the recently developed analytical microscale technologies. This technology offers unique advantages for automated nanoelectrospray including reduced sample consumption, improved detection sensitivity and enhanced data quality for proteomic studies. This review presents an overview and introduction of recent developments in chip devices coupled to electrospray mass spectrometers including the development of the automated nanoelectrospray ionization chip device for protein characterization. Applications using automated chip-based nanoelectrospray ionization technology in proteomic and bioanalytical studies are also extensively reviewed in the fields of high-throughput protein identification, protein post-translational modification studies, top-down proteomics, biomarker screening by pattern recognition, noncovalent protein-ligand binding for drug discovery and lipid analysis. Additionally, future trends in chip-based nanoelectrospray technology are discussed.
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Affiliation(s)
- Sheng Zhang
- Cornell University, 135 Biotechnology Building, Ithaca, NY 14853, USA.
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18
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Emilie-Laure Z. Large mixed complexes involving uracil, cytosine, thymine and/or 1-methyl uracil around Ca2+ ions: an electrospray ionization/MS study. JOURNAL OF MASS SPECTROMETRY : JMS 2013; 48:438-447. [PMID: 23584937 DOI: 10.1002/jms.3175] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2011] [Revised: 12/27/2012] [Accepted: 01/21/2013] [Indexed: 06/02/2023]
Abstract
We investigated the possible formation of mixed B(n)B'(n')Ca(2+) complexes where B and B' are two different nucleobases. Electrospray ionization (ESI) mass spectrometric experiments from solutions containing two different kinds of nucleobases and calcium ions were carried out to investigate the formation of magic number clusters that may be relevant in a biological point of view. The results presented here clearly show that mixed complexes can be formed and are stable in the gas phase. This represents an important step toward more complex solutions in which several nucleobases are present simultaneously and may compete in the formation of cationized clusters. We believe that thorough investigations on such systems may help understanding biological processes that may effect the tridimensional structure of the DNA macromolecule. The formation of mixed hexamers, decamers, dodecamers and tetradecamers are clearly favored from solution containing uracil (Ura), thymine (Thy) and Ca(2+), whereas mixed octamers are preferred from 1-methyl uracil (MeU), uracil and Ca(2+) mixtures. Cytosine (Cyto) can form mixed complexes with either uracil or 1-methyl uracil or thymine. On the other hand, the main species formed in these latter cases are mixed tetramers.
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Affiliation(s)
- Zins Emilie-Laure
- Laboratoire de Dynamique, Interactions et Réactivité (LADIR), UPMC Université Paris 06, CNRS, UMR 7075, 4 place Jussieu, F-75005, Paris, France
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19
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Kandiah M, Urban PL. Advances in ultrasensitive mass spectrometry of organic molecules. Chem Soc Rev 2013; 42:5299-322. [DOI: 10.1039/c3cs35389c] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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20
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Amoroso A, Boudet J, Berzigotti S, Duval V, Teller N, Mengin-Lecreulx D, Luxen A, Simorre JP, Joris B. A peptidoglycan fragment triggers β-lactam resistance in Bacillus licheniformis. PLoS Pathog 2012; 8:e1002571. [PMID: 22438804 PMCID: PMC3305447 DOI: 10.1371/journal.ppat.1002571] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2011] [Accepted: 01/24/2012] [Indexed: 01/29/2023] Open
Abstract
To resist to β-lactam antibiotics Eubacteria either constitutively synthesize a β-lactamase or a low affinity penicillin-binding protein target, or induce its synthesis in response to the presence of antibiotic outside the cell. In Bacillus licheniformis and Staphylococcus aureus, a membrane-bound penicillin receptor (BlaR/MecR) detects the presence of β-lactam and launches a cytoplasmic signal leading to the inactivation of BlaI/MecI repressor, and the synthesis of a β-lactamase or a low affinity target. We identified a dipeptide, resulting from the peptidoglycan turnover and present in bacterial cytoplasm, which is able to directly bind to the BlaI/MecI repressor and to destabilize the BlaI/MecI-DNA complex. We propose a general model, in which the acylation of BlaR/MecR receptor and the cellular stress induced by the antibiotic, are both necessary to generate a cell wall-derived coactivator responsible for the expression of an inducible β-lactam-resistance factor. The new model proposed confirms and emphasizes the role of peptidoglycan degradation fragments in bacterial cell regulation.
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Affiliation(s)
- Ana Amoroso
- Centre d'Ingénierie des Protéines, Institut de Chimie B6A, Sart-Tilman, Université de Liège, Liège, Belgium
- Cátedra de Microbiología, Facultad de Farmacia y Bioquímica Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Julien Boudet
- Institut de Biologie Structurale Jean-Pierre Ebel, CEA-CNRS-UJF, Grenoble, France
| | - Stéphanie Berzigotti
- Centre d'Ingénierie des Protéines, Institut de Chimie B6A, Sart-Tilman, Université de Liège, Liège, Belgium
| | - Valérie Duval
- Centre d'Ingénierie des Protéines, Institut de Chimie B6A, Sart-Tilman, Université de Liège, Liège, Belgium
| | - Nathalie Teller
- Chimie Organique de Synthèse, Institut de Chimie B6A, Sart-Tilman. Université de Liège, Liège, Belgium
| | - Dominique Mengin-Lecreulx
- Université de Paris-Sud 11 and CNRS, Institut de Biochimie et Biophysique Moléculaire et Cellulaire, Laboratoire des Enveloppes Bactériennes et Antibiotiques, UMR 8619, Orsay, France
| | - André Luxen
- Chimie Organique de Synthèse, Institut de Chimie B6A, Sart-Tilman. Université de Liège, Liège, Belgium
| | - Jean-Pierre Simorre
- Institut de Biologie Structurale Jean-Pierre Ebel, CEA-CNRS-UJF, Grenoble, France
| | - Bernard Joris
- Centre d'Ingénierie des Protéines, Institut de Chimie B6A, Sart-Tilman, Université de Liège, Liège, Belgium
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21
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Chen J, Canales L, Neal RE. Multi-Segment Direct Inject nano-ESI-LTQ-FT-ICR-MS/MS For Protein Identification. Proteome Sci 2011; 9:38. [PMID: 21736728 PMCID: PMC3142485 DOI: 10.1186/1477-5956-9-38] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2011] [Accepted: 07/07/2011] [Indexed: 12/27/2022] Open
Abstract
Reversed phase high performance liquid chromatography (HPLC) interfaced to electrospray tandem mass spectrometry (MS/MS) is commonly used for the identification of peptides from proteolytically cleaved proteins embedded in a polyacrylamide gel matrix as well as for metabolomics screening. HPLC separations are time consuming (30-60 min average), costly (columns and mobile phase reagents), and carry the risk of column carry over between samples. The use of a chip-based nano-ESI platform (Advion NanoMate) based on replaceable nano-tips for sample introduction eliminates sample cross-contamination, provides unchanging sample matrix, and enhances spray stability with attendant increases in reproducibility. Recent papers have established direct infusion nano-ESI-MS/MS utilizing the NanoMate for protein identification of gel spots based on full range MS scans with data dependent MS/MS. In a full range scan, discontinuous ion suppression due to sample matrix can impair identification of putative mass features of interest in both the proteomic and metabolomic workflows. In the current study, an extension of an established direct inject nano-ESI-MS/MS method is described that utilizes the mass filtering capability of an ion-trap for ion packet separation into four narrow mass ranges (50 amu overlap) with segment specific dynamic data dependent peak inclusion for MS/MS fragmentation (total acquisition time of 3 minutes). Comparison of this method with a more traditional nanoLC-MS/MS based protocol utilizing solvent/sample stream splitting to achieve nanoflow demonstrated comparable results for protein identification from polyacrylamide gel matrices. The advantages of this method include full automation, lack of cross-contamination, low cost, and high throughput.
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Affiliation(s)
- Jing Chen
- Dept of Environmental and Occupational Health Sciences, School of Public Health and Information Sciences, University of Louisville, 485 E, Gray Street, Louisville, KY 40202, USA.
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22
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A competitive binding study of chemokine, sulfated receptor, and glycosaminoglycan interactions by nano-electrospray ionization mass spectrometry. Anal Biochem 2010; 407:134-40. [PMID: 20696123 DOI: 10.1016/j.ab.2010.08.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2010] [Revised: 07/30/2010] [Accepted: 08/02/2010] [Indexed: 12/21/2022]
Abstract
Chemokines are secreted proteins that play roles in inducing chemotaxis, extravasation, and activation of leukocytes associated with inflammatory or homeostatic processes. Tyrosine sulfation of the chemokine receptor has been shown to be important for binding and signaling. We have applied a mass spectrometry method to measure the contribution of this posttranslational modification to binding of its ligand chemokine. Using nano-electrospray time-of-flight mass spectrometry (nano-ESI TOF MS), we determined the association constants of C-C motif chemokine 7 (CCL7) with C-C chemokine receptor type 2 (CCR2), monosulfated CCR2, and disulfated CCR2 peptides to be 1.1×10(4)M(-1), 3.9×10(4)M(-1), and 4.0×10(5)M(-1), respectively. To our knowledge, this is the first reported association constant measurement between a protein and sulfated peptide using MS. Furthermore, nano-ESI MS was used to characterize noncovalent binding interactions among CCL7, Arixtra (a pentasaccharide glycosaminoglycan [GAG] analog), and disulfated CCR2 peptide. A lack of observable ternary complex formation prompted investigation of competitive binding. Results of this study suggest that CCR2 competes partially with GAG for CCL7 binding and that disulfated CCR2 peptide has a higher binding affinity than Arixtra, which correlates with data from association constant measurements for CCL7-disulfated CCR2 and CCL7-Arixtra.
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23
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Afzal AJ, Natarajan A, Saini N, Iqbal MJ, Geisler M, El Shemy HA, Mungur R, Willmitzer L, Lightfoot DA. The nematode resistance allele at the rhg1 locus alters the proteome and primary metabolism of soybean roots. PLANT PHYSIOLOGY 2009; 151:1264-80. [PMID: 19429603 PMCID: PMC2773059 DOI: 10.1104/pp.109.138149] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2009] [Accepted: 05/03/2009] [Indexed: 05/19/2023]
Abstract
Heterodera glycines, the soybean cyst nematode (SCN), causes the most damaging chronic disease of soybean (Glycine max). Host resistance requires the resistance allele at rhg1. Resistance destroys the giant cells created in the plant's roots by the nematodes about 24 to 48 h after commencement of feeding. In addition, 4 to 8 d later, a systemic acquired resistance develops that discourages later infestations. The molecular mechanisms that control the rhg1-mediated resistance response appear to be multigenic and complex, as judged by transcript abundance changes, even in near isogenic lines (NILs). This study aimed to focus on key posttranscriptional changes by identifying proteins and metabolites that were increased in abundance in both resistant and susceptible NILs. Comparisons were made among NILs 10 d after SCN infestation and without SCN infestation. Two-dimensional gel electrophoresis resolved more than 1,000 protein spots on each gel. Only 30 protein spots with a significant (P < 0.05) difference in abundance of 1.5-fold or more were found among the four treatments. The proteins in these spots were picked, trypsin digested, and analyzed using quadrupole time-of-flight tandem mass spectrometry. Protein identifications could be made for 24 of the 30 spots. Four spots contained two proteins, so that 28 distinct proteins were identified. The proteins were grouped into six functional categories. Metabolite analysis by gas chromatography-mass spectrometry identified 131 metabolites, among which 58 were altered by one or more treatment; 28 were involved in primary metabolism. Taken together, the data showed that 17 pathways were altered by the rhg1 alleles. Pathways altered were associated with systemic acquired resistance-like responses, including xenobiotic, phytoalexin, ascorbate, and inositol metabolism, as well as primary metabolisms like amino acid synthesis and glycolysis. The pathways impacted by the rhg1 allelic state and SCN infestation agreed with transcript abundance analyses but identified a smaller set of key proteins. Six of the proteins lay within the same small region of the interactome identifying a key set of 159 interacting proteins involved in transcriptional control, nuclear localization, and protein degradation. Finally, two proteins (glucose-6-phosphate isomerase [EC 5.3.1.9] and isoflavone reductase [EC 1.3.1.45]) and two metabolites (maltose and an unknown) differed in resistant and susceptible NILs without SCN infestation and may form the basis of a new assay for the selection of resistance to SCN in soybean.
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Affiliation(s)
| | | | | | | | | | | | | | | | - David A. Lightfoot
- Department of Molecular Biology, Microbiology, and Biochemistry (A.J.A., A.N., H.A.E.S., R.M., D.A.L.), Genomics Core Facility and Center for Excellence in Soybean Research, Teaching, and Outreach, Department of Plant Soil and Agricultural Systems (A.J.A., N.S., H.A.E.S., D.A.L.), and Department of Plant Biology (M.G., D.A.L.), Southern Illinois University, Carbondale, Illinois 62901; Institute for Advanced Learning and Research, Institute for Sustainable and Renewable Resources, Danville, Virginia 24540 (M.J.I.); and Max Planck Institute for Molecular Plant Physiology, Potsdam 14476, Germany (R.M., L.W.)
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24
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Bovet C, Wortmann A, Eiler S, Granger F, Ruff M, Gerrits B, Moras D, Zenobi R. Estrogen receptor-ligand complexes measured by chip-based nanoelectrospray mass spectrometry: an approach for the screening of endocrine disruptors. Protein Sci 2007; 16:938-46. [PMID: 17400923 PMCID: PMC2206638 DOI: 10.1110/ps.062664107] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
In the present report, a method based on chip-based nanoelectrospray mass spectrometry (nanoESI-MS) is described to detect noncovalent ligand binding to the human estrogen receptor alpha ligand-binding domain (hERalpha LBD). This system represents an important environmental interest, because a wide variety of molecules, known as endocrine disruptors, can bind to the estrogen receptor (ER) and induce adverse health effects in wildlife and humans. Using proper experimental conditions, the nanoESI-MS approach allowed for the detection of specific ligand interactions with hERalpha LBD. The relative gas-phase stability of selected hERalpha LBD-ligand complexes did not mirror the binding affinity in solution, a result that demonstrates the prominent role of hydrophobic contacts for stabilizing ER-ligand complexes in solution. The best approach to evaluate relative solution-binding affinity by nanoESI-MS was to perform competitive binding experiments with 17beta-estradiol (E2) used as a reference ligand. Among the ligands tested, the relative binding affinity for hERalpha LBD measured by nanoESI-MS was 4-hydroxtamoxifen approximately diethylstilbestrol > E2 >> genistein >> bisphenol A, consistent with the order of the binding affinities in solution. The limited reproducibility of the bound to free protein ratio measured by nanoESI-MS for this system only allowed the binding constants (K(d)) to be estimated (low nanomolar range for E2). The specificity of nanoESI-MS combined with its speed (1 min/ligand), low sample consumption (90 pmol protein/ligand), and its sensitivity for ligand (30 ng/mL) demonstrates that this technique is a promising method for screening suspected endocrine disrupting compounds and to qualitatively evaluate their binding affinity.
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Affiliation(s)
- Cédric Bovet
- Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
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25
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Yang P, Cooks RG, Ouyang Z, Hawkridge AM, Muddiman DC. Gentle protein ionization assisted by high-velocity gas flow. Anal Chem 2007; 77:6174-83. [PMID: 16194076 DOI: 10.1021/ac050711l] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Gentle protein electrospray ionization is achieved using the high-velocity gas flow of an air amplifier to improve desolvation in conventional ESI and generate intact folded protein ions in the gas phase. Comparisons are made between the ESI spectra of a number of model proteins, including ubiquitin, cytochrome c, lysozyme, and myoglobin, over a range of pH values under optimized conditions, with and without using an air amplifier to achieve high-velocity gas flow. Previously reported increased ion signals are confirmed. In addition, the peaks recorded using the air amplifier are shown to be narrower, corresponding to more complete desolvation. Significant changes in the charge-state distribution also are observed, with a shift to lower charge state at high-velocity flow. The relationship between the observed charge-state distribution and protein conformation was explored by comparing the charge-state shifts and the distributions of charge states for proteins that are or are not stable in their native conformations in low pH solutions. The data suggest retention of native or nativelike protein conformations using the air amplifier in all cases examined. This is explained by a mechanism in which the air amplifier rapidly creates small droplets from the original large ESI droplets and these microdroplets then desolvate without a significant decrease in pH, resulting in retention of the folded protein conformations. Furthermore, the holoform of ionized myoglobin is visible at pH 3.5, a much lower value than the minimum needed to see this form in conventional ESI. These results provide evidence for the importance of the conditions used in the desolvation process for the preservation of the protein conformation and suggest that the conditions achieved when using high-velocity gas flows to assist droplet evaporation and ion desolvation are much gentler than those in conventional ESI experiments.
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Affiliation(s)
- Pengxiang Yang
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA
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Moravec T, Schmidt MA, Herman EM, Woodford-Thomas T. Production of Escherichia coli heat labile toxin (LT) B subunit in soybean seed and analysis of its immunogenicity as an oral vaccine. Vaccine 2007; 25:1647-57. [PMID: 17188785 DOI: 10.1016/j.vaccine.2006.11.010] [Citation(s) in RCA: 96] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2006] [Revised: 10/30/2006] [Accepted: 11/02/2006] [Indexed: 11/16/2022]
Abstract
The B subunit of the heat labile toxin of enterotoxigenic Escherichia coli (LTB) was used as a model immunogen for production in soybean seed. LTB expression was directed to the endoplasmic reticulum (ER) of seed storage parenchyma cells for sequestration in de novo synthesized inert protein accretions derived from the ER. Pentameric LTB accumulated to 2.4% of the total seed protein at maturity and was stable in desiccated seed. LTB-soybean extracts administered orally to mice induced both systemic IgG and IgA, and mucosal IgA antibody responses, and was particularly efficacious when used in a parenteral prime-oral gavage boost immunization strategy. Sera from immunized mice blocked ligand binding in vitro and immunized mice exhibited partial protection against LT challenge. Moreover, soybean-expressed LTB stimulated the antibody response against a co-administered antigen by 500-fold. These results demonstrate the utility of soybean as an efficient production platform for vaccines that can be used for oral delivery.
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Affiliation(s)
- Tomas Moravec
- Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, MO 63132, United States
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27
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Delvolvé A, Tabet JC, Bregant S, Afonso C, Burlina F, Fournier F. Charge dependent behavior of PNA/DNA/PNA triplexes in the gas phase. JOURNAL OF MASS SPECTROMETRY : JMS 2006; 41:1498-508. [PMID: 17103389 DOI: 10.1002/jms.1124] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Intact noncovalent complexes were studied in the gas phase using negative ion nano-ESI mass spectrometry. Among various noncovalent systems studied in the gas phase, the interaction of DNA strands with peptide nucleic acids (PNAs) presents a strong interest as biologically relevant systems. PNAs originally described by Nielsen are used as DNA mimics as possible medical agents by imprisoning DNA single strands into stable noncovalent complexes. Two types of PNAs were investigated in the PNA/DNA multiplex: the original Nielsen's PNA and a modified backbone PNA by the introduction of syn- and anti-(aminoethyl)thiazolidine rings. We first investigated the stoichiometry of PNA/DNA multiplexes formed in solution and observed them in the gas phase via qualitative kinetics of complementary strand associations. It resulted in observing PNA2/DNA triplexes (ts) as the multiply deprotonated species, most stable in both the solution and gas phase. Second, charge-dependant decompositions of these species were undertaken under low-energy collision conditions. It appears that covalent bond cleavages (base releasing or skeleton cleavage) occur from lower ts charge states rather than ts unzipping, which takes place from higher charge states. This behavior can be explained by considering the presence of zwitterions depending on the charge state. They result in strong salt-bridge interactions between the positively charged PNA side chain and the negatively charged DNA backbone. We propose a general model to clearly display the involved patterns in the noncovalent triplex decompositions. Third, the relative stability of three PNA2/DNA complexes was scrutinized in the gas phase by acquiring the breakdown curves of their ts(6-) form, corresponding to the ts unzipping. The chemical structures of the studied PNAs were chosen in order to evidence the possible influence of backbone stereochemistry on the rigidity of PNA2/DNA complexes. It provided significantly different stabilities via V(m) measurements. The relative gas-phase stability order obtained was compared to that found in solution by Chassaing et al., and shows qualitative agreement.
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Affiliation(s)
- Alice Delvolvé
- University Pierre et Marie Curie, CNRS-UMR 7613, Synthèse, Structure et Fonction de Molécules Bioactives, FR 2769, Case Courrier 45, 4 place Jussieu, 75005 Paris, France
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Hofstadler SA, Sannes-Lowery KA. Applications of ESI-MS in drug discovery: interrogation of noncovalent complexes. Nat Rev Drug Discov 2006; 5:585-95. [PMID: 16816839 DOI: 10.1038/nrd2083] [Citation(s) in RCA: 171] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
For many years, analytical mass spectrometry has had numerous supporting roles in the drug development process, including the assessment of compound purity; quantitation of absorption, distribution, metabolism and excretion; and compound-specific pharmacokinetic analyses. More recently, mass spectrometry has emerged as an effective technique for identifying lead compounds on the basis of the characterization of noncovalent ligand-macromolecular target interactions. This approach offers several attractive properties for screening applications in drug discovery compared with other strategies, including the small quantities of target and ligands required, and the capacity to study ligands or targets without having to label them. Here, we review the application of electrospray ionization mass spectrometry to the interrogation of noncovalent complexes, highlighting examples from drug discovery efforts aimed at a range of target classes.
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Affiliation(s)
- Steven A Hofstadler
- Ibis Therapeutics, A Division of ISIS Pharmaceuticals, 1891 Rutherford Road, Carlsbad, California 92008, USA.
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29
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Sheffield J, Taylor N, Fauquet C, Chen S. The cassava (Manihot esculenta Crantz) root proteome: Protein identification and differential expression. Proteomics 2006; 6:1588-98. [PMID: 16421938 DOI: 10.1002/pmic.200500503] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Using high-resolution 2-DE, we resolved proteins extracted from fibrous and tuberous root tissues of 3-month-old cassava plants. Gel image analysis revealed an average of 1467 electrophoretically resolved spots on the fibrous gels and 1595 spots on the tuberous gels in pH 3-10 range. Protein spots from both sets of gels were digested with trypsin. The digests were subjected to nanoelectrospray quadrupole TOF tandem mass analysis. Currently, we have obtained 299 protein identifications for 292 gel spots corresponding to 237 proteins. The proteins span various functional categories from energy, primary and secondary metabolism, disease and defense, destination and storage, transport, signal transduction, protein synthesis, cell structure, and transcription to cell growth and division. Gel image analysis has shown unique, as well as up- and down-regulated proteins, present in the tuberous and the fibrous tissues. Quantitative and qualitative analysis of the cassava root proteome is an important step towards further characterization of differentially expressed proteins and the elucidation of the mechanisms underlying the development and biological functions of the two types of roots.
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Affiliation(s)
- Jeanne Sheffield
- Proteomics and Mass Spectrometry Facility, Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
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30
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Anderson JC, Pascuzzi PE, Xiao F, Sessa G, Martin GB. Host-mediated phosphorylation of type III effector AvrPto promotes Pseudomonas virulence and avirulence in tomato. THE PLANT CELL 2006; 18:502-14. [PMID: 16399801 PMCID: PMC1356555 DOI: 10.1105/tpc.105.036590] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2005] [Revised: 11/29/2005] [Accepted: 12/12/2005] [Indexed: 05/06/2023]
Abstract
The AvrPto protein from Pseudomonas syringae pv tomato is delivered into plant cells by the bacterial type III secretion system, where it either promotes host susceptibility or, in tomato plants expressing the Pto kinase, elicits disease resistance. Using two-dimensional gel electrophoresis, we obtained evidence that AvrPto is phosphorylated when expressed in plant leaves. In vitro phosphorylation of AvrPto by plant extracts occurs independently of Pto and is due to a kinase activity that is conserved in tomato (Solanum lycopersicum), tobacco (Nicotiana tabacum), and Arabidopsis thaliana. Three Ser residues clustered in the C-terminal 18 amino acids of AvrPto were identified in vitro as putative phosphorylation sites, and one site at S149 was directly confirmed as an in vivo phosphorylation site by mass spectrometry. Substitution of Ala for S149 significantly decreased the ability of AvrPto to enhance disease symptoms and promote growth of P. s. tomato in susceptible tomato leaves. In addition, S149A significantly decreased the avirulence activity of AvrPto in resistant tomato plants. Our observations support a model in which AvrPto has evolved to mimic a substrate of a highly conserved plant kinase to enhance its virulence activity. Furthermore, residues of AvrPto that promote virulence are also monitored by plant defenses.
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Affiliation(s)
- Jeffrey C Anderson
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853-2703, USA
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31
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Ashcroft AE. Recent developments in electrospray ionisation mass spectrometry: noncovalently bound protein complexes. Nat Prod Rep 2005; 22:452-64. [PMID: 16047045 DOI: 10.1039/b417724j] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- Alison E Ashcroft
- Astbury Centre for Structural Molecular Biology, School of Biochemistry & Microbiology, The University of Leeds, UK
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32
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Vreuls C, Filée P, Van Melckebeke H, Aerts T, De Deyn P, Llabrès G, Matagne A, Simorre JP, Frère JM, Joris B. Guanidinium chloride denaturation of the dimeric Bacillus licheniformis BlaI repressor highlights an independent domain unfolding pathway. Biochem J 2005; 384:179-90. [PMID: 15285720 PMCID: PMC1134101 DOI: 10.1042/bj20040658] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The Bacillus licheniformis 749/I BlaI repressor is a prokaryotic regulator that, in the absence of a beta-lactam antibiotic, prevents the transcription of the blaP gene, which encodes the BlaP beta-lactamase. The BlaI repressor is composed of two structural domains. The 82-residue NTD (N-terminal domain) is a DNA-binding domain, and the CTD (C-terminal domain) containing the next 46 residues is a dimerization domain. Recent studies have shown the existence of the monomeric, dimeric and tetrameric forms of BlaI in solution. In the present study, we analyse the equilibrium unfolding of BlaI in the presence of GdmCl (guanidinium chloride) using different techniques: intrinsic and ANS (8-anilinonaphthalene-l-sulphonic acid) fluorescence, far- and near-UV CD spectroscopy, cross-linking, analytical ultracentrifugation, size exclusion chromatography and NMR spectroscopy. In addition, the intact NTD and CTD were purified after proteolysis of BlaI by papain, and their unfolding by GdmCl was also studied. GdmCl-induced equilibrium unfolding was shown to be fully reversible for BlaI and for the two isolated fragments. The results demonstrate that the NTD and CTD of BlaI fold/unfold independently in a four-step process, with no significant co-operative interactions between them. During the first step, the unfolding of the BlaI CTD occurs, followed in the second step by the formation of an 'ANS-bound' intermediate state. Cross-linking and analytical ultracentrifugation experiments suggest that the dissociation of the dimer into two partially unfolded monomers takes place in the third step. Finally, the unfolding of the BlaI NTD occurs at a GdmCl concentration of approx. 4 M. In summary, it is shown that the BlaI CTD is structured, more flexible and less stable than the NTD upon GdmCl denaturation. These results contribute to the characterization of the BlaI dimerization domain (i.e. CTD) involved in the induction process.
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Affiliation(s)
- Christelle Vreuls
- *Centre d’ingénierie des Protéines, Institut de Chimie B6a, Université de Liège, Sart-Tilman, B4000 Liège, Belgium
- †Laboratoire de Physique Biomédicale, Institut de Physique B5, Université de Liège, Sart-Tilman, B4000 Liège, Belgium
| | - Patrice Filée
- *Centre d’ingénierie des Protéines, Institut de Chimie B6a, Université de Liège, Sart-Tilman, B4000 Liège, Belgium
| | - Hélène Van Melckebeke
- ‡Institut de Biologie Structurale Jean-Pierre Ebel, CEA-CNRS-UJF, 38027 Grenoble, France
| | - Tony Aerts
- §Department of Biomedical Sciences, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp, Belgium
| | - Peter De Deyn
- §Department of Biomedical Sciences, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp, Belgium
| | - Gabriel Llabrès
- †Laboratoire de Physique Biomédicale, Institut de Physique B5, Université de Liège, Sart-Tilman, B4000 Liège, Belgium
| | - André Matagne
- *Centre d’ingénierie des Protéines, Institut de Chimie B6a, Université de Liège, Sart-Tilman, B4000 Liège, Belgium
| | - Jean-Pierre Simorre
- ‡Institut de Biologie Structurale Jean-Pierre Ebel, CEA-CNRS-UJF, 38027 Grenoble, France
| | - Jean-Marie Frère
- *Centre d’ingénierie des Protéines, Institut de Chimie B6a, Université de Liège, Sart-Tilman, B4000 Liège, Belgium
| | - Bernard Joris
- *Centre d’ingénierie des Protéines, Institut de Chimie B6a, Université de Liège, Sart-Tilman, B4000 Liège, Belgium
- To whom correspondence should be addressed (email )
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33
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Csiszar S, Thachuk M. Using ellipsoids to model charge distributions in gas phase protein complex ion dissociation. CAN J CHEM 2004. [DOI: 10.1139/v04-154] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Gas phase protein complex dissociation was modelled using ellipsoids on which discrete charges were placed in randomly chosen charge sites. A number of sizes, shapes, orientations, and types of ellipsoids were considered. For each case, charge transfer parameters and electrostatic energies were calculated as a function of the fractional surface area. It was found that to within 1015%, the charge on product ions after dissociation is distributed according to their fractional surface area. This can imply, for example, that in experiments measuring the dissociation of homodimers, charge asymmetries of greater than 1015% in the product ions signal that one of the ions has greatly increased its surface area, such as would occur with unfolding. This assumes that proton transfer occurs on a timescale fast enough that the dissociation products adopt the minimum electrostatic energy configuration. Calculation of this energy shows that it is minimized when one or more of the monomers is in an extended conformation.Key words: protein complex dissociation, ellipsoid charge model, charge asymmetry.
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34
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Lu H, Guo Y, Yang P. Using amino acids for probing structural information of cytochrome c by electrospray ionization mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2004; 15:1612-1615. [PMID: 15519228 DOI: 10.1016/j.jasms.2004.07.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2003] [Revised: 07/22/2004] [Accepted: 07/23/2004] [Indexed: 05/24/2023]
Abstract
By using electrospray ionization mass spectrometry (ESI-MS), protein complexes of cytochrome c with amino acids were studied. Different amino acids were investigated to explore these complexes. Using these amino acids, a strategy for probing the structure of cytochrome c was established. It was found that L-Arg and L-Glu could bind with cytochrome c to form noncovalent complexes. At low pH solution, complexes between the cytochrome c molecule with several L-Arg molecules (multiple L-Arg adducts) were formed, and the number of binding ligands depended on the charge state of cytochrome c. While in neutral solution, the cytochrome c molecule complexed with only one L-Arg molecule (single L-Arg adducts). As for L-Glu, only single L-Glu adducts were formed in both acidic and neutral solutions.
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Affiliation(s)
- Haojie Lu
- Shanghai Mass Spectrometry Center, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, People's Republic of China
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35
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Tang K, Page JS, Smith RD. Charge competition and the linear dynamic range of detection in electrospray ionization mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2004; 15:1416-1423. [PMID: 15465354 PMCID: PMC1829300 DOI: 10.1016/j.jasms.2004.04.034] [Citation(s) in RCA: 189] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2004] [Revised: 04/27/2004] [Accepted: 04/27/2004] [Indexed: 05/06/2023]
Abstract
An experimental investigation and theoretical analysis are reported on charge competition in electrospray ionization (ESI) and its effects on the linear dynamic range of ESI mass spectrometric (MS) measurements. The experiments confirmed the expected increase of MS sensitivities as the ESI flow rate decreases. However, different compounds show somewhat different mass spectral peak intensities even at the lowest flow rates, at the same concentration and electrospray operating conditions. MS response for each compound solution shows good linearity at lower concentrations and levels off at high concentration, consistent with analyte "saturation" in the ESI process. The extent of charge competition leading to saturation in the ESI process is consistent with the relative magnitude of excess charge in the electrospray compared to the total number of analyte molecules in the solution. This ESI capacity model allows one to predict the sample concentration limits for charge competition and the on-set of ionization suppression effects, as well as the linear dynamic range for ESI-MS. The implications for quantitative MS analysis and possibilities for effectively extending the dynamic range of ESI measurements are discussed.
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Affiliation(s)
- Keqi Tang
- Biological Sciences Division and Environmental and Molecular Sciences Laboratory, Pacific Northwest National Laboratory, MSIN K8-98, P.O. Box 999, 99352, Richland, WA, USA
| | - Jason S Page
- Biological Sciences Division and Environmental and Molecular Sciences Laboratory, Pacific Northwest National Laboratory, MSIN K8-98, P.O. Box 999, 99352, Richland, WA, USA
| | - Richard D Smith
- Biological Sciences Division and Environmental and Molecular Sciences Laboratory, Pacific Northwest National Laboratory, MSIN K8-98, P.O. Box 999, 99352, Richland, WA, USA.
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36
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Zhang S, Van Pelt CK, Wilson DB. Quantitative determination of noncovalent binding interactions using automated nanoelectrospray mass spectrometry. Anal Chem 2003; 75:3010-8. [PMID: 12964745 DOI: 10.1021/ac034089d] [Citation(s) in RCA: 114] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Electrospray ionization mass spectrometry (ESI-MS) has proven to be an extremely powerful tool for studying biomolecular structures and noncovalent interactions. Here we report a method using a fully automated, chip-based nanoESI-MS system to determine the dissociation constants (Kd) for the complexes of two different proteins with their ligands. The automated nanoelectrospray system, consisting of the NanoMate and ESI chip, serves functionally as a combination of autosampler and nanoelectrospray ionization source. This system provides all the advantages of conventional nanoelectrospray plus automated, high-throughput analyses without carryover. The automated nanoESI system was used to investigate quantitative noncovalent interactions between ribonuclease A (RNase A) and cytidylic acid ligands (2'-CMP, CTP), a well-characterized model protein-ligand complex, and between an inactive endocellulase mutant (Thermobifida fusca Cel6A D117Acd) and four oligosaccharide ligands (cellotriose, cellotetraose, cellopentaose, cellohexaose). Both titration and competitive binding approaches were performed prior to automated nanoESI-MS analysis with a Q-TOF mass spectrometer. Dissociation constants for each complex were calculated from the sum of ion peak areas of free and complexed proteins during the titration and competition experiments. The measured Kd values for the RNase A-CMP and Cel6A D117Acd-G3 complexes were found to be in excellent agreement with the available published values obtained by standard spectroscopic titration techniques. To our knowledge, this is the first report of using an ESI-MS approach to study the interactions between a cellulase and oligosaccharides. The results provide new insights for understanding the nature of cellulase-cellulose interactions.
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Affiliation(s)
- Sheng Zhang
- Advion BioSciences, Inc., 15 Catherwood Road, Ithaca, New York 14850, USA.
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37
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Benkestock K, Van Pelt CK, Akerud T, Sterling A, Edlund PO, Roeraade J. Automated nano-electrospray mass spectrometry for protein-ligand screening by noncovalent interaction applied to human H-FABP and A-FABP. JOURNAL OF BIOMOLECULAR SCREENING 2003; 8:247-56. [PMID: 12857378 DOI: 10.1177/1087057103008003002] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
A method for ligand screening by automated nano-electrospray ionization mass spectrometry (nano-ESI/MS) is described. The core of the system consisted of a chip-based platform for automated sample delivery from a 96-well plate and subsequent analysis based on noncovalent interactions. Human fatty acid binding protein, H-FABP (heart) and A-FABP (adipose), with small potential ligands was analyzed. The technique has been compared with a previously reported method based on nuclear magnetic resonance (NMR), and excellent correlation with the found hits was obtained. In the current MS screening method, the cycle time per sample was 1.1 min, which is approximately 50 times faster than NMR for single compounds and approximately 5 times faster for compound mixtures. High reproducibility was achieved, and the protein consumption was in the range of 88 to 100 picomoles per sample. Futhermore, a novel protocol for preparation of A-FABP without the natural ligand is presented. The described screening approach is suitable for ligand screening very early in the drug discovery process before conventional high-throughput screens (HTS) are developed and/or used as a secondary screening for ligands identified by HTS.
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38
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Filée P, Vreuls C, Herman R, Thamm I, Aerts T, De Deyn PP, Frère JM, Joris B. Dimerization and DNA binding properties of the Bacillus licheniformis 749/I BlaI repressor. J Biol Chem 2003; 278:16482-7. [PMID: 12615920 DOI: 10.1074/jbc.m210887200] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
In the absence of penicillin, the beta-lactamase encoding gene blaP of Bacillus licheniformis 749/I is negatively regulated by the transcriptional repressor BlaI. Three palindromic operator regions are recognized by BlaI: two in the blaP promoter (OP1 and OP2) and one (OP3) in the promoter of the blaI-blaR1 operon. In this study, the dissociation constant of the purified BlaI dimer was estimated at 25 microm by equilibrium ultracentrifugation. Quantitative Western blot analysis indicates that the intracellular concentrations of BlaI in B. licheniformis 749/I and Bacillus subtilis transformed by a multicopy plasmid harboring the beta-lactamase locus (blaP-blaI-blaR1) were lower than (1.9 microm) or in the same range as (75 microm) the dissociation constant, respectively. This suggests that BlaI is partially dimeric in the cytoplasm of these strains and interacts in vivo with its operators as a preformed dimer. This hypothesis is supported by band shift assays on an operator containing a randomized half-operator sequence. The global dissociation constants of the operator-BlaI dimer complexes were measured by band shift assays and estimated as K(d)(OP1) = 1.7 +/- 0.5 10(-15) m(2), K(d)(OP2) = 3.3 +/- 0.9 10(-15) m(2), and K(d)(OP3) = 10.5 +/- 2.5 10(-15) m(2). The role of the DNA binding properties of BlaI on the beta-lactamase regulation is discussed.
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Affiliation(s)
- Patrice Filée
- Centre d'ingénierie des Protéines, Institut de Chimie B6a, Université de Liège, Sart-Tilman, B4000 Liège, Belgium
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39
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Current literature in mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2002; 37:1298-1307. [PMID: 12489092 DOI: 10.1002/jms.259] [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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