1
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Czar MF, Marchand A, Zenobi R. A Modified Traveling Wave Ion Mobility Mass Spectrometer as a Versatile Platform for Gas-Phase Ion-Molecule Reactions. Anal Chem 2019; 91:6624-6631. [PMID: 31008583 DOI: 10.1021/acs.analchem.9b00541] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Taken individually, chemical labeling and mass spectrometry are two well-established tools for the structural characterization of biomolecular complexes. A way to combine their respective advantages is to perform gas-phase ion-molecule reactions (IMRs) inside the mass spectrometer. This is, however, not so well developed because of the limited range of usable chemicals and the lack of commercially available IMR devices. Here, we modified a traveling wave ion mobility mass spectrometer to enable IMRs in the trapping region of the instrument. Only one minor hardware modification is needed to allow vapors of a variety of liquid reagents to be leaked into the trap traveling wave ion guide of the instrument. A diverse set of IMRs can then readily be performed without any loss in instrument performance. We demonstrate the advantages of implementing IMR capabilities in general, and to this quadrupole-ion mobility-time-of-flight (Q-IM-TOF) mass spectrometer in particular, by exploiting the full functionality of the instrument, including mass selection, ion mobility separation, and post-mobility fragmentation. The potential to carry out gas-phase IMR kinetics experiments is also illustrated. We demonstrate the versatility of the setup using gas-phase IMRs of established utility for biological mass spectrometry, including hydrogen-deuterium exchange, ion-molecule proton transfer reactions, and covalent modification of DNA anions using trimethylsilyl chloride.
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Affiliation(s)
- Martin F Czar
- Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences , ETH Zurich , Zurich 8093 , Switzerland
| | - Adrien Marchand
- Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences , ETH Zurich , Zurich 8093 , Switzerland
| | - Renato Zenobi
- Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences , ETH Zurich , Zurich 8093 , Switzerland
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2
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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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3
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Shrivastav V, Nahin M, Hogan CJ, Larriba-Andaluz C. Benchmark Comparison for a Multi-Processing Ion Mobility Calculator in the Free Molecular Regime. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:1540-1551. [PMID: 28477243 DOI: 10.1007/s13361-017-1661-8] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 03/08/2017] [Accepted: 03/14/2017] [Indexed: 06/07/2023]
Abstract
A benchmark comparison between two ion mobility and collision cross-section (CCS) calculators, MOBCAL and IMoS, is presented here as a standard to test the efficiency and performance of both programs. Utilizing 47 organic ions, results are in excellent agreement between IMoS and MOBCAL in He and N2, when both programs use identical input parameters. Due to a more efficiently written algorithm and to its parallelization, IMoS is able to calculate the same CCS (within 1%) with a speed around two orders of magnitude faster than its MOBCAL counterpart when seven cores are used. Due to the high computational cost of MOBCAL in N2, reaching tens of thousands of seconds even for small ions, the comparison between IMoS and MOBCAL is stopped at 70 atoms. Large biomolecules (>10000 atoms) remain computationally expensive when IMoS is used in N2 (even when employing 16 cores). Approximations such as diffuse trajectory methods (DHSS, TDHSS) with and without partial charges and projected area approximation corrections can be used to reduce the total computational time by several folds without hurting the accuracy of the solution. These latter methods can in principle be used with coarse-grained model structures and should yield acceptable CCS results. Graphical Abstract ᅟ.
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Affiliation(s)
- Vaibhav Shrivastav
- Department of Mechanical Engineering, IUPUI, Indianapolis, IN, 46202, USA
| | - Minal Nahin
- Department of Mechanical Engineering, IUPUI, Indianapolis, IN, 46202, USA
| | - Christopher J Hogan
- Department of Mechanical Engineering, University of Minnesota, Minneapolis, MN, 55455, USA
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4
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Laszlo KJ, Munger EB, Bush MF. Effects of Solution Structure on the Folding of Lysozyme Ions in the Gas Phase. J Phys Chem B 2017; 121:2759-2766. [PMID: 28301724 PMCID: PMC5486214 DOI: 10.1021/acs.jpcb.7b00783] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The fidelity between the structures of proteins in solution and protein ions in the gas phase is critical to experiments that use gas-phase measurements to infer structures in solution. Here we generate ions of lysozyme, a 129-residue protein whose native tertiary structure contains four internal disulfide bonds, from three solutions that preserve varying extents of the original native structure. We then use cation-to-anion proton-transfer reactions (CAPTR) to reduce the charge states of those ions in the gas phase and ion mobility to probe their structures. The collision cross section (Ω) distributions of each CAPTR product depends to varying extents on the original solution, the charge state of the product, and the charge state of the precursor. For example, the Ω distributions of the 6+ ions depend strongly on the original solutions conditions and to a lesser extent on the charge state of the precursor. Energy-dependent experiments suggest that very different structures are accessible to disulfide-reduced and disulfide-intact ions, but similar Ω distributions are formed at high energy for disulfide-intact ions from denaturing and from aqueous conditions. The Ω distributions of the 3+ ions are all similar but exhibit subtle differences that depend more strongly on the original solutions conditions than other factors. More generally, these results suggest that specific CAPTR products may be especially sensitive to specific elements of structure in solution.
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Affiliation(s)
- Kenneth J. Laszlo
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195-1700, United States
| | - Eleanor B. Munger
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195-1700, United States
| | - Matthew F. Bush
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195-1700, United States
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5
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Laszlo KJ, Munger EB, Bush MF. Folding of Protein Ions in the Gas Phase after Cation-to-Anion Proton-Transfer Reactions. J Am Chem Soc 2016; 138:9581-8. [PMID: 27399988 PMCID: PMC4999245 DOI: 10.1021/jacs.6b04282] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The structure and folding of a protein in solution depends on noncovalent interactions within the protein and those with surrounding ions and molecules. Decoupling these interactions in solution is challenging, which has hindered the development of accurate physics-based models for structure prediction. Investigations of proteins in the gas phase can be used to selectively decouple factors affecting the structures of proteins. Here, we use cation-to-anion proton-transfer reactions (CAPTR) to reduce the charge states of denatured ubiquitin ions in the gas phase, and ion mobility to probe their structures. In CAPTR, a precursor charge state is selected (P) and reacted with monoanions to generate charge-reduced product ions (C). Following each CAPTR event, denatured ubiquitin ions (13+ to 6+) yield products that rapidly isomerize to structures that have smaller collision cross sections (Ω). The Ω values of CAPTR product ions depend strongly on C and very weakly on P. Pre- and post-CAPTR activation was then used to probe the potential-energy surfaces of the precursor and product ions, respectively. Post-CAPTR activation showed that ions of different P fold differently and populate different regions of the potential-energy surface of that ion. Finally, pre-CAPTR activation showed that the structures of protein ions can be indirectly investigated using ion mobility of their CAPTR product ions, even for subtle structural differences that are not apparent from ion mobility characterization of the activated precursor ions. More generally, these results show that CAPTR strongly complements existing techniques for characterizing the structures and dynamics of biological molecules in the gas phase.
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Affiliation(s)
- Kenneth J. Laszlo
- University of Washington, Department of Chemistry, Box 351700 Seattle, WA 98195-1700
| | - Eleanor B. Munger
- University of Washington, Department of Chemistry, Box 351700 Seattle, WA 98195-1700
| | - Matthew F. Bush
- University of Washington, Department of Chemistry, Box 351700 Seattle, WA 98195-1700
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6
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Ewing MA, Glover MS, Clemmer DE. Hybrid ion mobility and mass spectrometry as a separation tool. J Chromatogr A 2016; 1439:3-25. [DOI: 10.1016/j.chroma.2015.10.080] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 10/05/2015] [Accepted: 10/21/2015] [Indexed: 11/29/2022]
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7
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Seaiby C, Zabuga AV, Svendsen A, Rizzo TR. IR-induced conformational isomerization of a helical peptide in a cold ion trap. J Chem Phys 2016; 144:014304. [DOI: 10.1063/1.4939528] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Affiliation(s)
- Caroline Seaiby
- Laboratoire de Chimie Physique Moléculaire, Ecole Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
| | - Aleksandra V. Zabuga
- Laboratoire de Chimie Physique Moléculaire, Ecole Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
| | - Annette Svendsen
- Laboratoire de Chimie Physique Moléculaire, Ecole Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
| | - Thomas R. Rizzo
- Laboratoire de Chimie Physique Moléculaire, Ecole Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
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8
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Baldauf C, Rossi M. Going clean: structure and dynamics of peptides in the gas phase and paths to solvation. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2015; 27:493002. [PMID: 26598600 DOI: 10.1088/0953-8984/27/49/493002] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The gas phase is an artificial environment for biomolecules that has gained much attention both experimentally and theoretically due to its unique characteristic of providing a clean room environment for the comparison between theory and experiment. In this review we give an overview mainly on first-principles simulations of isolated peptides and the initial steps of their interactions with ions and solvent molecules: a bottom up approach to the complexity of biological environments. We focus on the accuracy of different methods to explore the conformational space, the connections between theory and experiment regarding collision cross section evaluations and (anharmonic) vibrational spectra, and the challenges faced in this field.
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Affiliation(s)
- Carsten Baldauf
- Fritz Haber Institute, Faradayweg 4-6, 14195 Berlin, Germany
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9
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Dickinson ER, Jurneczko E, Pacholarz KJ, Clarke DJ, Reeves M, Ball KL, Hupp T, Campopiano D, Nikolova PV, Barran PE. Insights into the conformations of three structurally diverse proteins: cytochrome c, p53, and MDM2, provided by variable-temperature ion mobility mass spectrometry. Anal Chem 2015; 87:3231-8. [PMID: 25629302 DOI: 10.1021/ac503720v] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Thermally induced conformational transitions of three proteins of increasing intrinsic disorder-cytochrome c, the tumor suppressor protein p53 DNA binding domain (p53 DBD), and the N-terminus of the oncoprotein murine double minute 2 (NT-MDM2)-have been studied by native mass spectrometry and variable-temperature drift time ion mobility mass spectrometry (VT-DT-IM-MS). Ion mobility measurements were carried out at temperatures ranging from 200 to 571 K. Multiple conformations are observable over several charge states for all three monomeric proteins, and for cytochrome c, dimers of significant intensity are also observed. Cytochrome c [M + 5H](5+) ions present in one conformer of CCS ∼1200 Å(2), undergoing compaction in line with the reported Tmelt = 360.15 K before slight unfolding at 571 K. The more extended [M + 7H](7+) cytochrome c monomer presents as two conformers undergoing similar compaction and structural rearrangements, prior to thermally induced unfolding. The [D + 11H](11+) dimer presents as two conformers, which undergo slight structural compaction or annealing before dissociation. p53 DBD follows a trend of structural collapse before an increase in the observed collision cross section (CCS), akin to that observed for cytochrome c but proceeding more smoothly. At 300 K, the monomeric charge states present in two conformational families, which compact to one conformer of CCS ∼1750 Å(2) at 365 K, in line with the low solution Tmelt = 315-317 K. The protein then extends to produce either a broad unresolved CCS distribution or, for z > 9, two conformers. NT-MDM2 exhibits a greater number of structural rearrangements, displaying charge-state-dependent unfolding pathways. DT-IM-MS experiments at 200 K resolve multiple conformers. Low charge state species of NT-MDM2 present as a single compact conformational family centered on CCS ∼1250 Å(2) at 300 K. This undergoes conformational tightening in line with the solution Tmelt = 348 K before unfolding at the highest temperatures. The more extended charge states present in two or more conformers at room temperature, undergoing thermally induced unfolding before significant structural collapse or annealing at high temperatures. Variable-temperature IM-MS is here shown to be an exciting approach to discern protein unfolding pathways for conformationally diverse proteins.
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Affiliation(s)
- Eleanor R Dickinson
- †Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, United Kingdom
| | - Ewa Jurneczko
- ‡School of Chemistry, University of Edinburgh, Edinburgh EH9 3JJ, United Kingdom
| | - Kamila J Pacholarz
- †Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, United Kingdom
| | - David J Clarke
- ‡School of Chemistry, University of Edinburgh, Edinburgh EH9 3JJ, United Kingdom
| | - Matthew Reeves
- ‡School of Chemistry, University of Edinburgh, Edinburgh EH9 3JJ, United Kingdom
| | - Kathryn L Ball
- §Institute of Genetics and Molecular Medicine, CRUK Cancer Research Centre, University of Edinburgh, Edinburgh EH4 2XR, United Kingdom
| | - Ted Hupp
- §Institute of Genetics and Molecular Medicine, CRUK Cancer Research Centre, University of Edinburgh, Edinburgh EH4 2XR, United Kingdom
| | - Dominic Campopiano
- ‡School of Chemistry, University of Edinburgh, Edinburgh EH9 3JJ, United Kingdom
| | - Penka V Nikolova
- ∥School of Biomedical Science, Institute of Pharmaceutical Sciences, King's College London, 150 Stamford Street, London SE1 9NH, United Kingdom
| | - Perdita E Barran
- †Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, United Kingdom
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Rajabi K. Time-resolved pulsed hydrogen/deuterium exchange mass spectrometry probes gaseous proteins structural kinetics. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:71-82. [PMID: 25318698 DOI: 10.1007/s13361-014-1004-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Revised: 09/10/2014] [Accepted: 09/11/2014] [Indexed: 06/04/2023]
Abstract
A pulsed hydrogen/deuterium exchange (HDX) method has been developed for rapid monitoring of the exchange kinetics of protein ions with D2O a few milliseconds after electrospray ionization (ESI). The stepwise gradual evolution of HDX of multiply charged protein ions was monitored using the pulsed HDX mass spectrometry technique. Upon introducing a very short pulse of D2O (in the μs to ms time scale) into the linear ion trap (LIT) of a time-of-flight (TOF) mass spectrometer, bimodal distributions were detected for the ions of cytochrome c and ubiquitin. Mechanistic details of HDX reactions for ubiquitin and cytochrome c in the gas phase were uncovered and the structural transitions were followed by analyzing the kinetics of HDX.
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Affiliation(s)
- Khadijeh Rajabi
- Department of Chemistry, University of British Columbia (UBC), 2036 Mail Mall, Vancouver, BC, V6T 1Z1, Canada,
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11
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Shvartsburg AA. Ultrahigh-Resolution Differential Ion Mobility Separations of Conformers for Proteins above 10 kDa: Onset of Dipole Alignment? Anal Chem 2014; 86:10608-15. [DOI: 10.1021/ac502389a] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Alexandre A. Shvartsburg
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, United States
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12
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Valentine SJ, Liu X, Plasencia MD, Hilderbrand AE, Kurulugama RT, Koeniger SL, Clemmer DE. Developing liquid chromatography ion mobility mass spectometry techniques. Expert Rev Proteomics 2014; 2:553-65. [PMID: 16097888 DOI: 10.1586/14789450.2.4.553] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
When a packet of ions in a buffer gas is exposed to a weak electric field, the ions will separate according to differences in their mobilities through the gas. This separation forms the basis of the analytical method known as ion mobility spectroscopy and is highly efficient, in that it can be carried out in a very short time frame (micro- to milliseconds). Recently, efforts have been made to couple the approach with liquid-phase separations and mass spectrometry in order to create a high-throughput and high-coverage approach for analyzing complex mixtures. This article reviews recent work to develop this approach for proteomics analyses. The instrumentation is described briefly. Several multidimensional data sets obtained upon analyzing complex mixtures are shown in order to illustrate the approach as well as provide a view of the limitations and required future work.
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Affiliation(s)
- Stephen J Valentine
- Predictive Physiology & Medicine, 1424 W. Adams Hill, Bloomington, IN 47403, USA.
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13
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Nonose S, Okamura T, Yamashita K, Sudo A. Temperature dependence of gas-phase conformations for ubiquitin ions characterized by proton transfer reactions. Chem Phys 2013. [DOI: 10.1016/j.chemphys.2013.02.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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14
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Gillig KJ, Chen CH. Critical examination of gas-phase protein conformation/multimer ion formation by electrospray ion mobility-mass spectrometry. Anal Chem 2013; 85:2177-82. [PMID: 23298466 DOI: 10.1021/ac3028849] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The generally accepted view of protein structure in the gas-phase is that protein ions produced by electrospray ionization (ESI) exist in a number of different states, and the resulting charge state distribution (CSD) and ion mobility spectrum is interpreted as evidence for protein ions retaining some memory of solution-phase conformation. Even with the inclusion of ion mobility information, reports of protein ion structure in the gas-phase are oftentimes in disagreement not only within the discipline but also as interpreted by other gas-phase techniques. The focus of this work will be to correctly distinguish truly different ion conformations formed by ESI versus homomultimeric complexes with the same m/z. The concentration of cytochrome c in solution was varied over a wide range, and the multiply charged multimers (MCMs) present in the ion mobility/mass spectrum were unambiguously assigned by m/z selection and dissociation prior to ion mobility/mass spectrometry analysis. The results revealed false negatives for protein oligomer formation and false positives for protein conformational states and no evidence that gas-phase cytochrome c ions retain memory of solution-phase conformation, characteristics of great importance for structural biology. The results also suggest that the total IM-MS distribution for a protein is the complex result of individual MCMs either surviving until detection (undissociated) or dissociating into lower order multimers or a number of product ions for each m/z.
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Affiliation(s)
- Kent J Gillig
- Genomics Research Center, Academia Sinica, 128 Academia Road, Nankang Sec. 2, Taipei 115, Taiwan
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15
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Warnke S, von Helden G, Pagel K. Protein Structure in the Gas Phase: The Influence of Side-Chain Microsolvation. J Am Chem Soc 2013; 135:1177-80. [DOI: 10.1021/ja308528d] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Stephan Warnke
- Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195 Berlin, Germany
| | - Gert von Helden
- Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195 Berlin, Germany
| | - Kevin Pagel
- Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195 Berlin, Germany
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16
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Ubiquinol-cytochrome c reductase (Complex III) electrochemistry at multi-walled carbon nanotubes/Nafion modified glassy carbon electrodes. Electrochim Acta 2012. [DOI: 10.1016/j.electacta.2011.11.121] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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17
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Deng Z, Thontasen N, Malinowski N, Rinke G, Harnau L, Rauschenbach S, Kern K. A close look at proteins: submolecular resolution of two- and three-dimensionally folded cytochrome c at surfaces. NANO LETTERS 2012; 12:2452-8. [PMID: 22530980 DOI: 10.1021/nl3005385] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Imaging of individual protein molecules at the single amino acid level has so far not been possible due to the incompatibility of proteins with the vacuum environment necessary for high-resolution scanning probe microscopy. Here we demonstrate electrospray ion beam deposition of selectively folded and unfolded cytochrome c protein ions on atomically defined solid surfaces in ultrahigh vacuum (10(-10) mbar) and achieve unprecedented resolution with scanning tunneling microscopy. On the surface folded proteins are found to retain their three-dimensional structure. Unfolded proteins are observed as extended polymer strands displaying submolecular features with resolution at the amino acid level. On weakly interacting surfaces, unfolded proteins refold into flat, irregular patches composed of individual molecules. This suggests the possibility of two-dimensionally confined folding of peptides of an appropriate sequence into regular two-dimensional structures as a new approach toward functional molecular surface coatings.
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Affiliation(s)
- Zhitao Deng
- Max-Planck-Institute for Solid State Research, Heisenbergstrasse 1, D-70569 Stuttgart, Germany
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18
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Vonderach M, Ehrler OT, Weis P, Kappes MM. Combining Ion Mobility Spectrometry, Mass Spectrometry, and Photoelectron Spectroscopy in a High-Transmission Instrument. Anal Chem 2011; 83:1108-15. [DOI: 10.1021/ac1029677] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Matthias Vonderach
- Abteilung für Physikalische Chemie Mikroskopischer Systeme, Institut für Physikalische Chemie, Karlsruher Institut für Technologie (KIT), Fritz-Haber Weg 2, 76128 Karlsruhe, Germany
| | - Oli T. Ehrler
- Abteilung für Physikalische Chemie Mikroskopischer Systeme, Institut für Physikalische Chemie, Karlsruher Institut für Technologie (KIT), Fritz-Haber Weg 2, 76128 Karlsruhe, Germany
| | - Patrick Weis
- Abteilung für Physikalische Chemie Mikroskopischer Systeme, Institut für Physikalische Chemie, Karlsruher Institut für Technologie (KIT), Fritz-Haber Weg 2, 76128 Karlsruhe, Germany
| | - Manfred M. Kappes
- Abteilung für Physikalische Chemie Mikroskopischer Systeme, Institut für Physikalische Chemie, Karlsruher Institut für Technologie (KIT), Fritz-Haber Weg 2, 76128 Karlsruhe, Germany
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19
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Chudinov AV, Sulimenkov IV, Pikhtelev AR, Kozlovskii VI. Study of H/D-exchange reaction kinetics of polypeptides. JOURNAL OF ANALYTICAL CHEMISTRY 2010. [DOI: 10.1134/s1061934810140121] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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20
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Uetrecht C, Rose RJ, van Duijn E, Lorenzen K, Heck AJR. Ion mobility mass spectrometry of proteins and proteinassemblies. Chem Soc Rev 2010; 39:1633-55. [DOI: 10.1039/b914002f] [Citation(s) in RCA: 381] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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21
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Segev E, Wyttenbach T, Bowers MT, Gerber RB. Conformational evolution of ubiquitin ions in electrospray mass spectrometry: molecular dynamics simulations at gradually increasing temperatures. Phys Chem Chem Phys 2008; 10:3077-82. [DOI: 10.1039/b718610j] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Nanita SC, Sokol E, Cooks RG. Alkali metal-cationized serine clusters studied by sonic spray ionization tandem mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2007; 18:856-68. [PMID: 17346986 DOI: 10.1016/j.jasms.2007.01.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2006] [Revised: 01/09/2007] [Accepted: 01/09/2007] [Indexed: 05/14/2023]
Abstract
Serine solutions containing salts of alkali metals yield magic number clusters of the type (Ser(4)+C)(+), (Ser(8)+C)(+), (Ser(12)+C)(+), and (Ser(17)+2C)(+2) (where C = Li(+), Na(+), K(+), Rb(+), or Cs(+)), in relative abundances which are strongly dependent on the cation size. Strong selectivity for homochirality is involved in the formation of serine tetramers cationized by K(+), Rb(+), and Cs(+). This is also the case for the octamers cationized by the smaller alkalis but there is a strong preference for heterochirality in the octamers cationized by the larger alkali cations. Tandem mass spectrometry shows that the octamers and dodecamers cationized by K(+), Rb(+), and Cs(+) dissociate mainly by the loss of Ser(4) units, suggesting that the neutral tetramers are the stable building blocks of the observed larger aggregates, (Ser(8)+C)(+) and (Ser(12)+C)(+). Remarkably, although the Ser(4) units are formed with a strong preference for homochirality, they aggregate further regardless of their handedness and, therefore, with a preference for the nominally racemic 4D:4L structure and an overall strong heterochiral preference. The octamers cationized by K(+), Rb(+), or Cs(+) therefore represent a new type of cluster ion that is homochiral in its internal subunits, which then assemble in a random fashion to form octamers. We tentatively interpret the homochirality of these tetramers as a consequence of assembly of the serine molecules around a central metal ion. The data provide additional evidence that the neutral serine octamer is homochiral and is readily cationized by smaller ions.
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Affiliation(s)
- Sergio C Nanita
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA
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23
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Koeniger SL, Clemmer DE. Resolution and structural transitions of elongated states of ubiquitin. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2007; 18:322-31. [PMID: 17084091 DOI: 10.1016/j.jasms.2006.09.025] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2006] [Revised: 09/21/2006] [Accepted: 09/28/2006] [Indexed: 05/11/2023]
Abstract
Electrospray ionization, combined with two-dimensional ion mobility spectrometry and mass spectrometry, is used to produce, select, and activate distributions of elongated ions, [M + 11H]11+ to [M + 13H]13+, of ubiquitin. The analysis makes it possible to examine state-to-state transitions for structural types, and transition diagrams associated with the efficiencies of structural changes are presented. The +11 and +12 charge states can form four resolvable states while only one state is formed for [M + 13H]13+. Some conformations, which appear to belong to the same family based on mobility analysis of different charge states, undergo similar transitions, others do not. Activation of ions that exist in low-abundance conformations, having mobilities that fall in between sharp peaks associated with higher abundances species, shows that the low-abundance forms undergo efficient (approximately 90 to 100%) conversion into states associated with well-defined peaks. This efficiency is significantly higher than the approximately 10 to 60% efficiency of transitions of structures associated with well-defined peaks. The formation of sharp features from a range of low-intensity species with different cross sections indicates that large regions of conformation space must be unfavorable or inaccessible in the gas phase. These results are compared with several previous IMS measurements of this system as well as information about gas-phase structure provided by other techniques.
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Affiliation(s)
- Stormy L Koeniger
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA
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24
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Chen X, Thachuk M. Collision-induced alignment of H2O+ drifting in helium. J Chem Phys 2006; 124:174501. [PMID: 16689577 DOI: 10.1063/1.2189235] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The collision-induced alignment of H(2)O(+) drifting in helium is studied with a molecular dynamics method that has been extended to treat nonlinear rigid ions. Rotational distribution functions and averaged quantities are presented in terms of the rho formalism [M. Thachuk, Phys. Rev. A 72, 032722 (2005)], and it is shown that this description gives a very good agreement with simulation results. In addition to velocity and angular velocity autocorrelation functions, a velocity-angular velocity cross correlation function is introduced. This cross correlation function provides insight into the dynamical nature of the alignment mechanism.
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Affiliation(s)
- Xin Chen
- Chemistry Department, University of British Columbia, Vancouver V6T 1Z1, Canada
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25
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Shvartsburg AA, Li F, Tang K, Smith RD. Characterizing the Structures and Folding of Free Proteins Using 2-D Gas-Phase Separations: Observation of Multiple Unfolded Conformers. Anal Chem 2006; 78:3304-15. [PMID: 16689531 DOI: 10.1021/ac060283z] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Understanding the 3-D structure and dynamics of proteins and other biological macromolecules in various environments is among the central challenges of chemistry. Electrospray ionization can often transfer ions from solution to gas phase with only limited structural distortion, allowing their profiling using mass spectrometry and other gas-phase approaches. Ion mobility spectrometry (IMS) can separate and characterize macroion conformations with high sensitivity and speed. However, IMS separation power is generally insufficient for full resolution of major structural variants of protein ions and elucidation of their interconversion dynamics. Here we report characterization of macromolecular conformations using field asymmetric waveform IMS (FAIMS) coupled to conventional IMS in conjunction with mass spectrometry. The collisional heating of ions in the electrodynamic funnel trap between FAIMS and IMS stages enables investigating the structural evolution of particular isomeric precursors as a function of the intensity and duration of activation that can be varied over large ranges. These new capabilities are demonstrated for ubiquitin and cytochrome c, two common model proteins for structure and folding studies. For nearly all charge states, two-dimensional FAIMS/IMS separations distinguish many more conformations than either FAIMS or IMS alone, including some with very low abundance. For cytochrome c in high charge states, we find several abundant "unfolded" isomer series not distinguishable by IMS, possibly corresponding to different "string of beads" geometries. The unfolding of specific ubiquitin conformers selected by FAIMS has been studied by employing their heating in the FAIMS/IMS interface.
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Affiliation(s)
- Alexandre A Shvartsburg
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, WA 99352, USA
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26
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Wang W, Kitova EN, Sun J, Klassen JS. Blackbody infrared radiative dissociation of nonspecific protein-carbohydrate complexes produced by nanoelectrospray ionization: the nature of the noncovalent interactions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2005; 16:1583-94. [PMID: 16087347 DOI: 10.1016/j.jasms.2005.05.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2005] [Revised: 05/16/2005] [Accepted: 05/18/2005] [Indexed: 05/03/2023]
Abstract
Gas-phase thermal dissociation experiments, implemented with blackbody infrared radiative dissociation (BIRD) and Fourier transform ion cyclotron resonance mass spectrometry, have been performed on a series of protonated and deprotonated 1:1 and protonated 1:2 protein-carbohydrate complexes formed by nonspecific interactions during the nanoflow electrospray (nanoES) ionization process. Nonspecific interactions between the proteins bovine carbonic anhydrase II (CA), bovine ubiquitin (Ubq), and bovine pancreatic trypsin inhibitor and several carbohydrates, ranging in size from mono- to tetrasaccharides, have been investigated. Over the range of temperatures studied (60-190 degrees C), BIRD of the protonated and deprotonated complexes proceeds exclusively by the loss of the carbohydrate in its neutral form. The rates of dissociation of the 1:1 complexes containing a mono- or disaccharide decrease with reaction time, suggesting the presence of two or more kinetically distinct structures produced during nanoES or by gas-phase processes. In contrast, the 1:1 complexes of the tri- and tetrasaccharides exhibit simple first-order dissociation kinetics, a result that, on its own, is suggestive of a single preferred carbohydrate binding site or multiple equivalent sites in the gas phase. A comparative analysis of the dissociation kinetics measured for protonated 1:1 and 1:2 complexes of Ubq with alphaTal[alphaAbe]alphaMan further supports the presence of a single preferred binding site. However, a similar analysis performed on the complexes of CA and alphaTal[alphaAbe]alphaMan suggests that equivalent but dependent carbohydrate binding sites exist in the gas phase. Analysis of the Arrhenius activation parameters (E(a) and A) determined for the dissociation of 1:1 complexes of CA with structurally related trisaccharides provides evidence that neutral intermolecular hydrogen bonds contribute, at least in part, to the stability of the gaseous complexes. Surprisingly, the E(a) values for the complexes of the same charge state are not sensitive to the structure (primary or higher order) of the protein, suggesting that the carbohydrates are able to form energetically equivalent interactions with the various functional groups presented by the protein. For a given protein-carbohydrate complex, the dissociation E(a) is sensitive to charge state, initially increasing and then decreasing with increasing charge. It is proposed that both ionic and neutral hydrogen bonds stabilize the nonspecific protein-carbohydrate complexes in the gas phase and that the relative contribution of the neutral and ionic interactions is strongly influenced by the charge state of the complex, with neutral interactions dominating at low charge states and ionic interactions dominating at high charge states.
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Affiliation(s)
- Weijie Wang
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
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Sowell RA, Koeniger SL, Valentine SJ, Moon MH, Clemmer DE. Nanoflow LC/IMS-MS and LC/IMS-CID/MS of protein mixtures. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2004; 15:1341-1353. [PMID: 15337515 DOI: 10.1016/j.jasms.2004.06.014] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2004] [Revised: 06/23/2004] [Accepted: 06/23/2004] [Indexed: 05/24/2023]
Abstract
A simple ion trap/ion mobility/time-of-flight (TOF) mass spectrometer has been coupled with nanoflow liquid chromatography to examine the feasibility of analyzing mixtures of intact proteins. In this approach proteins are separated using reversed-phase chromatography. As components elute from the column, they are electrosprayed into the gas phase and separated again in a drift tube prior to being dispersed and analyzed in a TOF mass spectrometer. The mobilities of ions through a buffer gas depend upon their collision cross sections and charge states; separation based on these gas-phase parameters provides a new means of simplifying mass spectra and characterizing mixtures. Additionally it is possible to induce dissociation at the exit of the drift tube and examine the fragmentation patterns of specific protein ion charge states and conformations. The approach is demonstrated by examining a simple three-component mixture containing ubiquitin, cytochrome c, and myoglobin and several larger prepared protein mixtures. The potential of this approach for use in proteomic applications is considered.
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Affiliation(s)
- Renã A Sowell
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA
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Valentine SJ, Koeniger SL, Clemmer DE. A Split-Field Drift Tube for Separation and Efficient Fragmentation of Biomolecular Ions. Anal Chem 2003; 75:6202-8. [PMID: 14616002 DOI: 10.1021/ac030111r] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A new ion mobility instrument that incorporates a low-field region for ion separation and a high-field region for collisional activation is described. In this approach, mixtures of ions are separated based on differences in their mobilities in a approximately 20-cm-long low-field ( approximately 5 V cm(-)(1)) region of a drift tube. As the ions approach the drift tube exit, they are exposed to a large focusing potential drop; at high fields, ions are efficiently collisionally activated and dissociate as they exit the drift tube. We have demonstrated this approach by examining the fragmentation pattern for electrosprayed bradykinin ions. These studies show that the activation process is highly tunable; it is possible to modulate the field such that precursor ion mass spectra as well as several high-field collision-induced fragmentation patterns can be obtained. The approach also appears to be a simple means of activating protein ions, as demonstrated by examining electrosprayed myoglobin ions.
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Valentine SJ, Clemmer DE. Temperature-dependent H/D exchange of compact and elongated cytochrome c ions in the gas phase. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2002; 13:506-517. [PMID: 12019975 DOI: 10.1016/s1044-0305(02)00372-0] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Isotopic exchange reactions of compact and elongated conformations of gaseous cytochrome c ions (+5 and +9 states) with D2O have been measured as a function of temperature (from 300 to approximately 440 K) using ion mobility techniques. Rate constants for those sites that exchange at high temperatures (>400 K) are about an order of magnitude smaller than rate constants for sites that exchange at 300 K. Although the exchange rates decrease, the maximum exchange levels for rapidly exchanging sites increase with temperature. At 300 K, exchange levels of 53 +/- 3 and 63 +/- 3 are measured for the compact and elongated states, respectively. From 300 to 335 K, the exchange levels increase slightly to approximately 60 to 70 hydrogens. Above 335 K, the levels increase to a value of approximately 200 for the +5 state and approximately 190 for the +9 state, near the maximum possible levels, 200 and 204 for these respective charge states. Molecular dynamics simulations have been carried out on structures having calculated cross sections that are near the experimental values in order to explore the exchange process. Overall, it appears that charge site and exchange site proximities are important factors in the exchange profiles for the elongated +9 ion and the compact +5 ion.
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30
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Arteca GA, Tapia O. Protein Denaturation in Vacuo. Behavior of the Four-α-Helix Bundle of Apocytochrome c‘ under Centrifugal Unfolding Conditions. J Phys Chem B 2002. [DOI: 10.1021/jp012692z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Gustavo A. Arteca
- Département de Chimie et Biochimie, Laurentian University, Ramsey Lake Road, Sudbury, Ontario P3E 2C6, Canada
| | - O. Tapia
- Department of Physical Chemistry, Uppsala University, Box 532, Uppsala S-751 21, Sweden
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31
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Abstract
In vacuo proteins provide a simple laboratory to explore the roles of sequence, temperature, charge state, and initial configuration in protein folding. Moreover, by the very absence of solvent, the study of anhydrous proteins in vacuo will also help us to understand specific environmental effects. From the experimental viewpoint, these systems are now beginning to be characterized at low resolution. Molecular dynamics (MD) simulations, in combination with tools for protein shape analysis, can complement experiments and provide further insights on the folding-unfolding transitions of these proteins. We review some aspects of this issue by using the results from a detailed MD study of hen egg-white lysozyme. For lysozyme ions, unfolding can be triggered by Coulombic repulsion. In neutral lysozyme, unfolding can be induced by centrifugal forces and also by weakening the monomer-monomer interaction. In both cases, the resulting unfolded transients can be used as initial configurations for relaxation dynamics. All trajectories are analyzed in terms of global molecular shape features of the backbone, including its anisometry and chain entanglement complexity. This strategy allows us to quantify separately the degree of polymer collapse and the evolution of large-scale folding features. Using these last two notions, we discuss some basic questions regarding the nature of the accessible paths associated with unfolding from, and refolding into, compact conformers.
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Affiliation(s)
- G A Arteca
- Département de Chimie et Biochimie, Laurentian University, Ramsey Lake Road, Sudbury, Ontario P3E 2C6, Canada.
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32
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Arteca GA, Reimann CT, Tapia O. Proteins in vacuo: denaturing and folding mechanisms studied with computer-simulated molecular dynamics. MASS SPECTROMETRY REVIEWS 2001; 20:402-422. [PMID: 11997946 DOI: 10.1002/mas.10012] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Mounting evidence from experiments suggests that the native fold in solution is metastable in dehydrated proteins. Results from a number of experiments that use mass spectrometry indicate also that folding-unfolding transitions take place in protein ions even in the absence of water. These observations on anhydrous proteins call for a re-evaluation of our understanding of the folding transition. In this context, computer-assisted simulations are an important complementary tool. Here, we provide an overview of recent progress on the simulation of proteins in vacuo. In particular, we discuss the response of proteins and protein ions to perturbations that trigger unfolding and re-folding transitions. By comparing the general patterns emerging from theory and experiment, we propose a series of new measurements that could help to validate, and improve, current simulation models.
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Affiliation(s)
- G A Arteca
- Département de Chimie et Biochimie, Laurentian University, Ramsey Lake Road, Sudbury, Ontario P3E 2C6, Canada
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33
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Arteca GA, Reimann CT, Tapia O. Transitions in Chain Entanglement and Compactness Associated with in Vacuo Unfolding of Lysozyme Ions. J Phys Chem B 2001. [DOI: 10.1021/jp0037955] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Gustavo A. Arteca
- Département de Chimie et Biochimie, Laurentian University, Sudbury, Ontario, Canada P3E 2C6, Department of Physical Chemistry, Uppsala University, Box 532, S-751 21 Uppsala, Sweden, and Department of Analytical Chemistry, Chemical Center, Lund University, Box 124, S-221 00 Lund, Sweden
| | - C. T. Reimann
- Département de Chimie et Biochimie, Laurentian University, Sudbury, Ontario, Canada P3E 2C6, Department of Physical Chemistry, Uppsala University, Box 532, S-751 21 Uppsala, Sweden, and Department of Analytical Chemistry, Chemical Center, Lund University, Box 124, S-221 00 Lund, Sweden
| | - O. Tapia
- Département de Chimie et Biochimie, Laurentian University, Sudbury, Ontario, Canada P3E 2C6, Department of Physical Chemistry, Uppsala University, Box 532, S-751 21 Uppsala, Sweden, and Department of Analytical Chemistry, Chemical Center, Lund University, Box 124, S-221 00 Lund, Sweden
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Abstract
This article provides a review of recent studies of the properties of unsolvated (and partially solvated) peptides and proteins. The methods used to produce vapor-phase peptide and protein ions are described along with some of the techniques used to study them, such as H/D exchange, blackbody infrared radiative dissociation, and ion mobility measurements. Studies of unsolvated peptides and proteins provide information about their intrinsic intramolecular interactions. The topics covered include the role of zwitterions and salt bridges in the vapor phase, Coulomb interactions in multiply charged ions, the unfolding and refolding of vapor-phase proteins, and the stability of unsolvated helices and sheets. Finally, dehydration and rehydration studies of proteins in the vapor phase are described. These can provide exquisitely detailed information about hydration interactions, such as the enthalpy and entropy changes associated with adsorbing individual water molecules.
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Affiliation(s)
- M F Jarrold
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, USa.
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36
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Arteca GA, Tapia O. Protein denaturation in vacuo: Mechanism for centrifugal unfolding of neutral lysozyme. J Chem Phys 2001. [DOI: 10.1063/1.1412865] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
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37
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Arteca GA, Reimann CT, Tapia O. Effect of a Variable Nonbonded Attractive Pair Interaction on the Relaxation Dynamics of in Vacuo Unfolded Lysozyme. J Phys Chem B 2000. [DOI: 10.1021/jp001841v] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Gustavo A. Arteca
- Département de chimie et biochimie, Laurentian University, Sudbury, Ontario, Canada P3E 2C6, Department of Physical Chemistry, Uppsala University, Box 532, S-751 21 Uppsala, Sweden, and Department of Analytical Chemistry, Chemical Center, University of Lund, Box 124, S-221 00 Lund, Sweden
| | - C. T. Reimann
- Département de chimie et biochimie, Laurentian University, Sudbury, Ontario, Canada P3E 2C6, Department of Physical Chemistry, Uppsala University, Box 532, S-751 21 Uppsala, Sweden, and Department of Analytical Chemistry, Chemical Center, University of Lund, Box 124, S-221 00 Lund, Sweden
| | - O. Tapia
- Département de chimie et biochimie, Laurentian University, Sudbury, Ontario, Canada P3E 2C6, Department of Physical Chemistry, Uppsala University, Box 532, S-751 21 Uppsala, Sweden, and Department of Analytical Chemistry, Chemical Center, University of Lund, Box 124, S-221 00 Lund, Sweden
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38
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Molecular shape analysis of simulated in vacuo unfolding of charged lysozyme: transitions in chain entanglement and anisometry. Chem Phys Lett 2000. [DOI: 10.1016/s0009-2614(00)00880-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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39
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Gidden J, Wyttenbach T, Jackson AT, Scrivens JH, Bowers MT. Gas-Phase Conformations of Synthetic Polymers: Poly(ethylene glycol), Poly(propylene glycol), and Poly(tetramethylene glycol). J Am Chem Soc 2000. [DOI: 10.1021/ja993096+] [Citation(s) in RCA: 132] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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40
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Valentine SJ, Counterman AE, Clemmer DE. A database of 660 peptide ion cross sections: use of intrinsic size parameters for bona fide predictions of cross sections. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 1999; 10:1188-211. [PMID: 10536822 DOI: 10.1016/s1044-0305(99)00079-3] [Citation(s) in RCA: 152] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
An ion trap/ion mobility/time-of-flight mass spectrometry technique has been used to measure collision cross sections for 660 peptide ions generated by tryptic digestion of 34 common proteins. Measured cross sections have been compiled into a database that contains peptide molecular weight and sequence information. The database is used to generate average intrinsic contributions to cross section (size parameters) for different amino acid residues by solving systems of equations that relate the unknown contributions of individual residues to the sequences and cross sections of database peptides. Size parameters are combined with information about amino acid composition to calculate cross sections for database peptides. Bona fide cross section predictions (made prior to measurement) for peptides observed in tryptic digests of sperm whale myoglobin and yeast enolase are made. Eight of 10 predicted cross sections are within 2% of the experimental values and all 10 are within 3.2%. The utility of size parameters for cross section prediction is explored and discussed.
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Affiliation(s)
- S J Valentine
- Department of Chemistry, Indiana University, Bloomington 47405, USA
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41
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Mao Y, Ratner MA, Jarrold MF. Molecular Dynamics Simulations of the Charge-Induced Unfolding and Refolding of Unsolvated Cytochrome c. J Phys Chem B 1999. [DOI: 10.1021/jp991093d] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yi Mao
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208
| | - Mark A. Ratner
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208
| | - Martin F. Jarrold
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208
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43
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wing NP, Cassady CJ. Effects of cysteic acid groups on the gas-phase reactivity and dissociation of [M + 4H]4+ ions from insulin chain B. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 1999; 10:928-940. [PMID: 10497806 DOI: 10.1016/s1044-0305(99)00074-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Gas-phase ion/molecule reactions and collision-induced dissociation (CID) were conducted on [M + 4H]4+ of insulin chain B. This Fourier transform mass spectrometry work involved ions from the oxidized peptide (with two cysteic acid residues) and its reduced form (with two cysteine residues). Kinetic behavior during deprotonation and hydrogen/deuterium exchange reactions indicates that insulin B (ox) ions have two distinct structural types. In contrast, insulin B (red) ions have only one major reacting population, which has a more compact structure than the oxidized ions. No significant differences in fragmentation patterns for the two insulin B (ox) populations were observed when CID was performed as a function of deprotonating reaction time. However, markedly different fragmentation was found between [M + 4H]4+ of insulin B (ox) and (red). Therefore, the presence of cysteic acid groups in insulin B (ox) significantly impacts dissociation and presumably structure. This suggests that some insulin B (ox) ions are zwitterionic, with the five basic sites protonated and one cysteic acid group deprotonated. Molecular dynamics calculations revealed several viable structures that are consistent with the experimental results. For example, the most stable form of the reduced ion, which is unprotonated at the His10, is very compact and has lost the alpha-helix of native insulin. Low energy structures for the oxidized ions include a zwitterion with an intraionic interaction between anionic Cyx7 and cationic His10, as well as a nonzwitterionic conformer that lacks a proton at Phe1; both structures retain the alpha-helix. These structures may account for the two experimentally observed isomers, although others are possible. In addition, experiments on oxidized insulin B were conducted from methanolic solution, which may denature the conformation, and pure aqueous solution, which may leave a native conformation. These differences in solvent composition had no effect on the gas-phase results.
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Affiliation(s)
- N P wing
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, USA
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44
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Arteca GA, Tapia O. Characterization of fold diversity among proteins with the same number of amino acid residues. JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES 1999; 39:642-9. [PMID: 10443026 DOI: 10.1021/ci990323i] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Chain entanglements provide a simple and global measure of folding in a macromolecule. The complexity of these entanglements can be expressed by the pattern of projected bond-bond crossings, or "overcrossings", associated with the molecular backbone. In this work, we use this approach to characterize quantitatively the range of tertiary folds observed in proteins with a given chain length. To discriminate among folding features, we use two shape descriptors derived from the probability distribution of overcrossings: the mean overcrossing number, N, and the most probable overcrossing number, N*. The values of N and N* relate to the content of secondary structure in a protein as well as its global three-dimensional organization. We propose a measure of folding diversity based on the properties of these descriptors. In addition, we discuss the application of our method to study how tertiary folds evolve during protein dynamics.
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Affiliation(s)
- G A Arteca
- Département de chimie et biochimie, Laurentian University, Sudbury, Ontario, Canada
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Candeias LP, Steenken S. Photoionization of Ferrocytochrome c by 248 nm Laser Light and the Observation of the Early Stages of Ferricytochrome c Unfolding in the Nanosecond-to-millisecond Timescale. Photochem Photobiol 1999. [DOI: 10.1111/j.1751-1097.1999.tb03345.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Mao Y, Woenckhaus J, Kolafa J, Ratner MA, Jarrold MF. Thermal Unfolding of Unsolvated Cytochrome c: Experiment and Molecular Dynamics Simulations. J Am Chem Soc 1999. [DOI: 10.1021/ja980324b] [Citation(s) in RCA: 81] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yi Mao
- Contribution from the Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208
| | - Jürgen Woenckhaus
- Contribution from the Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208
| | - Jiri Kolafa
- Contribution from the Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208
| | - Mark A. Ratner
- Contribution from the Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208
| | - Martin F. Jarrold
- Contribution from the Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208
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Marchi M, Ballone P. Adiabatic bias molecular dynamics: A method to navigate the conformational space of complex molecular systems. J Chem Phys 1999. [DOI: 10.1063/1.478259] [Citation(s) in RCA: 104] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Gidden J, Wyttenbach T, Batka JJ, Weis P, Jackson AT, Scrivens JH, Bowers MT. Folding Energetics and Dynamics of Macromolecules in the Gas Phase: Alkali Ion-Cationized Poly(ethylene terephthalate) Oligomers. J Am Chem Soc 1999. [DOI: 10.1021/ja9831047] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Miteva M, Demirev PA, Karshikoff AD. Multiply-Protonated Protein Ions in the Gas Phase: Calculation of the Electrostatic Interactions between Charged Sites. J Phys Chem B 1997. [DOI: 10.1021/jp972249h] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Maria Miteva
- Department of Bioscience at Novum, Karolinska Institute, 14157 Huddinge, Sweden, and Uppsala University, Division of Ion Physics, Box 534, 75121 Uppsala, Sweden
| | - Plamen A. Demirev
- Department of Bioscience at Novum, Karolinska Institute, 14157 Huddinge, Sweden, and Uppsala University, Division of Ion Physics, Box 534, 75121 Uppsala, Sweden
| | - Andrey D. Karshikoff
- Department of Bioscience at Novum, Karolinska Institute, 14157 Huddinge, Sweden, and Uppsala University, Division of Ion Physics, Box 534, 75121 Uppsala, Sweden
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Hudgins RR, Woenckhaus J, Jarrold MF. High resolution ion mobility measurements for gas phase proteins: correlation between solution phase and gas phase conformations. ACTA ACUST UNITED AC 1997. [DOI: 10.1016/s0168-1176(97)00182-1] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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