1
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Jordan JS, Lee KJ, Williams ER. Overcoming aggregation with laser heated nanoelectrospray mass spectrometry: thermal stability and pathways for loss of bicarbonate from carbonic anhydrase II. Analyst 2024; 149:2281-2290. [PMID: 38497240 DOI: 10.1039/d4an00229f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Variable temperature electrospray mass spectrometry is useful for multiplexed measurements of the thermal stabilities of biomolecules, but the ionization process can be disrupted by aggregation-prone proteins/complexes that have irreversible unfolding transitions. Resistively heating solutions containing a mixture of bovine carbonic anhydrase II (BCAII), a CO2 fixing enzyme involved in many biochemical pathways, and cytochrome c leads to complete loss of carbonic anhydrase signal and a significant reduction in cytochrome c signal above ∼72 °C due to aggregation. In contrast, when the tips of borosilicate glass nanoelectrospray emitters are heated with a laser, complete thermal denaturation curves for both proteins are obtained in <1 minute. The simultaneous measurements of the melting temperature of BCAII and BCAII bound to bicarbonate reveal that the bicarbonate stabilizes the folded form of this protein by ∼6.4 °C. Moreover, the temperature dependences of different bicarbonate loss pathways are obtained. Although protein analytes are directly heated by the laser for only 140 ms, heat conduction further up the emitter leads to a total analyte heating time of ∼41 s. Pulsed laser heating experiments could reduce this time to ∼0.5 s for protein aggregation that occurs on a faster time scale. Laser heating provides a powerful method for studying the detailed mechanisms of cofactor/ligand loss with increasing temperature and promises a new tool for studying the effect of ligands, drugs, growth conditions, buffer additives, or other treatments on the stabilities of aggregation-prone biomolecules.
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Affiliation(s)
- Jacob S Jordan
- Department of Chemistry, University of California, Berkeley, California, 94720-1460, USA.
| | - Katherine J Lee
- Department of Chemistry, University of California, Berkeley, California, 94720-1460, USA.
| | - Evan R Williams
- Department of Chemistry, University of California, Berkeley, California, 94720-1460, USA.
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2
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Cropley TC, Liu FC, Chai M, Bush MF, Bleiholder C. Metastability of Protein Solution Structures in the Absence of a Solvent: Rugged Energy Landscape and Glass-like Behavior. J Am Chem Soc 2024. [PMID: 38598661 DOI: 10.1021/jacs.3c12892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2024]
Abstract
Native ion mobility/mass spectrometry is well-poised to structurally screen proteomes but characterizes protein structures in the absence of a solvent. This raises long-standing unanswered questions about the biological significance of protein structures identified through ion mobility/mass spectrometry. Using newly developed computational and experimental ion mobility/ion mobility/mass spectrometry methods, we investigate the unfolding of the protein ubiquitin in a solvent-free environment. Our data suggest that the folded, solvent-free ubiquitin observed by ion mobility/mass spectrometry exists in a largely native fold with an intact β-grasp motif and α-helix. The ensemble of folded, solvent-free ubiquitin ions can be partitioned into kinetically stable subpopulations that appear to correspond to the structural heterogeneity of ubiquitin in solution. Time-resolved ion mobility/ion mobility/mass spectrometry measurements show that folded, solvent-free ubiquitin exhibits a strongly stretched-exponential time dependence, which simulations trace to a rugged energy landscape with kinetic traps. Unfolding rate constants are estimated to be approximately 800 to 20,000 times smaller than in the presence of water, effectively quenching the unfolding process on the time scale of typical ion mobility/mass spectrometry measurements. Our proposed unfolding pathway of solvent-free ubiquitin shares substantial characteristics with that established for the presence of solvent, including a polarized transition state with significant native content in the N-terminal β-hairpin and α-helix. Our experimental and computational data suggest that (1) the energy landscape governing the motions of folded, solvent-free proteins is rugged in analogy to that of glassy systems; (2) large-scale protein motions may at least partially be determined by the amino acid sequence of a polypeptide chain; and (3) solvent facilitates, rather than controls, protein motions.
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Affiliation(s)
- Tyler C Cropley
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32304, United States
| | - Fanny C Liu
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32304, United States
| | - Mengqi Chai
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32304, United States
| | - Matthew F Bush
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195-1700, United States
| | - Christian Bleiholder
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32304, United States
- Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32304, United States
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3
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Chen CJ, Williams ER. The role of analyte concentration in accelerated reaction rates in evaporating droplets. Chem Sci 2023; 14:4704-4713. [PMID: 37181782 PMCID: PMC10171075 DOI: 10.1039/d3sc00259d] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 04/04/2023] [Indexed: 05/16/2023] Open
Abstract
Accelerated reactions in microdroplets have been reported for a wide range of reactions with some microdroplet reactions occurring over a million times faster than the same reaction in bulk solution. Unique chemistry at the air-water interface has been implicated as a primary factor for accelerated reaction rates, but the role of analyte concentration in evaporating droplets has not been as well studied. Here, theta-glass electrospray emitters and mass spectrometry are used to rapidly mix two solutions on the low to sub-microsecond time scale and produce aqueous nanodrops with different sizes and lifetimes. We demonstrate that for a simple bimolecular reaction where surface chemistry does not appear to play a role, reaction rate acceleration factors are between 102 and 107 for different initial solution concentrations, and these values do not depend on nanodrop size. A rate acceleration factor of 107 is among the highest reported and can be attributed to concentration of analyte molecules, initially far apart in dilute solution, but brought into close proximity in the nanodrop through evaporation of solvent from the nanodrops prior to ion formation. These data indicate that analyte concentration phenomenon is a significant factor in reaction acceleration where droplet volume throughout the experiment is not carefully controlled.
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Affiliation(s)
- Casey J Chen
- Department of Chemistry, University of California Berkeley CA 94720 USA
| | - Evan R Williams
- Department of Chemistry, University of California Berkeley CA 94720 USA
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4
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Jordan JS, Williams ER. Laser Heating Nanoelectrospray Emitters for Fast Protein Melting Measurements with Mass Spectrometry. Anal Chem 2022; 94:16894-16900. [DOI: 10.1021/acs.analchem.2c04204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Jacob S. Jordan
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Evan R. Williams
- Department of Chemistry, University of California, Berkeley, California 94720, United States
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5
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Alexander Harrison J, Pruška A, Oganesyan I, Bittner P, Zenobi R. Temperature-Controlled Electrospray Ionization: Recent Progress and Applications. Chemistry 2021; 27:18015-18028. [PMID: 34632657 PMCID: PMC9298390 DOI: 10.1002/chem.202102474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Indexed: 11/11/2022]
Abstract
Native electrospray ionization (ESI) and nanoelectrospray ionization (nESI) allow researchers to analyze intact biomolecules and their complexes by mass spectrometry (MS). The data acquired using these soft ionization techniques provide a snapshot of a given biomolecules structure in solution. Over the last thirty years, several nESI and ESI sources capable of controlling spray solution temperature have been developed. These sources can be used to elucidate the thermodynamics of a given analyte, as well as provide structural information that cannot be readily obtained by other, more commonly used techniques. This review highlights how the field of temperature-controlled mass spectrometry has developed.
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Affiliation(s)
- Julian Alexander Harrison
- Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 3, 8093, Zurich, Switzerland
| | - Adam Pruška
- Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 3, 8093, Zurich, Switzerland
| | - Irina Oganesyan
- Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 3, 8093, Zurich, Switzerland
| | - Philipp Bittner
- Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 3, 8093, Zurich, Switzerland
| | - Renato Zenobi
- Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 3, 8093, Zurich, Switzerland
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6
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Laganowsky A, Clemmer DE, Russell DH. Variable-Temperature Native Mass Spectrometry for Studies of Protein Folding, Stabilities, Assembly, and Molecular Interactions. Annu Rev Biophys 2021; 51:63-77. [PMID: 34932911 PMCID: PMC9086101 DOI: 10.1146/annurev-biophys-102221-101121] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The structures and conformational dynamics of proteins, protein complexes, and their noncovalent interactions with other molecules are controlled specifically by the Gibbs free energy (entropy and enthalpy) of the system. For some organisms, temperature is highly regulated, but the majority of biophysical studies are carried out at room, nonphysiological temperature. In this review, we describe variable-temperature electrospray ionization (vT-ESI) mass spectrometry (MS)-based studies with unparalleled sensitivity, dynamic range, and selectivity for studies of both cold- and heat-induced chemical processes. Such studies provide direct determinations of stabilities, reactivities, and thermodynamic measurements for native and non-native structures of proteins and protein complexes and for protein-ligand interactions. Highlighted in this review are vT-ESI-MS studies that reveal 40 different conformers of chymotrypsin inhibitor 2, a classic two-state (native → unfolded) unfolder, and thermochemistry for a model membrane protein system binding lipid and its regulatory protein. Expected final online publication date for the Annual Review of Biophysics, Volume 51 is May 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Arthur Laganowsky
- Department of Chemistry, Texas A&M University, College Station, Texas, USA; ,
| | - David E Clemmer
- Department of Chemistry, Indiana University, Bloomington, Indiana, USA;
| | - David H Russell
- Department of Chemistry, Texas A&M University, College Station, Texas, USA; ,
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7
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El-Baba TJ, Raab SA, Buckley RP, Brown CJ, Lutomski CA, Henderson LW, Woodall DW, Shen J, Trinidad JC, Niu H, Jarrold MF, Russell DH, Laganowsky A, Clemmer DE. Thermal Analysis of a Mixture of Ribosomal Proteins by vT-ESI-MS: Toward a Parallel Approach for Characterizing the Stabilitome. Anal Chem 2021; 93:8484-8492. [PMID: 34101419 PMCID: PMC8546744 DOI: 10.1021/acs.analchem.1c00772] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The thermal stabilities of endogenous, intact proteins and protein assemblies in complex mixtures were characterized in parallel by means of variable-temperature electrospray ionization coupled to mass spectrometry (vT-ESI-MS). The method is demonstrated by directly measuring the melting transitions of seven proteins from a mixture of proteins derived from ribosomes. A proof-of-concept measurement of a fraction of an Escherichia coli lysate is provided to extend this approach to characterize the thermal stability of a proteome. As the solution temperature is increased, proteins and protein complexes undergo structural and organizational transitions; for each species, the folded ↔ unfolded and assembled ↔ disassembled populations are monitored based on changes in vT-ESI-MS charge state distributions and masses. The robustness of the approach illustrates a step toward the proteome-wide characterization of thermal stabilities and structural transitions-the stabilitome.
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Affiliation(s)
- Tarick J El-Baba
- Department of Chemistry, Indiana University, Bloomington, Indiana 47401, United States
| | - Shannon A Raab
- Department of Chemistry, Indiana University, Bloomington, Indiana 47401, United States
| | - Rachel P Buckley
- Department of Chemistry, Indiana University, Bloomington, Indiana 47401, United States
| | - Christopher J Brown
- Department of Chemistry, Indiana University, Bloomington, Indiana 47401, United States
| | - Corinne A Lutomski
- Department of Chemistry, Indiana University, Bloomington, Indiana 47401, United States
| | - Lucas W Henderson
- Department of Chemistry, Indiana University, Bloomington, Indiana 47401, United States
| | - Daniel W Woodall
- Department of Chemistry, Indiana University, Bloomington, Indiana 47401, United States
| | - Jiangchuan Shen
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47401, United States
| | - Jonathan C Trinidad
- Department of Chemistry, Indiana University, Bloomington, Indiana 47401, United States
| | - Hengyao Niu
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47401, United States
| | - Martin F Jarrold
- Department of Chemistry, Indiana University, Bloomington, Indiana 47401, United States
| | - David H Russell
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - David E Clemmer
- Department of Chemistry, Indiana University, Bloomington, Indiana 47401, United States
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8
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McCabe JW, Shirzadeh M, Walker TE, Lin CW, Jones BJ, Wysocki VH, Barondeau DP, Clemmer DE, Laganowsky A, Russell DH. Variable-Temperature Electrospray Ionization for Temperature-Dependent Folding/Refolding Reactions of Proteins and Ligand Binding. Anal Chem 2021; 93:6924-6931. [PMID: 33904705 DOI: 10.1021/acs.analchem.1c00870] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Stabilities and structure(s) of proteins are directly coupled to their local environment or Gibbs free energy landscape as defined by solvent, temperature, pressure, and concentration. Solution pH, ionic strength, cofactors, chemical chaperones, and osmolytes perturb the chemical potential and induce further changes in structure, stability, and function. At present, no single analytical technique can monitor these effects in a single measurement. Mass spectrometry and ion mobility-mass spectrometry play increasingly essential roles in studies of proteins, protein complexes, and even membrane protein complexes; however, with few exceptions, the effects of the solution temperature on the stability and structure(s) of analytes have not been thoroughly investigated. Here, we describe a new variable-temperature electrospray ionization (vT-ESI) source that utilizes a thermoelectric chip to cool and heat the solution contained within the static ESI emitter. This design allows for solution temperatures to be varied from ∼5 to 98 °C with short equilibration times (<2 min) between precisely controlled temperature changes. The performance of the apparatus for vT-ESI-mass spectrometry and vT-ESI-ion mobility-mass spectrometry studies of cold- and heat-folding reactions is demonstrated using ubiquitin and frataxin. Instrument performance for studies on temperature-dependent ligand binding is shown using the chaperonin GroEL.
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Affiliation(s)
- Jacob W McCabe
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Mehdi Shirzadeh
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Thomas E Walker
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Cheng-Wei Lin
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Benjamin J Jones
- Department of Chemistry, Ohio State University, Columbus, Ohio 43210, United States
| | - Vicki H Wysocki
- Department of Chemistry, Ohio State University, Columbus, Ohio 43210, United States
| | - David P Barondeau
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - David E Clemmer
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - David H Russell
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
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9
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McCabe JW, Hebert MJ, Shirzadeh M, Mallis CS, Denton JK, Walker TE, Russell DH. THE IMS PARADOX: A PERSPECTIVE ON STRUCTURAL ION MOBILITY-MASS SPECTROMETRY. MASS SPECTROMETRY REVIEWS 2021; 40:280-305. [PMID: 32608033 PMCID: PMC7989064 DOI: 10.1002/mas.21642] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 06/03/2020] [Indexed: 05/06/2023]
Abstract
Studies of large proteins, protein complexes, and membrane protein complexes pose new challenges, most notably the need for increased ion mobility (IM) and mass spectrometry (MS) resolution. This review covers evolutionary developments in IM-MS in the authors' and key collaborators' laboratories with specific focus on developments that enhance the utility of IM-MS for structural analysis. IM-MS measurements are performed on gas phase ions, thus "structural IM-MS" appears paradoxical-do gas phase ions retain their solution phase structure? There is growing evidence to support the notion that solution phase structure(s) can be retained by the gas phase ions. It should not go unnoticed that we use "structures" in this statement because an important feature of IM-MS is the ability to deal with conformationally heterogeneous systems, thus providing a direct measure of conformational entropy. The extension of this work to large proteins and protein complexes has motivated our development of Fourier-transform IM-MS instruments, a strategy first described by Hill and coworkers in 1985 (Anal Chem, 1985, 57, pp. 402-406) that has proved to be a game-changer in our quest to merge drift tube (DT) and ion mobility and the high mass resolution orbitrap MS instruments. DT-IMS is the only method that allows first-principles determinations of rotationally averaged collision cross sections (CSS), which is essential for studies of biomolecules where the conformational diversities of the molecule precludes the use of CCS calibration approaches. The Fourier transform-IM-orbitrap instrument described here also incorporates the full suite of native MS/IM-MS capabilities that are currently employed in the most advanced native MS/IM-MS instruments. © 2020 John Wiley & Sons Ltd. Mass Spec Rev.
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Affiliation(s)
- Jacob W McCabe
- Department of Chemistry, Texas A&M University, College Station, TX, 77843
| | - Michael J Hebert
- Department of Chemistry, Texas A&M University, College Station, TX, 77843
| | - Mehdi Shirzadeh
- Department of Chemistry, Texas A&M University, College Station, TX, 77843
| | | | - Joanna K Denton
- Department of Chemistry, Texas A&M University, College Station, TX, 77843
| | - Thomas E Walker
- Department of Chemistry, Texas A&M University, College Station, TX, 77843
| | - David H Russell
- Department of Chemistry, Texas A&M University, College Station, TX, 77843
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10
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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.
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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
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11
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Shirzadeh M, Poltash ML, Laganowsky A, Russell DH. Structural Analysis of the Effect of a Dual-FLAG Tag on Transthyretin. Biochemistry 2020; 59:1013-1022. [PMID: 32101399 PMCID: PMC7171973 DOI: 10.1021/acs.biochem.0c00105] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Recombinant proteins have increased our knowledge regarding the physiological role of proteins; however, affinity purification tags are often not cleaved prior to analysis, and their effects on protein structure, stability and assembly are often overlooked. In this study, the stabilizing effects of an N-terminus dual-FLAG (FT2) tag fusion to transthyretin (TTR), a construct used in previous studies, are investigated using native ion mobility-mass spectrometry (IM-MS). A combination of collision-induced unfolding and variable-temperature electrospray ionization is used to compare gas- and solution-phase stabilities of FT2-TTR to wild-type and C-terminal tagged TTR. Despite an increased stability of both gas- and solution-phase FT2-TTR, thermal degradation of FT2-TTR was observed at elevated temperatures, viz., backbone cleavage occurring between Lys9 and Cys10. This cleavage reaction is consistent with previously reported metalloprotease activity of TTR [Liz et al. 2009] and is suppressed by either metal chelation or excess zinc. This study brings to the fore the effect of affinity tag stabilization of TTR and emphasizes unprecedented detail afforded by native IM-MS to assess structural discrepancies of recombinant proteins from their wild-type counterparts.
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Affiliation(s)
- Mehdi Shirzadeh
- Department of Chemistry, Texas A & M University, College Station, Texas 77843, United States
| | - Michael L Poltash
- Department of Chemistry, Texas A & M University, College Station, Texas 77843, United States
| | - Arthur Laganowsky
- Department of Chemistry, Texas A & M University, College Station, Texas 77843, United States
| | - David H Russell
- Department of Chemistry, Texas A & M University, College Station, Texas 77843, United States
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12
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Brown CJ, Woodall DW, El-Baba TJ, Clemmer DE. Characterizing Thermal Transitions of IgG with Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:2438-2445. [PMID: 31363989 PMCID: PMC6866664 DOI: 10.1007/s13361-019-02292-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 07/15/2019] [Accepted: 07/16/2019] [Indexed: 06/02/2023]
Abstract
Variable temperature electrospray ionization (ESI) is coupled with mass spectrometry techniques in order to investigate structural transitions of monoclonal antibody immunoglobulin G (IgG) in a 100-mM ammonium acetate (pH 7.0) solution from 26 to 70 °C. At 26 °C, the mass spectrum for intact IgG shows six charge states + 22 to + 26. Upon increasing the solution temperature, the fraction of low-charge states decreases and new, higher-charge state ions are observed. Upon analysis, it appears that heating the solution aids in desolvation of the intact IgG precursor. Above ~ 50 °C, a cleavage event between the light and heavy chains is observed. An analysis of the kinetics for these processes at different temperatures yields transition state thermochemistry of ΔH‡ = 95 ± 10 kJ mol-1, ΔS‡ = 8 ± 1 J mol-1 K-1, and ΔG‡ = 92 ± 11 kJ mol-1. The mechanism for light chain dissociation appears to involve disulfide bond scrambling that ultimately results in a non-native Cys199-Cys217 disulfide bond in the light chain product. Above ~ 70 °C, we are unable to produce a stable ESI signal. The loss of signal is ascribed to aggregation that is primarily associated with the remaining portion of the antibody after having lost the light chain. Graphical Abstract.
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Affiliation(s)
- Christopher J Brown
- Department of Chemistry, Indiana University, 800 Kirkwood Avenue, Bloomington, IN, 47401, USA
| | - Daniel W Woodall
- Department of Chemistry, Indiana University, 800 Kirkwood Avenue, Bloomington, IN, 47401, USA
| | - Tarick J El-Baba
- Department of Chemistry, Indiana University, 800 Kirkwood Avenue, Bloomington, IN, 47401, USA
| | - David E Clemmer
- Department of Chemistry, Indiana University, 800 Kirkwood Avenue, Bloomington, IN, 47401, USA.
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13
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Giussani L, Tabacchi G, Coluccia S, Fois E. Confining a Protein-Containing Water Nanodroplet inside Silica Nanochannels. Int J Mol Sci 2019; 20:E2965. [PMID: 31216631 PMCID: PMC6627703 DOI: 10.3390/ijms20122965] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 06/10/2019] [Accepted: 06/14/2019] [Indexed: 02/01/2023] Open
Abstract
Incorporation of biological systems in water nanodroplets has recently emerged as a new frontier to investigate structural changes of biomolecules, with perspective applications in ultra-fast drug delivery. We report on the molecular dynamics of the digestive protein Pepsin subjected to a double confinement. The double confinement stemmed from embedding the protein inside a water nanodroplet, which in turn was caged in a nanochannel mimicking the mesoporous silica SBA-15. The nano-bio-droplet, whose size fits with the pore diameter, behaved differently depending on the protonation state of the pore surface silanols. Neutral channel sections allowed for the droplet to flow, while deprotonated sections acted as anchoring piers for the droplet. Inside the droplet, the protein, not directly bonded to the surface, showed a behavior similar to that reported for bulk water solutions, indicating that double confinement should not alter its catalytic activity. Our results suggest that nanobiodroplets, recently fabricated in volatile environments, can be encapsulated and stored in mesoporous silicas.
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Affiliation(s)
- Lara Giussani
- Dipartimento di Scienza e Alta Tecnologia and INSTM udr Como, Insubria University, Via Valleggio 9, I-22100 Como, Italy.
| | - Gloria Tabacchi
- Dipartimento di Scienza e Alta Tecnologia and INSTM udr Como, Insubria University, Via Valleggio 9, I-22100 Como, Italy.
| | - Salvatore Coluccia
- Dipartimento di Chimica, Turin University, Via P. Giuria 7, I-10125 Turin, Italy.
| | - Ettore Fois
- Dipartimento di Scienza e Alta Tecnologia and INSTM udr Como, Insubria University, Via Valleggio 9, I-22100 Como, Italy.
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14
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Conant CR, Fuller DR, Zhang Z, Woodall DW, Russell DH, Clemmer DE. Substance P in the Gas Phase: Conformational Changes and Dissociations Induced by Collisional Activation in a Drift Tube. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:932-945. [PMID: 30980379 PMCID: PMC6865269 DOI: 10.1007/s13361-019-02160-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 02/15/2019] [Accepted: 02/15/2019] [Indexed: 05/02/2023]
Abstract
The work presented below is related to our companion paper in this issue, entitled: Substance P in solution: trans-to-cis configurational changes of penultimate prolines initiate non-enzymatic peptide bond cleavages. Two-dimensional ion mobility spectrometry (IMS-IMS) and mass spectrometry techniques are used to investigate structural transitions for [M+3H]3+ ions of substance P (subP) upon collisional activation (CA) in the gas phase. In this approach, different conformations of ions having a specified mobility are selected after an initial IMS separation, collisionally activated to produce new conformers, and these product structures are separated again using a second IMS region. In this way, it is possible to follow folding and unfolding transitions of different conformations. The analysis shows evidence for five conformations. Unlike other systems, every transition is irreversible. Studies as a function of activation voltage are used to discern pathways of structural changes prior to reaching the energy required for dissociation. Thresholds associated with the onsets of transitions are calibrated to obtain estimates of the energetic barriers between different structures and semi-quantitative potential energy diagrams are presented. Overall, barriers associated with structural transitions of [subP+3H]3+ in the absence of solvent are on the order of ~ 40 kJ mol-1, substantially lower than the ~ 90 kJ mol-1 required for some similar structural transitions in solutions of ethanol. Comparisons of the transition energies in the gas phase with thermochemistry for similar transitions in solution provide clues about why reverse transitions are prohibited. Graphical Abstract.
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Affiliation(s)
- Christopher R Conant
- Department of Chemistry, Indiana University, 800 Kirkwood Avenue, Bloomington, IN, 47401, USA
| | - Daniel R Fuller
- Department of Chemistry, Indiana University, 800 Kirkwood Avenue, Bloomington, IN, 47401, USA
| | - Zhichao Zhang
- Department of Chemistry, Indiana University, 800 Kirkwood Avenue, Bloomington, IN, 47401, USA
| | - Daniel W Woodall
- Department of Chemistry, Indiana University, 800 Kirkwood Avenue, Bloomington, IN, 47401, USA
| | - David H Russell
- Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - David E Clemmer
- Department of Chemistry, Indiana University, 800 Kirkwood Avenue, Bloomington, IN, 47401, USA.
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15
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Sahota N, AbuSalim DI, Wang ML, Brown CJ, Zhang Z, El-Baba TJ, Cook SP, Clemmer DE. A microdroplet-accelerated Biginelli reaction: mechanisms and separation of isomers using IMS-MS. Chem Sci 2019; 10:4822-4827. [PMID: 31160956 PMCID: PMC6509997 DOI: 10.1039/c9sc00704k] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Accepted: 03/28/2019] [Indexed: 01/17/2023] Open
Abstract
Electrospray ionization (ESI) combined with ion mobility spectrometry (IMS) and mass spectrometry (MS) techniques is used to examine the Biginelli reaction in an ensemble of ions generated from droplets. We find evidence for rapid dihydropyrimidinone formation from condensation of ethyl acetoacetate, benzaldehyde, and urea on the very short timescales associated with the electrospray process (∼10 μs to ∼1.0 ms). Control bulk-solution reactions show no product formation even after several days. This implies that the in-droplet reaction rate is enhanced by an astonishing factor. Examination of the reaction conditions and characterization of the intermediates en route to product shows evidence for variations in the reaction mechanism. IMS separation shows that the Knoevenagel condensation intermediate from benzaldehyde and ethyl acetoacetate exists as both the cis- and trans-isomer, in a ∼5 to 1 ratio. We suggest that the dramatic acceleration arises because of increased reagent confinement as electrosprayed droplets shrink. The ability of IMS-MS to resolve intermediates (including isomers) provides a new means of understanding reaction pathways.
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Affiliation(s)
- Navneet Sahota
- Department of Chemistry , Indiana University , 800 East Kirkwood Avenue , Bloomington , IN 47405-7102 , USA . ;
| | - Deyaa I AbuSalim
- Department of Chemistry , Indiana University , 800 East Kirkwood Avenue , Bloomington , IN 47405-7102 , USA . ;
| | - Melinda L Wang
- Department of Chemistry , Indiana University , 800 East Kirkwood Avenue , Bloomington , IN 47405-7102 , USA . ;
| | - Christopher J Brown
- Department of Chemistry , Indiana University , 800 East Kirkwood Avenue , Bloomington , IN 47405-7102 , USA . ;
| | - Zhicaho Zhang
- Department of Chemistry , Indiana University , 800 East Kirkwood Avenue , Bloomington , IN 47405-7102 , USA . ;
| | - Tarick J El-Baba
- Department of Chemistry , Indiana University , 800 East Kirkwood Avenue , Bloomington , IN 47405-7102 , USA . ;
| | - Silas P Cook
- Department of Chemistry , Indiana University , 800 East Kirkwood Avenue , Bloomington , IN 47405-7102 , USA . ;
| | - David E Clemmer
- Department of Chemistry , Indiana University , 800 East Kirkwood Avenue , Bloomington , IN 47405-7102 , USA . ;
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Dehelean L, Sarbu M, Petrut A, Zamfir AD. Trends in Glycolipid Biomarker Discovery in Neurodegenerative Disorders by Mass Spectrometry. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1140:703-729. [DOI: 10.1007/978-3-030-15950-4_42] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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17
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Shrestha K, Alaulamie AA, Miandashti AR, Richardson HH. Time-resolved universal temperature measurements using NaYF 4:Er 3+,Yb 3+ upconverting nanoparticles in an electrospray jet. BEILSTEIN JOURNAL OF NANOTECHNOLOGY 2018; 9:2916-2924. [PMID: 30546988 PMCID: PMC6278772 DOI: 10.3762/bjnano.9.270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 10/25/2018] [Indexed: 05/09/2023]
Abstract
Hexagonal upconverting nanoparticles (UCNPs) of NaYF4:Er3+,Yb3+ (ca. 300 nm) have been widely used to measure the temperature at the nanoscale using luminescence ratio thermometry. However, several factors limit their applications. For example, changes in the peak shape, mainly is the S-band emission, hinders their ability to be used as a universal temperature sensor. Herein, we introduce a universal calibration protocol for NaYF4:Er3+,Yb3+ upconverting nanoparticles that is robust to environmental changes and gives a precise temperature measurement. We used this new procedure to calculate the temperature profile inside a Taylor cone generated with an electrospray jet. Inside the Taylor cone the fluid velocity increases toward the tip of the cone. A constant acquisition length leads to a decrease in excitation and acquisition time. This decrease in excitation time causes a peak shape change that corrupts the temperature measurement if the entire peak shape is integrated in the calibration. Our universal calibration circumvents this problem and can be used for time-resolved applications. The temperature at the end of the Taylor cone increases due to the creation of a whispering gallery mode cavity with 980 nm excitation. We use time-resolved energy balance equations to support our optical temperature measurements inside the Taylor cone. We believe that the findings of this paper provide a foundation for time-resolved temperature measurements using NaYF4:Er3+,Yb3+ upconverting nanoparticles and can be used to understand temperature-dependent reactions such as protein unfolding inside microjet/microdroplets and microfluidic systems.
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Affiliation(s)
- Kristina Shrestha
- Department of Chemistry and Biochemistry, Ohio University, Athens, Ohio 45701, USA
| | - Arwa A Alaulamie
- Department of Chemistry and Biochemistry, Ohio University, Athens, Ohio 45701, USA
- Department of Chemistry, College of Science, King Faisal University, Hofuf 31982, Saudi Arabia
| | | | - Hugh H Richardson
- Department of Chemistry and Biochemistry, Ohio University, Athens, Ohio 45701, USA
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