1
|
Lento C, Wilson DJ. Subsecond Time-Resolved Mass Spectrometry in Dynamic Structural Biology. Chem Rev 2021; 122:7624-7646. [PMID: 34324314 DOI: 10.1021/acs.chemrev.1c00222] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Life at the molecular level is a dynamic world, where the key players-proteins, oligonucleotides, lipids, and carbohydrates-are in a perpetual state of structural flux, shifting rapidly between local minima on their conformational free energy landscapes. The techniques of classical structural biology, X-ray crystallography, structural NMR, and cryo-electron microscopy (cryo-EM), while capable of extraordinary structural resolution, are innately ill-suited to characterize biomolecules in their dynamically active states. Subsecond time-resolved mass spectrometry (MS) provides a unique window into the dynamic world of biological macromolecules, offering the capacity to directly monitor biochemical processes and conformational shifts with a structural dimension provided by the electrospray charge-state distribution, ion mobility, covalent labeling, or hydrogen-deuterium exchange. Over the past two decades, this suite of techniques has provided important insights into the inherently dynamic processes that drive function and pathogenesis in biological macromolecules, including (mis)folding, complexation, aggregation, ligand binding, and enzyme catalysis, among others. This Review provides a comprehensive account of subsecond time-resolved MS and the advances it has enabled in dynamic structural biology, with an emphasis on insights into the dynamic drivers of protein function.
Collapse
Affiliation(s)
- Cristina Lento
- Department of Chemistry, York University, Toronto, Ontario M3J 1P3, Canada
| | - Derek J Wilson
- Department of Chemistry, York University, Toronto, Ontario M3J 1P3, Canada
| |
Collapse
|
2
|
Yan B, Bunch J. Probing Folded Proteins and Intact Protein Complexes by Desorption Electrospray Ionization Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:690-699. [PMID: 33605725 DOI: 10.1021/jasms.0c00417] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Native mass spectrometry (MS) enables the study of intact proteins as well as noncovalent protein-protein and protein-ligand complexes in their biological state. In this work, we present the application of a Waters desorption electrospray ionization (DESI) source with a prototype spray emitter for rapid surface measurements of folded and native protein structures. A comparison of DESI spray solvent shows that adding 50% methanol to 200 mM ammonium acetate solution does not reduce its performance in preserving folded protein structures. Instead, improved signal-to-noise (S/N) ratio is obtained, and less adducted peaks are detected by using this uncommon native MS solvent system. The standard DESI design with an inlet tube allows optimization of sampling temperature conditions to improve desolvation and therefore S/N ratio. Furthermore, tuning the inlet temperature enables the control and study of unfolding behavior of proteins from surface samples. The optimized condition for native DESI has been applied to several selected proteins and protein complexes with the molecular weight ranging from 8.6 to 66.4 kDa. Ions of folded proteins with narrow charge state distribution (CSD), or peaks showing noncovalent-bond-assembled intact protein complexes, are observed in the spectra. Evidence for the structural refolding of denatured proteins and protein complexes sampled with native solvent highlights the need for care when interpreting DESI native MS data, particularly for proteins with stable native structures.
Collapse
Affiliation(s)
- Bin Yan
- National Centre of Excellence in Mass Spectrometry Imaging, National Physical Laboratory, Hampton Road, Teddington TW11 0LW, U.K
| | - Josephine Bunch
- National Centre of Excellence in Mass Spectrometry Imaging, National Physical Laboratory, Hampton Road, Teddington TW11 0LW, U.K
- Department of Metabolism, Digestion and Reproduction, Imperial College London, South Kensington Campus, London SW7 2AZ, U.K
- Rosalind Franklin Institute, Harwell Campus, Didcot OX11 0FA, U.K
| |
Collapse
|
3
|
Woodall DW, Henderson LW, Raab SA, Honma K, Clemmer DE. Understanding the Thermal Denaturation of Myoglobin with IMS-MS: Evidence for Multiple Stable Structures and Trapped Pre-equilibrium States. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:64-72. [PMID: 32539412 PMCID: PMC7790998 DOI: 10.1021/jasms.0c00075] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Thermal denaturation of holomyoglobin (hMb) in solution (10 mM ammonium acetate at pH = 4.5, 6.8, and 9.0) was monitored by ion mobility spectrometry (IMS) and mass spectrometry (MS) techniques to characterize the stability and investigate structural changes involved in unfolding. We utilize two experimental approaches to induce thermal denaturation: a variable-temperature electrospray ionization (vT-ESI) source that heats the bulk solution in the ESI emitter, and a variable-power 10.6 μm CO2 laser that rapidly heats nanodroplets produced by ESI. These two approaches sample different time scales of the denaturation process; long time scales (seconds to minutes) where the system is at equilibrium using the vT-ESI approach and shorter time scales (μs) by rapid droplet heating in which the system is in a pre-equilibrium state. Increasing the solution temperature (from 28 to 95 °C in the vT-ESI experiments) shifts the charge state distribution from low charge states ([M + 7H]7+ to [M + 9H]9+) to more highly charged species. This is accompanied by loss of the heme group to yield the apomyoglobin (aMb) species, indicating that the protein has unfolded. Monitoring the formation of aMb and the shift in average charge states of aMb and hMb with solution temperature allows for relative quantitation of their individual stabilities, highlighting the stabilizing effects of heme binding. We compare the degree of unfolding induced by heating the bulk solution (using vT-ESI) to the laser droplet heating approach and find that the rapid nature of the laser heating approach allows for transient pre-equilibrium states to be sampled.
Collapse
Affiliation(s)
- Daniel W Woodall
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Lucas W Henderson
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Shannon A Raab
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Kenji Honma
- Graduate School of Material Science, University of Hyogo, 3-2-1 Kohto, Kamigori, Hyogo 678-1297, Japan
| | - David E Clemmer
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| |
Collapse
|
4
|
Bovine Hemoglobin Enzymatic Hydrolysis by a New Ecoefficient Process-Part I: Feasibility of Electrodialysis with Bipolar Membrane and Production of Neokyotorphin (α137-141). MEMBRANES 2020; 10:membranes10100257. [PMID: 32992811 PMCID: PMC7600281 DOI: 10.3390/membranes10100257] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 09/23/2020] [Accepted: 09/23/2020] [Indexed: 11/24/2022]
Abstract
Neokyotorphin (α137-141) is recognized as an antimicrobial peptide and a natural meat preservative. It is produced by conventional enzymatic hydrolysis of bovine hemoglobin, a major component of cruor, a by-product of slaughterhouses. However, during conventional hydrolysis, chemical agents are necessary to adjust and regulate the pH of the protein solution and the mineral salt content of the final hydrolysate is consequently high. To produce this peptide of interest without chemical agents and with a low salt concentration, electrodialysis with bipolar membrane (EDBM), an electromembrane process recognized as a green process, with two different membrane configurations (cationic (MCP) and anionic (AEM) membranes) was investigated. Hydrolysis in EDBM showed the same enzymatic mechanism, “Zipper”, and allowed the generation of α137-141 in the same concentration as observed in conventional hydrolysis (control). EDBM-MCP allowed the production of hydrolysates containing a low concentration of mineral salts but with fouling formation on MCP, while EDBM-AEM allowed the production of hydrolysates without fouling but with a similar salt concentration than the control. To the best of our knowledge, this was the first time that EDBM was demonstrated as a feasible and innovative technology to produce peptide hydrolysates from enzymatic hydrolysis.
Collapse
|
5
|
Pires IS, Belcher DA, Hickey R, Miller C, Badu‐Tawiah AK, Baek JH, Buehler PW, Palmer AF. Novel manufacturing method for producing apohemoglobin and its biophysical properties. Biotechnol Bioeng 2019; 117:125-145. [DOI: 10.1002/bit.27193] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 06/08/2019] [Accepted: 10/11/2019] [Indexed: 12/25/2022]
Affiliation(s)
- Ivan S. Pires
- William G. Lowrie Department of Chemical and Biomolecular EngineeringThe Ohio State University Columbus Ohio
| | - Donald A. Belcher
- William G. Lowrie Department of Chemical and Biomolecular EngineeringThe Ohio State University Columbus Ohio
| | - Richard Hickey
- William G. Lowrie Department of Chemical and Biomolecular EngineeringThe Ohio State University Columbus Ohio
| | - Colbert Miller
- Department of Chemistry and BiochemistryThe Ohio State University Columbus Ohio
| | | | - Jin Hyen Baek
- Laboratory of Biochemistry and Vascular Biology, Division of Hematology, Center for Biologics Evaluation and ResearchFood and Drug Administration Silver Spring Maryland
| | - Paul W. Buehler
- Laboratory of Biochemistry and Vascular Biology, Division of Hematology, Center for Biologics Evaluation and ResearchFood and Drug Administration Silver Spring Maryland
| | - Andre F. Palmer
- William G. Lowrie Department of Chemical and Biomolecular EngineeringThe Ohio State University Columbus Ohio
| |
Collapse
|
6
|
Sensitivity enhancement of electrochemical biosensor via cobalt nanoflowers on graphene and protein conformational intermediate. J Electroanal Chem (Lausanne) 2017. [DOI: 10.1016/j.jelechem.2017.06.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
7
|
Lento C, Wilson DJ. Unravelling the mysteries of sub-second biochemical processes using time-resolved mass spectrometry. Analyst 2017; 142:1640-1653. [DOI: 10.1039/c7an00338b] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Many important chemical and biochemical phenomena proceed on sub-second time scales.
Collapse
Affiliation(s)
| | - Derek J. Wilson
- Department of Chemistry
- York University
- Toronto
- Canada
- Centre for Research of Biomolecular Interactions
| |
Collapse
|
8
|
Pedro L, Van Voorhis WC, Quinn RJ. Optimization of Electrospray Ionization by Statistical Design of Experiments and Response Surface Methodology: Protein-Ligand Equilibrium Dissociation Constant Determinations. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:1520-30. [PMID: 27225419 PMCID: PMC4972871 DOI: 10.1007/s13361-016-1417-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2014] [Revised: 04/29/2016] [Accepted: 05/04/2016] [Indexed: 05/28/2023]
Abstract
Electrospray ionization mass spectrometry (ESI-MS) binding studies between proteins and ligands under native conditions require that instrumental ESI source conditions are optimized if relative solution-phase equilibrium concentrations between the protein-ligand complex and free protein are to be retained. Instrumental ESI source conditions that simultaneously maximize the relative ionization efficiency of the protein-ligand complex over free protein and minimize the protein-ligand complex dissociation during the ESI process and the transfer from atmospheric pressure to vacuum are generally specific for each protein-ligand system and should be established when an accurate equilibrium dissociation constant (KD) is to be determined via titration. In this paper, a straightforward and systematic approach for ESI source optimization is presented. The method uses statistical design of experiments (DOE) in conjunction with response surface methodology (RSM) and is demonstrated for the complexes between Plasmodium vivax guanylate kinase (PvGK) and two ligands: 5'-guanosine monophosphate (GMP) and 5'-guanosine diphosphate (GDP). It was verified that even though the ligands are structurally similar, the most appropriate ESI conditions for KD determination by titration are different for each. Graphical Abstract ᅟ.
Collapse
Affiliation(s)
- Liliana Pedro
- Eskitis Institute for Drug Discovery, Griffith University, Brisbane, Queensland, Australia
| | | | - Ronald J Quinn
- Eskitis Institute for Drug Discovery, Griffith University, Brisbane, Queensland, Australia.
| |
Collapse
|
9
|
Biophysical Methods to Investigate Intrinsically Disordered Proteins: Avoiding an “Elephant and Blind Men” Situation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 870:215-60. [DOI: 10.1007/978-3-319-20164-1_7] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
10
|
Martin NJ, Griffiths RL, Edwards RL, Cooper HJ. Native Liquid Extraction Surface Analysis Mass Spectrometry: Analysis of Noncovalent Protein Complexes Directly from Dried Substrates. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:1320-7. [PMID: 25990922 PMCID: PMC4494149 DOI: 10.1007/s13361-015-1152-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Revised: 03/24/2015] [Accepted: 03/27/2015] [Indexed: 05/18/2023]
Abstract
Liquid extraction surface analysis (LESA) mass spectrometry is a promising tool for the analysis of intact proteins from biological substrates. Here, we demonstrate native LESA mass spectrometry of noncovalent protein complexes of myoglobin and hemoglobin from a range of surfaces. Holomyoglobin, in which apomyoglobin is noncovalently bound to the prosthetic heme group, was observed following LESA mass spectrometry of myoglobin dried onto glass and polyvinylidene fluoride surfaces. Tetrameric hemoglobin [(αβ)2(4H)] was observed following LESA mass spectrometry of hemoglobin dried onto glass and polyvinylidene fluoride (PVDF) surfaces, and from dried blood spots (DBS) on filter paper. Heme-bound dimers and monomers were also observed. The 'contact' LESA approach was particularly suitable for the analysis of hemoglobin tetramers from DBS.
Collapse
Affiliation(s)
- Nicholas J. Martin
- />School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT UK
| | - Rian L. Griffiths
- />School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT UK
| | - Rebecca L. Edwards
- />School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT UK
- />Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, TN 37232 USA
| | - Helen J. Cooper
- />School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT UK
| |
Collapse
|
11
|
Cui W, Zhang H, Blankenship RE, Gross ML. Electron-capture dissociation and ion mobility mass spectrometry for characterization of the hemoglobin protein assembly. Protein Sci 2015; 24:1325-32. [PMID: 26032343 DOI: 10.1002/pro.2712] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 05/19/2015] [Indexed: 12/12/2022]
Abstract
Native spray has the potential to probe biophysical properties of protein assemblies. Here we report an investigation using both ECD top-down sequencing with an FTICR mass spectrometer and ion mobility (IM) measurements on a Q-TOF to investigate the collisionally induced unfolding of a native-like heterogeneous tetrameric assembly, human hemoglobin (hHb), in the gas phase. To our knowledge, this is the first report combining ECD and ion-mobility data on the same target protein assembly to delineate the effects of collisional activation on both assembly size and the extent and location of fragmentation. Although the collision-induced unfolding of the hemoglobin assembly is clearly seen by both IMMS and ECD, the latter delineates the regions that increasingly unfold as the collision energy is increased. The results are consistent with previous outcomes for homogeneous protein assemblies and reinforce our interpretation that activation opens the structure of the protein assembly from the flexible regions to make available ECD fragmentation, without dissociating the component proteins.
Collapse
Affiliation(s)
- Weidong Cui
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri, 63130
| | - Hao Zhang
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri, 63130
| | - Robert E Blankenship
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri, 63130.,Department of Biology, Washington University in St. Louis, St. Louis, Missouri, 63130
| | - Michael L Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri, 63130
| |
Collapse
|
12
|
DeMuth JC, Bu J, McLuckey SA. Electrospray droplet exposure to polar vapors: delayed desolvation of protein complexes. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2015; 29:973-981. [PMID: 26407312 DOI: 10.1002/rcm.7188] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Revised: 02/08/2015] [Accepted: 03/05/2015] [Indexed: 06/05/2023]
Abstract
RATIONALE Fragile non-covalent complexes are susceptible to dissociation upon introduction into and transmission through the mass spectrometer. The exposure of nanoelectrospray droplets to various polar vapors, which are introduced into the curtain gas, is shown to stabilize non-covalent protein complexes even under relatively energetic ion transfer conditions. This study probes the mechanism by which polar vapor exposure appears to stabilize non-covalent protein complex ions in the gas phase. METHODS Holomyoglobin and hemoglobin were dissolved in either aqueous 1 mM ammonium acetate or ammonium bicarbonate solutions and ionized via nanoelectrospray ionization in the positive polarity. Polar vapors were entrained within the counter-current drying gas and exposed to nanoelectrospray droplets for circa 1 ms within the interface of a quadrupole/time-of-flight mass spectrometer. Mass spectra were acquired using various voltage gradients within the mass spectrometer. RESULTS In the absence of added reagent vapors, significant fragmentation of holomyoglobin ions is noted with high voltage gradients for ions either entering or departing q0, a transmission quadrupole closely coupled to the skimmer exit. However, upon the introduction of reagent vapors, essentially 100% of the holomyoglobin complex can be preserved. Significant stabilization is noted at both relatively high q0 entrance and exit gradients when ions are transmitted through q0. These results indicate that upon vapor exposure the holomyoglobin ions are not completely desolvated as they enter or exit q0 under normal ion transmission conditions. CONCLUSIONS The apparent stabilization of protein complexes and other non-covalent complexes noted here and elsewhere is attributed to the delayed desolvation of the ions. This allows the solvated ions to be transmitted through relatively high voltage gradients without disrupting the non-covalent interactions holding the complexes together.
Collapse
Affiliation(s)
- J Corinne DeMuth
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907-2084, USA
| | - Jiexun Bu
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907-2084, USA
| | - Scott A McLuckey
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907-2084, USA
| |
Collapse
|
13
|
Wohlgemuth I, Lenz C, Urlaub H. Studying macromolecular complex stoichiometries by peptide-based mass spectrometry. Proteomics 2015; 15:862-79. [PMID: 25546807 PMCID: PMC5024058 DOI: 10.1002/pmic.201400466] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 11/24/2014] [Accepted: 12/22/2014] [Indexed: 11/11/2022]
Abstract
A majority of cellular functions are carried out by macromolecular complexes. A host of biochemical and spectroscopic methods exists to characterize especially protein/protein complexes, however there has been a lack of a universal method to determine protein stoichiometries. Peptide‐based MS, especially as a complementary method to the MS analysis of intact protein complexes, has now been developed to a point where it can be employed to assay protein stoichiometries in a routine manner. While the experimental demands are still significant, peptide‐based MS has been successfully applied to analyze stoichiometries for a variety of protein complexes from very different biological backgrounds. In this review, we discuss the requirements especially for targeted MS acquisition strategies to be used in this context, with a special focus on the interconnected experimental aspects of sample preparation, protein digestion, and peptide stability. In addition, different strategies for the introduction of quantitative peptide standards and their suitability for different scenarios are compared.
Collapse
Affiliation(s)
- Ingo Wohlgemuth
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Goettingen, Germany
| | | | | |
Collapse
|
14
|
Fotouhi L, Yousefinejad S, Salehi N, Saboury AA, Sheibani N, Moosavi-Movahedi AA. Application of merged spectroscopic data combined with chemometric analysis for resolution of hemoglobin intermediates during chemical unfolding. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 136 Pt C:1974-1981. [PMID: 25468440 PMCID: PMC6690049 DOI: 10.1016/j.saa.2014.10.120] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Revised: 10/21/2014] [Accepted: 10/28/2014] [Indexed: 06/04/2023]
Abstract
Using tetradecyltrimethylammonium bromide (TTAB) as a surfactant denaturant, and augmentation of different spectroscopic data, helped to detect the intermediates of hemoglobin (Hb) during unfolding process. UV-vis, fluorescence, and circular dichroism spectroscopy were used simultaneously to monitor different aspects of hemoglobin species from the tertiary or secondary structure points of view. Application of the multivariate curve resolution-alternating least square (MCR-ALS), using the initial estimates of spectral profiles and appropriate constraints on different parts of augmented spectroscopic data, showed good efficiency for characterization of intermediates during Hb unfolding. These results indicated the existence of five protein species, including three intermediate-like compounds in this process. The unfolding pathway in the presence of TTAB included conversion of oxyhemoglobin into deoxyhemoglobin, and then ferrylhemoglobin, ferrihemoglobin or aquamethemoglobin, which finally transformed into hemichrome. This is the first application of chemometric analysis on the merged spectroscopic data related to chemical denaturation of a protein. These types of analysis in multisubunit proteins not only increase the domain of information, but also can reduce the ambiguities of the obtained results.
Collapse
Affiliation(s)
- L Fotouhi
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - S Yousefinejad
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - N Salehi
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - A A Saboury
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran; Center of Excellence in Biothermodynamics, University of Tehran, Tehran, Iran
| | - N Sheibani
- Department of Ophthalmology and Visual Sciences and McPherson Eye Research Institute, School of Medicine and Public Health, University of Wisconsin, Madison, WI, USA
| | - A A Moosavi-Movahedi
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran; Center of Excellence in Biothermodynamics, University of Tehran, Tehran, Iran.
| |
Collapse
|
15
|
Liuni P, Deng B, Wilson DJ. Comparing equilibrium and kinetic protein unfolding using time-resolved electrospray-coupled ion mobility mass spectrometry. Analyst 2015; 140:6973-9. [DOI: 10.1039/c5an00843c] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
We apply a new hyphenated method, TRESI-IMS-MS, to compare equilibrium and kinetic unfolding intermediates of cytochrome c.
Collapse
Affiliation(s)
- Peter Liuni
- Department of Chemistry and Centre for Research in Mass Spectrometry
- York University
- Toronto
- Canada
| | - Bin Deng
- Department of Chemistry and Centre for Research in Mass Spectrometry
- York University
- Toronto
- Canada
| | - Derek J. Wilson
- Department of Chemistry and Centre for Research in Mass Spectrometry
- York University
- Toronto
- Canada
| |
Collapse
|
16
|
Schermann SM, Simmons DA, Konermann L. Mass spectrometry-based approaches to protein–ligand interactions. Expert Rev Proteomics 2014; 2:475-85. [PMID: 16097882 DOI: 10.1586/14789450.2.4.475] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
One of the greatest current challenges in proteomics is to develop an understanding of cellular communication and regulation processes, most of which involve noncovalent interactions of proteins with various binding partners. Mass spectrometry plays an important role in all aspects of these research efforts. This article provides a survey of mass spectrometry-based approaches for exploring protein-ligand interactions. A wide array of techniques is available, and the choice of method depends on the specific problem at hand. For example, the high-throughput screening of compound libraries for binding to a specific receptor requires different approaches than structural studies on multiprotein complexes. This review is directed to readers wishing to obtain a concise yet comprehensive overview of existing experimental techniques. Specific emphasis is placed on emerging methods that have been developed within the last few years.
Collapse
Affiliation(s)
- Sonya M Schermann
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.
| | | | | |
Collapse
|
17
|
Liu J, Dong Y, Zheng J, He Y, Sheng Q. Investigation on the conformation change of hemoglobin immobilized on MPA-modified electrode by electrochemical method. ANAL SCI 2013; 29:1075-81. [PMID: 24212734 DOI: 10.2116/analsci.29.1075] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The conformation change of bovine hemoglobin (Hb) during the unfolding process induced by urea and acid was investigated by an electrochemical method. Hb unfolding induced by urea of different concentrations was realized by bonding Hb onto a 3-mercaptopropionic acid (MPA) modified gold electrode. The difference in unfolding percentage showed that the Hb unfolding induced by urea was a two-step, three-state transition process, while the unfolding induced by acid was a two-state transition process. The results obtained by the electrochemical method coincided closely with those obtained by UV-vis spectroscopy and fluorescence spectroscopy. Some thermodynamic parameters during the conformational change were also calculated to study the intermediate state during the Hb unfolding process. The present work may lead to an easy and effective way to study metalloproteins unfolding, and holds great promise for the design of novel sensitive biosensors.
Collapse
Affiliation(s)
- Jianbo Liu
- Institute of Analytical Science/Shaanxi Provincial Key Laboratory of Electroanalytical Chemistry, Northwest University
| | | | | | | | | |
Collapse
|
18
|
Microscopy ambient ionization top-down mass spectrometry reveals developmental patterning. Proc Natl Acad Sci U S A 2013; 110:14855-60. [PMID: 23969833 DOI: 10.1073/pnas.1310618110] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
There is immense cellular and molecular heterogeneity in biological systems. Here, we demonstrate the utility of integrating an inverted light microscope with an ambient ionization source, nanospray electrospray desorption ionization, attached to a high-resolution mass spectrometer to characterize the molecular composition of mouse spinal cords. We detected a broad range of molecules, including peptides and proteins, as well as metabolites such as lipids, sugars, and other small molecules, including S-adenosyl methionine and glutathione, through top-down MS. Top-down analysis revealed variation in the expression of Hb, including the transition from fetal to adult Hb and heterogeneity in Hb subunits consistent with the genetic diversity of the mouse models. Similarly, temporal changes to actin-sequestering proteins β-thymosins during development were observed. These results demonstrate that interfacing microscopy with ambient ionization provides the means to perform targeted in situ ambient top-down mass spectral analysis to study the pattern of proteins, lipids, and sugars in biologically heterogeneous samples.
Collapse
|
19
|
Resetca D, Wilson DJ. Characterizing rapid, activity-linked conformational transitions in proteins via sub-second hydrogen deuterium exchange mass spectrometry. FEBS J 2013; 280:5616-25. [DOI: 10.1111/febs.12332] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Revised: 04/26/2013] [Accepted: 05/01/2013] [Indexed: 01/01/2023]
Affiliation(s)
- Diana Resetca
- Department of Chemistry; York University; Toronto Ontario Canada
| | - Derek J. Wilson
- Department of Chemistry; York University; Toronto Ontario Canada
- Center for Research in Mass Spectrometry; Department of Chemistry; York University; Toronto Ontario Canada
| |
Collapse
|
20
|
Protein structure preservation by MWCNTs/RTIL nano-composite. Int J Biol Macromol 2013; 56:169-74. [DOI: 10.1016/j.ijbiomac.2013.02.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Revised: 02/02/2013] [Accepted: 02/04/2013] [Indexed: 11/18/2022]
|
21
|
Kaltashov IA, Bobst CE, Abzalimov RR. Mass spectrometry-based methods to study protein architecture and dynamics. Protein Sci 2013; 22:530-44. [PMID: 23436701 DOI: 10.1002/pro.2238] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2012] [Revised: 02/11/2013] [Accepted: 02/13/2013] [Indexed: 11/09/2022]
Abstract
Mass spectrometry is now an indispensable tool in the armamentarium of molecular biophysics, where it is used for tasks ranging from protein sequencing and mapping of post-translational modifications to studies of higher order structure, conformational dynamics, and interactions of proteins with small molecule ligands and other biopolymers. This mini-review highlights several popular mass spectrometry-based tools that are now commonly used for structural studies of proteins beyond their covalent structure with a particular emphasis on hydrogen exchange and direct electrospray ionization mass spectrometry.
Collapse
Affiliation(s)
- Igor A Kaltashov
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, Massachusetts, USA.
| | | | | |
Collapse
|
22
|
Deng L, Kitova EN, Klassen JS. Dissociation kinetics of the streptavidin-biotin interaction measured using direct electrospray ionization mass spectrometry analysis. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:49-56. [PMID: 23247970 DOI: 10.1007/s13361-012-0533-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2012] [Revised: 10/31/2012] [Accepted: 11/02/2012] [Indexed: 06/01/2023]
Abstract
Dissociation rate constants (k (off)) for the model high affinity interaction between biotin (B) and the homotetramer of natural core streptavidin (S(4)) were measured at pH 7 and temperatures ranging from 15 to 45 °C using electrospray ionization mass spectrometry (ESI-MS). Two different approaches to data analysis were employed, one based on the initial rate of dissociation of the (S(4) + 4B) complex, the other involving nonlinear fitting of the time-dependent relative abundances of the (S(4) + iB) species. The two methods were found to yield k (off) values that are in good agreement, within a factor of two. The Arrhenius parameters for the dissociation of the biotin-streptavidin interaction in solution were established from the k (off) values determined by ESI-MS and compared with values measured using a radiolabeled biotin assay. Importantly, the dissociation activation energies determined by ESI-MS agree, within 1 kcal mol(-1), with the reported value. In addition to providing a quantitative measure of k (off), the results of the ESI-MS measurements revealed that the apparent cooperative distribution of (S(4) + iB) species observed at short reaction times is of kinetic origin and that sequential binding of B to S(4) occurs in a noncooperative fashion with the four ligand binding sites being kinetically and thermodynamically equivalent and independent.
Collapse
Affiliation(s)
- Lu Deng
- Department of Chemistry and Alberta Glycomics Centre, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | | | | |
Collapse
|
23
|
Abzalimov RR, Frimpong AK, Kaltashov IA. Detection and characterization of large-scale protein conformational transitions in solution using charge-state distribution analysis in ESI-MS. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2012; 896:365-73. [PMID: 22821537 DOI: 10.1007/978-1-4614-3704-8_24] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
Abstract
Ion charge-state distribution analysis in electro-spray ionization mass spectrometry (ESI-MS) is a robust and fast technique for direct detection and characterization of coexisting protein conformations in solution. Compact folded proteins give rise to ESI-generated ions carrying a relatively small number of charges, whereas less compact conformers accommodate upon ESI a larger number of charges depending on the extent of their unfolding. A chemometric approach [1] based upon factor analysis is applied to determine contributions from individual conformers to the overall CSD. Here we present basic guidelines for the use of this MS-based technique: from the preparation of suitable solutions for ESI-MS to the acquisition of reliable MS data and their subsequent analysis.
Collapse
Affiliation(s)
- Rinat R Abzalimov
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, MA, USA
| | | | | |
Collapse
|
24
|
Hilton GR, Benesch JLP. Two decades of studying non-covalent biomolecular assemblies by means of electrospray ionization mass spectrometry. J R Soc Interface 2012; 9:801-16. [PMID: 22319100 PMCID: PMC3306659 DOI: 10.1098/rsif.2011.0823] [Citation(s) in RCA: 112] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2011] [Accepted: 01/16/2012] [Indexed: 12/31/2022] Open
Abstract
Mass spectrometry (MS) is a recognized approach for characterizing proteins and the complexes they assemble into. This application of a long-established physico-chemical tool to the frontiers of structural biology has stemmed from experiments performed in the early 1990s. While initial studies focused on the elucidation of stoichiometry by means of simple mass determination, developments in MS technology and methodology now allow researchers to address questions of shape, inter-subunit connectivity and protein dynamics. Here, we chart the remarkable rise of MS and its application to biomolecular complexes over the last two decades.
Collapse
Affiliation(s)
| | - Justin L. P. Benesch
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX3 1QZ, UK
| |
Collapse
|
25
|
Pacholarz KJ, Garlish RA, Taylor RJ, Barran PE. Mass spectrometry based tools to investigate protein–ligand interactions for drug discovery. Chem Soc Rev 2012; 41:4335-55. [DOI: 10.1039/c2cs35035a] [Citation(s) in RCA: 113] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
|
26
|
Rob T, Wilson DJ. Time-resolved mass spectrometry for monitoring millisecond time-scale solution-phase processes. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2012; 18:205-214. [PMID: 22641726 DOI: 10.1255/ejms.1176] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Many chemical and biochemical reactions equilibrate within a few seconds of initiation under "native" conditions. To understand the microscopic processes underlying these reactions, the most direct approach is to monitor the reaction as equilibrium is established (i.e. the reaction kinetics). However, this requires the ability to characterize the reaction mixture on the millisecond time-scale. In this review, we survey the contributions of time-resolved mass spectrometry (TR-MS) to the characterization of millisecond time-scale (bio)chemical processes, with a focus on biochemical applications. Compared to conventional time-resolved techniques, which use optical detection, the primary advantage of TR-MS is the ability to detect virtually all reactive species simultaneously. This provides a singularly high detail account of the reaction without the need for a chromophoric change on turnover or artificial chromophoric probes. To provide millisecond time-resolution, TR-MS set-ups usually employ continuous-flow rapid mixers, corresponding either to a fixed "tee" that provides a single reaction time-point or an adjustable position mixer that allows continuous reaction monitoring. TR-MS has been used to monitor processes with rates up to 500 s(-1) and to provide a detailed account of complex reactions involving 10 co- populated species. This corresponds to significantly lower time-resolution than optical methods, which can measure rates in excess of 900 s(-1) under ideal conditions, but substantially more detail (optical studies are typically limited to one or two analytes). TR-MS has been implemented on a number of platforms, including capillary and microfluidic set-ups. Capillary-based implementations are straightforward to fabricate and provide the most efficient rapid mixing. Microfluidic implementations have also been devised to enable multi-step experimental workflows that incorporate TR-MS. As a general method for time-resolved measurements, the applications for TR-MS are wide ranging. TR-MS has been used to identify intermediates in organic reactions, reveal protein (un)folding mechanisms, monitor enzyme catalysis in the pre-steady-state and, in conjunction with hydrogen-deuterium exchange, characterize protein conformational dynamics. While not without limitations, TR-MS represents a powerful alternative for measuring solution phase processes on the millisecond time-scale and a new, promising approach for revealing mechanistic details in (bio)chemical reactions.
Collapse
Affiliation(s)
- Tamanna Rob
- Department of Chemistry, York University, 4700 Keele St, Toronto, Ontario, M3J 1P3 Canada
| | | |
Collapse
|
27
|
Bobst CE, Kaltashov IA. Advanced mass spectrometry-based methods for the analysis of conformational integrity of biopharmaceutical products. Curr Pharm Biotechnol 2011; 12:1517-29. [PMID: 21542797 PMCID: PMC3375681 DOI: 10.2174/138920111798357311] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2010] [Accepted: 01/12/2011] [Indexed: 01/07/2023]
Abstract
Mass spectrometry has already become an indispensable tool in the analytical armamentarium of the biopharmaceutical industry, although its current uses are limited to characterization of covalent structure of recombinant protein drugs. However, the scope of applications of mass spectrometry-based methods is beginning to expand to include characterization of the higher order structure and dynamics of biopharmaceutical products, a development which is catalyzed by the recent progress in mass spectrometry-based methods to study higher order protein structure. The two particularly promising methods that are likely to have the most significant and lasting impact in many areas of biopharmaceutical analysis, direct ESI MS and hydrogen/deuterium exchange, are focus of this article.
Collapse
Affiliation(s)
- Cedric E. Bobst
- Department of Chemistry, University of Massachusetts-Amherst
| | | |
Collapse
|
28
|
Ferguson CN, Benchaar SA, Miao Z, Loo JA, Chen H. Direct ionization of large proteins and protein complexes by desorption electrospray ionization-mass spectrometry. Anal Chem 2011; 83:6468-73. [PMID: 21774530 DOI: 10.1021/ac201390w] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Desorption electrospray ionization-mass spectrometry (DESI-MS) has advantages for rapid sample analysis with little or no sample pretreatment, but performance for large biomolecules has not been demonstrated. In this study, liquid sample DESI, an extended version of DESI used for analysis of liquid samples, was shown to have capabilities for direct ionization of large noncovalent protein complexes (>45 kDa) and proteins (up to 150 kDa). Protein complex ions (e.g., superoxide dismutase, enolase, and hemoglobin) desorbed from solution by liquid sample DESI were measured intact, indicating the capability of DESI for preserving weak noncovalent interactions. Doping the DESI spray solvent with supercharging reagents resulted in protein complex ions having increased multiple charging without complex dissociation. Ion mobility measurements of model protein cytochrome c showed that the supercharging reagent favored the more compact conformation for the lower charged protein ions. Liquid sample DESI of hydrophobic peptide gramicidin D suggests that the ionization mechanism involves a droplet pick-up mixing process. Measurement of liquid samples significantly extends the mass range of DESI-MS, allowing the analysis of high-mass proteins such as 150 kDa immunoglobulin G (IgG) and thus represents the largest protein successfully ionized by DESI to date.
Collapse
Affiliation(s)
- Carly N Ferguson
- Department of Chemistry and Biochemistry, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, California 90095, USA
| | | | | | | | | |
Collapse
|
29
|
Kitova EN, Soya N, Klassen JS. Identifying Specific Small-Molecule Interactions Using Electrospray Ionization Mass Spectrometry. Anal Chem 2011; 83:5160-7. [DOI: 10.1021/ac200244u] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Elena N. Kitova
- Alberta Ingenuity Centre for Carbohydrate Science and Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G2
| | - Naoto Soya
- Alberta Ingenuity Centre for Carbohydrate Science and Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G2
| | - John S. Klassen
- Alberta Ingenuity Centre for Carbohydrate Science and Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G2
| |
Collapse
|
30
|
Shao Q, Wu P, Gu P, Xu X, Zhang H, Cai C. Electrochemical and Spectroscopic Studies on the Conformational Structure of Hemoglobin Assembled on Gold Nanoparticles. J Phys Chem B 2011; 115:8627-37. [DOI: 10.1021/jp203344u] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Qian Shao
- Jiangsu Key Laboratory of New Power Batteries, Jiangsu Key Laboratory of Biofunctional Materials, Laboratory of Electrochemistry, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210097, People's Republic of China
| | - Ping Wu
- Jiangsu Key Laboratory of New Power Batteries, Jiangsu Key Laboratory of Biofunctional Materials, Laboratory of Electrochemistry, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210097, People's Republic of China
| | - Piao Gu
- Jiangsu Key Laboratory of New Power Batteries, Jiangsu Key Laboratory of Biofunctional Materials, Laboratory of Electrochemistry, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210097, People's Republic of China
| | - Xiaoqing Xu
- Jiangsu Key Laboratory of New Power Batteries, Jiangsu Key Laboratory of Biofunctional Materials, Laboratory of Electrochemistry, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210097, People's Republic of China
- Department of Pharmacy, College of Jiangsu Jiankang Profession, Nanjing 210029, People's Republic of China
| | - Hui Zhang
- Jiangsu Key Laboratory of New Power Batteries, Jiangsu Key Laboratory of Biofunctional Materials, Laboratory of Electrochemistry, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210097, People's Republic of China
| | - Chenxin Cai
- Jiangsu Key Laboratory of New Power Batteries, Jiangsu Key Laboratory of Biofunctional Materials, Laboratory of Electrochemistry, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210097, People's Republic of China
| |
Collapse
|
31
|
Miao Z, Chen H, Liu P, Liu Y. Development of Submillisecond Time-Resolved Mass Spectrometry Using Desorption Electrospray Ionization. Anal Chem 2011; 83:3994-7. [DOI: 10.1021/ac200842e] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Zhixin Miao
- Department of Chemistry and Biochemistry, Center for Intelligent Chemical Instrumentation, Ohio University, Athens, Ohio 45701, United States
| | - Hao Chen
- Department of Chemistry and Biochemistry, Center for Intelligent Chemical Instrumentation, Ohio University, Athens, Ohio 45701, United States
| | - Pengyuan Liu
- Department of Chemistry and Biochemistry, Center for Intelligent Chemical Instrumentation, Ohio University, Athens, Ohio 45701, United States
| | - Yan Liu
- Department of Chemistry and Biochemistry, Center for Intelligent Chemical Instrumentation, Ohio University, Athens, Ohio 45701, United States
| |
Collapse
|
32
|
Direct probing of the folding/unfolding event of bovine hemoglobin at montmorillonite clay modified electrode by adsorptive-transfer voltammetry. Talanta 2011; 84:148-54. [DOI: 10.1016/j.talanta.2010.12.038] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2010] [Revised: 12/16/2010] [Accepted: 12/21/2010] [Indexed: 11/22/2022]
|
33
|
Chevreux G, Atmanene C, Lopez P, Ouazzani J, Van Dorsselaer A, Badet B, Badet-Denisot MA, Sanglier-Cianférani S. Monitoring the dynamics of monomer exchange using electrospray mass spectrometry: the case of the dimeric glucosamine-6-phosphate synthase. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2011; 22:431-439. [PMID: 21472562 DOI: 10.1007/s13361-010-0054-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2010] [Revised: 11/28/2010] [Accepted: 12/10/2010] [Indexed: 05/30/2023]
Abstract
Escherichia coli glucosamine-6-phosphate synthase (GlmS) is a dimeric enzyme from the glutamine-dependent amidotransferases family, which catalyses the conversion of D-fructose-6-phosphate (Fru6P) and glutamine (Gln) into D-glucosamine-6-phosphate (GlcN6P) and glutamate, respectively. Extensive X-ray crystallography investigations have been reported, highlighting the importance of the dimeric association to form the sugar active site as well as significant conformational changes of the protein upon substrate and product binding. In the present work, an approach based on time-resolved noncovalent mass spectrometry has been developed to study the dynamics of GlmS subunit exchange. Using (14)N versus (15)N labeled proteins, the kinetics of GlmS subunit exchange was monitored with the wild-type enzyme in the presence of different substrates and products as well as with the protein bearing a key amino acid mutation specially designed to weaken the dimer interface. Determination of rate constants of subunit exchange revealed important modifications of the protein dynamics: while glutamine, glutamate, and K603A mutation accelerates subunit exchange, Fru6P and GlcN6P totally prevent it. These results are described in light of the available structural information, providing additional useful data for both the characterization of GlmS catalytic process and the design of new GlmS inhibitors. Finally, time-resolved noncovalent MS can be proposed as an additional biophysical technique for real-time monitoring of protein dynamics.
Collapse
Affiliation(s)
- Guillaume Chevreux
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), Université de Strasbourg, IPHC, 25 rue Becquerel 67087, Strasbourg, France
| | | | | | | | | | | | | | | |
Collapse
|
34
|
Kang Y, Terrier P, Douglas DJ. Mass spectra and ion collision cross sections of hemoglobin. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2011; 22:290-299. [PMID: 21472588 DOI: 10.1007/s13361-010-0026-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2010] [Revised: 10/02/2010] [Accepted: 10/28/2010] [Indexed: 05/30/2023]
Abstract
Mass spectra of commercially obtained hemoglobin (Hb) show higher levels of monomer and dimer ions, heme-deficient dimer ions, and apo-monomer ions than hemoglobin freshly prepared from blood. This has previously been attributed to oxidation of commercial Hb. Further, it has been reported that that dimer ions from commercial bovine Hb have lower collision cross sections than low charge state monomer ions. To investigate these effects further, we have recorded mass spectra of fresh human Hb, commercial human and bovine Hb, fresh human Hb oxidized with H(2)O(2), lyophilized fresh human Hb, fresh human Hb both lyophilized and chemically oxidized, and commercial human Hb oxidized with H(2)O(2). Masses of α-monomer ions of all hemoglobins agree with the masses expected from the sequences within 3 Da or better. Mass spectra of the β chains of commercial Hb and oxidized fresh human Hb show a peak or shoulder on the high mass side, consistent with oxidation of the protein. Both commercial proteins and oxidized fresh human Hb produce heme-deficient dimers with masses 32 Da greater than expected and higher levels of monomer and dimer ions than fresh Hb. Lyophilization or oxidation of Hb both produce higher levels of monomer and dimer ions in mass spectra. Fresh human Hb, commercial human Hb, commercial bovine Hb, and oxidized commercial human Hb all give dimer ions with cross sections greater than monomer ions. Thus, neither oxidation of Hb or the difference in sequence between human and bovine Hb make substantial differences to cross sections of ions.
Collapse
Affiliation(s)
- Yang Kang
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
| | | | | |
Collapse
|
35
|
Wang X, Zhao W, Lin X, Su B, Liu J. Observation of symmetric denaturation of hemoglobin subunits by electrospray ionization mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2010; 45:1306-1311. [PMID: 20963788 DOI: 10.1002/jms.1843] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2010] [Accepted: 09/01/2010] [Indexed: 05/30/2023]
Abstract
Electrospray ionization mass spectrometry (ESI-MS) has been used to characterize the denaturation of porcine hemoglobin (Hb) induced by solvent changes. This work provides evidence for the symmetric nature of Hb denaturation and demonstrates that heme losses from α- and β-monomers occur in parallel, in response to the addition of acid and organic co-solvents in solution. When subject to one of the following solution conditions (pH 3.2-4.0 or 15-30% acetonitrile-water or 30-45% methanol-water solution), α- and β-globins undergo symmetric dissociation to release the heme groups, which is detected by ESI-MS. Circular dichroism (CD) and fluorescence spectroscopy (FS) data show that the acid-induced and organic solvent-induced heme release, as observed in the mass spectra, can probably be ascribed to different aspects of the conformational changes taking place in the protein. The acidity of the solvent has a significant effect on the secondary structure, whereas organic content level in solution (15-30% acetonitrile or 30-45% methanol) tends to destroy the tertiary structure of Hb globins, both leading to release of the heme from each subunit.
Collapse
Affiliation(s)
- Xian Wang
- Key Laboratory of Analytical Chemistry of the State Ethnic Affairs Commission, College of Chemistry and Materials Science, South-Central University for Nationalities, Wuhan, Hubei 430074, People's Republic of China.
| | | | | | | | | |
Collapse
|
36
|
Zhao X, Mai Z, Dai Z, Zou X. Electrochemically Monitoring the Acid and Acidic Urea-Induced Unfolding of Hemoglobin and Its Electrocatalytic Ability. ELECTROANAL 2010. [DOI: 10.1002/elan.201000113] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
37
|
Henning S, Mormann M, Peter-Katalinić J, Pohlentz G. Direct analysis of α- and β-chains of hemoglobins from mammalian blood samples by nanoESI mass spectrometry during in-capillary proteolytic digestion. Amino Acids 2010; 41:343-50. [DOI: 10.1007/s00726-010-0671-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2010] [Accepted: 06/17/2010] [Indexed: 02/02/2023]
|
38
|
Mai Z, Zhao X, Dai Z, Zou X. Contributions of Components in Guanidine Hydrochloride to Hemoglobin Unfolding Investigated by Protein Film Electrochemistry. J Phys Chem B 2010; 114:7090-7. [DOI: 10.1021/jp101082d] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Zhibin Mai
- School of Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou 510275, People's Republic of China, and College of Light Industry and Food Science, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, People's Republic of China
| | - Xiaojuan Zhao
- School of Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou 510275, People's Republic of China, and College of Light Industry and Food Science, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, People's Republic of China
| | - Zong Dai
- School of Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou 510275, People's Republic of China, and College of Light Industry and Food Science, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, People's Republic of China
| | - Xiaoyong Zou
- School of Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou 510275, People's Republic of China, and College of Light Industry and Food Science, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, People's Republic of China
| |
Collapse
|
39
|
Mai Z, Zhao X, Dai Z, Zou X. Direct electrochemistry of hemoglobin adsorbed on self-assembled monolayers with different head groups or chain length. Talanta 2010; 81:167-75. [DOI: 10.1016/j.talanta.2009.11.053] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2009] [Revised: 11/19/2009] [Accepted: 11/23/2009] [Indexed: 10/20/2022]
|
40
|
Frimpong AK, Abzalimov RR, Uversky VN, Kaltashov IA. Characterization of intrinsically disordered proteins with electrospray ionization mass spectrometry: conformational heterogeneity of alpha-synuclein. Proteins 2010; 78:714-22. [PMID: 19847913 DOI: 10.1002/prot.22604] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Conformational heterogeneity of alpha-synuclein was studied with electrospray ionization mass spectrometry by analyzing protein ion charge state distributions, where the extent of multiple charging reflects compactness of the protein conformations in solution. Although alpha-synuclein lacks a single well-defined structure under physiological conditions, it was found to sample four distinct conformational states, ranging from a highly structured one to a random coil. The compact highly structured state of alpha-synuclein is present across the entire range of conditions tested (pH ranging from 2.5 to 10, alcohol content from 0% to 60%), but is particularly abundant in acidic solutions. The only other protein state populated in acidic solutions is a partially folded intermediate state lacking stable tertiary structure. Another, more compact intermediate state is induced by significant amounts of ethanol used as a co-solvent and appears to represent a partially folded conformation with high beta-sheet content. Protein dimerization is observed throughout the entire range of conditions tested, although only acidic solutions favor formation of highly structured dimers of alpha-synuclein. These dimers are likely to present the earliest stages in protein aggregation leading to globular oligomers and, subsequently, protofibrils.
Collapse
Affiliation(s)
- Agya K Frimpong
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | | | | | | |
Collapse
|
41
|
Li X, Zheng W, Zhang L, Yu P, Lin Y, Su L, Mao L. Effective Electrochemical Method for Investigation of Hemoglobin Unfolding Based on the Redox Property of Heme Groups at Glassy Carbon Electrodes. Anal Chem 2009; 81:8557-63. [DOI: 10.1021/ac9015215] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Xianchan Li
- Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences (CAS), Beijing 100190, China
| | - Wei Zheng
- Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences (CAS), Beijing 100190, China
| | - Limin Zhang
- Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences (CAS), Beijing 100190, China
| | - Ping Yu
- Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences (CAS), Beijing 100190, China
| | - Yuqing Lin
- Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences (CAS), Beijing 100190, China
| | - Lei Su
- Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences (CAS), Beijing 100190, China
| | - Lanqun Mao
- Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences (CAS), Beijing 100190, China
| |
Collapse
|
42
|
Pimenova T, Pereira CP, Schaer DJ, Zenobi R. Characterization of high molecular weight multimeric states of human haptoglobin and hemoglobin-based oxygen carriers by high-mass MALDI MS. J Sep Sci 2009; 32:1224-30. [DOI: 10.1002/jssc.200800625] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
|
43
|
Wright PJ, Douglas DJ. Gas-phase H/D exchange and collision cross sections of hemoglobin monomers, dimers, and tetramers. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2009; 20:484-495. [PMID: 19101164 DOI: 10.1016/j.jasms.2008.11.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2008] [Revised: 11/10/2008] [Accepted: 11/11/2008] [Indexed: 05/27/2023]
Abstract
The conformations of gas-phase ions of hemoglobin, and its dimer and monomer subunits have been studied with H/D exchange and cross section measurements. During the H/D exchange measurements, tetramers undergo slow dissociation to dimers, and dimers to monomers, but this did not prevent drawing conclusions about the relative exchange levels of monomers, dimers, and tetramers. Assembly of the monomers into tetramers, hexamers, and octamers causes the monomers to exchange a greater fraction of their hydrogens. Dimer ions, however, exchange a lower fraction of their hydrogens than monomers or tetramers. Solvation of tetramers affects the exchange kinetics. Solvation molecules do not appear to exchange, and solvation lowers the overall exchange level of the tetramers. Cross section measurements show that monomer ions in low charge states, and tetramer ions have compact structures, comparable in size to the native conformations in solution. Dimers have remarkably compact structures, considerably smaller than the native conformation in solution and smaller than might be expected from the monomer or tetramer cross sections. This is consistent with the relatively low level of exchange of the dimers.
Collapse
Affiliation(s)
- P John Wright
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
| | | |
Collapse
|
44
|
Rob T, Wilson DJ. A versatile microfluidic chip for millisecond time-scale kinetic studies by electrospray mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2009; 20:124-130. [PMID: 18845447 DOI: 10.1016/j.jasms.2008.09.005] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2008] [Revised: 09/01/2008] [Accepted: 09/01/2008] [Indexed: 05/26/2023]
Abstract
An electrospray coupled microfluidic reactor for the measurement of millisecond time-scale, solution phase kinetics is introduced. The device incorporates a simple two-channel design that is etched into polymethyl methacrylate (PMMA) by laser ablation. The outlet of the device is laser cut to a sharp tip, facilitating low dead volume 'on chip' electrospray. Fabrication is fast, straightforward and highly reproducible, supporting rapid prototyping and large-scale reproduction. Device performance is characterized using a cytochrome c unfolding reaction. Unfolding processes with rates in excess of 30 s(-1) are easily measured, including the appearance of a 'native-like' intermediate that is maximally populated 180 ms post reaction initiation. To extract reliable rates from the data, a theoretical framework for the analysis of kinetics acquired under square-channel laminar flow is introduced.
Collapse
Affiliation(s)
- Tamanna Rob
- Center for Research in Mass Spectrometry, Department of Chemistry, York University, Toronto, Ontario, Canada
| | | |
Collapse
|
45
|
Konermann L, Messinger J, Hillier W. Mass Spectrometry-Based Methods for Studying Kinetics and Dynamics in Biological Systems. BIOPHYSICAL TECHNIQUES IN PHOTOSYNTHESIS 2008. [DOI: 10.1007/978-1-4020-8250-4_9] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
|
46
|
Chapter 2 Characterization of Protein Higher Order Structure and Dynamics with ESI MS. ACTA ACUST UNITED AC 2008. [DOI: 10.1016/s0166-526x(08)00202-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
|
47
|
Nabuchi Y, Murao N, Asoh Y, Takayama M. Probing the Unfolding and Refolding Processes of Carbonic Anhydrase 2 Using Electrospray Ionization Mass Spectrometry Combined with pH Jump. Anal Chem 2007; 79:8342-9. [PMID: 17900145 DOI: 10.1021/ac071130u] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A novel method for proving the time course of the unfolding and refolding processes of metalloprotein bovine carbonic anhydrase 2 (CA2) is demonstrated using electrospray ionization mass spectrometry (ESI MS) combined with pH jumps between 3.6 and 4.4. The shift in mass accompanied by the release or coordination of a zinc ion and the change in the charge state distribution were measured to evaluate the folding process. The time course of the ESI mass spectra revealed the existence of four types of ions in the experimental system, i.e., lower charged apo-CA2 and holo-CA2 ions and higher charged apo-CA2 and holo-CA2 ions. The deconvolution spectrum of the ion peak ensemble for each type of ion was processed and time course plots of the relative intensities of the four ions were prepared in order to analyze the folding processes. These analyses revealed the coexistence of two folding states of the lower and higher charged apo-CA2 under the condition of pH 3.6. The lower and higher charged apoproteins spontaneously refolded to the lower charged holoprotein by a pH jump from 3.6 to 4.4 without the addition of an extra zinc ion. The higher charged holoprotein observed during both the unfolding and refolding processes was considered to be an intermediate of the change in folding. The present study indicates that ESI MS combined with pH jump would be a powerful method to probe the unfolding and refolding of proteins. This method simultaneously measures mass spectra and analyzes the folding processes as a function of time using deconvolution spectra constructed by selecting a suitable m/z range for the analysis from the peaks of charge state distributions.
Collapse
Affiliation(s)
- Yoshiaki Nabuchi
- Fuji Gotemba Research Laboratories, Chugai Pharmaceutical Co., Ltd., Gotemba, Shizuoka 412-8513, Japan.
| | | | | | | |
Collapse
|
48
|
Benesch JLP, Ruotolo BT, Simmons DA, Robinson CV. Protein complexes in the gas phase: technology for structural genomics and proteomics. Chem Rev 2007; 107:3544-67. [PMID: 17649985 DOI: 10.1021/cr068289b] [Citation(s) in RCA: 344] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Justin L P Benesch
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | | | | | | |
Collapse
|
49
|
Kuprowski MC, Boys BL, Konermann L. Analysis of protein mixtures by electrospray mass spectrometry: effects of conformation and desolvation behavior on the signal intensities of hemoglobin subunits. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2007; 18:1279-85. [PMID: 17500007 DOI: 10.1016/j.jasms.2007.04.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2007] [Revised: 03/31/2007] [Accepted: 04/05/2007] [Indexed: 05/15/2023]
Abstract
The determination of solution-phase protein concentration ratios based on ESI-MS intensity ratios is not always straightforward. For example, equimolar mixtures of hemoglobin alpha- and beta-subunits consistently result in much higher peak intensities for the alpha-chain. The current work explores the origin of this effect. Under mildly acidic conditions (pH 3.4) alpha-globin is extensively unfolded, whereas beta-globin retains residual structure. Because of its greater nonpolar character, the more unfolded alpha-subunit can more effectively compete for charge. This leads to suppression of beta-globin signals under conditions where the protein ion yield is limited by the charge concentration on the initially formed ESI droplets. More balanced intensities are observed when operating under charge excess conditions and/or in a solvent environment where both proteins are unfolded to a similar degree (pH 2.2). However, even in these cases the overall alpha-globin peak intensity is still twice as high as that of the beta-subunit. The persistent imbalance under these conditions originates from the different declustering behaviors of the two proteins. A considerable fraction of beta-globin undergoes incomplete desolvation during ESI, thereby reducing the intensity of bare [beta + zH](z+) ions. When including the contributions of incompletely desolvated species, the overall alpha:beta ion intensity ratio is close to unity. The alpha:beta intensity imbalance can also be eliminated by a strongly elevated declustering potential in the ion sampling interface. In conclusion, important factors that have to be considered for the ESI-MS analysis of protein mixtures are (1) conformational effects, resulting in differential surface activities, and (2) dissimilarities in the protein desolvation behavior.
Collapse
Affiliation(s)
- Mark C Kuprowski
- Department of Chemistry, The University of Western Ontario, London, Ontario, Canada
| | | | | |
Collapse
|
50
|
Abstract
The fact that ions of macromolecular complexes produced by electrospray ionization can be maintained intact in a mass spectrometer has stimulated exciting new lines of research. In this review we chart the progress of this research from the observation of simple homo-oligomers to complex heterogeneous macromolecular assemblies of mega-Dalton proportions. The applications described herein not only confirm the status of mass spectrometry (MS) as a structural biology approach to complement X-ray analysis or electron microscopy, but also highlight unique attributes of the methodology. This is exemplified in studies of the biogenesis of macromolecular complexes and in the exchange of subunits between macromolecular complexes. Moreover, recent successes in revealing the overall subunit architecture of complexes are set to promote MS from a complementary approach to a structural biology tool in its own right.
Collapse
Affiliation(s)
- Michal Sharon
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom.
| | | |
Collapse
|