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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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2
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Esser TK, Böhning J, Önür A, Chinthapalli DK, Eriksson L, Grabarics M, Fremdling P, Konijnenberg A, Makarov A, Botman A, Peter C, Benesch JLP, Robinson CV, Gault J, Baker L, Bharat TAM, Rauschenbach S. Cryo-EM of soft-landed β-galactosidase: Gas-phase and native structures are remarkably similar. SCIENCE ADVANCES 2024; 10:eadl4628. [PMID: 38354247 PMCID: PMC10866560 DOI: 10.1126/sciadv.adl4628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 01/11/2024] [Indexed: 02/16/2024]
Abstract
Native mass spectrometry (MS) has become widely accepted in structural biology, providing information on stoichiometry, interactions, homogeneity, and shape of protein complexes. Yet, the fundamental assumption that proteins inside the mass spectrometer retain a structure faithful to native proteins in solution remains a matter of intense debate. Here, we reveal the gas-phase structure of β-galactosidase using single-particle cryo-electron microscopy (cryo-EM) down to 2.6-Å resolution, enabled by soft landing of mass-selected protein complexes onto cold transmission electron microscopy (TEM) grids followed by in situ ice coating. We find that large parts of the secondary and tertiary structure are retained from the solution. Dehydration-driven subunit reorientation leads to consistent compaction in the gas phase. By providing a direct link between high-resolution imaging and the capability to handle and select protein complexes that behave problematically in conventional sample preparation, the approach has the potential to expand the scope of both native mass spectrometry and cryo-EM.
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Affiliation(s)
- Tim K. Esser
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
- Kavli Institute for NanoScience Discovery, Dorothy Crowfoot Hodgkin Building, Oxford OX1 3QU, UK
- Thermo Fisher Scientific, 1 Boundary Park, Hemel Hempstead, Hertfordshire HP2 7GE, UK
| | - Jan Böhning
- Structural Studies Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Alpcan Önür
- Department of Chemistry, University of Konstanz, Konstanz 78457, Germany
| | - Dinesh K. Chinthapalli
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
- Kavli Institute for NanoScience Discovery, Dorothy Crowfoot Hodgkin Building, Oxford OX1 3QU, UK
| | - Lukas Eriksson
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
- Kavli Institute for NanoScience Discovery, Dorothy Crowfoot Hodgkin Building, Oxford OX1 3QU, UK
| | - Marko Grabarics
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
- Kavli Institute for NanoScience Discovery, Dorothy Crowfoot Hodgkin Building, Oxford OX1 3QU, UK
| | - Paul Fremdling
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | | | - Alexander Makarov
- Thermo Fisher Scientific, Bremen 28199, Germany
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands
| | - Aurelien Botman
- Thermo Fisher Scientific, 5350 NE Dawson Creek Drive, Hillsboro, OR 97124, USA
| | - Christine Peter
- Department of Chemistry, University of Konstanz, Konstanz 78457, Germany
| | - Justin L. P. Benesch
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
- Kavli Institute for NanoScience Discovery, Dorothy Crowfoot Hodgkin Building, Oxford OX1 3QU, UK
| | - Carol V. Robinson
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
- Kavli Institute for NanoScience Discovery, Dorothy Crowfoot Hodgkin Building, Oxford OX1 3QU, UK
| | - Joseph Gault
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Lindsay Baker
- Kavli Institute for NanoScience Discovery, Dorothy Crowfoot Hodgkin Building, Oxford OX1 3QU, UK
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Tanmay A. M. Bharat
- Structural Studies Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Stephan Rauschenbach
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
- Kavli Institute for NanoScience Discovery, Dorothy Crowfoot Hodgkin Building, Oxford OX1 3QU, UK
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3
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Strauß M, Shayeghi A, Mauser MF, Geyer P, Kostersitz T, Salapa J, Dobrovolskiy O, Daly S, Commandeur J, Hua Y, Köhler V, Mayor M, Benserhir J, Bruschini C, Charbon E, Castaneda M, Gevers M, Gourgues R, Kalhor N, Fognini A, Arndt M. Highly sensitive single-molecule detection of macromolecule ion beams. SCIENCE ADVANCES 2023; 9:eadj2801. [PMID: 38039360 PMCID: PMC10691769 DOI: 10.1126/sciadv.adj2801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 11/02/2023] [Indexed: 12/03/2023]
Abstract
The analysis of proteins in the gas phase benefits from detectors that exhibit high efficiency and precise spatial resolution. Although modern secondary electron multipliers already address numerous analytical requirements, additional methods are desired for macromolecules at energies lower than currently used in post-acceleration detection. Previous studies have proven the sensitivity of superconducting detectors to high-energy particles in time-of-flight mass spectrometry. Here, we demonstrate that superconducting nanowire detectors are exceptionally well suited for quadrupole mass spectrometry and exhibit an outstanding quantum yield at low-impact energies. At energies as low as 100 eV, the sensitivity of these detectors surpasses conventional ion detectors by three orders of magnitude, and they offer the possibility to discriminate molecules by their impact energy and charge. We demonstrate three developments with these compact and sensitive devices, the recording of 2D ion beam profiles, photochemistry experiments in the gas phase, and advanced cryogenic electronics to pave the way toward highly integrated detectors.
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Affiliation(s)
- Marcel Strauß
- Faculty of Physics and Vienna Doctoral School of Physics (VDSP) and Vienna Center for Quantum Science and Technology (VCQ), University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria
| | - Armin Shayeghi
- Faculty of Physics and Vienna Doctoral School of Physics (VDSP) and Vienna Center for Quantum Science and Technology (VCQ), University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria
- Institute for Quantum Optics and Quantum Information (IQOQI) Vienna, Austrian Academy of Sciences, Boltzmanngasse 3, A-1090 Vienna, Austria
| | - Martin F. X. Mauser
- Faculty of Physics and Vienna Doctoral School of Physics (VDSP) and Vienna Center for Quantum Science and Technology (VCQ), University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria
| | - Philipp Geyer
- Faculty of Physics and Vienna Doctoral School of Physics (VDSP) and Vienna Center for Quantum Science and Technology (VCQ), University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria
| | - Tim Kostersitz
- Faculty of Physics and Vienna Doctoral School of Physics (VDSP) and Vienna Center for Quantum Science and Technology (VCQ), University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria
| | - Julia Salapa
- Faculty of Physics and Vienna Doctoral School of Physics (VDSP) and Vienna Center for Quantum Science and Technology (VCQ), University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria
| | - Oleksandr Dobrovolskiy
- Faculty of Physics and Vienna Doctoral School of Physics (VDSP) and Vienna Center for Quantum Science and Technology (VCQ), University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria
| | - Steven Daly
- MSVision, Televisieweg 40, 1322 AM Almere, The Netherlands
| | - Jan Commandeur
- MSVision, Televisieweg 40, 1322 AM Almere, The Netherlands
| | - Yong Hua
- Department of Chemistry, University of Basel, St. Johannsring 19, CH-4056 Basel, Switzerland
| | - Valentin Köhler
- Department of Chemistry, University of Basel, St. Johannsring 19, CH-4056 Basel, Switzerland
| | - Marcel Mayor
- Department of Chemistry, University of Basel, St. Johannsring 19, CH-4056 Basel, Switzerland
| | - Jad Benserhir
- Advanced Quantum Architecture Laboratory, EPFL, Rue de la Maladière 71b, CH-2002 Neuchâtel, Switzerland
| | - Claudio Bruschini
- Advanced Quantum Architecture Laboratory, EPFL, Rue de la Maladière 71b, CH-2002 Neuchâtel, Switzerland
| | - Edoardo Charbon
- Advanced Quantum Architecture Laboratory, EPFL, Rue de la Maladière 71b, CH-2002 Neuchâtel, Switzerland
| | - Mario Castaneda
- Single Quantum, Rotterdamseweg 394, 2629 HH, Delft, The Netherlands
| | - Monique Gevers
- Single Quantum, Rotterdamseweg 394, 2629 HH, Delft, The Netherlands
| | - Ronan Gourgues
- Single Quantum, Rotterdamseweg 394, 2629 HH, Delft, The Netherlands
| | - Nima Kalhor
- Single Quantum, Rotterdamseweg 394, 2629 HH, Delft, The Netherlands
| | - Andreas Fognini
- Single Quantum, Rotterdamseweg 394, 2629 HH, Delft, The Netherlands
| | - Markus Arndt
- Faculty of Physics and Vienna Doctoral School of Physics (VDSP) and Vienna Center for Quantum Science and Technology (VCQ), University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria
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4
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Hua Y, Strauss M, Fisher S, Mauser MFX, Manchet P, Smacchia M, Geyer P, Shayeghi A, Pfeffer M, Eggenweiler TH, Daly S, Commandeur J, Mayor M, Arndt M, Šolomek T, Köhler V. Giving the Green Light to Photochemical Uncaging of Large Biomolecules in High Vacuum. JACS AU 2023; 3:2790-2799. [PMID: 37885583 PMCID: PMC10598566 DOI: 10.1021/jacsau.3c00351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 10/02/2023] [Accepted: 10/02/2023] [Indexed: 10/28/2023]
Abstract
The isolation of biomolecules in a high vacuum enables experiments on fragile species in the absence of a perturbing environment. Since many molecular properties are influenced by local electric fields, here we seek to gain control over the number of charges on a biopolymer by photochemical uncaging. We present the design, modeling, and synthesis of photoactive molecular tags, their labeling to peptides and proteins as well as their photochemical validation in solution and in the gas phase. The tailored tags can be selectively cleaved off at a well-defined time and without the need for any external charge-transferring agents. The energy of a single or two green photons can already trigger the process, and it is soft enough to ensure the integrity of the released biomolecular cargo. We exploit differences in the cleavage pathways in solution and in vacuum and observe a surprising robustness in upscaling the approach from a model system to genuine proteins. The interaction wavelength of 532 nm is compatible with various biomolecular entities, such as oligonucleotides or oligosaccharides.
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Affiliation(s)
- Yong Hua
- Department
of Chemistry, University of Basel, St. Johannsring 19, CH-4056 Basel, Switzerland
| | - Marcel Strauss
- Vienna
Faculty of Physics, University of Vienna,
VDSP & VCQ, Boltzmanngasse 5, A-1090 Vienna, Austria
| | - Sergey Fisher
- Van’t
Hoff Institute for Molecular Sciences (HIMS), University of Amsterdam, PO Box 94157, 1090 GD Amsterdam, The Netherlands
| | - Martin F. X. Mauser
- Vienna
Faculty of Physics, University of Vienna,
VDSP & VCQ, Boltzmanngasse 5, A-1090 Vienna, Austria
| | - Pierre Manchet
- Vienna
Faculty of Physics, University of Vienna,
VDSP & VCQ, Boltzmanngasse 5, A-1090 Vienna, Austria
| | - Martina Smacchia
- Vienna
Faculty of Physics, University of Vienna,
VDSP & VCQ, Boltzmanngasse 5, A-1090 Vienna, Austria
| | - Philipp Geyer
- Vienna
Faculty of Physics, University of Vienna,
VDSP & VCQ, Boltzmanngasse 5, A-1090 Vienna, Austria
| | - Armin Shayeghi
- Vienna
Faculty of Physics, University of Vienna,
VDSP & VCQ, Boltzmanngasse 5, A-1090 Vienna, Austria
| | - Michael Pfeffer
- Department
of Chemistry, University of Basel, St. Johannsring 19, CH-4056 Basel, Switzerland
| | - Tim Henri Eggenweiler
- Department
of Chemistry, University of Basel, St. Johannsring 19, CH-4056 Basel, Switzerland
| | - Steven Daly
- MS
Vision, Televisieweg
40, 1322 AM Almere, The Netherlands
| | - Jan Commandeur
- MS
Vision, Televisieweg
40, 1322 AM Almere, The Netherlands
| | - Marcel Mayor
- Department
of Chemistry, University of Basel, St. Johannsring 19, CH-4056 Basel, Switzerland
- Institute
for Nanotechnology (INT), Karlsruhe Institute
of Technology (KIT), P.O. Box 3640, DE-76021 Karlsruhe Eggenstein-Leopoldshafen, Germany
- Lehn Institute
of Functional Materials, School of Chemistry, Sun Yat-Sen University, Guangzhou 510274, P. R. China
| | - Markus Arndt
- Vienna
Faculty of Physics, University of Vienna,
VDSP & VCQ, Boltzmanngasse 5, A-1090 Vienna, Austria
| | - Tomáš Šolomek
- Van’t
Hoff Institute for Molecular Sciences (HIMS), University of Amsterdam, PO Box 94157, 1090 GD Amsterdam, The Netherlands
| | - Valentin Köhler
- Department
of Chemistry, University of Basel, St. Johannsring 19, CH-4056 Basel, Switzerland
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5
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Moore CC, Staroverov VN, Konermann L. Using Density Functional Theory for Testing the Robustness of Mobile-Proton Molecular Dynamics Simulations on Electrosprayed Ions: Structural Implications for Gaseous Proteins. J Phys Chem B 2023; 127:4061-4071. [PMID: 37116098 DOI: 10.1021/acs.jpcb.3c01581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Abstract
Current experiments only provide low-resolution information on gaseous protein ions generated by electrospray ionization (ESI). Molecular dynamics (MD) simulations can yield complementary insights. Unfortunately, conventional MD does not capture the mobile nature of protons in gaseous proteins. Mobile-proton MD (MPMD) overcomes this limitation. Earlier MPMD data at 300 K indicated that protein ions generated by "native" ESI retain solution-like structures with a hydrophobic core and zwitterionic exterior [Bakhtiari, M.; Konermann, L. J. Phys. Chem. B 2019, 123, 1784-1796]. MPMD redistributes protons using electrostatic and proton affinity calculations. The robustness of this approach has never been scrutinized. Here, we close this gap by benchmarking MPMD against density functional theory (DFT) at the B3LYP/6-31G* level, which is well suited for predicting proton affinities. The computational cost of DFT necessitated the use of small peptides. The MPMD energetic ranking of proton configurations was found to be consistent with DFT single-point energies, implying that MPMD can reliably identify favorable protonation sites. Peptide MPMD runs converged to DFT-optimized structures only when applying 300-500 K temperature cycling, which was necessary to prevent trapping in local minima. Temperature cycling MPMD was then applied to gaseous protein ions. Native ubiquitin converted to slightly expanded structures with a zwitterionic core and a nonpolar exterior. Our data suggest that such inside-out protein structures are intrinsically preferred in the gas phase, and that they form in ESI experiments after moderate collisional excitation. This is in contrast to native ESI (with minimal collisional excitation, simulated by MPMD at 300 K), where kinetic trapping promotes the survival of solution-like structures. In summary, this work validates the MPMD approach for simulations on gaseous peptides and proteins.
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Affiliation(s)
- Conrad C Moore
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Viktor N Staroverov
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
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6
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Christofi E, Barran P. Ion Mobility Mass Spectrometry (IM-MS) for Structural Biology: Insights Gained by Measuring Mass, Charge, and Collision Cross Section. Chem Rev 2023; 123:2902-2949. [PMID: 36827511 PMCID: PMC10037255 DOI: 10.1021/acs.chemrev.2c00600] [Citation(s) in RCA: 43] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Indexed: 02/26/2023]
Abstract
The investigation of macromolecular biomolecules with ion mobility mass spectrometry (IM-MS) techniques has provided substantial insights into the field of structural biology over the past two decades. An IM-MS workflow applied to a given target analyte provides mass, charge, and conformation, and all three of these can be used to discern structural information. While mass and charge are determined in mass spectrometry (MS), it is the addition of ion mobility that enables the separation of isomeric and isobaric ions and the direct elucidation of conformation, which has reaped huge benefits for structural biology. In this review, where we focus on the analysis of proteins and their complexes, we outline the typical features of an IM-MS experiment from the preparation of samples, the creation of ions, and their separation in different mobility and mass spectrometers. We describe the interpretation of ion mobility data in terms of protein conformation and how the data can be compared with data from other sources with the use of computational tools. The benefit of coupling mobility analysis to activation via collisions with gas or surfaces or photons photoactivation is detailed with reference to recent examples. And finally, we focus on insights afforded by IM-MS experiments when applied to the study of conformationally dynamic and intrinsically disordered proteins.
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Affiliation(s)
- Emilia Christofi
- Michael Barber Centre for Collaborative
Mass Spectrometry, Manchester Institute of Biotechnology, University of Manchester, Princess Street, Manchester M1 7DN, United Kingdom
| | - Perdita Barran
- Michael Barber Centre for Collaborative
Mass Spectrometry, Manchester Institute of Biotechnology, University of Manchester, Princess Street, Manchester M1 7DN, United Kingdom
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7
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Ashworth EK, Langeland J, Stockett MH, Lindkvist TT, Kjær C, Bull JN, Nielsen SB. Cryogenic Fluorescence Spectroscopy of Ionic Fluorones in Gaseous and Condensed Phases: New Light on Their Intrinsic Photophysics. J Phys Chem A 2022; 126:9553-9563. [PMID: 36529970 DOI: 10.1021/acs.jpca.2c07231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Fluorescence spectroscopy of gas-phase ions generated through electrospray ionization is an emerging technique able to probe intrinsic molecular photophysics directly without perturbations from solvent interactions. While there is ample scope for the ongoing development of gas-phase fluorescence techniques, the recent expansion into low-temperature operating conditions accesses a wealth of data on intrinsic fluorophore photophysics, offering enhanced spectral resolution compared with room-temperature measurements, without matrix effects hindering the excited-state dynamics. This perspective reviews current progress on understanding the photophysics of anionic fluorone dyes, which exhibit an unusually large Stokes shift in the gas phase, and discusses how comparison of gas- and condensed-phase fluorescence spectra can fingerprint structural dynamics. The capacity for temperature-dependent measurements of both fluorescence emission and excitation spectra helps establish the foundation for the use of fluorone dyes as fluorescent tags in macromolecular structure determination. We suggest ideas for technique development.
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Affiliation(s)
- Eleanor K Ashworth
- School of Chemistry, University of East Anglia, NorwichNR4 7TJ, United Kingdom
| | - Jeppe Langeland
- Department of Physics and Astronomy, Aarhus University, Aarhus8000, Denmark
| | - Mark H Stockett
- Department of Physics, Stockholm University, SE-10691Stockholm, Sweden
| | | | - Christina Kjær
- Department of Physics and Astronomy, Aarhus University, Aarhus8000, Denmark
| | - James N Bull
- School of Chemistry, University of East Anglia, NorwichNR4 7TJ, United Kingdom
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8
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Ujma J, Jhingree J, Norgate E, Upton R, Wang X, Benoit F, Bellina B, Barran P. Protein Unfolding in Freeze Frames: Intermediate States are Revealed by Variable-Temperature Ion Mobility-Mass Spectrometry. Anal Chem 2022; 94:12248-12255. [PMID: 36001095 PMCID: PMC9453741 DOI: 10.1021/acs.analchem.2c03066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The gas phase is an idealized laboratory for the study of protein structure, from which it is possible to examine stable and transient forms of mass-selected ions in the absence of bulk solvent. With ion mobility-mass spectrometry (IM-MS) apparatus built to operate at both cryogenic and elevated temperatures, we have examined conformational transitions that occur to the monomeric proteins: ubiquitin, lysozyme, and α-synuclein as a function of temperature and in source activation. We rationalize the experimental observations with a temperature-dependent framework model and comparison to known conformers. Data from ubiquitin show unfolding transitions that proceed through diverse and highly elongated intermediate states, which converge to more compact structures. These findings contrast with data obtained from lysozyme─a protein where (un)-folding plasticity is restricted by four disulfide linkages, although this is alleviated in its reduced form. For structured proteins, collision activation of the protein ions in-source enables subsequent "freezing" or thermal annealing of unfolding intermediates, whereas disordered proteins restructure substantially at 250 K even without activation, indicating that cold denaturation can occur without solvent. These data are presented in the context of a toy model framework that describes the relative occupancy of the available conformational space.
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Affiliation(s)
- Jakub Ujma
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Jacquelyn Jhingree
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Emma Norgate
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Rosie Upton
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Xudong Wang
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Florian Benoit
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Bruno Bellina
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Perdita Barran
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
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9
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Bian X, Zhuang X, Zheng Z, Liu S, Liu Z, Song F. Unfolding and aggregation of oxidized metal-deficient superoxide dismutase and isoflavone inhibition based on ion mobility mass spectrometry and ThT fluorescence assay. Arch Biochem Biophys 2022; 727:109306. [DOI: 10.1016/j.abb.2022.109306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 05/30/2022] [Accepted: 05/31/2022] [Indexed: 11/02/2022]
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10
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Grabarics M, Lettow M, Kirschbaum C, Greis K, Manz C, Pagel K. Mass Spectrometry-Based Techniques to Elucidate the Sugar Code. Chem Rev 2022; 122:7840-7908. [PMID: 34491038 PMCID: PMC9052437 DOI: 10.1021/acs.chemrev.1c00380] [Citation(s) in RCA: 61] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Indexed: 12/22/2022]
Abstract
Cells encode information in the sequence of biopolymers, such as nucleic acids, proteins, and glycans. Although glycans are essential to all living organisms, surprisingly little is known about the "sugar code" and the biological roles of these molecules. The reason glycobiology lags behind its counterparts dealing with nucleic acids and proteins lies in the complexity of carbohydrate structures, which renders their analysis extremely challenging. Building blocks that may differ only in the configuration of a single stereocenter, combined with the vast possibilities to connect monosaccharide units, lead to an immense variety of isomers, which poses a formidable challenge to conventional mass spectrometry. In recent years, however, a combination of innovative ion activation methods, commercialization of ion mobility-mass spectrometry, progress in gas-phase ion spectroscopy, and advances in computational chemistry have led to a revolution in mass spectrometry-based glycan analysis. The present review focuses on the above techniques that expanded the traditional glycomics toolkit and provided spectacular insight into the structure of these fascinating biomolecules. To emphasize the specific challenges associated with them, major classes of mammalian glycans are discussed in separate sections. By doing so, we aim to put the spotlight on the most important element of glycobiology: the glycans themselves.
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Affiliation(s)
- Márkó Grabarics
- Institute
of Chemistry and Biochemistry, Freie Universität
Berlin, Arnimallee 22, 14195 Berlin, Germany
- Department
of Molecular Physics, Fritz Haber Institute
of the Max Planck Society, Faradayweg 4−6, 14195 Berlin, Germany
| | - Maike Lettow
- Institute
of Chemistry and Biochemistry, Freie Universität
Berlin, Arnimallee 22, 14195 Berlin, Germany
- Department
of Molecular Physics, Fritz Haber Institute
of the Max Planck Society, Faradayweg 4−6, 14195 Berlin, Germany
| | - Carla Kirschbaum
- Institute
of Chemistry and Biochemistry, Freie Universität
Berlin, Arnimallee 22, 14195 Berlin, Germany
- Department
of Molecular Physics, Fritz Haber Institute
of the Max Planck Society, Faradayweg 4−6, 14195 Berlin, Germany
| | - Kim Greis
- Institute
of Chemistry and Biochemistry, Freie Universität
Berlin, Arnimallee 22, 14195 Berlin, Germany
- Department
of Molecular Physics, Fritz Haber Institute
of the Max Planck Society, Faradayweg 4−6, 14195 Berlin, Germany
| | - Christian Manz
- Institute
of Chemistry and Biochemistry, Freie Universität
Berlin, Arnimallee 22, 14195 Berlin, Germany
- Department
of Molecular Physics, Fritz Haber Institute
of the Max Planck Society, Faradayweg 4−6, 14195 Berlin, Germany
| | - Kevin Pagel
- Institute
of Chemistry and Biochemistry, Freie Universität
Berlin, Arnimallee 22, 14195 Berlin, Germany
- Department
of Molecular Physics, Fritz Haber Institute
of the Max Planck Society, Faradayweg 4−6, 14195 Berlin, Germany
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11
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Barnes LF, Draper BE, Jarrold MF. Analysis of Recombinant Adenovirus Vectors by Ion Trap Charge Detection Mass Spectrometry: Accurate Molecular Weight Measurements beyond 150 MDa. Anal Chem 2022; 94:1543-1551. [PMID: 35023731 DOI: 10.1021/acs.analchem.1c02439] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Adenovirus is one of the largest nonenveloped, double-stranded DNA viruses. It is widely used as a gene therapy vector and has recently received a lot of attention as a novel vaccine platform for SARS-CoV-2. Human adenovirus 5 (HAdV5) contains over 2500 protein molecules and has a 36 kbp genome. Adenovirus is well beyond the range of conventional mass spectrometry, and it was unclear how well such a large complex could be desolvated. Here, we report molecular weight (MW) distributions measured for HAdV5 and for 11 recombinant AdV vectors with genomes of varying lengths. The MW distributions were recorded using ion trap charge detection mass spectrometry (CDMS), a single-particle technique where m/z and charge are measured for individual ions. The results show that ions as large as 150 MDa can be effectively desolvated and accurate MW distributions obtained. The MW distribution for HAdV5 contains a narrow peak at 156.1 MDa, assigned to the infectious virus. A smaller peak at 129.6 MDa is attributed to incomplete particles that have not packaged a genome. The ions in the 129.6 MDa peak have a much lower average charge than those in the peak at 156.1 MDa. This is attributed to the empty particles missing some or all of the fibers that decorate the surface of the virion. The MW measured for the mature virus (156.1 MDa) is much larger than that predicted from sequence masses and copy numbers of the constituents (142.5 MDa). Measurements performed for recombinant AdV as a function of genome length show that for every 1 MDa increase in the genome MW, the MW of the mature virus increases by around 2.3 MDa. The additional 1.3 MDa is attributed to core proteins that are copackaged with the DNA. This observation suggests that the discrepancy between the measured and expected MWs for mature HAdV5 is due to an underestimate in the copy numbers of the core proteins.
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Affiliation(s)
- Lauren F Barnes
- Chemistry Department, Indiana University, 800 E Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Benjamin E Draper
- Megadalton Solutions, Inc., 3750 E Bluebird Lane, Bloomington, Indiana 47401, United States
| | - Martin F Jarrold
- Chemistry Department, Indiana University, 800 E Kirkwood Avenue, Bloomington, Indiana 47405, United States
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12
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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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13
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The concept of protein folding/unfolding and its impacts on human health. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2021. [PMID: 34090616 DOI: 10.1016/bs.apcsb.2021.01.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2023]
Abstract
Proteins have evolved in specific 3D structures and play different functions in cells and determine various reactions and pathways. The newly synthesized amino acid chains once depart ribosome must crumple into three-dimensional structures so can be biologically active. This process of protein that makes a functional molecule is called protein folding. The protein folding is both a biological and a physicochemical process that depends on the sequence of it. In fact, this process occurs more complicated and in some cases and in exposure to some molecules like glucose (glycation), mistaken folding leads to amyloid structures and fatal disorders called conformational diseases. Such conditions are detected by the quality control system of the cell and these abnormal proteins undergo renovation or degradation. This scenario takes place by the chaperones, chaperonins, and Ubiquitin-proteasome complex. Understanding of protein folding mechanisms from different views including experimental and computational approaches has revealed some intermediate ensembles such as molten globule and has been subjected to biophysical and molecular biology attempts to know more about prevalent conformational diseases.
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14
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Deep learning the collisional cross sections of the peptide universe from a million experimental values. Nat Commun 2021; 12:1185. [PMID: 33608539 PMCID: PMC7896072 DOI: 10.1038/s41467-021-21352-8] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 01/22/2021] [Indexed: 01/09/2023] Open
Abstract
The size and shape of peptide ions in the gas phase are an under-explored dimension for mass spectrometry-based proteomics. To investigate the nature and utility of the peptide collisional cross section (CCS) space, we measure more than a million data points from whole-proteome digests of five organisms with trapped ion mobility spectrometry (TIMS) and parallel accumulation-serial fragmentation (PASEF). The scale and precision (CV < 1%) of our data is sufficient to train a deep recurrent neural network that accurately predicts CCS values solely based on the peptide sequence. Cross section predictions for the synthetic ProteomeTools peptides validate the model within a 1.4% median relative error (R > 0.99). Hydrophobicity, proportion of prolines and position of histidines are main determinants of the cross sections in addition to sequence-specific interactions. CCS values can now be predicted for any peptide and organism, forming a basis for advanced proteomics workflows that make full use of the additional information. Proteomics has been advanced by algorithms that can predict different peptide features, but predicting peptide collisional cross sections (CCS) has remained challenging. Here, the authors measure over one million CCS values of tryptic peptides and develop a deep learning model for peptide CCS prediction.
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15
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Barth M, Schmidt C. Native mass spectrometry-A valuable tool in structural biology. JOURNAL OF MASS SPECTROMETRY : JMS 2020; 55:e4578. [PMID: 32662584 DOI: 10.1002/jms.4578] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 05/18/2020] [Accepted: 05/19/2020] [Indexed: 05/16/2023]
Abstract
Proteins and the complexes they form with their ligands are the players of cellular action. Their function is directly linked with their structure making the structural analysis of protein-ligand complexes essential. Classical techniques of structural biology include X-ray crystallography, nuclear magnetic resonance spectroscopy and recently distinguished cryo-electron microscopy. However, protein-ligand complexes are often dynamic and heterogeneous and consequently challenging for these techniques. Alternative approaches are therefore needed and gained importance during the last decades. One alternative is native mass spectrometry, which is the analysis of intact protein complexes in the gas phase. To achieve this, sample preparation and instrument conditions have to be optimised. Native mass spectrometry then reveals stoichiometry, protein interactions and topology of protein assemblies. Advanced techniques such as ion mobility and high-resolution mass spectrometry further add to the range of applications and deliver information on shape and microheterogeneity of the complexes. In this tutorial, we explain the basics of native mass spectrometry including sample requirements, instrument modifications and interpretation of native mass spectra. We further discuss the developments of native mass spectrometry and provide example spectra and applications.
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Affiliation(s)
- Marie Barth
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Institute for Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Carla Schmidt
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Institute for Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle, Germany
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16
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Thomas DA, Chang R, Mucha E, Lettow M, Greis K, Gewinner S, Schöllkopf W, Meijer G, von Helden G. Probing the conformational landscape and thermochemistry of DNA dinucleotide anions via helium nanodroplet infrared action spectroscopy. Phys Chem Chem Phys 2020; 22:18400-18413. [PMID: 32797142 DOI: 10.1039/d0cp02482a] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Isolation of biomolecules in vacuum facilitates characterization of the intramolecular interactions that determine three-dimensional structure, but experimental quantification of conformer thermochemistry remains challenging. Infrared spectroscopy of molecules trapped in helium nanodroplets is a promising methodology for the measurement of thermochemical parameters. When molecules are captured in a helium nanodroplet, the rate of cooling to an equilibrium temperature of ca. 0.4 K is generally faster than the rate of isomerization, resulting in "shock-freezing" that kinetically traps molecules in local conformational minima. This unique property enables the study of temperature-dependent conformational equilibria via infrared spectroscopy at 0.4 K, thereby avoiding the deleterious effects of spectral broadening at higher temperatures. Herein, we demonstrate the first application of this approach to ionic species by coupling electrospray ionization mass spectrometry (ESI-MS) with helium nanodroplet infrared action spectroscopy to probe the structure and thermochemistry of deprotonated DNA dinucleotides. Dinucleotide anions were generated by ESI, confined in an ion trap at temperatures between 90 and 350 K, and entrained in traversing helium nanodroplets. The infrared action spectra of the entrained ions show a strong dependence on pre-pickup ion temperature, consistent with the preservation of conformer population upon cooling to 0.4 K. Non-negative matrix factorization was utilized to identify component conformer infrared spectra and determine temperature-dependent conformer populations. Relative enthalpies and entropies of conformers were subsequently obtained from a van't Hoff analysis. IR spectra and conformer thermochemistry are compared to results from ion mobility spectrometry (IMS) and electronic structure methods. The implementation of ESI-MS as a source of dopant molecules expands the diversity of molecules accessible for thermochemical measurements, enabling the study of larger, non-volatile species.
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Affiliation(s)
- Daniel A Thomas
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany.
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17
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Charles L, Chendo C, Poyer S. Ion mobility spectrometry - Mass spectrometry coupling for synthetic polymers. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2020; 34 Suppl 2:e8624. [PMID: 31658387 DOI: 10.1002/rcm.8624] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 09/27/2019] [Accepted: 09/28/2019] [Indexed: 06/10/2023]
Abstract
This review covers applications of ion mobility spectrometry (IMS) hyphenated to mass spectrometry (MS) in the field of synthetic polymers. MS has become an essential technique in polymer science, but increasingly complex samples produced to provide desirable macroscopic properties of high-performance materials often require separation of species prior to their mass analysis. Similar to liquid chromatography, the IMS dimension introduces shape selectivity but enables separation at a much faster rate (milliseconds vs minutes). As a post-ionization technique, IMS can be hyphenated to MS to perform a double separation dimension of gas-phase ions, first as a function on their mobility (determined by their charge state and collision cross section, CCS), then as a function of their m/z ratio. Implemented with a variety of ionization techniques, such coupling permits the spectral complexity to be reduced, to enhance the dynamic range of detection, or to achieve separation of isobaric ions prior to their activation in MS/MS experiments. Coupling IMS to MS also provides valuable information regarding the 3D structure of polymer ions in the gas phase and regarding how to address the question of how charges are distributed within the structure. Moreover, the ability of IMS to separate multiply charged species generated by electrospray ionization yields typical IMS-MS 2D maps that permit the conformational dynamics of synthetic polymer chains to be described as a function of their length.
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Affiliation(s)
- Laurence Charles
- Aix Marseille Univ, CNRS, ICR, Institut de Chimie Radicalaire, 13397, Marseille Cedex 20, France
| | - Christophe Chendo
- Aix Marseille Univ, CNRS, ICR, Institut de Chimie Radicalaire, 13397, Marseille Cedex 20, France
| | - Salomé Poyer
- Aix Marseille Univ, CNRS, ICR, Institut de Chimie Radicalaire, 13397, Marseille Cedex 20, France
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18
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Nonose S. Temperature-Resolved Proton Transfer Reactions of Biomolecular Ions. Mass Spectrom (Tokyo) 2020; 9:A0083. [PMID: 32547897 PMCID: PMC7242783 DOI: 10.5702/massspectrometry.a0083] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 02/17/2020] [Indexed: 11/23/2022] Open
Abstract
Temperature-resolved proton transfer reactions of multiply-protonated angiotensin I, disulfide-intact and -reduced lysozyme, and ubiquitin ions to primary, secondary and aromatic amines were examined in the gas phase. Absolute reaction rate constants for the proton transfer were determined from the intensities of the parent and product ions in mass spectra. Dramatic changes were observed in the distribution of product ions and the reaction rate constants. In particular, the rate constants for disulfide-intact lysozyme ions changed more drastically with the change in charge state and temperature compared to the corresponding values for disulfide-reduced ions. Proton transfer reactions were enhanced or suppressed as the result of the formation of complexes between the ions with gaseous molecules, which is related to changes in their conformation with changing.
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Affiliation(s)
- Shinji Nonose
- Graduate School of Nanobioscience, Yokohama City University, 22-2 Seto, Kanazawa-ku, Yokohama 236-0027, Japan
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19
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Shayeghi A, Rieser P, Richter G, Sezer U, Rodewald JH, Geyer P, Martinez TJ, Arndt M. Matter-wave interference of a native polypeptide. Nat Commun 2020; 11:1447. [PMID: 32193414 PMCID: PMC7081299 DOI: 10.1038/s41467-020-15280-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 02/26/2020] [Indexed: 11/12/2022] Open
Abstract
The de Broglie wave nature of matter is a paradigmatic example of quantum physics and it has been exploited in precision measurements of forces and fundamental constants. However, matter-wave interferometry has remained an outstanding challenge for natural polypeptides, building blocks of life, which are fragile and difficult to handle. Here, we demonstrate the wave nature of gramicidin, a natural antibiotic composed of 15 amino acids. Its center of mass is delocalized over more than 20 times the molecular size in our time-domain Talbot-Lau interferometer. We compare the observed interference fringes with a model that includes both a rigorous treatment of the peptide’s quantum wave nature as well as a quantum chemical assessment of its optical properties to distinguish our result from classical predictions. The realization of quantum optics with this prototypical biomolecule paves the way for quantum-assisted measurements on a large class of biologically relevant molecules. Matter-wave interferometry of complex molecules is challenging due to difficulties in preparing and detecting molecular beams. Here the authors demonstrate quantum behavior of a polypeptide using matter-wave interference in an all-optical time-domain Talbot-Lau interferometer.
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Affiliation(s)
- A Shayeghi
- Faculty of Physics, University of Vienna, VCQ, Boltzmanngasse 5, A-1090, Vienna, Austria
| | - P Rieser
- Faculty of Physics, University of Vienna, VCQ, Boltzmanngasse 5, A-1090, Vienna, Austria
| | - G Richter
- Faculty of Physics, University of Vienna, VCQ, Boltzmanngasse 5, A-1090, Vienna, Austria
| | - U Sezer
- Faculty of Physics, University of Vienna, VCQ, Boltzmanngasse 5, A-1090, Vienna, Austria
| | - J H Rodewald
- Centre for Cold Matter, Blackett Laboratory, Imperial College London, Prince Consort Road, London, SW7 2AZ, United Kingdom
| | - P Geyer
- Faculty of Physics, University of Vienna, VCQ, Boltzmanngasse 5, A-1090, Vienna, Austria
| | - T J Martinez
- Department of Chemistry and the PULSE Institute, Stanford University, Stanford, CA, 94305, USA.,SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - M Arndt
- Faculty of Physics, University of Vienna, VCQ, Boltzmanngasse 5, A-1090, Vienna, Austria.
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20
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Fan J, Lian P, Li M, Liu X, Zhou X, Ouyang Z. Ion Mobility Separation Using a Dual-LIT Miniature Mass Spectrometer. Anal Chem 2020; 92:2573-2579. [PMID: 31940171 DOI: 10.1021/acs.analchem.9b04271] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Ion mobility (IM) has been increasingly used in combination with mass spectrometry (MS) for chemical and biological analysis. While implementation of IM with MS usually requires complex instrumentation with delicate controls, in this study we explored the potential of performing IM separation using dual-linear ion traps (LITs) in a miniature mass spectrometer, which was originally developed for performing comprehensive MS/MS scan functions with a simple instrumentation configuration. The IM separation was achieved by ion transfer between the LITs with dynamic gas flow. Its performance was characterized for analysis of a broad range of chemical and biological compounds including small organic compounds such as trisaccharides, raffinose, cellotriose, and melezitose, as well as protein conformers. The demonstrated technique serves as another example of developing powerful hybrid instrument functions with simple configurations and miniaturized sizes.
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Affiliation(s)
- Jingjin Fan
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument , Tsinghua University , Beijing 100084 , China
| | - Penglong Lian
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument , Tsinghua University , Beijing 100084 , China
| | - Ming Li
- NCS Testing Technology Company, Limited , Beijing 100081 , China
| | - Xinwei Liu
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument , Tsinghua University , Beijing 100084 , China
| | - Xiaoyu Zhou
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument , Tsinghua University , Beijing 100084 , China
| | - Zheng Ouyang
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument , Tsinghua University , Beijing 100084 , China
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21
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Soorkia S, Jouvet C, Grégoire G. UV Photoinduced Dynamics of Conformer-Resolved Aromatic Peptides. Chem Rev 2019; 120:3296-3327. [DOI: 10.1021/acs.chemrev.9b00316] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Satchin Soorkia
- Institut des Sciences Moléculaires d’Orsay (ISMO), CNRS, Univ. Paris-Sud, Université Paris-Saclay, F-91405 Orsay, France
| | - Christophe Jouvet
- CNRS, Aix Marseille Université, PIIM UMR 7345, 13397, Marseille, France
| | - Gilles Grégoire
- Institut des Sciences Moléculaires d’Orsay (ISMO), CNRS, Univ. Paris-Sud, Université Paris-Saclay, F-91405 Orsay, France
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22
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Gantman T, Goldstein M, Segev E, Gerber RB. Conformers of Ubiquitin 6+ for Different Charge Distributions: Atomistic Structures and Ion Mobility Cross Sections. J Phys Chem B 2019; 123:6401-6409. [DOI: 10.1021/acs.jpcb.9b02720] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Tamara Gantman
- The Fritz Haber Research Center for Molecular Dynamics, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Moshe Goldstein
- The Fritz Haber Research Center for Molecular Dynamics, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
- Department of Computer Science, Jerusalem College of Technology (JCT), Jerusalem 9372115, Israel
| | - Elad Segev
- The Fritz Haber Research Center for Molecular Dynamics, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
- Department of Applied Mathematics, Holon Institute of Technology, Holon 5810201, Israel
| | - R. Benny Gerber
- The Fritz Haber Research Center for Molecular Dynamics, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
- Department of Chemistry, University of California, Irvine, California 92697, United States
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23
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Trimpin S, Inutan ED, Karki S, Elia EA, Zhang WJ, Weidner SM, Marshall DD, Hoang K, Lee C, Davis ETJ, Smith V, Meher AK, Cornejo MA, Auner GW, McEwen CN. Fundamental Studies of New Ionization Technologies and Insights from IMS-MS. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:1133-1147. [PMID: 31062287 DOI: 10.1007/s13361-019-02194-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 03/13/2019] [Accepted: 03/13/2019] [Indexed: 06/09/2023]
Abstract
Exceptional ion mobility spectrometry mass spectrometry (IMS-MS) developments by von Helden, Jarrold, and Clemmer provided technology that gives a view of chemical/biological compositions previously not achievable. The ionization method of choice used with IMS-MS has been electrospray ionization (ESI). In this special issue contribution, we focus on fundamentals of heretofore unprecedented means for transferring volatile and nonvolatile compounds into gas-phase ions singly and multiply charged. These newer ionization processes frequently lead to different selectivity relative to ESI and, together with IMS-MS, may provide a more comprehensive view of chemical compositions directly from their original environment such as surfaces, e.g., tissue. Similarities of results using solvent- and matrix-assisted ionization are highlighted, as are differences between ESI and the inlet ionization methods, especially with mixtures such as bacterial extracts. Selectivity using different matrices is discussed, as are results which add to our fundamental knowledge of inlet ionization as well as pose additional avenues for inquiry. IMS-MS provides an opportunity for comparison studies relative to ESI and will prove valuable using the new ionization technologies for direct analyses. Our hypothesis is that some ESI-IMS-MS applications will be replaced by the new ionization processes and by understanding mechanistic aspects to aid enhanced source and method developments this will be hastened.
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Affiliation(s)
- Sarah Trimpin
- Department of Chemistry, Wayne State University, Detroit, MI, USA.
- Cardiovascular Research Institute, School of Medicine, Wayne State University, Detroit, MI, USA.
- MSTM, LLC, Newark, DE, USA.
| | - Ellen D Inutan
- Department of Chemistry, Wayne State University, Detroit, MI, USA
- MSTM, LLC, Newark, DE, USA
- Mindanao State University-Iligan Institute of Technology, Iligan City, Philippines
| | - Santosh Karki
- Department of Chemistry, Wayne State University, Detroit, MI, USA
- MSTM, LLC, Newark, DE, USA
| | | | - Wen-Jing Zhang
- Department of Chemistry, Wayne State University, Detroit, MI, USA
| | - Steffen M Weidner
- Bundesanstalt für Materialforschung und -prüfung (BAM), Berlin, Germany
| | - Darrell D Marshall
- Department of Chemistry, Wayne State University, Detroit, MI, USA
- MSTM, LLC, Newark, DE, USA
| | - Khoa Hoang
- University of the Sciences, Philadelphia, PA, USA
| | - Chuping Lee
- Department of Chemistry, Wayne State University, Detroit, MI, USA
- MSTM, LLC, Newark, DE, USA
| | - Eric T J Davis
- Department of Chemistry, Wayne State University, Detroit, MI, USA
| | | | - Anil K Meher
- Department of Chemistry, Wayne State University, Detroit, MI, USA
| | - Mario A Cornejo
- Department of Chemistry, Wayne State University, Detroit, MI, USA
| | - Gregory W Auner
- Department of Surgery, School of Medicine, Wayne State University, Detroit, MI, USA
| | - Charles N McEwen
- MSTM, LLC, Newark, DE, USA
- University of the Sciences, Philadelphia, PA, USA
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24
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Schätti J, Kriegleder M, Debiossac M, Kerschbaum M, Geyer P, Mayor M, Arndt M, Köhler V. Neutralization of insulin by photocleavage under high vacuum. Chem Commun (Camb) 2019; 55:12507-12510. [DOI: 10.1039/c9cc05712a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Electrosprayed peptide ion beams are charge manipulated by photocleavage of chemical tags.
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Affiliation(s)
- Jonas Schätti
- Department of Chemistry
- University of Basel
- CH Basel
- Switzerland
| | | | | | | | - Philipp Geyer
- Faculty of Physics
- University of Vienna
- A-1090 Vienna
- Austria
| | - Marcel Mayor
- Department of Chemistry
- University of Basel
- CH Basel
- Switzerland
- Institute of Nanotechnology
| | - Markus Arndt
- Faculty of Physics
- University of Vienna
- A-1090 Vienna
- Austria
| | - Valentin Köhler
- Department of Chemistry
- University of Basel
- CH Basel
- Switzerland
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25
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Pushing the mass limit for intact launch and photoionization of large neutral biopolymers. Commun Chem 2018. [DOI: 10.1038/s42004-018-0095-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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26
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Przygońska K, Poznański J, Mistarz UH, Rand KD, Dadlez M. Side-chain moieties from the N-terminal region of Aβ are Involved in an oligomer-stabilizing network of interactions. PLoS One 2018; 13:e0201761. [PMID: 30080867 PMCID: PMC6078298 DOI: 10.1371/journal.pone.0201761] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 07/20/2018] [Indexed: 12/31/2022] Open
Abstract
Oligomeric forms of the Aβ peptide represent the most probable neurotoxic agent in Alzheimer’s disease. The dynamic and heterogeneous character of these oligomers makes their structural characterization by classic methods difficult. Native mass spectrometry, when supported by additional gas phase techniques, like ion mobility separation and hydrogen-deuterium exchange (IM-HDX-MS), enable analysis of different oligomers coexisting in the sample and may provide species-specific structural information for each oligomeric form populated in the gas phase. Here, we have combined these three techniques to obtain insight into the structural properties of oligomers of Aβ1–40 and two variants with scrambled sequences. Gas-phase HDX-MS revealed a sequence-specific engagement of the side-chains of residues located at the N-terminal part of the peptide in a network of oligomer-stabilizing interactions. Oligomer-specific interactions were no longer observed in the case of the fully scrambled sequence. Also, the ability to form alternative structures, observed for WT Aβ peptide, was lost upon scrambling. Our data underscore a role for the N-terminal residues in shaping the equilibria of oligomeric forms. Although the peptide lacking the N-terminal 1–16 residues (p3 peptide) is thought to be benign, the role of the N-terminus has not been sufficiently characterized yet. We speculate that the interaction networks revealed here may be crucial for enabling structural transitions necessary to obtain mature parallel cross-β structures from smaller antiparallel oligomers. We provide a hypothetical molecular model of the trajectory that allows a gradual conversion from antiparallel to parallel oligomers without decomposition of oligomers. Oligomer-defining interactions involving the Aβ peptide N-terminus may be important in production of the neurotoxic forms and thus should not be neglected.
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Affiliation(s)
- Kaja Przygońska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Jarosław Poznański
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Ulrik H. Mistarz
- Department of Pharmacy, University of Copenhagen, Copenhagen, Denmark
| | - Kasper D. Rand
- Department of Pharmacy, University of Copenhagen, Copenhagen, Denmark
| | - Michał Dadlez
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
- Institute of Genetics and Biotechnology, Department of Biology, University of Warsaw, Warsaw, Poland
- * E-mail:
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27
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Luo B, Yang M, Jiang P, Lan F, Wu Y. Multi-affinity sites of magnetic guanidyl-functionalized metal-organic framework nanospheres for efficient enrichment of global phosphopeptides. NANOSCALE 2018; 10:8391-8396. [PMID: 29701230 DOI: 10.1039/c8nr01914b] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Magnetic guanidyl-functionalized metal-organic framework (MOF) nanospheres with multi-affinity sites composed of an inherent Zn-O cluster based on MOAC and specific recognized groups (amino group and guanidyl group) were for the first time synthesized by a combination strategy of epitaxial growth and post-synthetic modification of magnetic amino-derived MOFs, and they exhibit great potential for efficient enrichment of global phosphopeptides.
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Affiliation(s)
- Bin Luo
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu, 610064, China.
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28
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How can native mass spectrometry contribute to characterization of biomacromolecular higher-order structure and interactions? Methods 2018; 144:3-13. [PMID: 29704661 DOI: 10.1016/j.ymeth.2018.04.025] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 04/03/2018] [Accepted: 04/21/2018] [Indexed: 01/16/2023] Open
Abstract
Native mass spectrometry (MS) is an emerging approach for characterizing biomacromolecular structure and interactions under physiologically relevant conditions. In native MS measurement, intact macromolecules or macromolecular complexes are directly ionized from a non-denaturing solvent, and key noncovalent interactions that hold the complexes together can be preserved for MS analysis in the gas phase. This technique provides unique multi-level structural information such as conformational changes, stoichiometry, topology and dynamics, complementing conventional biophysical techniques. Despite the maturation of native MS and greatly expanded range of applications in recent decades, further dissemination is needed to make the community aware of such a technique. In this review, we attempt to provide an overview of the current body of knowledge regarding major aspects of native MS and explain how such technique contributes to the characterization of biomacromolecular higher-order structure and interactions.
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29
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Debiossac M, Schätti J, Kriegleder M, Geyer P, Shayeghi A, Mayor M, Arndt M, Köhler V. Tailored photocleavable peptides: fragmentation and neutralization pathways in high vacuum. Phys Chem Chem Phys 2018; 20:11412-11417. [PMID: 29645042 PMCID: PMC5932999 DOI: 10.1039/c8cp01058g] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 03/23/2018] [Indexed: 01/31/2023]
Abstract
Photocleavable tags (PCTs) have the potential for excellent spatio-temporal control over the release of subunits of complex molecules. Here, we show that electrosprayed oligopeptides, functionalized by a tailored ortho-nitroarylether can undergo site-specific photo-activated cleavage under UV irradiation (266 nm) in high vacuum. The comparison of UV photodissociation (UVPD) and collision-induced dissociation (CID) points to the thermal nature of the cleavage mechanism, a picture corroborated by the temperature dependence of the process. Two competing photodissociation pathways can be identified. In one case a phenolate anion is separated from a neutral zwitterion. In the other case a neutral phenol derivative leaves a negatively charged peptide behind. To understand the factors favoring one channel over the other, we investigate the influence of the peptide length, the nature of the phenolic group and the position of the nitro-group (ortho vs. para). The observed gas phase cleavage of a para-nitro benzylic ether markedly differs from the established behavior in solution.
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Affiliation(s)
- M. Debiossac
- Faculty of Physics, University of Vienna , VCQ, Boltzmanngasse 5 , A-1090 Vienna , Austria .
| | - J. Schätti
- Department of Chemistry, University of Basel , Mattenstrasse 24a, BPR 1096 , CH-4058 Basel , Switzerland .
| | - M. Kriegleder
- Faculty of Physics, University of Vienna , VCQ, Boltzmanngasse 5 , A-1090 Vienna , Austria .
| | - P. Geyer
- Faculty of Physics, University of Vienna , VCQ, Boltzmanngasse 5 , A-1090 Vienna , Austria .
| | - A. Shayeghi
- Faculty of Physics, University of Vienna , VCQ, Boltzmanngasse 5 , A-1090 Vienna , Austria .
| | - M. Mayor
- Department of Chemistry, University of Basel , Mattenstrasse 24a, BPR 1096 , CH-4058 Basel , Switzerland .
- Institute of Nanotechnology (INT), Karlsruhe Institute of Technology (KIT) , Hermann-von-Helmholtz-Platz 1 , D-76344 Eggenstein-Leopoldshafen , Germany
- Lehn Institute of Functional Materials (LIFM), Sun Yat-Sen University (SYSU) , Xingang Rd. W. , Guangzhou , China
| | - M. Arndt
- Faculty of Physics, University of Vienna , VCQ, Boltzmanngasse 5 , A-1090 Vienna , Austria .
| | - V. Köhler
- Department of Chemistry, University of Basel , Mattenstrasse 24a, BPR 1096 , CH-4058 Basel , Switzerland .
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30
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Chakraborty S, Endres KJ, Bera R, Wojtas L, Moorefield CN, Saunders MJ, Das N, Wesdemiotis C, Newkome GR. Concentration dependent supramolecular interconversions of triptycene-based cubic, prismatic, and tetrahedral structures. Dalton Trans 2018; 47:14189-14194. [DOI: 10.1039/c7dt04571a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
New insight into the molecular fission–fusion process is obtained with the characterization of a stable intermediate prismatic cage.
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Affiliation(s)
| | | | - Ranajit Bera
- Department of Chemistry
- Indian Institute of Technology Patna
- Patna 801106
- India
| | - Lukasz Wojtas
- Department of Chemistry
- University of South Florida
- Tampa
- USA
| | | | - Mary Jane Saunders
- Department of Biological Sciences
- Florida Atlantic University
- Boca Raton
- USA
| | - Neeladri Das
- Department of Chemistry
- Indian Institute of Technology Patna
- Patna 801106
- India
| | - Chrys Wesdemiotis
- Departments of Polymer Science
- University of Akron
- Akron
- USA
- Departments of Chemistry
| | - George R. Newkome
- Departments of Polymer Science
- University of Akron
- Akron
- USA
- Departments of Chemistry
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31
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32
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Yefremova Y, Danquah BD, Opuni KF, El-Kased R, Koy C, Glocker MO. Mass spectrometric characterization of protein structures and protein complexes in condensed and gas phase. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2017; 23:445-459. [PMID: 29183193 DOI: 10.1177/1469066717722256] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Proteins are essential for almost all physiological processes of life. They serve a myriad of functions which are as varied as their unique amino acid sequences and their corresponding three-dimensional structures. To fulfill their tasks, most proteins depend on stable physical associations, in the form of protein complexes that evolved between themselves and other proteins. In solution (condensed phase), proteins and/or protein complexes are in constant energy exchange with the surrounding solvent. Albeit methods to describe in-solution thermodynamic properties of proteins and of protein complexes are well established and broadly applied, they do not provide a broad enough access to life-science experimentalists to study all their proteins' properties at leisure. This leaves great desire to add novel methods to the analytical biochemist's toolbox. The development of electrospray ionization created the opportunity to characterize protein higher order structures and protein complexes rather elegantly by simultaneously lessening the need of sophisticated sample preparation steps. Electrospray mass spectrometry enabled us to translate proteins and protein complexes very efficiently into the gas phase under mild conditions, retaining both, intact protein complexes, and gross protein structures upon phase transition. Moreover, in the environment of the mass spectrometer (gas phase, in vacuo), analyte molecules are free of interactions with surrounding solvent molecules and, therefore, the energy of inter- and intramolecular forces can be studied independently from interference of the solvating environment. Provided that gas phase methods can give information which is relevant for understanding in-solution processes, gas phase protein structure studies and/or investigations on the characterization of protein complexes has rapidly gained more and more attention from the bioanalytical scientific community. Recent reports have shown that electrospray mass spectrometry provides direct access to six prime protein complex properties: stabilities, compositions, binding surfaces (epitopes), disassembly processes, stoichiometries, and thermodynamic parameters.
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Affiliation(s)
- Yelena Yefremova
- 1 Proteome Center Rostock, University of Rostock, Rostock, Germany
| | - Bright D Danquah
- 1 Proteome Center Rostock, University of Rostock, Rostock, Germany
| | | | - Reham El-Kased
- 3 Microbiology and Immunology, Faculty of Pharmacy, The British University in Egypt, Cairo, Egypt
| | - Cornelia Koy
- 1 Proteome Center Rostock, University of Rostock, Rostock, Germany
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33
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Yang Y, Liao G, Kong X. Charge-state Resolved Infrared Multiple Photon Dissociation (IRMPD) Spectroscopy of Ubiquitin Ions in the Gas Phase. Sci Rep 2017; 7:16592. [PMID: 29185478 PMCID: PMC5707388 DOI: 10.1038/s41598-017-16831-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 11/16/2017] [Indexed: 11/25/2022] Open
Abstract
In this study, we obtained for the first time the direct infrared multiple photon dissociation (IRMPD) spectra of ubiquitin ions in the range 2700-3750 cm-1. Ubiquitin ions with different charge states showed absorption in the two regions of 2940-3000 cm-1 and 3280-3400 cm-1. The increase of the charge state of ubiquitin ions broadened the absorption peak on the high-frequency side in the second region, indicating some hydrogen bonds were weakened due to Coulomb interaction. It is also found that the relative intensity of the absorption peak in the first region compared to the absorption peak in the second region increased with increasing charge state, making the IRMPD spectra charge-state resolved. Although it is usually reasonable to suggest the origin of the absorption in the range 2940-3000 cm-1 as the C-H bond stretching modes, the results show significantly reduced absorption after the deuteration of all labile hydrogen atoms. A possible explanation for this is that the coupling coefficients between the C-H vibrational mode and other selective modes decreased greatly after the deuteration, reducing the rate of energy redistribution and probability of consecutive IR absorption.
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Affiliation(s)
- Yijie Yang
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Guanhua Liao
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Xianglei Kong
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, China.
- Collaborative Innovation Center of Chemical Science and Engineering, Nankai University, Tianjin, 300071, China.
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34
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Xie TZ, Wu X, Endres KJ, Guo Z, Lu X, Li J, Manandhar E, Ludlow JM, Moorefield CN, Saunders MJ, Wesdemiotis C, Newkome GR. Supercharged, Precise, Megametallodendrimers via a Single-Step, Quantitative, Assembly Process. J Am Chem Soc 2017; 139:15652-15655. [DOI: 10.1021/jacs.7b10328] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
| | | | | | | | - Xiaocun Lu
- Beckman Institute, 405 North
Mathews Avenue, Urbana, Illinois 61801, United States
| | | | | | | | - Charles N. Moorefield
- Dendronex, LLC, 109 Runway Drive,
Reese Technology Center, Lubbock, Texas 79416, United States
| | - Mary Jane Saunders
- Department
of Biological Sciences, Florida Atlantic University, 777 Glades Road, Boca Raton, Florida 33431, United States
| | | | - George R. Newkome
- Center
for
Molecular Biology and Biotechnology, Florida Atlantic University, Jupiter, Florida 33428, United States
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35
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Mairhofer L, Eibenberger S, Cotter JP, Romirer M, Shayeghi A, Arndt M. Quantum-Assisted Metrology of Neutral Vitamins in the Gas Phase. Angew Chem Int Ed Engl 2017; 56:10947-10951. [PMID: 28599088 PMCID: PMC5582605 DOI: 10.1002/anie.201704916] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Indexed: 11/11/2022]
Abstract
It has recently been shown that matter-wave interferometry can be used to imprint a periodic nanostructure onto a molecular beam, which provides a highly sensitive tool for beam displacement measurements. Herein, we used this feature to measure electronic properties of provitamin A, vitamin E, and vitamin K1 in the gas phase for the first time. The shift of the matter-wave fringes in a static electric field encodes the molecular susceptibility and the time-averaged dynamic electric dipole moment. The dependence of the fringe pattern on the intensity of the central light-wave diffraction grating was used to determine the molecular optical polarizability. Comparison of our experimental findings with molecular dynamics simulations and density functional theory provides a rich picture of the electronic structures and dynamics of these biomolecules in the gas phase with β-carotene as a particularly interesting example.
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Affiliation(s)
- Lukas Mairhofer
- Faculty of Physics, VCQUniversity of ViennaBoltzmanngasse 51090ViennaAustria
| | - Sandra Eibenberger
- Faculty of Physics, VCQUniversity of ViennaBoltzmanngasse 51090ViennaAustria
- Lyman LaboratoryHarvard UniversityDepartment of Physics17 Oxford StreetCambridgeMA02138USA
| | - Joseph P. Cotter
- Faculty of Physics, VCQUniversity of ViennaBoltzmanngasse 51090ViennaAustria
- Centre for cold matterBlackett LaboratoryImperial CollegePrince Consort RoadLondonSW7 2BWUK
| | - Marion Romirer
- Faculty of Physics, VCQUniversity of ViennaBoltzmanngasse 51090ViennaAustria
| | - Armin Shayeghi
- Faculty of Physics, VCQUniversity of ViennaBoltzmanngasse 51090ViennaAustria
| | - Markus Arndt
- Faculty of Physics, VCQUniversity of ViennaBoltzmanngasse 51090ViennaAustria
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36
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Mairhofer L, Eibenberger S, Cotter JP, Romirer M, Shayeghi A, Arndt M. Quanteninterferenzexperimente für die Vermessung von Vitaminen in der Gasphase. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201704916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Lukas Mairhofer
- Fakultät für Physik, VCQ; Universität Wien; Boltzmanngasse 5 1090 Wien Österreich
| | - Sandra Eibenberger
- Fakultät für Physik, VCQ; Universität Wien; Boltzmanngasse 5 1090 Wien Österreich
- Lyman Laboratory; Harvard University; Department of Physics; 17 Oxford Street Cambridge MA 02138 USA
| | - Joseph P. Cotter
- Fakultät für Physik, VCQ; Universität Wien; Boltzmanngasse 5 1090 Wien Österreich
- Centre for cold matter; Blackett Laboratory; Imperial College; Prince Consort Road London SW7 2BW Großbritannien
| | - Marion Romirer
- Fakultät für Physik, VCQ; Universität Wien; Boltzmanngasse 5 1090 Wien Österreich
| | - Armin Shayeghi
- Fakultät für Physik, VCQ; Universität Wien; Boltzmanngasse 5 1090 Wien Österreich
| | - Markus Arndt
- Fakultät für Physik, VCQ; Universität Wien; Boltzmanngasse 5 1090 Wien Österreich
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37
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Schätti J, Sezer U, Pedalino S, Cotter JP, Arndt M, Mayor M, Köhler V. Tailoring the volatility and stability of oligopeptides. JOURNAL OF MASS SPECTROMETRY : JMS 2017; 52:550-556. [PMID: 28608445 PMCID: PMC5601229 DOI: 10.1002/jms.3959] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2017] [Revised: 06/08/2017] [Accepted: 06/08/2017] [Indexed: 06/07/2023]
Abstract
Amino acids are essential building blocks of life, and fluorinated derivatives have gained interest in chemistry and medicine. Modern mass spectrometry has enabled the study of oligo- and polypeptides as isolated entities in the gas phase, but predominantly as singly or even multiply charged species. While laser desorption of neutral peptides into adiabatically expanding supersonic noble gas jets is possible, UV-VIS spectroscopy, electric or magnetic deflectometry as well as quantum interferometry would profit from the possibility to prepare thermally slow molecular beams. This has typically been precluded by the fragility of the peptide bond and the fact that a peptide would rather 'fry', i.e. denature and fragment than 'fly'. Here, we explore how tailored perfluoroalkyl functionalization can reduce the intermolecular binding and thus increase the volatility of peptides and compare it to previously explored methylation, acylation and amidation of peptides. We show that this strategy is essential and enables the formation of thermal beams of intact neutral tripeptides, whereas only fragments were observed for an extensively fluoroalkyl-decorated nonapeptide. © 2017 The Authors. Journal of Mass Spectrometry Published by John Wiley & Sons Ltd.
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Affiliation(s)
- J. Schätti
- University of BaselDepartment of ChemistryBasel4056Switzerland
| | - U. Sezer
- University of ViennaFaculty of PhysicsBoltzmanngasse 51090ViennaAustria
| | - S. Pedalino
- University of ViennaFaculty of PhysicsBoltzmanngasse 51090ViennaAustria
| | - J. P. Cotter
- University of ViennaFaculty of PhysicsBoltzmanngasse 51090ViennaAustria
| | - M. Arndt
- University of ViennaFaculty of PhysicsBoltzmanngasse 51090ViennaAustria
| | - M. Mayor
- University of BaselDepartment of ChemistryBasel4056Switzerland
- Karlsruhe Institute of TechnologyInstitute for NanotechnologyHermann‐von‐Helmholtz‐Platz 176344Eggenstein‐LeopoldshafenGermany
| | - V. Köhler
- University of BaselDepartment of ChemistryBasel4056Switzerland
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38
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Zhang Z, Wang H, Wang X, Li Y, Song B, Bolarinwa O, Reese RA, Zhang T, Wang XQ, Cai J, Xu B, Wang M, Liu C, Yang HB, Li X. Supersnowflakes: Stepwise Self-Assembly and Dynamic Exchange of Rhombus Star-Shaped Supramolecules. J Am Chem Soc 2017; 139:8174-8185. [PMID: 28558196 DOI: 10.1021/jacs.7b01326] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
With the goal of increasing the complexity of metallo-supramolecules, two rhombus star-shaped supramolecular architectures, namely, supersnowflakes, were designed and assembled using multiple 2,2':6',2″-terpyridine (tpy) ligands in a stepwise manner. In the design of multicomponent self-assembly, ditopic and tritopic ligands were bridged through Ru(II) with strong coordination to form metal-organic ligands for the subsequent self-assembly with a hexatopic ligand and Zn(II). The combination of Ru(II)-organic ligands with high stability and Zn(II) ions with weak coordination played a key role in the self-assembly of giant heteroleptic supersnowflakes, which encompassed three types of tpy-based organic ligands and two metal ions. With such a stepwise strategy, the self-sorting of individual building blocks was prevented from forming the undesired assemblies, e.g., small macrocycles and coordination polymers. Furthermore, the intra- and intermolecular dynamic exchange study of two supersnowflakes by NMR and mass spectrometry revealed the remarkable stability of these giant supramolecular complexes.
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Affiliation(s)
- Zhe Zhang
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, School of Chemistry, Central China Normal University , Wuhan, Hubei 430079, China.,Department of Chemistry, University of South Florida , Tampa, Florida 33620, United States
| | - Heng Wang
- Department of Chemistry, University of South Florida , Tampa, Florida 33620, United States
| | - Xu Wang
- Department of Chemistry, Texas State University , San Marcos, Texas 78666, United States
| | - Yiming Li
- Department of Chemistry, University of South Florida , Tampa, Florida 33620, United States
| | - Bo Song
- Department of Chemistry, University of South Florida , Tampa, Florida 33620, United States
| | - Olapeju Bolarinwa
- Department of Chemistry, University of South Florida , Tampa, Florida 33620, United States
| | - R Alexander Reese
- Single Molecule Study Laboratory, College of Engineering and Nanoscale Science and Engineering Center, University of Georgia , Athens, Georgia 30602, United States
| | - Tong Zhang
- Single Molecule Study Laboratory, College of Engineering and Nanoscale Science and Engineering Center, University of Georgia , Athens, Georgia 30602, United States
| | - Xu-Qing Wang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, Department of Chemistry, East China Normal University , Shanghai 200062, China
| | - Jianfeng Cai
- Department of Chemistry, University of South Florida , Tampa, Florida 33620, United States
| | - Bingqian Xu
- Single Molecule Study Laboratory, College of Engineering and Nanoscale Science and Engineering Center, University of Georgia , Athens, Georgia 30602, United States
| | - Ming Wang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University , Changchun, Jilin 130012, China
| | - Changlin Liu
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, School of Chemistry, Central China Normal University , Wuhan, Hubei 430079, China
| | - Hai-Bo Yang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, Department of Chemistry, East China Normal University , Shanghai 200062, China
| | - Xiaopeng Li
- Department of Chemistry, University of South Florida , Tampa, Florida 33620, United States
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39
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Li J, Lyu W, Rossetti G, Konijnenberg A, Natalello A, Ippoliti E, Orozco M, Sobott F, Grandori R, Carloni P. Proton Dynamics in Protein Mass Spectrometry. J Phys Chem Lett 2017; 8:1105-1112. [PMID: 28207277 DOI: 10.1021/acs.jpclett.7b00127] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Native electrospray ionization/ion mobility-mass spectrometry (ESI/IM-MS) allows an accurate determination of low-resolution structural features of proteins. Yet, the presence of proton dynamics, observed already by us for DNA in the gas phase, and its impact on protein structural determinants, have not been investigated so far. Here, we address this issue by a multistep simulation strategy on a pharmacologically relevant peptide, the N-terminal residues of amyloid-β peptide (Aβ(1-16)). Our calculations reproduce the experimental maximum charge state from ESI-MS and are also in fair agreement with collision cross section (CCS) data measured here by ESI/IM-MS. Although the main structural features are preserved, subtle conformational changes do take place in the first ∼0.1 ms of dynamics. In addition, intramolecular proton dynamics processes occur on the picosecond-time scale in the gas phase as emerging from quantum mechanics/molecular mechanics (QM/MM) simulations at the B3LYP level of theory. We conclude that proton transfer phenomena do occur frequently during fly time in ESI-MS experiments (typically on the millisecond time scale). However, the structural changes associated with the process do not significantly affect the structural determinants.
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Affiliation(s)
- Jinyu Li
- College of Chemistry, Fuzhou University , 350002 Fuzhou, China
| | - Wenping Lyu
- Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich , 52425 Jülich, Germany
- Faculty of Mathematics, Computer Science and Natural Sciences, RWTH-Aachen University , 52056 Aachen, Germany
- Computation-Based Science and Technology Research Center, Cyprus Institute , 2121 Aglantzia, Nicosia, Cyprus
| | - Giulia Rossetti
- Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich , 52425 Jülich, Germany
- Department of Hematology, Oncology, Hemostaseology, and Stem Cell Transplantation, Faculty of Medicine, RWTH Aachen University , 52062 Aachen, Germany
- Jülich Supercomputing Centre (JSC), Forschungszentrum Jülich , D-52425 Jülich, Germany
| | - Albert Konijnenberg
- Biomolecular & Analytical Mass Spectrometry group, Department of Chemistry, University of Antwerp , 2000 Antwerpen, Belgium
| | - Antonino Natalello
- Department of Biotechnology and Biosciences, University of Milano-Bicocca , Piazza della Scienza 2, 20126 Milan, Italy
| | - Emiliano Ippoliti
- Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich , 52425 Jülich, Germany
| | - Modesto Orozco
- Joint BSC-IRB Program on Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology , Baldiri Reixac 10, Barcelona 08028, Spain
- Departament de Bioquímica i Biomedicina, Facultat de Biologia, Universitat de Barcelona , Avgda Diagonal 647, Barcelona 08028, Spain
| | - Frank Sobott
- Biomolecular & Analytical Mass Spectrometry group, Department of Chemistry, University of Antwerp , 2000 Antwerpen, Belgium
- Astbury Centre for Structural Molecular Biology, University of Leeds , Leeds LS2 9JT, United Kingdom
- School of Molecular and Cellular Biology, University of Leeds , Leeds LS2 9JT, United Kingdom
| | - Rita Grandori
- Department of Biotechnology and Biosciences, University of Milano-Bicocca , Piazza della Scienza 2, 20126 Milan, Italy
| | - Paolo Carloni
- Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich , 52425 Jülich, Germany
- JARA-HPC, 52425 Jülich, Germany
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40
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Chakraborty S, Hong W, Endres KJ, Xie TZ, Wojtas L, Moorefield CN, Wesdemiotis C, Newkome GR. Terpyridine-Based, Flexible Tripods: From a Highly Symmetric Nanosphere to Temperature-Dependent, Irreversible, 3D Isomeric Macromolecular Nanocages. J Am Chem Soc 2017; 139:3012-3020. [DOI: 10.1021/jacs.6b11784] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
| | | | | | | | - Lukasz Wojtas
- Department
of Chemistry, University of South Florida, 4202 East Fowler Avenue, Tampa, Florida 33620, United States
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41
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Yao Y, Chakraborty S, Zhu S, Endres KJ, Xie TZ, Hong W, Manandhar E, Moorefield CN, Wesdemiotis C, Newkome GR. Stepwise, multicomponent assembly of a molecular trapezoid possessing three different metals. Chem Commun (Camb) 2017; 53:8038-8041. [DOI: 10.1039/c7cc04080f] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
A novel terpyridine-based, trapezoidal architecture was synthesized by a coordination-driven multicomponent assembly and features three different tpy–M2+–tpy bonds (M2+ = Ru2+, Fe2+, and Zn2+) in the macrocyclic ring.
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Affiliation(s)
- Yuchen Yao
- Departments of Polymer Science
- University of Akron
- Akron
- USA
| | | | - Shiying Zhu
- Departments of Polymer Science
- University of Akron
- Akron
- USA
| | | | - Ting-Zheng Xie
- Departments of Polymer Science
- University of Akron
- Akron
- USA
| | - Wei Hong
- Departments of Polymer Science
- University of Akron
- Akron
- USA
| | | | | | - Chrys Wesdemiotis
- Departments of Polymer Science
- University of Akron
- Akron
- USA
- Departments of Chemistry
| | - George R. Newkome
- Departments of Polymer Science
- University of Akron
- Akron
- USA
- Departments of Chemistry
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42
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Xie TZ, Endres KJ, Guo Z, Ludlow JM, Moorefield CN, Saunders MJ, Wesdemiotis C, Newkome GR. Controlled Interconversion of Superposed-Bistriangle, Octahedron, and Cuboctahedron Cages Constructed Using a Single, Terpyridinyl-Based Polyligand and Zn2+. J Am Chem Soc 2016; 138:12344-7. [DOI: 10.1021/jacs.6b07969] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
| | | | | | | | | | - Mary Jane Saunders
- Department of Biological Sciences, Florida Atlantic University, Boca
Raton, Florida 33431, United States
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43
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Chakraborty S, Sarkar R, Endres K, Xie TZ, Ghosh M, Moorefield CN, Saunders MJ, Wesdemiotis C, Newkome GR. Programmed Molecular Engineering: Stepwise, Multicomponent Assembly of a Dimetallic Metallotriangulane. European J Org Chem 2016. [DOI: 10.1002/ejoc.201600883] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Sourav Chakraborty
- Department of Polymer Science; The University of Akron; 44325-4717 Akron OH USA
| | - Rajarshi Sarkar
- Department of Chemistry; The University of Akron; 44325-3601 Akron OH USA
| | - Kevin Endres
- Department of Polymer Science; The University of Akron; 44325-4717 Akron OH USA
| | - Ting-Zheng Xie
- Department of Polymer Science; The University of Akron; 44325-4717 Akron OH USA
| | - Monoj Ghosh
- Department of Polymer Engineering; The University of Akron; 44325-0301 Akron USA
| | | | - Mary Jane Saunders
- Department of Biological Science; Florida Atlantic University; 33431 Boca Raton FL USA
| | - Chrys Wesdemiotis
- Department of Polymer Science; The University of Akron; 44325-4717 Akron OH USA
- Department of Chemistry; The University of Akron; 44325-3601 Akron OH USA
| | - George R. Newkome
- Department of Polymer Science; The University of Akron; 44325-4717 Akron OH USA
- Department of Chemistry; The University of Akron; 44325-3601 Akron OH USA
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44
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Liu C, Li Z, Wang H. Drag force and transport property of a small cylinder in free molecule flow: A gas-kinetic theory analysis. Phys Rev E 2016; 94:023102. [PMID: 27627388 DOI: 10.1103/physreve.94.023102] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Indexed: 06/06/2023]
Abstract
Analytical expressions are derived for aerodynamic drag force on small cylinders in the free molecule flow using the gas-kinetic theory. The derivation considers the effect of intermolecular interactions between the cylinder and gas media. Two limiting collision models, specular and diffuse scattering, are investigated in two limiting cylinder orientations with respect to the drift velocity. The earlier solution of Dahneke [B. E. Dahneke, J. Aerosol Sci. 4, 147 (1973)10.1016/0021-8502(73)90066-9] is shown to be a special case of the current expressions in the rigid-body limit of collision. Drag force expressions are obtained for cylinders that undergo Brownian rotation and for those that align with the drift velocity. The validity of the theoretical expressions is tested against experimental mobility data available for carbon nanotubes.
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Affiliation(s)
- Changran Liu
- Department of Mechanical Engineering, Stanford University, Stanford, California 94305, USA
| | - Zhigang Li
- Department of Mechanical and Aerospace Engineering, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Hai Wang
- Department of Mechanical Engineering, Stanford University, Stanford, California 94305, USA
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45
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Akashi S, Downard KM. Effect of charge on the conformation of highly basic peptides including the tail regions of histone proteins by ion mobility mass spectrometry. Anal Bioanal Chem 2016; 408:6637-48. [DOI: 10.1007/s00216-016-9777-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Revised: 06/28/2016] [Accepted: 07/06/2016] [Indexed: 10/21/2022]
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46
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Pepin R, Petrone A, Laszlo KJ, Bush MF, Li X, Tureček F. Does Thermal Breathing Affect Collision Cross Sections of Gas-Phase Peptide Ions? An Ab Initio Molecular Dynamics Study. J Phys Chem Lett 2016; 7:2765-71. [PMID: 27389035 PMCID: PMC5032842 DOI: 10.1021/acs.jpclett.6b01187] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Ab initio molecular dynamics (AIMD) with density functional theory (DFT) was applied to explore conformational motions and collision cross sections (Ω) of folded (2) and extended (7) conformers of doubly charged peptide ions, (Ala-Ala-Leu-Arg + 2H)(2+), in the gas phase at 300 and 473 K. The experimental Ω of (Ala-Ala-Leu-Arg +2H)(2+) was measured as 149 ± 1.2 Å(2) at 298 K. Thermally distributed mean values of Ω for 2 and 7 at 300 and 473 K were only 0.8-1.1% larger than for the equilibrium 0 K structures. Long (>10 ps) trajectory calculations indicated entropy-driven conformational change of 2 to 7 that occurred at random within a ∼ 4 ps time window. The experimental Ω was found to fit the calculated population averaged values for 2 and 7, indicating a rapid conformer interconversion. Overall, thermal breathing had only a minor effect on the peptide ion collision cross sections.
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47
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Wang M, Wang K, Wang C, Huang M, Hao XQ, Shen MZ, Shi GQ, Zhang Z, Song B, Cisneros A, Song MP, Xu B, Li X. Self-Assembly of Concentric Hexagons and Hierarchical Self-Assembly of Supramolecular Metal–Organic Nanoribbons at the Solid/Liquid Interface. J Am Chem Soc 2016; 138:9258-68. [DOI: 10.1021/jacs.6b04959] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ming Wang
- Department of Chemistry and Biochemistry & Materials Science, Engineering, and Commercialization Program, Texas State University, San Marcos, Texas 78666, United States
- State
Key Laboratory of Supramolecular Structure and Materials, College
of Chemistry, Jilin University, Changchun, Jilin 130012, People’s Republic of China
| | - Kun Wang
- Single
Molecule Study Laboratory, College of Engineering and Nanoscale Science
and Engineering Center, University of Georgia, Athens, Georgia 30602, United States
| | - Chao Wang
- Department of Chemistry and Biochemistry & Materials Science, Engineering, and Commercialization Program, Texas State University, San Marcos, Texas 78666, United States
| | - Mingjun Huang
- Department
of Polymer Science, College of Polymer Science and Polymer Engineering, The University of Akron, Akron, Ohio 44325, United States
| | - Xin-Qi Hao
- College
of Chemistry and Molecular Engineering, Zhengzhou University, Zhengzhou 450001, People’s Republic of China
| | - Ming-Zhan Shen
- College
of Chemistry and Molecular Engineering, Zhengzhou University, Zhengzhou 450001, People’s Republic of China
| | - Guo-Qing Shi
- College
of Chemistry and Molecular Engineering, Zhengzhou University, Zhengzhou 450001, People’s Republic of China
- College of
Food and Biological Engineering, Zhengzhou University of Light Industry, Zhengzhou 450002, People’s Republic of China
| | - Zhe Zhang
- Department of Chemistry and Biochemistry & Materials Science, Engineering, and Commercialization Program, Texas State University, San Marcos, Texas 78666, United States
- College
of Chemistry, Central China Normal University, Wuhan 430079, People’s Republic of China
| | - Bo Song
- Department of Chemistry and Biochemistry & Materials Science, Engineering, and Commercialization Program, Texas State University, San Marcos, Texas 78666, United States
| | - Alejandro Cisneros
- Department of Chemistry and Biochemistry & Materials Science, Engineering, and Commercialization Program, Texas State University, San Marcos, Texas 78666, United States
| | - Mao-Ping Song
- College
of Chemistry and Molecular Engineering, Zhengzhou University, Zhengzhou 450001, People’s Republic of China
| | - Bingqian Xu
- Single
Molecule Study Laboratory, College of Engineering and Nanoscale Science
and Engineering Center, University of Georgia, Athens, Georgia 30602, United States
| | - Xiaopeng Li
- Department of Chemistry and Biochemistry & Materials Science, Engineering, and Commercialization Program, Texas State University, San Marcos, Texas 78666, United States
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48
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49
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Coordination-Driven, Self-Assembly of a Polycyclic, Terpyridine-Based Nanobelt. J Inorg Organomet Polym Mater 2016. [DOI: 10.1007/s10904-016-0393-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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50
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Loo RRO, Loo JA. Salt Bridge Rearrangement (SaBRe) Explains the Dissociation Behavior of Noncovalent Complexes. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:975-90. [PMID: 27052739 PMCID: PMC4865452 DOI: 10.1007/s13361-016-1375-3] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2016] [Revised: 02/28/2016] [Accepted: 03/01/2016] [Indexed: 05/11/2023]
Abstract
Native electrospray ionization-mass spectrometry, with gas-phase activation and solution compositions that partially release subcomplexes, can elucidate topologies of macromolecular assemblies. That so much complexity can be preserved in gas-phase assemblies is remarkable, although a long-standing conundrum has been the differences between their gas- and solution-phase decompositions. Collision-induced dissociation of multimeric noncovalent complexes typically distributes products asymmetrically (i.e., by ejecting a single subunit bearing a large percentage of the excess charge). That unexpected behavior has been rationalized as one subunit "unfolding" to depart with more charge. We present an alternative explanation based on heterolytic ion-pair scission and rearrangement, a mechanism that inherently partitions charge asymmetrically. Excessive barriers to dissociation are circumvented in this manner, when local charge rearrangements access a lower-barrier surface. An implication of this ion pair consideration is that stability differences between high- and low-charge state ions usually attributed to Coulomb repulsion may, alternatively, be conveyed by attractive forces from ion pairs (salt bridges) stabilizing low-charge state ions. Should the number of ion pairs be roughly inversely related to charge, symmetric dissociations would be favored from highly charged complexes, as observed. Correlations between a gas-phase protein's size and charge reflect the quantity of restraining ion pairs. Collisionally-facilitated salt bridge rearrangement (SaBRe) may explain unusual size "contractions" seen for some activated, low charge state complexes. That some low-charged multimers preferentially cleave covalent bonds or shed small ions to disrupting noncovalent associations is also explained by greater ion pairing in low charge state complexes. Graphical Abstract ᅟ.
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Affiliation(s)
- Rachel R Ogorzalek Loo
- Department of Biological Chemistry, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA, 90095, USA.
| | - Joseph A Loo
- Department of Biological Chemistry, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA, 90095, USA.
- UCLA/DOE Institute for Genomics and Proteomics, University of California-Los Angeles, Los Angeles, CA, 90095, USA.
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, CA, 90095, USA.
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