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Kubyshkin V, Rubini M. Proline Analogues. Chem Rev 2024; 124:8130-8232. [PMID: 38941181 DOI: 10.1021/acs.chemrev.4c00007] [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: 06/30/2024]
Abstract
Within the canonical repertoire of the amino acid involved in protein biogenesis, proline plays a unique role as an amino acid presenting a modified backbone rather than a side-chain. Chemical structures that mimic proline but introduce changes into its specific molecular features are defined as proline analogues. This review article summarizes the existing chemical, physicochemical, and biochemical knowledge about this peculiar family of structures. We group proline analogues from the following compounds: substituted prolines, unsaturated and fused structures, ring size homologues, heterocyclic, e.g., pseudoproline, and bridged proline-resembling structures. We overview (1) the occurrence of proline analogues in nature and their chemical synthesis, (2) physicochemical properties including ring conformation and cis/trans amide isomerization, (3) use in commercial drugs such as nirmatrelvir recently approved against COVID-19, (4) peptide and protein synthesis involving proline analogues, (5) specific opportunities created in peptide engineering, and (6) cases of protein engineering with the analogues. The review aims to provide a summary to anyone interested in using proline analogues in systems ranging from specific biochemical setups to complex biological systems.
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Affiliation(s)
| | - Marina Rubini
- School of Chemistry, University College Dublin, Belfield, Dublin 4, Ireland
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2
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Grifnée E, Kune C, Delvaux C, Tilmant T, Quinton L, Matagne A, Mazzucchelli G, Far J, De Pauw E. Investigation of Structure-Stabilizing Elements in Proteins by Ion Mobility Mass Spectrometry and Collision-Induced Unfolding. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:1076-1088. [PMID: 38660944 DOI: 10.1021/jasms.3c00398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
A recently developed proteolytic reactor, designed for protein structural investigation, was coupled to ion mobility mass spectrometry to monitor collisional cross section (CCS) evolution of model proteins undergoing trypsin-mediated mono enzymatic digestion. As peptides are released during digestion, the CCS of the remaining protein structure may deviate from the classical 2/3 power of the CCS-mass relationship for spherical structures. The classical relationship between CCS and mass (CCS = A × M2/3) for spherical structures, assuming a globular shape in the gas phase, may deviate as stabilizing elements are lost during digestion. In addition, collision-induced unfolding (CIU) experiments on partially digested proteins provided insights into the CCS resilience in the gas phase to ion activation, potentially due to the presence of stabilizing elements. The study initially investigated a model peptide ModBea (3 kDa), assessing the impact of disulfide bridges on CCS resilience in both reduced and oxidized forms. Subsequently, β-lactoglobulin (2 disulfide bridges), calmodulin (Ca2+ coordination cation), and cytochrome c (heme) were selected to investigate the influence of common structuring elements on CCS resilience. CIU experiments probed the unfolding process, evaluating the effect of losing specific peptides on the energy landscapes of partially digested proteins. Comparisons of the TWCCSN2→He to trend curves describing the CCS/mass relationship revealed that proteins with structure-stabilizing elements consistently exhibit TWCCSN2→He and greater resilience toward CIU compared to proteins lacking these elements. The integration of online digestion, ion mobility, and CIU provides a valuable tool for identifying structuring elements in biopolymers in the gas phase.
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Affiliation(s)
- Elodie Grifnée
- Mass Spectrometry Laboratory, MolSys Research Unit, Quartier Agora, University of Liège, Allée du Six Août 11, B-4000 Liège, Belgium
| | - Christopher Kune
- Mass Spectrometry Laboratory, MolSys Research Unit, Quartier Agora, University of Liège, Allée du Six Août 11, B-4000 Liège, Belgium
| | - Cédric Delvaux
- Mass Spectrometry Laboratory, MolSys Research Unit, Quartier Agora, University of Liège, Allée du Six Août 11, B-4000 Liège, Belgium
| | - Thomas Tilmant
- Mass Spectrometry Laboratory, MolSys Research Unit, Quartier Agora, University of Liège, Allée du Six Août 11, B-4000 Liège, Belgium
| | - Loïc Quinton
- Mass Spectrometry Laboratory, MolSys Research Unit, Quartier Agora, University of Liège, Allée du Six Août 11, B-4000 Liège, Belgium
| | - André Matagne
- Laboratory of Enzymology and Protein Folding, Center for Protein Engineering, InBioS Research Unit, University of Liège, B-4000 Liège, Belgium
| | - Gabriel Mazzucchelli
- Mass Spectrometry Laboratory, MolSys Research Unit, Quartier Agora, University of Liège, Allée du Six Août 11, B-4000 Liège, Belgium
| | - Johann Far
- Mass Spectrometry Laboratory, MolSys Research Unit, Quartier Agora, University of Liège, Allée du Six Août 11, B-4000 Liège, Belgium
| | - Edwin De Pauw
- Mass Spectrometry Laboratory, MolSys Research Unit, Quartier Agora, University of Liège, Allée du Six Août 11, B-4000 Liège, Belgium
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3
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Schramm HM, Tamadate T, Hogan CJ, Clowers BH. Ion-neutral clustering alters gas-phase hydrogen-deuterium exchange rates. Phys Chem Chem Phys 2023; 25:4959-4968. [PMID: 36722872 DOI: 10.1039/d2cp04388b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The rates and mechanisms of chemical reactions that occur at a phase boundary often differ considerably from chemical behavior in bulk solution, but remain difficult to quantify. Ion-neutral interactions are one such class of chemical reactions whose behavior during the nascent stages of solvation differs from bulk solution while occupying critical roles in aerosol formation, atmospheric chemistry, and gas-phase ion separations. Through a gas-phase ion separation technique utilizing a counter-current flow of deuterated vapor, we quantify the degree of hydrogen-deuterium exchange (HDX) and ion-neutral clustering on a series of model chemical systems (i.e. amino acids). By simultaneously quantifying the degree of vapor association and HDX, the effects of cluster formation on reaction kinetics are realized. These results imply that cluster formation cannot be ignored when modeling complex nucleation processes and biopolymer structural dynamics.
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Affiliation(s)
- Haley M Schramm
- Department of Chemistry, Washington State University, Pullman, WA 99163, USA.
| | - Tomoya Tamadate
- Department of Mechanical Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Christopher J Hogan
- Department of Mechanical Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Brian H Clowers
- Department of Chemistry, Washington State University, Pullman, WA 99163, USA.
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4
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Hueber A, Green M, Ujma J, Richardson K, Gimbert Y, Cenac N, Bertrand-Michel J, Tabet JC. Energy-Resolved Ion Mobility Spectrometry: Composite Breakdown Curves for Distinguishing Isomeric Product Ions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:36-47. [PMID: 36488200 DOI: 10.1021/jasms.2c00233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Identification of lipopeptides (LpAA) synthesized from bacteria involves the study of structural characterization. Twenty LpAA have been characterized using commercial tandem high-resolution mass spectrometers in negative electrospray, employing nonresonant excitation in "RF only" collision cells and generally behave identically. However, [LpAA-H]- (AA = Asp or Glu) shows surprising fragmentation pathways, yielding a complementary fatty acid carboxylate and dehydrated amino acid fragment anions. In this study, the dissociation mechanisms of [C12Glu-H]- were determinate using energy-resolved mass spectrometry (ERMS). Product ion breakdown profiles are, generally, unimodal with full width at half-maximum (fwhm) increasing as product ion m/z ratios decrease, except for the two product ions of interest (fatty acid carboxylate and dehydrated glutamate) characterized by broad and composite profiles. Such behavior was already shown for other ions using a custom-built guided ion beam mass spectrometer. In this study, we investigate the meaning of these particular profiles from an ERMS breakdown, using fragmentation mechanisms depending on the collision energy. ERMS on line with ion mobility spectrometry (IMS), here called ER-IMS, provides a way to probe such questions. Broad or composite profiles imply that the corresponding product ions may be generated by two (or more) pathways, resulting in common or isomeric product ion structures. ER-IMS analysis indicates that the fatty acid carboxylate product ion is produced with a common structure through different pathways, while dehydrated glutamate has two isomeric forms depending on the mechanism involved. Drift time values correlate with the calculated collision cross section that confirms the product ion structures and fragmentation mechanisms.
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Affiliation(s)
- Amandine Hueber
- MetaboHUB-MetaToul, National Infrastructure of Metabolomics and Fluxomics, ToulouseF-31077, France
- IRSD, Université de Toulouse, INSERM, INRA, INP ENVT, Université de Toulouse 3 Paul Sabatier, ToulouseF-31024, France
- I2MC, INSERM, Université Toulouse 3 Paul Sabatier, ToulouseF-31432, France
| | - Martin Green
- Waters Corporation, Stamford Avenue, Altrincham Road, WilmslowSK9 4AX, United Kingdom
| | - Jakub Ujma
- Waters Corporation, Stamford Avenue, Altrincham Road, WilmslowSK9 4AX, United Kingdom
| | - Keith Richardson
- Waters Corporation, Stamford Avenue, Altrincham Road, WilmslowSK9 4AX, United Kingdom
| | - Yves Gimbert
- Sorbonne Université, Faculté des Sciences et de l'Ingénierie, Institut Parisien de Chimie Moléculaire (IPCM), F-75005Paris, France
- Département de chimie Moléculaire, UMR CNRS, 5250, Université Grenoble Alpes, F-38050Grenoble, France
| | - Nicolas Cenac
- IRSD, Université de Toulouse, INSERM, INRA, INP ENVT, Université de Toulouse 3 Paul Sabatier, ToulouseF-31024, France
| | - Justine Bertrand-Michel
- MetaboHUB-MetaToul, National Infrastructure of Metabolomics and Fluxomics, ToulouseF-31077, France
- I2MC, INSERM, Université Toulouse 3 Paul Sabatier, ToulouseF-31432, France
| | - Jean-Claude Tabet
- MetaboHUB-MetaToul, National Infrastructure of Metabolomics and Fluxomics, ToulouseF-31077, France
- Sorbonne Université, Faculté des Sciences et de l'Ingénierie, Institut Parisien de Chimie Moléculaire (IPCM), F-75005Paris, France
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé, F-91191Gif-sur-Yvette, France
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5
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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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6
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Britt HM, Cragnolini T, Thalassinos K. Integration of Mass Spectrometry Data for Structural Biology. Chem Rev 2021; 122:7952-7986. [PMID: 34506113 DOI: 10.1021/acs.chemrev.1c00356] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Mass spectrometry (MS) is increasingly being used to probe the structure and dynamics of proteins and the complexes they form with other macromolecules. There are now several specialized MS methods, each with unique sample preparation, data acquisition, and data processing protocols. Collectively, these methods are referred to as structural MS and include cross-linking, hydrogen-deuterium exchange, hydroxyl radical footprinting, native, ion mobility, and top-down MS. Each of these provides a unique type of structural information, ranging from composition and stoichiometry through to residue level proximity and solvent accessibility. Structural MS has proved particularly beneficial in studying protein classes for which analysis by classic structural biology techniques proves challenging such as glycosylated or intrinsically disordered proteins. To capture the structural details for a particular system, especially larger multiprotein complexes, more than one structural MS method with other structural and biophysical techniques is often required. Key to integrating these diverse data are computational strategies and software solutions to facilitate this process. We provide a background to the structural MS methods and briefly summarize other structural methods and how these are combined with MS. We then describe current state of the art approaches for the integration of structural MS data for structural biology. We quantify how often these methods are used together and provide examples where such combinations have been fruitful. To illustrate the power of integrative approaches, we discuss progress in solving the structures of the proteasome and the nuclear pore complex. We also discuss how information from structural MS, particularly pertaining to protein dynamics, is not currently utilized in integrative workflows and how such information can provide a more accurate picture of the systems studied. We conclude by discussing new developments in the MS and computational fields that will further enable in-cell structural studies.
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Affiliation(s)
- Hannah M Britt
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, United Kingdom
| | - Tristan Cragnolini
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, United Kingdom.,Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, United Kingdom
| | - Konstantinos Thalassinos
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, United Kingdom.,Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, United Kingdom
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7
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Zhang Z, Conant CR, El-Baba TJ, Raab SA, Fuller DR, Hales DA, Clemmer DE. Diketopiperazine Formation from FPG nK ( n = 1-9) Peptides: Rates of Structural Rearrangements and Mechanisms. J Phys Chem B 2021; 125:8107-8116. [PMID: 34270248 PMCID: PMC10661757 DOI: 10.1021/acs.jpcb.1c03515] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Peptides with penultimate proline residues undergo trans → cis isomerization of the Phe1-Pro2 peptide bond followed by spontaneous bond cleavage at the Pro2-Xxx3 bond (where Xxx is another amino acid residue), leading to cleavage of the Pro2-Xxx3 bond and formation of a diketopiperazine (DKP). In this paper, ion mobility spectrometry and mass spectrometry techniques were used to study the dissociation kinetics of nine peptides [Phe1-Pro2-Glyn-Lysn+3 (n = 1-9)] in ethanol. Shorter (n = 1-3) peptides are found to be more stable than longer (n = 4-9) peptides. Alanine substitution studies indicate that, when experiments are initiated, the Phe1-Pro2 bond of the n = 9 peptide exists exclusively in the cis configuration, while the n = 1-8 peptides appear to exist initially with both cis- and trans-Phe1-Pro2 configured bonds. Molecular dynamics simulations indicate that intramolecular hydrogen bonding interactions stabilize conformations of shorter peptides, thus inhibiting DKP formation. Similar stabilizing interactions appear less frequently in longer peptides. In addition, in smaller peptides, the N-terminal amino group is more likely to be charged compared to the same group in longer peptides, which would inhibit the dissociation through the DKP formation mechanism. Analysis of temperature-dependent kinetics measurements provides insight about the mechanism of bond cleavage. The analysis gives the following transition state thermochemistry: ΔG⧧ values range from 94.6 ± 0.9 to 101.5 ± 1.9 kJ·mol-1, values of ΔH⧧ range from 89.1 ± 0.9 to 116.7 ± 1.5 kJ·mol-1, and ΔS⧧ values range from -25.4 ± 2.6 to 50.8 ± 4.2 J·mol-1·K-1. Proposed mechanisms and thermochemistry are discussed.
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Affiliation(s)
- Zhichao Zhang
- Department of Chemistry, Indiana University, Bloomington, Indiana, United States
| | - Christopher R Conant
- Department of Chemistry, Indiana University, Bloomington, Indiana, United States
| | - Tarick J El-Baba
- Department of Chemistry, Indiana University, Bloomington, Indiana, United States
| | - Shannon A Raab
- Department of Chemistry, Indiana University, Bloomington, Indiana, United States
| | - Daniel R Fuller
- Department of Chemistry, Indiana University, Bloomington, Indiana, United States
| | - David A Hales
- Department of Chemistry, Hendrix College, Conway, Arkansas, United States
| | - David E Clemmer
- Department of Chemistry, Indiana University, Bloomington, Indiana, United States
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8
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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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9
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Zhang ZC, Raab SA, Hales DA, Clemmer DE. Influence of Solvents upon Diketopiperazine Formation of FPG8K. J Phys Chem B 2021; 125:2952-2959. [DOI: 10.1021/acs.jpcb.1c00269] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Zhi-chao Zhang
- Department of Chemistry, Indiana University, 800 Kirkwood Avenue, Bloomington, Indiana 47401, United States
| | - Shannon A. Raab
- Department of Chemistry, Indiana University, 800 Kirkwood Avenue, Bloomington, Indiana 47401, United States
| | - David A. Hales
- Department of Chemistry, Indiana University, 800 Kirkwood Avenue, Bloomington, Indiana 47401, United States
- Department of Chemistry, Hendrix College, Conway, Arkansas 72032, United States
| | - David E. Clemmer
- Department of Chemistry, Indiana University, 800 Kirkwood Avenue, Bloomington, Indiana 47401, United States
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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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Raab SA, El-Baba TJ, Woodall DW, Liu W, Liu Y, Baird Z, Hales DA, Laganowsky A, Russell DH, Clemmer DE. Evidence for Many Unique Solution Structures for Chymotrypsin Inhibitor 2: A Thermodynamic Perspective Derived from vT-ESI-IMS-MS Measurements. J Am Chem Soc 2020; 142:17372-17383. [PMID: 32866376 DOI: 10.1021/jacs.0c05365] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Chymotrypsin inhibitor 2 (CI-2) is a classic model for two-state cooperative protein folding and is one of the most extensively studied systems. Alan Fersht, a pioneer in the field of structural biology, has studied the wild-type (wt) and over 100 mutant forms of CI-2 with traditional analytical and biochemical techniques. Here, we examine wt CI-2 and three mutant forms (A16G, K11A, L32A) to demonstrate the utility of variable-temperature (vT) electrospray ionization (ESI) paired with ion mobility spectrometry (IMS) and mass spectrometry (MS) to map the free energy folding landscape. As the solution temperature is increased, the abundance of each of the six ESI charge states for wt CI-2 and each mutant is found to vary independently. These results require that at least six unique types of CI-2 solution conformers are present. Ion mobility analysis reveals that within each charge state there are additional conformers having distinct solution temperature profiles. A model of the data at ∼30 different temperatures for all four systems suggests the presence of 41 unique CI-2 solution conformations. A thermodynamic analysis of this system yields values of ΔCp as well as ΔG, ΔH, and ΔS for each state at every temperature studied. Detailed energy landscapes derived from these data provide a rare glimpse into Anfinsen's thermodynamic hypothesis and the process of thermal denaturation, normally thought of as a cooperative two-state transition involving the native state and unstructured denatured species. Specifically, as the temperature is varied, the entropies and enthalpies of different conformers undergo dramatic changes in magnitude and relative order to maintain the delicate balance associated with equilibrium.
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Affiliation(s)
- Shannon A Raab
- Department of Chemistry, Indiana University, 800 Kirkwood Avenue, Bloomington, Indiana 47401, United States
| | - Tarick J El-Baba
- Department of Chemistry, Indiana University, 800 Kirkwood Avenue, Bloomington, Indiana 47401, United States
| | - Daniel W Woodall
- Department of Chemistry, Indiana University, 800 Kirkwood Avenue, Bloomington, Indiana 47401, United States
| | - Wen Liu
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Yang Liu
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Zane Baird
- Baxter Healthcare Corporation, 927 South Curry Pike, Bloomington, Indiana 47403, United States
| | - David A Hales
- Department of Chemistry, Hendrix College, Conway, Arkansas 72032, 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
| | - David E Clemmer
- Department of Chemistry, Indiana University, 800 Kirkwood Avenue, Bloomington, Indiana 47401, United States
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12
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Silzel JW, Murphree TA, Paranji RK, Guttman MM, Julian RR. Probing the Stability of Proline Cis/Trans Isomers in the Gas Phase with Ultraviolet Photodissociation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:1974-1980. [PMID: 32808771 DOI: 10.1021/jasms.0c00242] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Although most peptide bonds in proteins exist in the trans configuration, when cis peptide bonds do occur, they can have major impact on protein structure and function. The rapid identification of cis peptide bonds is therefore an important task. Peptide bonds containing proline are more likely to adopt the cis configuration because the ring connecting the side chain and backbone in proline flattens the energetic landscape relative to amino acids with free side chains. Examples of cis proline isomers have been identified in both solution and in the gas phase by a variety of structure-probing methods. Mass spectrometry is an attractive potential method for identifying cis proline due to its speed and sensitivity; however, the question remains of whether cis/trans proline isomers originating in solution are preserved during ionization and manipulation within a mass spectrometer. Herein, we investigate the gas-phase stability of isolated solution-phase cis and trans proline isomers using a synthetic peptide sequence with a Tyr-Pro-Pro motif. A variety of dissociation methods were explored to evaluate their potential to distinguish cis/trans configuration, including collision-induced dissociation, radical-directed dissociation, and photodissociation. Only photodissociation employed in conjunction with extremely gentle electrospray and charge solvation by 18-crown-6 ether was able to distinguish cis/trans isomers for our model peptide, suggesting that any thermal activation during transfer or while in the gas phase leads to isomer scrambling. Furthermore, the necessity for 18-crown-6 suggests that intramolecular charge solvation taking place during electrospray ionization can override cis/trans isomer homogeneity. Overall, the results suggest that solution-phase cis/trans proline isomers are fragile and easily lost during electrospray, requiring careful selection of instrument parameters and consideration of charge solvation to prevent cis/trans scrambling.
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Affiliation(s)
- Jacob W Silzel
- Department of Chemistry, University of California, 501 Big Springs Road, Riverside, California 92521, United States
| | - Taylor A Murphree
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Rajan K Paranji
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Miklos M Guttman
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Ryan R Julian
- Department of Chemistry, University of California, 501 Big Springs Road, Riverside, California 92521, United States
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13
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Woodall DW, Brown CJ, Raab SA, El-Baba TJ, Laganowsky A, Russell DH, Clemmer DE. Melting of Hemoglobin in Native Solutions as measured by IMS-MS. Anal Chem 2020; 92:3440-3446. [PMID: 31990187 PMCID: PMC7480357 DOI: 10.1021/acs.analchem.9b05561] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Thermally induced structural transitions of the quaternary structure of the hemoglobin tetramer (human) in aqueous solution (150 mM ammonium acetate) were investigated using a variable temperature electrospray ionization (vt-ESI) technique in combination with ion mobility spectrometry (IMS) and mass spectrometry (MS) measurements. At low solution temperatures (28 to ∼40 °C), a heterotetrameric (α2β2) complex is the most abundant species that is observed. When the solution temperature is increased, this assembly dissociates into heterodimers (holo αβ forms) before ultimately forming insoluble aggregates at higher temperatures (>60 °C). In addition to the holo αβ forms, a small population of αβ dimers containing only a single heme ligand and having a dioxidation modification mapping to the β subunit are observed. The oxidized heterodimers are less stable than the unmodified holo-heterodimer. The Cys93 residue of the β subunit is the primary site of dioxidation. The close proximity of this post translational modification to both the αβ subunit interface and the heme binding site suggests that this modification is coupled to the loss of the heme and decreased protein stability. Changes in the charge state and collision cross sections of these species indicate that the tetramers and dimers favor less compact structures at elevated temperatures (prior to temperatures where dissociation dominates).
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Affiliation(s)
- Daniel W Woodall
- Department of Chemistry , Indiana University , Bloomington , Indiana 47405 , United States
| | - Christopher J Brown
- Department of Chemistry , Indiana University , Bloomington , Indiana 47405 , United States
| | - Shannon A Raab
- Department of Chemistry , Indiana University , Bloomington , Indiana 47405 , United States
| | - Tarick J El-Baba
- 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
| | - David E Clemmer
- Department of Chemistry , Indiana University , Bloomington , Indiana 47405 , United States
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14
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Huang MC, Chen WH, Huang CW, Huang KY, Horng JC, Hayashi M, Chen IC. Investigation of the cis– trans structures and isomerization of oligoprolines by using Raman spectroscopy and density functional theory calculations: solute–solvent interactions and effects of terminal positively charged amino acid residues. RSC Adv 2020; 10:34493-34500. [PMID: 35514408 PMCID: PMC9056779 DOI: 10.1039/d0ra05746k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 09/08/2020] [Indexed: 11/29/2022] Open
Abstract
Using low-wavenumber Raman spectroscopy in combination with theoretical calculations via solid-state density functional theory (DFT)-D3, we studied the vibrational structures and interaction with solvent of poly-l-proline and the oligoproline P12 series. The P12 series includes P12, the positively charged amino acid residue (arginine and lysine) N-terminus proline oligomers RP11 and KP11, and the C-terminus P11R and P11K. We assigned the spring-type phonon mode to 74–76 cm−1 bands for the PPI and PPII conformers and the carbonyl group ring-opening mode 122 cm−1 in the PPI conformer of poly-l-proline. Amide I and II were assigned based on the results of mode analysis for O, N, and C atom displacements. The broad band feature of the H-bond transverse mode in the Raman spectra indicates that the positively charged proline oligomers PPII form H-bonds with water in the solid phase, whereas P12 is relatively more hydrophobic. In propanol, the PPI conformer of the P12 series forms less H-bond network with the solvent. The PPII conformer exhibits a distinct Raman band at 310 cm−1, whereas the PPI has bands at 365, 660, and 960 cm−1 with reasonable intensity that can be used to quantitatively determine these two conformational forms. The 365 cm−1 mode comprising the motion of a C
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O group turning to the helix axis was used to monitor the isomerization reaction PPI ↔ PPII. In pure propanol, RP11 and KP11 were found to have mostly PPI present, but P11R and P11K preferred PPII. After adding 20% water, the PPI in P11R and P11K was completely converted to PPII, whereas a small fraction of PPI remained in RP11 and KP11. The substituted positively charged amino acid affected the balance of the PPI/PPII population ratio. The low-wavenumber Raman spectra in combination with theoretical calculations via solid-state density functional theory (DFT)-D3 are displayed. The vibrational structures and interaction with solvent of poly-l-proline and the oligoproline P12 series are identified.![]()
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Affiliation(s)
- Mei-Chun Huang
- Department of Chemistry
- National Tsing Hua University
- Hsinchu
- Republic of China
| | - Wei-Hao Chen
- Department of Chemistry
- National Tsing Hua University
- Hsinchu
- Republic of China
| | - Chen-Wei Huang
- Department of Chemistry
- National Tsing Hua University
- Hsinchu
- Republic of China
| | - Kuei-Yen Huang
- Department of Chemistry
- National Tsing Hua University
- Hsinchu
- Republic of China
| | - Jia-Cherng Horng
- Department of Chemistry
- National Tsing Hua University
- Hsinchu
- Republic of China
| | - Michitoshi Hayashi
- Center for Condensed Matter Sciences
- National Taiwan University
- Taipei
- Republic of China
| | - I.-Chia Chen
- Department of Chemistry
- National Tsing Hua University
- Hsinchu
- Republic of China
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15
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Duez Q, Metwally H, Hoyas S, Lemaur V, Cornil J, De Winter J, Konermann L, Gerbaux P. Effects of electrospray mechanisms and structural relaxation on polylactide ion conformations in the gas phase: insights from ion mobility spectrometry and molecular dynamics simulations. Phys Chem Chem Phys 2020; 22:4193-4204. [DOI: 10.1039/c9cp06391a] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Gas-phase polymer ions may retain structural features associated with their electrospray formation mechanisms.
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Affiliation(s)
- Quentin Duez
- Organic Synthesis and Mass Spectrometry Laboratory
- Center of Innovation and Research in Materials and Polymers (CIRMAP) – University of Mons (UMONS)
- B-7000 Mons
- Belgium
- Laboratory for Chemistry of Novel Materials
| | - Haidy Metwally
- Department of Chemistry
- The University of Western Ontario
- London
- Canada
| | - Sébastien Hoyas
- Organic Synthesis and Mass Spectrometry Laboratory
- Center of Innovation and Research in Materials and Polymers (CIRMAP) – University of Mons (UMONS)
- B-7000 Mons
- Belgium
- Laboratory for Chemistry of Novel Materials
| | - Vincent Lemaur
- Laboratory for Chemistry of Novel Materials
- Center of Innovation and Research in Materials and Polymers (CIRMAP) – University of Mons (UMONS)
- B-7000 Mons
- Belgium
| | - Jérôme Cornil
- Laboratory for Chemistry of Novel Materials
- Center of Innovation and Research in Materials and Polymers (CIRMAP) – University of Mons (UMONS)
- B-7000 Mons
- Belgium
| | - Julien De Winter
- Organic Synthesis and Mass Spectrometry Laboratory
- Center of Innovation and Research in Materials and Polymers (CIRMAP) – University of Mons (UMONS)
- B-7000 Mons
- Belgium
| | - Lars Konermann
- Department of Chemistry
- The University of Western Ontario
- London
- Canada
| | - Pascal Gerbaux
- Organic Synthesis and Mass Spectrometry Laboratory
- Center of Innovation and Research in Materials and Polymers (CIRMAP) – University of Mons (UMONS)
- B-7000 Mons
- Belgium
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16
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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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17
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Mallis CS, Saha ML, Stang PJ, Russell DH. Topological Characterization of Coordination-Driven Self-assembly Complexes: Applications of Ion Mobility-Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:1654-1662. [PMID: 31317343 DOI: 10.1007/s13361-019-02276-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 05/30/2019] [Accepted: 06/21/2019] [Indexed: 06/10/2023]
Abstract
Coordination-driven self-assembly (CDSA) is increasingly used to synthesize coordination complexes containing metal-centered electron acceptors and typically nitrogen-containing electron donors. Characterization of the structures obtained from CDSA via crystallographic or spectroscopic means is limited due to difficulties in forming single crystals for X-ray studies and overlapping precursor and product signals in NMR. Here, we employ ion mobility-mass spectrometry (IM-MS), which provides a direct measure of size and shape of the CDSA complexes, to study the intact reaction products of a rhomboid-shaped complex. This approach negates the need for product isolation and crystallization and allows for tracking of the product distribution as a function of time. A potential challenge of IM-MS is that the size/shape of the observed CDSA complexes can vary with internal energy; however, we show that proper tuning of the instrument reduces the effects of collisional activation thereby allowing for retention of ion conformations that reflect solution-phase ion structures. Graphical Abstract.
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Affiliation(s)
| | - Manik Lal Saha
- Department of Chemistry, University of Utah, Salt Lake City, UT, 84112, USA
| | - Peter J Stang
- Department of Chemistry, University of Utah, Salt Lake City, UT, 84112, USA
| | - David H Russell
- Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA.
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18
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Decroo C, Colson E, Lemaur V, Caulier G, De Winter J, Cabrera-Barjas G, Cornil J, Flammang P, Gerbaux P. Ion mobility mass spectrometry of saponin ions. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2019; 33 Suppl 2:22-33. [PMID: 29873851 DOI: 10.1002/rcm.8193] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 05/25/2018] [Accepted: 05/28/2018] [Indexed: 06/08/2023]
Affiliation(s)
- Corentin Decroo
- Organic Synthesis and Mass Spectrometry Lab, Interdisciplinary Center for Mass Spectrometry, Research Institute for Biosciences, University of Mons - UMONS, 23 Place du Parc, B-7000, Mons, Belgium
- Laboratory for Chemistry of Novel Materials, Center of Innovation and Research in Materials and Polymers, Research Institute for Science and Engineering of Materials, University of Mons - UMONS, 23 Place du Parc, 7000, Mons, Belgium
- Biology of Marine Organisms and Biomimetics Unit, Research Institute for Biosciences, University of Mons - UMONS, 23 Place du Parc, B-7000, Mons, Belgium
| | - Emmanuel Colson
- Organic Synthesis and Mass Spectrometry Lab, Interdisciplinary Center for Mass Spectrometry, Research Institute for Biosciences, University of Mons - UMONS, 23 Place du Parc, B-7000, Mons, Belgium
- Biology of Marine Organisms and Biomimetics Unit, Research Institute for Biosciences, University of Mons - UMONS, 23 Place du Parc, B-7000, Mons, Belgium
| | - Vincent Lemaur
- Laboratory for Chemistry of Novel Materials, Center of Innovation and Research in Materials and Polymers, Research Institute for Science and Engineering of Materials, University of Mons - UMONS, 23 Place du Parc, 7000, Mons, Belgium
| | - Guillaume Caulier
- Biology of Marine Organisms and Biomimetics Unit, Research Institute for Biosciences, University of Mons - UMONS, 23 Place du Parc, B-7000, Mons, Belgium
| | - Julien De Winter
- Organic Synthesis and Mass Spectrometry Lab, Interdisciplinary Center for Mass Spectrometry, Research Institute for Biosciences, University of Mons - UMONS, 23 Place du Parc, B-7000, Mons, Belgium
| | - Gustavo Cabrera-Barjas
- Unit for Technology Development (UDT), University of Concepción, Av. Cordillera 2634, Parque Industrial Coronel, P.O. Box 4051 mail 3, Coronel, Región del Bío Bío, Chile
| | - Jérôme Cornil
- Laboratory for Chemistry of Novel Materials, Center of Innovation and Research in Materials and Polymers, Research Institute for Science and Engineering of Materials, University of Mons - UMONS, 23 Place du Parc, 7000, Mons, Belgium
| | - Patrick Flammang
- Biology of Marine Organisms and Biomimetics Unit, Research Institute for Biosciences, University of Mons - UMONS, 23 Place du Parc, B-7000, Mons, Belgium
| | - Pascal Gerbaux
- Organic Synthesis and Mass Spectrometry Lab, Interdisciplinary Center for Mass Spectrometry, Research Institute for Biosciences, University of Mons - UMONS, 23 Place du Parc, B-7000, Mons, Belgium
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19
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Conant CR, Fuller DR, El-Baba TJ, Zhang Z, Russell DH, Clemmer DE. Substance P in Solution: Trans-to-Cis Configurational Changes of Penultimate Prolines Initiate Non-enzymatic Peptide Bond Cleavages. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:919-931. [PMID: 30980380 PMCID: PMC6824264 DOI: 10.1007/s13361-019-02159-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 02/15/2019] [Accepted: 02/15/2019] [Indexed: 05/02/2023]
Abstract
We report ion mobility spectrometry and mass spectrometry studies of the non-enzymatic step-by-step degradation of substance P (subP), an 11-residue neuropeptide, with the sequence Arg1-Pro2-Lys3-Pro4-Gln5-Gln6-Phe7-Phe8-Gly9-Leu10-Met11-NH2, in ethanol. At elevated solution temperatures (55 to 75 °C), several reactions are observed, including a protonation event, i.e., [subP+2H]2+ + H+ → [subP+3H]3+, that appears to be regulated by a configurational change and two sequential bond cleavages (the Pro2-Lys3 peptide bond is cleaved to form the smaller nonapeptide Lys3-Met11-NH2 [subP(3-11)], and subsequently, subP(3-11) is cleaved at the Pro4-Gln5 peptide bond to yield the heptapeptide Gln5-Met11-NH2 [subP(5-11)]). Each of the product peptides [subP(3-11) and subP(5-11)] is accompanied by a complementary diketopiperazine (DKP): cyclo-Arg1-Pro2 (cRP) for the first cleavage, and cyclo-Lys3-Pro4 (cKP) for the second. Insight about the mechanism of degradation is obtained by comparing kinetics calculations of trial model mechanisms with experimental data. The best model of our experimental data indicates that the initial cleavage of subP is regulated by a conformational change, likely a trans→cis isomerization of the Arg1-Pro2 peptide bond. The subP(3-11) product has a long lifetime (t1/2 ~ 30 h at 55 °C) and appears to transition through several structural intermediates prior to dissociation, suggesting that subP(3-11) is initially formed with a Lys3-trans-Pro4 peptide bond configuration and that slow trans→cis isomerization regulates the second bond cleavage event as well. From these data and our model mechanisms, we obtain transition state thermochemistry ranging from ΔH‡ = 41 to 85 kJ mol-1 and ΔS‡ = - 43 to - 157 J mol-1 K-1 for each step in the reaction. 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
| | - Tarick J El-Baba
- 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
| | - 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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20
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Duez Q, Liénard R, Moins S, Lemaur V, Coulembier O, Cornil J, Gerbaux P, De Winter J. One Step Further in the Characterization of Synthetic Polymers by Ion Mobility Mass Spectrometry: Evaluating the Contribution of End-groups. Polymers (Basel) 2019; 11:E688. [PMID: 30995722 PMCID: PMC6523221 DOI: 10.3390/polym11040688] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 04/09/2019] [Accepted: 04/10/2019] [Indexed: 12/20/2022] Open
Abstract
Several families of polymers possessing various end-groups are characterized by ion mobility mass spectrometry (IMMS). A significant contribution of the end-groups to the ion collision cross section (CCS) is observed, although their role is neglected in current fitting models described in literature. Comparing polymers prepared from different synthetic procedures might thus, be misleading with the current theoretical treatments. We show that this issue is alleviated by comparing the CCS of various polymer ions (polyesters and polyethers) as a function of the number of atoms in the macroion instead of the usual representation involving the degree of polymerization. Finally, we extract the atom number density from the spectra which gives us the possibility to evaluate the compaction of polymer ions, and by extension to discern isomeric polymers.
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Affiliation(s)
- Quentin Duez
- Organic Synthesis and Mass Spectrometry Laboratory, Interdisciplinary Center for Mass Spectrometry (CISMa), University of Mons, UMONS, 23 Place du Parc, 7000 Mons, Belgium.
- Laboratory for Chemistry of Novel Materials, Center of Innovation and Research in Materials and Polymers (CIRMAP), University of Mons, UMONS, 23 Place du Parc, 7000 Mons, Belgium.
| | - Romain Liénard
- Organic Synthesis and Mass Spectrometry Laboratory, Interdisciplinary Center for Mass Spectrometry (CISMa), University of Mons, UMONS, 23 Place du Parc, 7000 Mons, Belgium.
- Laboratory of Polymeric and Composite Materials, Center of Innovation and Research in Materials and Polymers (CIRMAP), University of Mons, UMONS, 23 Place du Parc, 7000 Mons, Belgium.
| | - Sébastien Moins
- Laboratory of Polymeric and Composite Materials, Center of Innovation and Research in Materials and Polymers (CIRMAP), University of Mons, UMONS, 23 Place du Parc, 7000 Mons, Belgium.
| | - Vincent Lemaur
- Laboratory for Chemistry of Novel Materials, Center of Innovation and Research in Materials and Polymers (CIRMAP), University of Mons, UMONS, 23 Place du Parc, 7000 Mons, Belgium.
| | - Olivier Coulembier
- Laboratory of Polymeric and Composite Materials, Center of Innovation and Research in Materials and Polymers (CIRMAP), University of Mons, UMONS, 23 Place du Parc, 7000 Mons, Belgium.
| | - Jérôme Cornil
- Laboratory for Chemistry of Novel Materials, Center of Innovation and Research in Materials and Polymers (CIRMAP), University of Mons, UMONS, 23 Place du Parc, 7000 Mons, Belgium.
| | - Pascal Gerbaux
- Organic Synthesis and Mass Spectrometry Laboratory, Interdisciplinary Center for Mass Spectrometry (CISMa), University of Mons, UMONS, 23 Place du Parc, 7000 Mons, Belgium.
| | - Julien De Winter
- Organic Synthesis and Mass Spectrometry Laboratory, Interdisciplinary Center for Mass Spectrometry (CISMa), University of Mons, UMONS, 23 Place du Parc, 7000 Mons, Belgium.
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21
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El-Baba TJ, Fuller DR, Hales DA, Russell DH, Clemmer DE. Solvent Mediation of Peptide Conformations: Polyproline Structures in Water, Methanol, Ethanol, and 1-Propanol as Determined by Ion Mobility Spectrometry-Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:77-84. [PMID: 30069641 PMCID: PMC6503664 DOI: 10.1007/s13361-018-2034-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 07/03/2018] [Accepted: 07/07/2018] [Indexed: 05/30/2023]
Abstract
Ion mobility spectrometry and circular dichroism spectroscopy are used to examine the populations of the small model peptide, polyproline-13 in water, methanol, ethanol, and 1-propanol over a range of solution temperatures (from 288 to 318 K). At low temperatures, the less-polar solvents (1-propanol and ethanol) favor the all-cis polyproline I helix (PPI); as the temperature is increased, the trans-configured polyproline II helix (PPII) is formed. In polar solvents (methanol and water), PPII is favored at all temperatures. From the experimental data, we determine the relative stabilities of the eight structures in methanol, ethanol, and 1-propanol, as well as four in water, all with respect to PPII. Although these conformers show relatively small differences in free energies, substantial variability is observed in the enthalpies and entropies across the structures and solvents. This requires that enthalpies and entropies be highly correlated: in 1-propanol, cis-configured PPI conformations are energetically favorable but entropically disfavored. In more polar solvents, PPI is enthalpically less favorable and entropy favors trans-configured forms. While either ΔH0 or ΔS0 can favor different structures, no conformation in any solvent is simultaneously energetically and entropically stabilized. These data present a rare opportunity to examine the origin of conformational stability. Graphical Abstract ᅟ.
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Affiliation(s)
- Tarick J El-Baba
- 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
| | - David A Hales
- Department of Chemistry, Hendrix College, Conway, AR, 72032, 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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22
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Huang KY, Horng JC. Impacts of the Terminal Charged Residues on Polyproline Conformation. J Phys Chem B 2018; 123:138-147. [DOI: 10.1021/acs.jpcb.8b10864] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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23
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Bell MR, Cruzeiro VWD, Cismesia AP, Tesler LF, Roitberg AE, Polfer NC. Probing the Structures of Solvent-Complexed Ions Formed in Electrospray Ionization Using Cryogenic Infrared Photodissociation Spectroscopy. J Phys Chem A 2018; 122:7427-7436. [DOI: 10.1021/acs.jpca.8b05896] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Matthew R. Bell
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611-7200, United States
| | - Vinícius Wilian D. Cruzeiro
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611-7200, United States
| | - Adam P. Cismesia
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611-7200, United States
| | - Larry F. Tesler
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611-7200, United States
| | - Adrian E. Roitberg
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611-7200, United States
| | - Nicolas C. Polfer
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611-7200, United States
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24
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Garabedian A, Leng F, Ridgeway ME, Park MA, Fernandez-Lima F. Tailoring peptide conformational space with organic gas modifiers in TIMS-MS. ACTA ACUST UNITED AC 2018. [DOI: 10.1007/s12127-018-0231-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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25
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Gustafson E, Mortensen DN, Dearden DV. Quantitative Collision Cross-Sections from FTICR Linewidth Measurements: Improvements in Theory and Experiment. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:251-259. [PMID: 28733966 DOI: 10.1007/s13361-017-1738-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Revised: 06/13/2017] [Accepted: 06/14/2017] [Indexed: 06/07/2023]
Abstract
Two corrections to the equation used in the cross-sectional areas by Fourier transform ion cyclotron resonance ("CRAFTI") technique are identified. In CRAFTI, ion collision cross-sections are obtained from the pressure-dependent ion linewidths in Fourier transform mass spectra. The effects of these corrections on the accuracy of the cross-sections obtained using the CRAFTI technique are evaluated experimentally using the 20 biogenic amino acids and several crown ether complexes with protonated alkyl monoamines. Good absolute agreement is obtained between the CRAFTI cross-sections and the corresponding cross-sections obtained using both static drift ion mobility spectrometry and computational simulations. These results indicate that the CRAFTI cross-sections obtained using the updated equation presented here are quantitatively descriptive of the size and shape of the gas-phase ions. Cross-sections that differ by less than 3% are measured for the isobaric isomers n-butylamine and tert-butylamine complexed with the crown ethers. This level of precision is similar to what has been achieved previously using traveling wave ion mobility devices. These results indicate that CRAFTI can be used to probe subtle structural differences between ions with approximately the same precision as that achieved in traveling wave ion mobility devices. Graphical Abstract ᅟ.
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Affiliation(s)
- Elaura Gustafson
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, 84602-5700, USA
| | - Daniel N Mortensen
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, 84602-5700, USA
| | - David V Dearden
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, 84602-5700, USA.
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26
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Mortensen DN, Williams ER. Microsecond and nanosecond polyproline II helix formation in aqueous nanodrops measured by mass spectrometry. Chem Commun (Camb) 2018; 52:12218-12221. [PMID: 27711437 DOI: 10.1039/c6cc06423j] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The 1.5 μs and <400 ns time constants for the formation of polyproline II helix structures in 21 and 16 residue peptides, respectively, are measured using rapid mixing from theta-glass emitters coupled with mass spectrometry. Results from these studies should serve as useful benchmarks for comparison with computational simulation results.
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Affiliation(s)
- Daniel N Mortensen
- 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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27
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Haler JRN, Kune C, Massonnet P, Comby-Zerbino C, Jordens J, Honing M, Mengerink Y, Far J, De Pauw E. Comprehensive Ion Mobility Calibration: Poly(ethylene oxide) Polymer Calibrants and General Strategies. Anal Chem 2017; 89:12076-12086. [DOI: 10.1021/acs.analchem.7b02564] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Jean R. N. Haler
- Mass
Spectrometry Laboratory, University of Liège, Quartier Agora, Allée du
Six Aout 11, B-4000 Liège, Belgium
| | - Christopher Kune
- Mass
Spectrometry Laboratory, University of Liège, Quartier Agora, Allée du
Six Aout 11, B-4000 Liège, Belgium
| | - Philippe Massonnet
- Mass
Spectrometry Laboratory, University of Liège, Quartier Agora, Allée du
Six Aout 11, B-4000 Liège, Belgium
| | - Clothilde Comby-Zerbino
- Institut
Lumière Matière, Université de Lyon, Université Lyon 1, CNRS, 69100 Villeurbanne, France
| | | | | | | | - Johann Far
- Mass
Spectrometry Laboratory, University of Liège, Quartier Agora, Allée du
Six Aout 11, B-4000 Liège, Belgium
| | - Edwin De Pauw
- Mass
Spectrometry Laboratory, University of Liège, Quartier Agora, Allée du
Six Aout 11, B-4000 Liège, Belgium
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28
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Duez Q, Chirot F, Liénard R, Josse T, Choi C, Coulembier O, Dugourd P, Cornil J, Gerbaux P, De Winter J. Polymers for Traveling Wave Ion Mobility Spectrometry Calibration. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:2483-2491. [PMID: 28762031 DOI: 10.1007/s13361-017-1762-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Revised: 06/30/2017] [Accepted: 07/09/2017] [Indexed: 06/07/2023]
Abstract
One of the main issues when using traveling wave ion mobility spectrometry (TWIMS) for the determination of collisional cross-section (CCS) concerns the need for a robust calibration procedure built from referent ions of known CCS. Here, we implement synthetic polymer ions as CCS calibrants in positive ion mode. Based on their intrinsic polydispersities, polymers offer in a single sample the opportunity to generate, upon electrospray ionization, numerous ions covering a broad mass range and a large CCS window for different charge states at a time. In addition, the key advantage of polymer ions as CCS calibrants lies in the robustness of their gas-phase structure with respect to the instrumental conditions, making them less prone to collisional-induced unfolding (CIU) than protein ions. In this paper, we present a CCS calibration procedure using sodium cationized polylactide and polyethylene glycol, PLA and PEG, as calibrants with reference CCS determined on a home-made drift tube. Our calibration procedure is further validated by testing the polymer calibration to determine CCS of numerous different ions for which CCS are reported in the literature. Graphical Abstract ᅟ.
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Affiliation(s)
- Quentin Duez
- Organic Synthesis and Mass Spectrometry Laboratory, Interdisciplinary Center for Mass Spectrometry (CISMa), University of Mons (UMons), Place du Parc, 23, Mons, 7000, Belgium
- Laboratory for Chemistry of Novel Materials, Center of Innovation and Research in Materials and Polymers (CIRMAP), University of Mons (UMons), Place du Parc, 23, Mons, 7000, Belgium
| | - Fabien Chirot
- Université Lyon, Université Claude Bernard Lyon 1, ENS de Lyon, CNRS, Institut des Sciences Analytiques, UMR 5280, 5 rue de la Doua, F-69100, Villeurbanne, France
| | - Romain Liénard
- Organic Synthesis and Mass Spectrometry Laboratory, Interdisciplinary Center for Mass Spectrometry (CISMa), University of Mons (UMons), Place du Parc, 23, Mons, 7000, Belgium
- Laboratory of Polymeric and Composite Materials, Center of Innovation and Research in Materials and Polymers (CIRMAP), University of Mons, UMons, 23 Place du Parc, 7000, Mons, Belgium
| | - Thomas Josse
- Organic Synthesis and Mass Spectrometry Laboratory, Interdisciplinary Center for Mass Spectrometry (CISMa), University of Mons (UMons), Place du Parc, 23, Mons, 7000, Belgium
- Laboratory of Polymeric and Composite Materials, Center of Innovation and Research in Materials and Polymers (CIRMAP), University of Mons, UMons, 23 Place du Parc, 7000, Mons, Belgium
| | - ChangMin Choi
- Université Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622, Lyon, France
| | - Olivier Coulembier
- Laboratory of Polymeric and Composite Materials, Center of Innovation and Research in Materials and Polymers (CIRMAP), University of Mons, UMons, 23 Place du Parc, 7000, Mons, Belgium
| | - Philippe Dugourd
- Université Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622, Lyon, France
| | - Jérôme Cornil
- Laboratory for Chemistry of Novel Materials, Center of Innovation and Research in Materials and Polymers (CIRMAP), University of Mons (UMons), Place du Parc, 23, Mons, 7000, Belgium
| | - Pascal Gerbaux
- Organic Synthesis and Mass Spectrometry Laboratory, Interdisciplinary Center for Mass Spectrometry (CISMa), University of Mons (UMons), Place du Parc, 23, Mons, 7000, Belgium
| | - Julien De Winter
- Organic Synthesis and Mass Spectrometry Laboratory, Interdisciplinary Center for Mass Spectrometry (CISMa), University of Mons (UMons), Place du Parc, 23, Mons, 7000, Belgium.
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29
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Mortensen DN, Susa AC, Williams ER. Collisional Cross-Sections with T-Wave Ion Mobility Spectrometry without Experimental Calibration. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:1282-1292. [PMID: 28432656 DOI: 10.1007/s13361-017-1669-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 03/21/2017] [Accepted: 03/27/2017] [Indexed: 06/07/2023]
Abstract
A method for relating traveling-wave ion mobility spectrometry (TWIMS) drift times with collisional cross-sections using computational simulations is presented. This method is developed using SIMION modeling of the TWIMS potential wave and equations that describe the velocity of ions in gases induced by electric fields. The accuracy of this method is assessed by comparing the collisional cross-sections of 70 different reference ions obtained using this method with those obtained from static drift tube ion mobility measurements. The cross-sections obtained here with low wave velocities are very similar to those obtained using static drift (average difference = 0.3%) for ions formed from both denaturing and buffered aqueous solutions. In contrast, the cross-sections obtained with high wave velocities are significantly greater, especially for ions formed from buffered aqueous solutions. These higher cross-sections at high wave velocities may result from high-order factors not accounted for in the model presented here or from the protein ions unfolding during TWIMS. Results from this study demonstrate that collisional cross-sections can be obtained from single TWIMS drift time measurements, but that low wave velocities and gentle instrument conditions should be used in order to minimize any uncertainties resulting from high-order effects not accounted for in the present model and from any protein unfolding that might occur. Thus, the method presented here eliminates the need to calibrate TWIMS drift times with collisional cross-sections measured using other ion mobility devices. Graphical Abstract ᅟ.
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Affiliation(s)
- Daniel N Mortensen
- Department of Chemistry, University of California, Berkeley, CA, 94720-1460, USA
| | - Anna C Susa
- Department of Chemistry, University of California, Berkeley, CA, 94720-1460, USA
| | - Evan R Williams
- Department of Chemistry, University of California, Berkeley, CA, 94720-1460, USA.
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30
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Clemmer DE, Russell DH, Williams ER. Characterizing the Conformationome: Toward a Structural Understanding of the Proteome. Acc Chem Res 2017; 50:556-560. [PMID: 28945417 DOI: 10.1021/acs.accounts.6b00548] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
While non-native protein conformations such as folding intermediates are rarely observed in solution such species are often stabilized as gaseous ions during electrospray ionization for mass spectrometry. This opens the possibility of large scale efforts to capture information about many non-native structures such as folding intermediates or malformed conformations having deleterious effects: studies of the conformationome.
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Affiliation(s)
- David E. Clemmer
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - David H. Russell
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Evan R. Williams
- Department of Chemistry, University of California, Berkeley 94720, United States
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31
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Abutokaikah MT, Guan S, Bythell BJ. Stereochemical Sequence Ion Selectivity: Proline versus Pipecolic-acid-containing Protonated Peptides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:182-189. [PMID: 27730525 DOI: 10.1007/s13361-016-1510-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 09/12/2016] [Accepted: 09/15/2016] [Indexed: 06/06/2023]
Abstract
Substitution of proline by pipecolic acid, the six-membered ring congener of proline, results in vastly different tandem mass spectra. The well-known proline effect is eliminated and amide bond cleavage C-terminal to pipecolic acid dominates instead. Why do these two ostensibly similar residues produce dramatically differing spectra? Recent evidence indicates that the proton affinities of these residues are similar, so are unlikely to explain the result [Raulfs et al., J. Am. Soc. Mass Spectrom. 25, 1705-1715 (2014)]. An additional hypothesis based on increased flexibility was also advocated. Here, we provide a computational investigation of the "pipecolic acid effect," to test this and other hypotheses to determine if theory can shed additional light on this fascinating result. Our calculations provide evidence for both the increased flexibility of pipecolic-acid-containing peptides, and structural changes in the transition structures necessary to produce the sequence ions. The most striking computational finding is inversion of the stereochemistry of the transition structures leading to "proline effect"-type amide bond fragmentation between the proline/pipecolic acid-congeners: R (proline) to S (pipecolic acid). Additionally, our calculations predict substantial stabilization of the amide bond cleavage barriers for the pipecolic acid congeners by reduction in deleterious steric interactions and provide evidence for the importance of experimental energy regime in rationalizing the spectra. Graphical Abstract ᅟ.
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Affiliation(s)
- Maha T Abutokaikah
- Department of Chemistry and Biochemistry, University of Missouri, St. Louis, MO, 63121, USA
| | - Shanshan Guan
- Department of Chemistry and Biochemistry, University of Missouri, St. Louis, MO, 63121, USA
| | - Benjamin J Bythell
- Department of Chemistry and Biochemistry, University of Missouri, St. Louis, MO, 63121, USA.
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32
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Creese AJ, Cooper HJ. Separation of cis and trans Isomers of Polyproline by FAIMS Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:2071-2074. [PMID: 27704474 PMCID: PMC5088216 DOI: 10.1007/s13361-016-1482-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 07/12/2016] [Accepted: 08/12/2016] [Indexed: 06/06/2023]
Abstract
High field asymmetric waveform ion mobility spectrometry (FAIMS) is well-established as a tool for separating peptide isomers (sequence inversions and post-translationally modified localization variants). Here, we demonstrate the FAIMS is able to differentiate cis and trans isomers of polyproline. Polyproline assumes an all-cis conformation-the PPI helix-in 1-propanol, and an all-trans conformation-the PPII helix-in aqueous solutions. Differentiation of these conformers may be achieved both through use of a cylindrical FAIMS device and a miniaturized ultrahigh field planar FAIMS device. Graphical Abstract ᅟ.
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Affiliation(s)
- Andrew J Creese
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Helen J Cooper
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
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33
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El-Baba TJ, Kim D, Rogers DB, Khan FA, Hales DA, Russell DH, Clemmer DE. Long-Lived Intermediates in a Cooperative Two-State Folding Transition. J Phys Chem B 2016; 120:12040-12046. [PMID: 27933943 DOI: 10.1021/acs.jpcb.6b08932] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Biomolecular folding often occurs through a cooperative two-state reactant ↔ product transition; the term cooperative does not convey that intermediate structures are nonexistent but rather that these states are not observable by existing experimental techniques. Because of this, few intermediates have been studied and characterized. Recently, ion mobility spectrometry (IMS) measurements revealed that the oligomer polyproline-13 (Pro13, which in propanol (PrOH) favors the right-handed helical PPI structure having adjacent pyrrolidine rings in a cis configuration) folds through six sequential long-lived intermediates as it converts to the all-trans-configured PPII structure that is favored in aqueous solutions. Here, we examine the PPIPrOH → PPIIaq folding transition for a HisPro13 sequence, i.e., Pro13 having a single histidine residue added to the N-terminus. Remarkably, the IMS measurements show that, upon addition of histidine, all of the IMS peaks associated with intermediate structures disappear. Instead, HisPro13 folds via a cooperative two-state transition, delayed by a significant induction period. The induction period is temperature dependent-shifting the transition to longer times at lower temperatures. Equilibrium studies show that the HisPro13 PPIPrOH → PPIIaq transition is endothermic but favored entropically. From these clues, we propose a sequential folding mechanism and develop a model that suggests that ∼13-17 long-lived intermediates are likely responsible for the induction period. In this model, intermediates are separated by average individual activation barriers of ∼90 kJ·mol-1, and are entropically favorable.
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Affiliation(s)
- Tarick J El-Baba
- Department of Chemistry, Indiana University , 800 Kirkwood Avenue, Bloomington, Indiana 47401, United States
| | - Doyong Kim
- Department of Chemistry, Texas A&M University , College Station, Texas 77843, United States
| | - Dylan B Rogers
- Department of Chemistry, Hendrix College , Conway, Arkansas 72032, United States
| | - Faizan A Khan
- Department of Chemistry, Hendrix College , Conway, Arkansas 72032, United States
| | - David A Hales
- Department of Chemistry, Hendrix College , Conway, Arkansas 72032, United States
| | - David H Russell
- Department of Chemistry, Texas A&M University , College Station, Texas 77843, United States
| | - David E Clemmer
- Department of Chemistry, Indiana University , 800 Kirkwood Avenue, Bloomington, Indiana 47401, United States
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34
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Garabedian A, Butcher D, Lippens JL, Miksovska J, Chapagain PP, Fabris D, Ridgeway ME, Park MA, Fernandez-Lima F. Structures of the kinetically trapped i-motif DNA intermediates. Phys Chem Chem Phys 2016; 18:26691-26702. [PMID: 27711445 PMCID: PMC5652045 DOI: 10.1039/c6cp04418b] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
In the present work, the conformational dynamics and folding pathways of i-motif DNA were studied in solution and in the gas-phase as a function of the solution pH conditions using circular dichroism (CD), photoacoustic calorimetry analysis (PAC), trapped ion mobility spectrometry-mass spectrometry (TIMS-MS), and molecular dynamics (MD). Solution studies showed at thermodynamic equilibrium the existence of a two-state folding mechanism, whereas during the pH = 7.0 → 4.5 transition a fast and slow phase (ΔHfast + ΔHslow = 43 ± 7 kcal mol-1) with a volume change associated with the formation of hemiprotonated cytosine base pairs and concomitant collapse of the i-motif oligonucleotide into a compact conformation were observed. TIMS-MS experiments showed that gas-phase, kinetically trapped i-motif DNA intermediates produced by nanoESI are preserved, with relative abundances depending on the solution pH conditions. In particular, a folded i-motif DNA structure was observed in nanoESI-TIMS-MS for low charge states in both positive and negative ion mode (e.g., z = ±3 to ±5) at low pH conditions. As solution pH increases, the cytosine neutralization leads to the loss of cytosine-cytosine+ (C·CH+) base pairing in the CCC strands and in those conditions we observe partially unfolded i-motif DNA conformations in nanoESI-TIMS-MS for higher charge states (e.g., z = -6 to -9). Collisional induced activation prior to TIMS-MS showed the existence of multiple local free energy minima, associated with the i-motif DNA unfolding at z = -6 charge state. For the first time, candidate gas-phase structures are proposed based on mobility measurements of the i-motif DNA unfolding pathway. Moreover, the inspection of partially unfolded i-motif DNA structures (z = -7 and z = -8 charge states) showed that the presence of inner cations may or may not induce conformational changes in the gas-phase. For example, incorporation of ammonium adducts does not lead to major conformational changes while sodium adducts may lead to the formation of sodium mediated bonds between two negatively charged sides inducing the stabilization towards more compact structures in new local, free energy minima in the gas-phase.
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Affiliation(s)
- Alyssa Garabedian
- Department of Chemistry and Biochemistry, Florida International University, Miami, USA.
| | - David Butcher
- Department of Chemistry and Biochemistry, Florida International University, Miami, USA.
| | | | - Jaroslava Miksovska
- Department of Chemistry and Biochemistry, Florida International University, Miami, USA. and Biomolecular Science Institute, Florida International University, Miami, USA
| | - Prem P Chapagain
- Biomolecular Science Institute, Florida International University, Miami, USA and Department of Physics, Florida International University, Miami, USA
| | | | | | - Melvin A Park
- Bruker Daltonics Inc., Billerica, Massachusetts, USA
| | - Francisco Fernandez-Lima
- Department of Chemistry and Biochemistry, Florida International University, Miami, USA. and Biomolecular Science Institute, Florida International University, Miami, USA
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35
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Benigni P, Marin R, Molano-Arevalo JC, Garabedian A, Wolff JJ, Ridgeway ME, Park MA, Fernandez-Lima F. Towards the Analysis of High Molecular Weight Proteins and Protein complexes using TIMS-MS. INTERNATIONAL JOURNAL FOR ION MOBILITY SPECTROMETRY : OFFICIAL PUBLICATION OF THE INTERNATIONAL SOCIETY FOR ION MOBILITY SPECTROMETRY 2016; 19:95-104. [PMID: 27818614 PMCID: PMC5091298 DOI: 10.1007/s12127-016-0201-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 05/26/2016] [Accepted: 05/29/2016] [Indexed: 01/02/2023]
Abstract
In the present work, we demonstrate the potential and versatility of TIMS for the analysis of proteins, DNA-protein complexes and protein-protein complexes in their native and denatured states. In addition, we show that accurate CCS measurement are possible and in good agreement with previously reported CCS values using other IMS analyzers (<5% difference). The main challenges for the analysis of high mass proteins and protein complexes in the mobility and m/z domain are described. That is, the analysis of high molecular weight systems in their native state may require the use of higher electric fields or a compromise in the TIMS mobility resolution by reducing the bath gas velocity in order to effectively trap at lower electric fields. This is the first report of CCS measurements of high molecular weight biomolecules and biomolecular complexes (~ 150 kDa) using TIMS-MS.
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Affiliation(s)
- Paolo Benigni
- Department of Chemistry & Biochemistry, Florida International University, Miami, FL 33199, USA
| | - Rebecca Marin
- Department of Chemistry & Biochemistry, Florida International University, Miami, FL 33199, USA
| | | | - Alyssa Garabedian
- Department of Chemistry & Biochemistry, Florida International University, Miami, FL 33199, USA
| | | | | | - Melvin A. Park
- Bruker Daltonics, Inc., Billerica, Massachusetts 01821, USA
| | - Francisco Fernandez-Lima
- Department of Chemistry & Biochemistry, Florida International University, Miami, FL 33199, USA
- Biomolecular Science Institute, Florida International University, Miami, FL 33199, USA
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36
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Lietz CB, Chen Z, Yun Son C, Pang X, Cui Q, Li L. Multiple gas-phase conformations of proline-containing peptides: is it always cis/trans isomerization? Analyst 2016; 141:4863-9. [PMID: 27434776 PMCID: PMC4972606 DOI: 10.1039/c5an00835b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Ion mobility-mass spectrometry (IM-MS) is often employed to look at the secondary, tertiary, and quaternary structures of naked peptides and proteins in the gas-phase. Recently, it has offered a unique glimpse into proline-containing peptides and their cis/trans Xxx-Pro isomers. An experimental "signature" has been identified wherein a proline-containing peptide has its Pro residues substituted with another amino acid and the presence or absence of conformations in the IM-MS spectra is observed. Despite the high probability that one could attribute these conformations to cis/trans isomers, it is also possible that cis/trans isomers are not the cause of the additional conformations in proline-containing peptides. However, the experimental evidence of such a system has not been demonstrated or reported. Herein, we present the IM-MS analysis of Neuropeptide Y's wild-type (WT) signal sequence and Leu7Pro (L7P) mutant. Although comparison of arrival times and collision cross-sections of [M + 4H](4+) ions yields the cis/trans "signature", molecular dynamics indicates that a cis-Pro7 is not very stable and that trans-Pro7 conformations of the same cross-section arise with equal frequency. We believe that this work further underscores the importance of theoretical calculations in IM-MS structural assignments.
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Affiliation(s)
- Christopher B Lietz
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA.
| | - Zhengwei Chen
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA.
| | - Chang Yun Son
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA.
| | - Xueqin Pang
- School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53705, USA
| | - Qiang Cui
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA.
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA. and School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53705, USA
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37
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Beveridge R, Migas LG, Payne KAP, Scrutton NS, Leys D, Barran PE. Mass spectrometry locates local and allosteric conformational changes that occur on cofactor binding. Nat Commun 2016; 7:12163. [PMID: 27418477 PMCID: PMC4947166 DOI: 10.1038/ncomms12163] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 06/08/2016] [Indexed: 11/09/2022] Open
Abstract
Fdc1 is a decarboxylase enzyme that requires the novel prenylated FMN cofactor for activity. Here, we use it as an exemplar system to show how native top-down and bottom-up mass spectrometry can measure the structural effect of cofactor binding by a protein. For Fdc1(Ubix), the cofactor confers structural stability to the enzyme. IM-MS shows the holo protein to exist in four closely related conformational families, the populations of which differ in the apo form; the two smaller families are more populated in the presence of the cofactor and depopulated in its absence. These findings, supported by MD simulations, indicate a more open structure for the apo form. HDX-MS reveals that while the dominant structural changes occur proximal to the cofactor-binding site, rearrangements on cofactor binding are evident throughout the protein, predominantly attributable to allosteric conformational tightening, consistent with IM-MS data.
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Affiliation(s)
- Rebecca Beveridge
- Michael Barber Centre for Collaborative Mass Spectrometry, School of Chemistry, Centre for Synthetic Biology of Fine and Speciality Chemicals, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
| | - Lukasz G Migas
- Michael Barber Centre for Collaborative Mass Spectrometry, School of Chemistry, Centre for Synthetic Biology of Fine and Speciality Chemicals, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
| | - Karl A P Payne
- Michael Barber Centre for Collaborative Mass Spectrometry, School of Chemistry, Centre for Synthetic Biology of Fine and Speciality Chemicals, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
| | - Nigel S Scrutton
- Michael Barber Centre for Collaborative Mass Spectrometry, School of Chemistry, Centre for Synthetic Biology of Fine and Speciality Chemicals, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
| | - David Leys
- Michael Barber Centre for Collaborative Mass Spectrometry, School of Chemistry, Centre for Synthetic Biology of Fine and Speciality Chemicals, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
| | - Perdita E Barran
- Michael Barber Centre for Collaborative Mass Spectrometry, School of Chemistry, Centre for Synthetic Biology of Fine and Speciality Chemicals, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
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Benigni P, Fernandez-Lima F. Oversampling Selective Accumulation Trapped Ion Mobility Spectrometry Coupled to FT-ICR MS: Fundamentals and Applications. Anal Chem 2016; 88:7404-12. [DOI: 10.1021/acs.analchem.6b01946] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Paolo Benigni
- Department of Chemistry and Biochemistry and ‡Biomolecular Sciences
Institute, Florida International University, Miami, Florida 33199, United States
| | - Francisco Fernandez-Lima
- Department of Chemistry and Biochemistry and ‡Biomolecular Sciences
Institute, Florida International University, Miami, Florida 33199, United States
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Shi L, Holliday AE, Bohrer BC, Kim D, Servage KA, Russell DH, Clemmer DE. "Wet" Versus "Dry" Folding of Polyproline. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:1037-47. [PMID: 27059978 PMCID: PMC5152579 DOI: 10.1007/s13361-016-1372-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 02/20/2016] [Accepted: 02/22/2016] [Indexed: 05/06/2023]
Abstract
When the all-cis polyproline-I helix (PPI, favored in 1-propanol) of polyproline-13 is introduced into water, it folds into the all-trans polyproline-II (PPII) helix through at least six intermediates [Shi, L., Holliday, A.E., Shi, H., Zhu, F., Ewing, M.A., Russell, D.H., Clemmer, D.E.: Characterizing intermediates along the transition from PPI to PPII using ion mobility-mass spectrometry. J. Am. Chem. Soc. 136, 12702-12711 (2014)]. Here, we show that the solvent-free intermediates refold into the all-cis PPI helix with high (>90%) efficiency. Moreover, in the absence of solvent, each intermediate appears to utilize the same small set of pathways observed for the solution-phase PPII → PPI transition upon immersion of PPIIaq in 1-propanol. That folding in solution (under conditions where water is displaced by propanol) and folding in vacuo (where energy required for folding is provided by collisional activation) occur along the same pathway is remarkable. Implicit in this statement is that 1-propanol mimics a "dry" environment, similar to the gas phase. We note that intermediates with structures that are similar to PPIIaq can form PPII under the most gentle activation conditions-indicating that some transitions observed in water (i.e., "wet" folding, are accessible (albeit inefficient) in vacuo. Lastly, these "dry" folding experiments show that PPI (all cis) is favored under "dry" conditions, which underscores the role of water as the major factor promoting preference for trans proline. Graphical Abstract ᅟ.
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Affiliation(s)
- Liuqing Shi
- Department of Chemistry, Indiana University, Bloomington, IN, 47405, USA
| | - Alison E Holliday
- Department of Chemistry, Moravian College, Bethlehem, PA, 18018, USA
| | - Brian C Bohrer
- Department of Chemistry, University of Southern Indiana, Evansville, IN, 47712, USA
| | - Doyong Kim
- Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - Kelly A Servage
- Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - David H Russell
- Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA.
| | - David E Clemmer
- Department of Chemistry, Indiana University, Bloomington, IN, 47405, USA.
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