1
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Ion Mobility Mass Spectrometry for Structural Elucidation of Petroleum Compounds. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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2
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Pham KN, Fernandez-Lima F. Structural Characterization of Human Histone H4.1 by Tandem Nonlinear and Linear Ion Mobility Spectrometry Complemented with Molecular Dynamics Simulations. ACS OMEGA 2021; 6:29567-29576. [PMID: 34778628 PMCID: PMC8582071 DOI: 10.1021/acsomega.1c03744] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 10/15/2021] [Indexed: 06/13/2023]
Abstract
Extracellular histone H4 is an attractive drug target owing to its roles in organ failure in sepsis and other diseases. To identify inhibitors using in silico methods, information on histone H4 structural dynamics and three-dimensional (3D) structural coordinates is required. Here, DNA-free histone H4 type 1 (H4.1) was characterized by utilizing tandem nonlinear and linear ion mobility spectrometry (FAIMS-TIMS) coupled to mass spectrometry (MS) complemented with molecular dynamics (MD) simulations. The gas-phase structures of H4.1 are dependent on the starting solution conditions, evidenced by differences in charge state distributions, mobility distributions, and collision-induced unfolding (CIU) pathways. The experimental results show that H4.1 adopts diverse conformational types from compact (C) to partially folded (P) and subsequently elongated (E) structures. Molecular dynamics simulations provided candidate structures for the histone H4.1 monomer in solution and for the gas-phase structures observed using FAIMS-IMS-TOF MS as a function of the charge state and mobility distribution. A combination of the FAIMS-TIMS experimental results with theoretical dipole calculations reveals the important role of charge distribution in the dipole alignment of H4.1 elongated structures at high electric fields. A comparison of the secondary and primary structures of DNA-free H2A.1 and H4.1 is made based on the experimental IMS-MS and MD findings.
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Affiliation(s)
- Khoa N. Pham
- Department
of Chemistry and Biochemistry, Florida International
University, Miami, Florida 33199, United States
| | - Francisco Fernandez-Lima
- Department
of Chemistry and Biochemistry, Florida International
University, Miami, Florida 33199, United States
- Biomolecular
Science Institute, Florida International
University, Miami, Florida 33199, United
States
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3
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Pham KN, Mamun Y, Fernandez-Lima F. Structural Heterogeneity of Human Histone H2A.1. J Phys Chem B 2021; 125:4977-4986. [PMID: 33974801 PMCID: PMC8568062 DOI: 10.1021/acs.jpcb.1c00335] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Histones are highly basic chromatin proteins that tightly package and order eukaryotic DNA into nucleosomes. While the atomic structure of the nucleosomes has been determined, the three-dimensional structure of DNA-free histones remains unresolved. Here, we combine tandem nonlinear and linear ion mobility spectrometry (FAIMS-TIMS) coupled to mass spectrometry in parallel with molecular modeling to study the conformational space of a DNA-free histone H2A type 1 (H2A.1). Experimental results showed the dependence of the gas-phase structures on the starting solution conditions, characterized by charge state distributions, mobility distributions, and collision-induced-unfolding pathways. The measured H2A.1 gas-phase structures showed a high diversity of structural features ranging from compact (C) to partially folded (P) and then highly elongated (E) conformations. Molecular dynamics simulations provided candidate structures for the solution H2A.1 native conformation with folded N- and C-terminal tails, as well as gas-phase candidate structures associated with the mobility trends. Complementary collision cross section and dipole calculations showed that the charge distribution in the case of elongated gas-phase structures, where basic and acidic residues are mostly exposed (e.g., z > 15+), is sufficient to induce differences in the dipole alignment at high electric fields, in good agreement with the trends observed during the FAIMS-TIMS experiments.
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Affiliation(s)
- Khoa N Pham
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States
| | - Yasir Mamun
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States
| | - Francisco Fernandez-Lima
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States.,Biomolecular Science Institute, Florida International University, Miami, Florida 33199, United States
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4
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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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5
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Le Fèvre A, Dugourd P, Chirot F. Exploring Conformational Landscapes Using Trap and Release Tandem Ion Mobility Spectrometry. Anal Chem 2021; 93:4183-4190. [PMID: 33625848 DOI: 10.1021/acs.analchem.0c04520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The dynamics and thermodynamics of structural changes in isolated glu-fibrinopeptide B (GluFib) were investigated by tandem ion mobility spectrometry (IMS). Doubly protonated GluFib2+ ions were first selected by IMS and then stored for a controlled duration in a thermalized ion trap. Temperature-induced conformational changes were finally monitored by IMS as a function of trapping time. Based on this procedure, isomerization rates and equilibrium populations of the different conformers were determined as a function of temperature. We demonstrate that the measured thermodynamic quantities can be directly compared to simulated observables from ensemble molecular modeling based on appropriate order parameters. We obtained good qualitative agreement with replica-exchange molecular dynamics simulations based on the AMOEBA force field and processed using the weighted histogram analysis method. This suggests that the balance between Coulomb repulsion and optimal charge solvation is the main source of the observed conformational bistability. Our results emphasize the differences between the kinetically driven quasi-equilibrium distributions obtained after collisional activation and the thermodynamically driven distributions from the present equilibrium experiments due to entropic effects. As a consequence, our measurements not only allow straightforward determination of Arrhenius activation energies but also yield the relative enthalpy and entropy changes associated to a structural transition.
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Affiliation(s)
- Aurélien Le Fèvre
- Université Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5280 Institut des Sciences Analytiques, 5 rue de la Doua, Villeurbanne F-69100, France
| | - Philippe Dugourd
- Université Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5306 Institut Lumière Matière, 5 rue de la Doua, Villeurbanne F-69100, France
| | - Fabien Chirot
- Université Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5280 Institut des Sciences Analytiques, 5 rue de la Doua, Villeurbanne F-69100, France
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6
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Porter J, Dit Fouque KJ, Miksovska J, Fernandez-Lima F. Salt bridges govern the structural heterogeneity of heme protein interactions and porphyrin networks: microperoxidase-11. RSC Adv 2020; 10:33861-33867. [PMID: 35519052 PMCID: PMC9056719 DOI: 10.1039/d0ra04956e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 09/01/2020] [Indexed: 11/21/2022] Open
Abstract
In this work, a proteolytic digest of cytochrome c (microperoxidase 11, MP-11) was used as a model to study the structural aspects of heme protein interactions and porphyrin networks. The MP-11 structural heterogeneity was studied as a function of the starting pH (e.g., pH 3.1-6.1) and concentration (e.g., 1-50 μM) conditions and adduct coordination. Trapped ion mobility spectrometry coupled to mass spectrometry (TIMS-MS) showed the MP-11 structural dependence of the charge state distribution and molecular ion forms with the starting pH conditions. The singly charged (e.g., [M]+, [M - 2H + NH4]+, [M - H + Na]+ and [M - H + K]+) and doubly charged (e.g., [M + H]2+, [M - H + NH4]2+, [M + Na]2+ and [M + K]2+) molecular ion forms were observed for all solvent conditions, although the structural heterogeneity (e.g., number of mobility bands) significantly varied with the pH value and ion form. The MP-11 dimer formation as a model for heme-protein protein interactions showed that dimer formation is favored toward more neutral pH and favored when assisted by salt bridges (e.g., NH4 +, Na+ and K+ vs. H+). Inspection of the dimer mobility profiles (2+ and 3+ charge states) showed a high degree of structural heterogeneity as a function of the solution pH and ion form; the observation of common mobility bands suggest that the different salt bridges can stabilize similar structural motifs. In addition, the salt bridge influence on the MP-11 dimer formations was measured using collision induced dissociation and showed a strong dependence with the type of salt bridge (i.e., a CE50 of 10.0, 11.5, 11.8 and 13.0 eV was observed for [2M + H]3+, [2M - H + NH4]3+, [2M + Na]3+ and [2M + K]3+, respectively). Measurements of the dimer equilibrium constant showed that the salt bridge interactions increase the binding strength of the dimeric species.
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Affiliation(s)
- J Porter
- Department of Chemistry and Biochemistry, Florida International University Miami FL 33199 USA
| | - K Jeanne Dit Fouque
- Department of Chemistry and Biochemistry, Florida International University Miami FL 33199 USA
| | - J Miksovska
- Department of Chemistry and Biochemistry, Florida International University Miami FL 33199 USA
- Biomolecular Science Institute, Florida International University Miami FL 33199 USA
| | - F Fernandez-Lima
- Department of Chemistry and Biochemistry, Florida International University Miami FL 33199 USA
- Biomolecular Science Institute, Florida International University Miami FL 33199 USA
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7
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Lim D, Park Y, Chang R, Ahmed A, Kim S. Application of molecular dynamics simulation to improve the theoretical prediction for collisional cross section of aromatic compounds with long alkyl chains in crude oils. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2019; 33:650-656. [PMID: 30710409 DOI: 10.1002/rcm.8400] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 01/21/2019] [Accepted: 01/23/2019] [Indexed: 06/09/2023]
Abstract
RATIONALE Molecular dynamics (MD) simulations with finite temperature were performed to improve the theoretical prediction of collisional cross section (CCS) values, especially for aromatic compounds containing long alkyl chains. METHODS In this study, the CCS values of 11 aromatic compounds with long alkyl chains were calculated by MD simulations while considering internal energy at 300, 500, and 700 K, and the results were compared with experimentally determined values. RESULTS The CCS values calculated at higher energies showed better agreement with the experimental values. Polycyclic aromatic hydrocarbons (PAHs) such as pentacene and benz[b]anthracene were also investigated, and better agreement between the theoretical and experimental results was observed when higher temperature (or higher internal energy) was considered. CONCLUSIONS The data presented in this study show that the internal degrees of freedom of ions must be considered to accurately predict the CCS values of aromatic compounds with a flexible structure measured by ion mobility mass spectrometry.
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Affiliation(s)
- Dongwan Lim
- Department of Chemistry, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Yunjae Park
- Department of Chemistry, Kwangwoon University, Seoul, 01897, Republic of Korea
| | - Rakwoo Chang
- Department of Chemistry, Kwangwoon University, Seoul, 01897, Republic of Korea
| | - Arif Ahmed
- Department of Chemistry, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Sunghwan Kim
- Department of Chemistry, Kyungpook National University, Daegu, 41566, Republic of Korea
- Green Nano Center, Department of Chemistry, Daegu, 41566, Republic of Korea
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8
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Molano-Arevalo JC, Gonzalez W, Jeanne Dit Fouque K, Miksovska J, Maitre P, Fernandez-Lima F. Insights from ion mobility-mass spectrometry, infrared spectroscopy, and molecular dynamics simulations on nicotinamide adenine dinucleotide structural dynamics: NAD +vs. NADH. Phys Chem Chem Phys 2018; 20:7043-7052. [PMID: 29473073 DOI: 10.1039/c7cp05602h] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Nicotinamide adenine dinucleotide (NAD) is found in all living cells where the oxidized (NAD+) and reduced (NADH) forms play important roles in many enzymatic reactions. However, little is known about NAD+ and NADH conformational changes and kinetics as a function of the cell environment. In the present work, an analytical workflow is utilized to study NAD+ and NADH dynamics as a function of the organic content in solution using fluorescence lifetime spectroscopy and in the gas-phase using trapped ion mobility spectrometry coupled to mass spectrometry (TIMS-MS) and infrared multiple photon dissociation (IRMPD) spectroscopy. NAD solution time decay studies showed a two-component distribution, assigned to changes from a "close" to "open" conformation with the increase of the organic content. NAD gas-phase studies using nESI-TIMS-MS displayed two ion mobility bands for NAD+ protonated and sodiated species, while four and two ion mobility bands were observed for NADH protonated and sodiated species, respectively. Changes in the mobility profiles were observed for NADH as a function of the starting solution conditions and the time after desolvation, while NAD+ profiles showed no dependence. IRMPD spectroscopy of NAD+ and NADH protonated species in the 800-1800 and 3200-3700 cm-1 spectral regions showed common and signature bands between the NAD forms. Candidate structures were proposed for NAD+ and NADH kinetically trapped intermediates of the protonated and sodiated species, based on their collision cross sections and IR profiles. Results showed that NAD+ and NADH species exist in open, stack, and closed conformations and that the driving force for conformational dynamics is hydrogen bonding of the N-H-O and O-H-O forms with ribose rings.
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Gunzer F. Evaluation of calculated negative mode ion mobilities of small molecules in air. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2017; 23:369-375. [PMID: 29183198 DOI: 10.1177/1469066717729299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Ion mobility spectrometry is a well-known technique employed for the detection and analysis of gaseous substances. In pharmaceutical applications, it is furthermore used for structural analysis of compounds, especially in combination with mass spectrometry. In this field, the comparison of calculated collision cross sections and ion mobilities of theoretic model compounds with experimental values measured with ion mobility spectrometers helps to determine the compound's structure. For positive mode ion mobility spectrometry, the calculated mobilities using the Trajectory Method show in general a deviation of 10% or less from experimental values. In this article, it was analyzed how well the calculated values reproduce the experimental values obtained with negative mode ion mobility spectrometry including symmetric and asymmetric analyte clusters. Furthermore, the influence of four different partial charge models on the results was investigated.
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Affiliation(s)
- Frank Gunzer
- Department of Electronics Engineering, Information Engineering and Technology Faculty, German University in Cairo, Entrance El Tagamoa El Khames, New Cairo, Egypt
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10
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D'Atri V, Causon T, Hernandez-Alba O, Mutabazi A, Veuthey JL, Cianferani S, Guillarme D. Adding a new separation dimension to MS and LC-MS: What is the utility of ion mobility spectrometry? J Sep Sci 2017; 41:20-67. [PMID: 29024509 DOI: 10.1002/jssc.201700919] [Citation(s) in RCA: 114] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 09/19/2017] [Accepted: 09/19/2017] [Indexed: 12/12/2022]
Abstract
Ion mobility spectrometry is an analytical technique known for more than 100 years, which entails separating ions in the gas phase based on their size, shape, and charge. While ion mobility spectrometry alone can be useful for some applications (mostly security analysis for detecting certain classes of narcotics and explosives), it becomes even more powerful in combination with mass spectrometry and high-performance liquid chromatography. Indeed, the limited resolving power of ion mobility spectrometry alone can be tackled when combining this analytical strategy with mass spectrometry or liquid chromatography with mass spectrometry. Over the last few years, the hyphenation of ion mobility spectrometry to mass spectrometry or liquid chromatography with mass spectrometry has attracted more and more interest, with significant progresses in both technical advances and pioneering applications. This review describes the theoretical background, available technologies, and future capabilities of these techniques. It also highlights a wide range of applications, from small molecules (natural products, metabolites, glycans, lipids) to large biomolecules (proteins, protein complexes, biopharmaceuticals, oligonucleotides).
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Affiliation(s)
- Valentina D'Atri
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Geneva, Switzerland
| | - Tim Causon
- Division of Analytical Chemistry, Department of Chemistry, University of Natural Resources and Life Sciences (BOKU Vienna), Vienna, Austria
| | - Oscar Hernandez-Alba
- BioOrganic Mass Spectrometry Laboratory (LSMBO), IPHC, Université de Strasbourg, CNRS, Strasbourg, France
| | - Aline Mutabazi
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Geneva, Switzerland
| | - Jean-Luc Veuthey
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Geneva, Switzerland
| | - Sarah Cianferani
- BioOrganic Mass Spectrometry Laboratory (LSMBO), IPHC, Université de Strasbourg, CNRS, Strasbourg, France
| | - Davy Guillarme
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Geneva, Switzerland
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Fouque KJD, Garabedian A, Porter J, Baird M, Pang X, Williams TD, Li L, Shvartsburg A, Fernandez-Lima F. Fast and Effective Ion Mobility-Mass Spectrometry Separation of d-Amino-Acid-Containing Peptides. Anal Chem 2017; 89:11787-11794. [PMID: 28982001 PMCID: PMC5677546 DOI: 10.1021/acs.analchem.7b03401] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Despite often minute concentrations in vivo, d-amino acid containing peptides (DAACPs) are crucial to many life processes. Standard proteomics protocols fail to detect them as d/l substitutions do not affect the peptide parent and fragment masses. The differences in fragment yields are often limited, obstructing the investigations of important but low abundance epimers in isomeric mixtures. Separation of d/l-peptides using ion mobility spectrometry (IMS) was impeded by small collision cross section differences (commonly ∼1%). Here, broad baseline separation of DAACPs with up to ∼30 residues employing trapped IMS with resolving power up to ∼340, followed by time-of-flight mass spectrometry is demonstrated. The d/l-pairs coeluting in one charge state were resolved in another, and epimers merged as protonated species were resolved upon metalation, effectively turning the charge state and cationization mode into extra separation dimensions. Linear quantification down to 0.25% proved the utility of high resolution IMS-MS for real samples with large interisomeric dynamic range. Very close relative mobilities found for DAACP pairs using traveling-wave IMS (TWIMS) with different ion sources and faster IMS separations showed the transferability of results across IMS platforms. Fragmentation of epimers can enhance their identification and further improve detection and quantification limits, and we demonstrate the advantages of online mobility separated collision-induced dissociation (CID) followed by high resolution mass spectrometry (TIMS-CID-MS) for epimer analysis.
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Affiliation(s)
- Kevin Jeanne Dit Fouque
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA
| | - Alyssa Garabedian
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA
| | - Jacob Porter
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA
| | - Matthew Baird
- Department of Chemistry, Wichita State University, Wichita, KS 67260, USA
| | - Xueqin Pang
- School of Pharmacy and Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Todd D. Williams
- Mass Spectrometry Laboratory, University of Kansas, Lawrence, KS 66045, USA
| | - Lingjun Li
- School of Pharmacy and Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53705, USA
| | | | - Francisco Fernandez-Lima
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA
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12
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Molano-Arevalo JC, Dit Fouque KJ, Pham K, Miksovska J, Ridgeway ME, Park MA, Fernandez-Lima F. Characterization of Intramolecular Interactions of Cytochrome c Using Hydrogen-Deuterium Exchange-Trapped Ion Mobility Spectrometry-Mass Spectrometry and Molecular Dynamics. Anal Chem 2017; 89:8757-8765. [PMID: 28742962 PMCID: PMC5653375 DOI: 10.1021/acs.analchem.7b00844] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Globular proteins, such as cytochrome c (cyt c), display an organized native conformation, maintained by a hydrogen bond interaction network. In the present work, the structural interrogation of kinetically trapped intermediates of cyt c was performed by correlating the ion-neutral collision cross section (CCS) and charge state with the starting solution conditions and time after desolvation using collision induced activation (CIA), time-resolved hydrogen/deuterium back exchange (HDX) and trapped ion mobility spectrometry-mass spectrometry (TIMS-MS). The high ion mobility resolving power of the TIMS analyzer allowed the identification of new ion mobility bands, yielding a total of 63 mobility bands over the +6 to +21 charge states and 20 mobility bands over the -5 to -10 charge states. Mobility selected HDX rates showed that for the same charge state, conformers with larger CCS present faster HDX rates in both positive and negative ion mode, suggesting that the charge sites and neighboring exchange sites on the accessible surface area define the exchange rate regardless of the charge state. Complementary molecular dynamic simulations permitted the generation of candidate structures and a mechanistic model of the folding transitions from native (N) to molten globule (MG) to kinetic intermediates (U) pathways. Our results suggest that cyt c major structural unfolding is associated with the distancing of the N- and C-terminal helices and subsequent solvent exposure of the hydrophobic, heme-containing cavity.
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Affiliation(s)
| | - Kevin Jeanne Dit Fouque
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA
| | - Khoa Pham
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA
| | - Jaroslava Miksovska
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199
| | | | - Melvin A. Park
- Bruker Daltonics, Inc., Billerica, Massachusetts, 01821, USA
| | - Francisco Fernandez-Lima
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199
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13
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Wagner ND, Clemmer DE, Russell DH. ESI-IM-MS and Collision-Induced Unfolding That Provide Insight into the Linkage-Dependent Interfacial Interactions of Covalently Linked Diubiquitin. Anal Chem 2017; 89:10094-10103. [DOI: 10.1021/acs.analchem.7b02932] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Nicole D. Wagner
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - David E. Clemmer
- Department
of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - David H. Russell
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
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14
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Ghassabi Kondalaji S, Khakinejad M, Tafreshian A, J Valentine S. Comprehensive Peptide Ion Structure Studies Using Ion Mobility Techniques: Part 1. An Advanced Protocol for Molecular Dynamics Simulations and Collision Cross-Section Calculation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:947-959. [PMID: 28211014 PMCID: PMC5942881 DOI: 10.1007/s13361-017-1599-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 01/07/2017] [Accepted: 01/09/2017] [Indexed: 05/02/2023]
Abstract
Collision cross-section (CCS) measurements with a linear drift tube have been utilized to study the gas-phase conformers of a model peptide (acetyl-PAAAAKAAAAKAAAAKAAAAK). Extensive molecular dynamics (MD) simulations have been conducted to derive an advanced protocol for the generation of a comprehensive pool of in-silico structures; both higher energy and more thermodynamically stable structures are included to provide an unbiased sampling of conformational space. MD simulations at 300 K are applied to the in-silico structures to more accurately describe the gas-phase transport properties of the ion conformers including their dynamics. Different methods used previously for trajectory method (TM) CCS calculation employing the Mobcal software [1] are evaluated. A new method for accurate CCS calculation is proposed based on clustering and data mining techniques. CCS values are calculated for all in-silico structures, and those with matching CCS values are chosen as candidate structures. With this approach, more than 300 candidate structures with significant structural variation are produced; although no final gas-phase structure is proposed here, in a second installment of this work, gas-phase hydrogen deuterium exchange data will be utilized as a second criterion to select among these structures as well as to propose relative populations for these ion conformers. Here the need to increase conformer diversity and accurate CCS calculation is demonstrated and the advanced methods are discussed. Graphical Abstract ᅟ.
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Affiliation(s)
| | - Mahdiar Khakinejad
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, 26506, USA
| | - Amirmahdi Tafreshian
- Department of Statistics, West Virginia University, P.O. Box 6330, Morgantown, WV, 26506, USA
| | - Stephen J Valentine
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, 26506, USA.
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15
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Young MN, Bleiholder C. Molecular Structures and Momentum Transfer Cross Sections: The Influence of the Analyte Charge Distribution. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:619-627. [PMID: 28251573 DOI: 10.1007/s13361-017-1605-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 12/19/2016] [Accepted: 12/20/2016] [Indexed: 06/06/2023]
Abstract
Structure elucidation by ion mobility spectrometry-mass spectrometry methods is based on the comparison of an experimentally measured momentum transfer cross-section to cross-sections calculated for model structures. Thus, it is imperative that the calculated cross-section must be accurate. However, it is not fully understood how important it is to accurately model the charge distribution of an analyte ion when calculating momentum transfer cross-sections. Here, we calculate and compare momentum transfer cross-sections for carbon clusters that differ in mass, charge state, and mode of charge distribution, and vary temperature and polarizability of the buffer gas. Our data indicate that the detailed distribution of the ion charge density is intimately linked to the contribution of glancing collisions to the momentum transfer cross-section. The data suggest that analyte ions with molecular mass ~3 kDa or momentum transfer cross-section 400-500 Å2 would be significantly influenced by the charge distribution in nitrogen buffer gas. Our data further suggest that accurate structure elucidation on the basis of IMS-MS data measured in nitrogen buffer gas must account for the molecular charge distribution even for systems as large as C960 (~12 kDa) when localized charges are present and/or measurements are conducted under cryogenic temperatures. Finally, our data underscore that accurate structure elucidation is unlikely if ion mobility data recorded in one buffer gas is converted into other buffer gases when electronic properties of the buffer gases differ. Graphical Abstract ᅟ.
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Affiliation(s)
- Meggie N Young
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, 32306, USA
| | - Christian Bleiholder
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, 32306, USA.
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL, 32306, USA.
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16
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Lietz CB, Chen Z, Yun Son C, Pang X, Cui Q, Li L. Multiple gas-phase conformations of proline-containing peptides: is it always cis/trans isomerization? Analyst 2016; 141:4863-9. [PMID: 27434776 PMCID: PMC4972606 DOI: 10.1039/c5an00835b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Ion mobility-mass spectrometry (IM-MS) is often employed to look at the secondary, tertiary, and quaternary structures of naked peptides and proteins in the gas-phase. Recently, it has offered a unique glimpse into proline-containing peptides and their cis/trans Xxx-Pro isomers. An experimental "signature" has been identified wherein a proline-containing peptide has its Pro residues substituted with another amino acid and the presence or absence of conformations in the IM-MS spectra is observed. Despite the high probability that one could attribute these conformations to cis/trans isomers, it is also possible that cis/trans isomers are not the cause of the additional conformations in proline-containing peptides. However, the experimental evidence of such a system has not been demonstrated or reported. Herein, we present the IM-MS analysis of Neuropeptide Y's wild-type (WT) signal sequence and Leu7Pro (L7P) mutant. Although comparison of arrival times and collision cross-sections of [M + 4H](4+) ions yields the cis/trans "signature", molecular dynamics indicates that a cis-Pro7 is not very stable and that trans-Pro7 conformations of the same cross-section arise with equal frequency. We believe that this work further underscores the importance of theoretical calculations in IM-MS structural assignments.
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Affiliation(s)
- Christopher B Lietz
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA.
| | - Zhengwei Chen
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA.
| | - Chang Yun Son
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA.
| | - Xueqin Pang
- School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53705, USA
| | - Qiang Cui
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA.
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA. and School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53705, USA
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17
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Benigni P, Fernandez-Lima F. Oversampling Selective Accumulation Trapped Ion Mobility Spectrometry Coupled to FT-ICR MS: Fundamentals and Applications. Anal Chem 2016; 88:7404-12. [DOI: 10.1021/acs.analchem.6b01946] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Paolo Benigni
- Department of Chemistry and Biochemistry and ‡Biomolecular Sciences
Institute, Florida International University, Miami, Florida 33199, United States
| | - Francisco Fernandez-Lima
- Department of Chemistry and Biochemistry and ‡Biomolecular Sciences
Institute, Florida International University, Miami, Florida 33199, United States
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18
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19
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Isomer Separation of Polybrominated Diphenyl Ether Metabolites using nanoESI-TIMS-MS. ACTA ACUST UNITED AC 2016; 19:69-76. [PMID: 27642261 DOI: 10.1007/s12127-016-0198-z] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
In this paper, high-resolution nano-electrospray ionization-trapped ion mobility spectrometry coupled to mass spectrometry (nESI-TIMS-MS) is used for the study of hydroxylated polybrominated diphenyl ether (OH-PBDE) metabolites. In particular, experimental ion-neutral collision cross sections (CCS) were measured for five structural OH-PBDE isomers using TIMS-MS. Candidate structures were proposed for each IMS band observed in good agreement with the experimental CCS measurements (5% error). The analytical power of TIMS-MS to baseline and partially separate structural isomers of OH-BDE in binary and ternary mixtures is shown for single charge species with a mobility resolving power of RIMS ~ 400. This work provides the proof of concept for the analysis of low concentration OH-PBDE in environmental samples based on accurate collision cross section and mass measurements without the need for derivatization and pre-fractionation protocols, thus significantly reducing the cost and analysis time.
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20
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Brack W, Ait-Aissa S, Burgess RM, Busch W, Creusot N, Di Paolo C, Escher BI, Mark Hewitt L, Hilscherova K, Hollender J, Hollert H, Jonker W, Kool J, Lamoree M, Muschket M, Neumann S, Rostkowski P, Ruttkies C, Schollee J, Schymanski EL, Schulze T, Seiler TB, Tindall AJ, De Aragão Umbuzeiro G, Vrana B, Krauss M. Effect-directed analysis supporting monitoring of aquatic environments--An in-depth overview. THE SCIENCE OF THE TOTAL ENVIRONMENT 2016; 544:1073-118. [PMID: 26779957 DOI: 10.1016/j.scitotenv.2015.11.102] [Citation(s) in RCA: 219] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 11/20/2015] [Accepted: 11/20/2015] [Indexed: 05/18/2023]
Abstract
Aquatic environments are often contaminated with complex mixtures of chemicals that may pose a risk to ecosystems and human health. This contamination cannot be addressed with target analysis alone but tools are required to reduce this complexity and identify those chemicals that might cause adverse effects. Effect-directed analysis (EDA) is designed to meet this challenge and faces increasing interest in water and sediment quality monitoring. Thus, the present paper summarizes current experience with the EDA approach and the tools required, and provides practical advice on their application. The paper highlights the need for proper problem formulation and gives general advice for study design. As the EDA approach is directed by toxicity, basic principles for the selection of bioassays are given as well as a comprehensive compilation of appropriate assays, including their strengths and weaknesses. A specific focus is given to strategies for sampling, extraction and bioassay dosing since they strongly impact prioritization of toxicants in EDA. Reduction of sample complexity mainly relies on fractionation procedures, which are discussed in this paper, including quality assurance and quality control. Automated combinations of fractionation, biotesting and chemical analysis using so-called hyphenated tools can enhance the throughput and might reduce the risk of artifacts in laboratory work. The key to determining the chemical structures causing effects is analytical toxicant identification. The latest approaches, tools, software and databases for target-, suspect and non-target screening as well as unknown identification are discussed together with analytical and toxicological confirmation approaches. A better understanding of optimal use and combination of EDA tools will help to design efficient and successful toxicant identification studies in the context of quality monitoring in multiply stressed environments.
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Affiliation(s)
- Werner Brack
- UFZ Helmholtz Centre for Environmental Research, Permoserstraße 15, 04318 Leipzig, Germany; RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Selim Ait-Aissa
- Institut National de l'Environnement Industriel et des Risques INERIS, BP2, 60550 Verneuil-en-Halatte, France
| | - Robert M Burgess
- US Environmental Protection Agency, Office of Research and Development, National Health and Environmental Effects Research Laboratory, Atlantic Ecology Division, Narragansett, RI, USA
| | - Wibke Busch
- UFZ Helmholtz Centre for Environmental Research, Permoserstraße 15, 04318 Leipzig, Germany
| | - Nicolas Creusot
- Institut National de l'Environnement Industriel et des Risques INERIS, BP2, 60550 Verneuil-en-Halatte, France
| | | | - Beate I Escher
- UFZ Helmholtz Centre for Environmental Research, Permoserstraße 15, 04318 Leipzig, Germany; Eberhard Karls University Tübingen, 72074 Tübingen, Germany
| | - L Mark Hewitt
- Water Science and Technology Directorate, Environment Canada, 867 Lakeshore Road, Burlington, Ontario L7S 1A1, Canada
| | - Klara Hilscherova
- Masaryk University, Research Centre for Toxic Compounds in the Environment (RECETOX), Kamenice 753/5, 625 00 Brno, Czech Republic
| | - Juliane Hollender
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
| | - Henner Hollert
- RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Willem Jonker
- VU University, BioMolecular Analysis Group, Amsterdam, The Netherlands
| | - Jeroen Kool
- VU University, BioMolecular Analysis Group, Amsterdam, The Netherlands
| | - Marja Lamoree
- VU Amsterdam, Institute for Environmental Studies, Amsterdam, The Netherlands
| | - Matthias Muschket
- UFZ Helmholtz Centre for Environmental Research, Permoserstraße 15, 04318 Leipzig, Germany
| | - Steffen Neumann
- Leibniz Institute of Plant Biochemistry, Halle (Saale), Germany
| | - Pawel Rostkowski
- NILU - Norwegian Institute for Air Research, Instituttveien 18, 2007 Kjeller, Norway
| | | | - Jennifer Schollee
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
| | - Emma L Schymanski
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
| | - Tobias Schulze
- UFZ Helmholtz Centre for Environmental Research, Permoserstraße 15, 04318 Leipzig, Germany
| | | | - Andrew J Tindall
- WatchFrag, Bâtiment Genavenir 3, 1 Rue Pierre Fontaine, 91000 Evry, France
| | | | - Branislav Vrana
- Masaryk University, Research Centre for Toxic Compounds in the Environment (RECETOX), Kamenice 753/5, 625 00 Brno, Czech Republic
| | - Martin Krauss
- UFZ Helmholtz Centre for Environmental Research, Permoserstraße 15, 04318 Leipzig, Germany
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21
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Gunzer F. Comparison of Experimental and Calculated Ion Mobilities of Small Molecules in Air. JOURNAL OF ANALYTICAL METHODS IN CHEMISTRY 2016; 2016:6246415. [PMID: 27298751 PMCID: PMC4889856 DOI: 10.1155/2016/6246415] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 05/05/2016] [Indexed: 05/06/2023]
Abstract
Ion mobility spectrometry is a well-known technique for analyzing gases. Examples are military applications, but also safety related applications, for example, for protection of employees in industries working with hazardous gases. In the last 15 years, this technique has been further developed as a tool for structural analysis, for example, in pharmaceutical applications. In particular, the collision cross section, which is related to the mobility, is of interest here. With help of theoretic principles, it is possible to develop molecular models that can be verified by the comparison of their calculated cross sections with experimental data. In this paper, it is analyzed how well the ion trajectory method is suitable to reproduce the measured ion mobility of small organic molecules such as the water clusters forming the positively charged reactant ions, simple aromatic substances, and n-alkanes.
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Affiliation(s)
- Frank Gunzer
- Information Engineering and Technology Faculty, German University in Cairo, El Tagamoa El Khames, Cairo, Egypt
- *Frank Gunzer:
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22
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Benigni P, Marin R, Fernandez-Lima F. Towards unsupervised polyaromatic hydrocarbons structural assignment from SA-TIMS-FTMS data. ACTA ACUST UNITED AC 2015; 18:151-157. [PMID: 26525904 DOI: 10.1007/s12127-015-0175-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
With the advent of high resolution ion mobility analyzers and their coupling to ultrahigh resolution mass spectrometers, there is a need to further develop a theoretical workflow capable of correlating experimental accurate mass and mobility measurements with tridimensional candidate structures. In the present work, a general workflow is described for unsupervised tridimensional structural assignment based on accurate mass measurements, mobility measurements, in silico 2D-3D structure generation, and theoretical mobility calculations. In particular, the potential of this workflow will be shown for the analysis of polyaromatic hydrocarbons from Coal Tar SRM 1597a using selected accumulation - trapped ion mobility spectrometry (SA-TIMS) coupled to Fourier transform-ion cyclotron resonance mass spectrometry (FT-ICR MS). The proposed workflow can be adapted to different IMS scenarios, can utilize different collisional cross-section calculators and has the potential to include MSn and IMSn measurements for faster and more accurate tridimensional structural assignment.
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Affiliation(s)
- Paolo Benigni
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL, USA
| | - Rebecca Marin
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL, USA
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23
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Schenk ER, Nau F, Fernandez-Lima F. Theoretical predictor for candidate structure assignment from IMS data of biomolecule-related conformational space. INTERNATIONAL JOURNAL FOR ION MOBILITY SPECTROMETRY : OFFICIAL PUBLICATION OF THE INTERNATIONAL SOCIETY FOR ION MOBILITY SPECTROMETRY 2015; 18:23-29. [PMID: 27330407 PMCID: PMC4909055 DOI: 10.1007/s12127-015-0165-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The ability to correlate experimental ion mobility data with candidate structures from theoretical modeling provides a powerful analytical and structural tool for the characterization of biomolecules. In the present paper, a theoretical workflow is described to generate and assign candidate structures for experimental trapped ion mobility and H/D exchange (HDX-TIMS-MS) data following molecular dynamics simulations and statistical filtering. The applicability of the theoretical predictor is illustrated for a peptide and protein example with multiple conformations and kinetic intermediates. The described methodology yields a low computational cost and a simple workflow by incorporating statistical filtering and molecular dynamics simulations. The workflow can be adapted to different IMS scenarios and CCS calculators for a more accurate description of the IMS experimental conditions. For the case of the HDX-TIMS-MS experiments, molecular dynamics in the "TIMS box" accounts for a better sampling of the molecular intermediates and local energy minima.
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Affiliation(s)
- Emily R Schenk
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA
| | - Frederic Nau
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA
| | - Francisco Fernandez-Lima
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA; Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
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24
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Benigni P, Thompson CJ, Ridgeway ME, Park MA, Fernandez-Lima F. Targeted high-resolution ion mobility separation coupled to ultrahigh-resolution mass spectrometry of endocrine disruptors in complex mixtures. Anal Chem 2015; 87:4321-5. [PMID: 25818070 PMCID: PMC4867114 DOI: 10.1021/ac504866v] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Traditional separation and detection of targeted compounds from complex mixtures from environmental matrices requires the use of lengthy prefractionation steps and high-resolution mass analyzers due to the large number of chemical components and their large structural diversity (highly isomeric). In the present work, selected accumulation trapped ion mobility spectrometry (SA-TIMS) is coupled to Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) for direct separation and characterization of targeted endocrine-disrupting compounds (EDC) from a complex environmental matrix in a single analysis. In particular, targeted identification based on high-resolution mobility (R ∼ 70-120) and ultrahigh-resolution mass measurements (R > 400 000) of seven commonly targeted EDC and their isobars (e.g., bisphenol A, (Z)- and (E)-diethylstilbestrol, hexestrol, estrone, α-estradiol, and 17-ethynylestradiol) is shown from a complex mixture of water-soluble organic matter (e.g., Suwannee River Fulvic Acid Standard II) complemented with reference standard measurements and theoretical calculations (<3% error).
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Affiliation(s)
- Paolo Benigni
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States
| | | | - Mark E. Ridgeway
- Bruker Daltonics Inc., Billerica, Massachusetts 01821, United States
| | - Melvin A. Park
- Bruker Daltonics Inc., Billerica, Massachusetts 01821, United States
| | - Francisco Fernandez-Lima
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States
- Biomolecular Sciences Institute, Florida International University, Miami, Florida 33199, United States
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25
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Yang L, Liu CW, Shao Q, Zhang J, Gao YQ. From thermodynamics to kinetics: enhanced sampling of rare events. Acc Chem Res 2015; 48:947-55. [PMID: 25781363 DOI: 10.1021/ar500267n] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Despite great advances in molecular dynamics simulations, there remain large gaps between the simulations and experimental observations in terms of the time and length scales that can be approached. Developing fast and accurate algorithms and methods is of ultimate importance to bridge these gaps. In this Account, we briefly summarize recent efforts in such directions. In particular, we focus on integrated tempering sampling. The efficiency of this sampling method has been demonstrated by applications to a range of chemical and biological problems: protein folding, molecular cluster structure searches, and chemical reactions. The combination of integrated tempering sampling and a trajectory sampling method allows the calculation of rate constants and reaction pathways without predefined collective coordinates.
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Affiliation(s)
| | | | - Qiang Shao
- Drug
Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
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26
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Schenk ER, Almeida R, Miksovska J, Ridgeway ME, Park MA, Fernandez-Lima F. Kinetic intermediates of holo- and apo-myoglobin studied using HDX-TIMS-MS and molecular dynamic simulations. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:555-63. [PMID: 25690175 PMCID: PMC4402236 DOI: 10.1007/s13361-014-1067-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Revised: 12/01/2014] [Accepted: 12/07/2014] [Indexed: 05/05/2023]
Abstract
In the present work, the kinetic intermediates of holo- and apo-myoglobin were studied by correlating the ion-neutral collision cross section and time resolved H/D back exchange rate simultaneously in a trapped ion mobility spectrometer coupled to a mass spectrometer (HDX-TIMS-MS). The high mobility resolution of the TIMS cell permitted the observation of multiple IMS bands and complementary molecular dynamics simulations resulted in the assignment of candidate structures for each experimental condition studied (e.g., holo [M + 8H](+8)-[M + 9H](+9) and apo [M + 9H](+9)-[M + 19H](+19)). Inspection of the kinetic intermediates suggests that the tertiary structure of apomyoglobin unfolds quickly upon the loss of the Fe protoporphyrin IX that stabilizes the interactions between the A, G, and H helices. In the absence of the porphyrin heme, the apomyoglobin unfolds to Xn kinetic intermediates that vary in the extent of unfolding as a result of the observed charge state.
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Affiliation(s)
- Emily R. Schenk
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
| | - Raybel Almeida
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA
| | - Jaroslava Miksovska
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA
| | | | | | - Francisco Fernandez-Lima
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
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27
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Molano-Arevalo JC, Hernandez DR, Gonzalez WG, Miksovska J, Ridgeway ME, Park MA, Fernandez-Lima F. Flavin adenine dinucleotide structural motifs: from solution to gas phase. Anal Chem 2014; 86:10223-30. [PMID: 25222439 PMCID: PMC4204916 DOI: 10.1021/ac5023666] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
![]()
Flavin
adenine dinucleotide (FAD) is involved in important metabolic
reactions where the biological function is intrinsically related to
changes in conformation. In the present work, FAD conformational changes
were studied in solution and in gas phase by measuring the fluorescence
decay time and ion-neutral collision cross sections (CCS, in a trapped
ion mobility spectrometer, TIMS) as a function of the solvent conditions
(i.e., organic content) and gas-phase collisional partner (i.e., N2 doped with organic molecules). Changes in the fluorescence
decay suggest that FAD can exist in four conformations in solution,
where the abundance of the extended conformations increases with the
organic content. TIMS-MS experiments showed that FAD can exist in
the gas phase as deprotonated (M = C27H31N9O15P2) and protonated forms (M = C27H33N9O15P2) and
that multiple conformations (up to 12) can be observed as a function
of the starting solution for the [M + H]+ and [M + Na]+molecular ions. In addition, changes in the relative abundances
of the gas-phase structures were observed from a “stack”
to a “close” conformation when organic molecules were
introduced in the TIMS cell as collision partners. Candidate structures
optimized at the DFT/B3LYP/6-31G(d,p) were proposed for each IMS band,
and results showed that the most abundant IMS band corresponds to
the most stable candidate structure. Solution and gas-phase experiments
suggest that the driving force that stabilizes the different conformations
is based on the interaction of the adenine and isoalloxazine rings
that can be tailored by the “solvation” effect created
with the organic molecules.
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Affiliation(s)
- Juan Camilo Molano-Arevalo
- Department of Chemistry and Biochemistry, Florida International University , Miami, Florida 33199, United States
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28
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Hernandez DR, DeBord JD, Ridgeway ME, Kaplan DA, Park MA, Fernandez-Lima F. Ion dynamics in a trapped ion mobility spectrometer. Analyst 2014; 139:1913-21. [PMID: 24571000 PMCID: PMC4144823 DOI: 10.1039/c3an02174b] [Citation(s) in RCA: 187] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
In the present paper, theoretical simulations and experimental observations are used to describe the ion dynamics in a trapped ion mobility spectrometer. In particular, the ion motion, ion transmission and mobility separation are discussed as a function of the bath gas velocity, radial confinement, analysis time and speed. Mobility analysis and calibration procedure are reported for the case of sphere-like molecules for positive and negative ion modes. Results showed that a maximal mobility resolution can be achieved by optimizing the gas velocity, radial confinement (RF amplitude) and ramp speed (voltage range and ramp time). The mobility resolution scales with the electric field and gas velocity and R = 100-250 can be routinely obtained at room temperature.
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Affiliation(s)
- Diana Rosa Hernandez
- Department of Chemistry and Biochemistry, Florida International University, Miami, USA. ; Fax: +1 305 348 3772; Tel: +1 305 348 2037
| | - John Daniel DeBord
- Department of Chemistry and Biochemistry, Florida International University, Miami, USA. ; Fax: +1 305 348 3772; Tel: +1 305 348 2037
| | | | | | - Melvin A. Park
- Bruker Daltonics, Inc., Billerica, Massachusetts 01821, USA
| | - Francisco Fernandez-Lima
- Department of Chemistry and Biochemistry, Florida International University, Miami, USA. ; Fax: +1 305 348 3772; Tel: +1 305 348 2037
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29
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Hsu PJ. A new perspective of shape recognition to discover the phase transition of finite-size clusters. J Comput Chem 2014; 35:1082-92. [DOI: 10.1002/jcc.23593] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2013] [Revised: 02/07/2014] [Accepted: 03/10/2014] [Indexed: 01/04/2023]
Affiliation(s)
- Po-Jen Hsu
- Department of Physics; National Central University; Chungli 320 Taiwan
- Molecular Science and Technology Program, Taiwan International Graduate Program; Academia Sinica; Taipei 115 Taiwan
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30
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Ahmed A, Cho Y, Giles K, Riches E, Lee JW, Kim HI, Choi CH, Kim S. Elucidating Molecular Structures of Nonalkylated and Short-Chain Alkyl (n < 5, (CH2)n) Aromatic Compounds in Crude Oils by a Combination of Ion Mobility and Ultrahigh-Resolution Mass Spectrometries and Theoretical Collisional Cross-Section Calculations. Anal Chem 2014; 86:3300-7. [DOI: 10.1021/ac4032737] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Arif Ahmed
- Kyungpook National University, Department of Chemistry, Daegu, 702-701 Republic of Korea
| | - Yunju Cho
- Kyungpook National University, Department of Chemistry, Daegu, 702-701 Republic of Korea
| | | | | | - Jong Wha Lee
- Pohang University of Science and Technology, Pohang, 790-784, Republic of Korea
| | - Hugh I. Kim
- Pohang University of Science and Technology, Pohang, 790-784, Republic of Korea
| | - Cheol Ho Choi
- Kyungpook National University, Department of Chemistry, Daegu, 702-701 Republic of Korea
- Green-Nano Materials
Research Center, Daegu, 702-701 Republic of Korea
| | - Sunghwan Kim
- Kyungpook National University, Department of Chemistry, Daegu, 702-701 Republic of Korea
- Green-Nano Materials
Research Center, Daegu, 702-701 Republic of Korea
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31
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Schenk E, Mendez V, Landrum JT, Ridgeway ME, Park MA, Fernandez-Lima F. Direct observation of differences of carotenoid polyene chain cis/trans isomers resulting from structural topology. Anal Chem 2014; 86:2019-24. [PMID: 24428664 PMCID: PMC3983025 DOI: 10.1021/ac403153m] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Accepted: 01/15/2014] [Indexed: 02/07/2023]
Abstract
In the present paper, trapped ion mobility spectrometry (TIMS) and theoretical calculations have been used to study carotenoid geometrical motifs generated by photoisomerization from the all-trans geometry. Multiple geometric isomers of the carotenoids lutein and zeaxanthin were separated using TIMS (R > 110) for [M](+), [M + H](+), and [M - 18](+) molecular species. Comparison of observed cross sections with those obtained from molecular dynamics calculations showed that the number of cis double bonds and s-cis single bonds in the polyene chain determine the topology space of the carotenoid. The intensities of IMS signals are correlated with the relative stability of these geometric isomers.1,2 The most stable isomer is the all-trans geometry regardless of the ionization state ([M - 18](+), [M](+), and [M + H](+)), and structural stability decreases with the increasing number of cis and/or s-cis bonds in the polyene chain.
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Affiliation(s)
- Emily
R. Schenk
- Department
of Chemistry and Biochemistry, Florida International
University, Miami, FL 33199, U.S.A.
| | - Vanesa Mendez
- Department
of Chemistry and Biochemistry, Florida International
University, Miami, FL 33199, U.S.A.
| | - John T. Landrum
- Department
of Chemistry and Biochemistry, Florida International
University, Miami, FL 33199, U.S.A.
| | | | - Melvin A. Park
- Bruker
Daltonics,
Inc., Billerica, Massachusetts 01821, USA
| | - Francisco Fernandez-Lima
- Department
of Chemistry and Biochemistry, Florida International
University, Miami, FL 33199, U.S.A.
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Schenk ER, Ridgeway ME, Park MA, Leng F, Fernandez-Lima F. Isomerization kinetics of AT hook decapeptide solution structures. Anal Chem 2014; 86:1210-4. [PMID: 24364733 PMCID: PMC3935383 DOI: 10.1021/ac403386q] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The mammalian high mobility group protein HMGA2 contains three DNA binding motifs associated with many physiological functions including oncogenesis, obesity, stem cell youth, human height, and human intelligence. In the present paper, trapped ion mobility spectrometry-mass spectrometry (TIMS-MS) has been utilized to study the conformational dynamics of the third DNA binding motif using the "AT hook" decapeptide unit (Lys(1)-Arg(2)-Prol(3)-Arg(4)-Gly(5)-Arg(6)-Prol(7)-Arg(8)-Lys(9)-Trp(10), ATHP) as a function of the solvent state. Solvent state distributions were preserved during electrospray ion formation, and multiple IMS bands were identified for the [M + 2H](2+) and for the [M + 3H](3+) charge states. Conformational isomer interconversion rates were measured as a function of the trapping time for the [M + 2H](2+) and [M + 3H](3+) charge states. Candidate structures were proposed for all IMS bands observed. Protonation site, proline residue conformation, and side chain orientations were identified as the main motifs governing the conformational interconversion processes. Conformational dynamics from the solvent state distribution to the gas-phase "de-solvated" state distribution demonstrated that ATHP is "structured", and relative abundances are associated with the relative stability between the proposed conformers. The most stable ATHP [M + 2H](2+) conformation at the "de-solvated" state corresponds to the AT hook motif observed in AT-rich DNA regions.
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Affiliation(s)
- Emily R. Schenk
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA
| | | | - Melvin A. Park
- Bruker Daltonics, Inc., Billerica, Massachusetts 01821, USA
| | - Fenfei Leng
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA
| | - Francisco Fernandez-Lima
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA
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Ouyang H, Larriba-Andaluz C, Oberreit DR, Hogan CJ. The collision cross sections of iodide salt cluster ions in air via differential mobility analysis-mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:1833-1847. [PMID: 24026975 DOI: 10.1007/s13361-013-0724-8] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2013] [Revised: 07/30/2013] [Accepted: 07/30/2013] [Indexed: 06/02/2023]
Abstract
To date, most collision cross section (CCS) predictions have invoked gas molecule impingement-reemission rules in which specular and elastic scattering of spherical gas molecules from rigid polyatomic surfaces are assumed. Although such predictions have been shown to agree well with CCSs measured in helium bath gas, a number of studies reveal that these predictions do not agree with CCSs for ions in diatomic gases, namely, air and molecular nitrogen. To further examine the validity of specular-elastic versus diffuse-inelastic scattering models, we measured the CCSs of positively charged metal iodide cluster ions of the form [MI]n[M(+)]z, where M = Na, K, Rb, or Cs, n = 1 - 25, and z = 1 - 2. Measurements were made in air via differential mobility analysis mass spectrometry (DMA-MS). The CCSs measured are compared with specular-elastic as well as diffuse-inelastic scattering model predictions with candidate ion structures determined from density functional theory. It is found that predictions from diffuse-inelastic collision models agree well (within 5%) with measurements from sodium iodide cluster ions, while specular-elastic collision model predictions are in better agreement with cesium iodide cluster ion measurements. The agreement with diffuse-inelastic and specular-elastic predictions decreases and increases, respectively, with increasing cation mass. However, even when diffuse-inelastic cluster ion predictions disagree with measurements, the disagreement is of a near-constant factor for all ions, indicating that a simple linear rescaling collapses predictions to measurements. Conversely, rescaling cannot be used to collapse specular-elastic predictions to measurements; hence, although the precise impingement reemission rules remain ambiguous, they are not specular-elastic.
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Affiliation(s)
- Hui Ouyang
- Department of Mechanical Engineering, University of Minnesota, Minneapolis, MN, 55455, USA
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Comparison of reactant and analyte ions for 63Nickel, corona discharge, and secondary electrospray ionization sources with ion mobility-mass spectrometry. Talanta 2013; 107:225-32. [DOI: 10.1016/j.talanta.2013.01.009] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Revised: 01/08/2013] [Accepted: 01/08/2013] [Indexed: 11/19/2022]
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Lapthorn C, Pullen F, Chowdhry BZ. Ion mobility spectrometry-mass spectrometry (IMS-MS) of small molecules: separating and assigning structures to ions. MASS SPECTROMETRY REVIEWS 2013; 32:43-71. [PMID: 22941854 DOI: 10.1002/mas.21349] [Citation(s) in RCA: 183] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2011] [Revised: 01/29/2012] [Accepted: 03/08/2012] [Indexed: 05/11/2023]
Abstract
The phenomenon of ion mobility (IM), the movement/transport of charged particles under the influence of an electric field, was first observed in the early 20th Century and harnessed later in ion mobility spectrometry (IMS). There have been rapid advances in instrumental design, experimental methods, and theory together with contributions from computational chemistry and gas-phase ion chemistry, which have diversified the range of potential applications of contemporary IMS techniques. Whilst IMS-mass spectrometry (IMS-MS) has recently been recognized for having significant research/applied industrial potential and encompasses multi-/cross-disciplinary areas of science, the applications and impact from decades of research are only now beginning to be utilized for "small molecule" species. This review focuses on the application of IMS-MS to "small molecule" species typically used in drug discovery (100-500 Da) including an assessment of the limitations and possibilities of the technique. Potential future developments in instrumental design, experimental methods, and applications are addressed. The typical application of IMS-MS in relation to small molecules has been to separate species in fairly uniform molecular classes such as mixture analysis, including metabolites. Separation of similar species has historically been challenging using IMS as the resolving power, R, has been low (3-100) and the differences in collision cross-sections that could be measured have been relatively small, so instrument and method development has often focused on increasing resolving power. However, IMS-MS has a range of other potential applications that are examined in this review where it displays unique advantages, including: determination of small molecule structure from drift time, "small molecule" separation in achiral and chiral mixtures, improvement in selectivity, identification of carbohydrate isomers, metabonomics, and for understanding the size and shape of small molecules. This review provides a broad but selective overview of current literature, concentrating on IMS-MS, not solely IMS, and small molecule applications.
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Affiliation(s)
- Cris Lapthorn
- School of Science, University of Greenwich, Medway Campus, Chatham, Kent ME4 4TB, UK
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Zakharova NL, Crawford CL, Hauck BC, Quinton JK, Seims WF, Hill HH, Clark AE. An assessment of computational methods for obtaining structural information of moderately flexible biomolecules from ion mobility spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:792-805. [PMID: 22359091 DOI: 10.1007/s13361-012-0339-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2011] [Revised: 01/11/2012] [Accepted: 01/13/2012] [Indexed: 05/22/2023]
Abstract
When utilized in conjunction with modeling, the collision cross section (Ω) from ion mobility spectrometry can be used to deduce the gas phase structures of analyte ions. Gas phase conformations are determined computationally, and their Ω calculated using an approximate method, the results of which are compared with experimental data. Though prior work has focused upon rigid small molecules or large biomolecules, correlation of computational and experimental Ω has not been thoroughly examined for analytes with intermediate conformational flexibility, which constitute a large fraction of the molecules studied in the field. Here, the computational paradigm for calculating Ω has been tested for the tripeptides WGY, YGW, and YWG (Y = tyrosine, W = tryptophan, G = glycine). Experimental data indicate that Ω(exp) (YWG) > Ω(exp) (WGY) ≈ Ω(exp) (YGW). The energy distributions of conformations obtained from tiers of simulated annealing molecular dynamics (SAMD) were analyzed using a wide array of density functionals. These quantum mechanical energy distributions do not agree with the MD data, which leads to structural differences between the SAMD and DFT conformations. The latter structures are obtained by reoptimization of the SAMD geometries, and are the only suite of structures that reproduce the experimental trend in analyte separability. In the absence of fitting Lennard Jones potentials that reproduce experimental results for the Trajectory Method, the Exact Hard Sphere Scattering method produced numerical values that are in best agreement with the experimental cross sections obtained in He drift gas.
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Affiliation(s)
- Natalia L Zakharova
- Department of Chemistry, Washington State University, Pullman, WA 99164, USA
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Chen L, Gao YQ, Russell DH. How Alkali Metal Ion Binding Alters the Conformation Preferences of Gramicidin A: A Molecular Dynamics and Ion Mobility Study. J Phys Chem A 2011; 116:689-96. [DOI: 10.1021/jp209430q] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Liuxi Chen
- Laboratory for Biological Mass Spectrometry, Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Yi Qin Gao
- Beijing National Lab for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China 100871
| | - David H. Russell
- Laboratory for Biological Mass Spectrometry, Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
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38
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Fernandez-Lima F, Kaplan DA, Suetering J, Park MA. Gas-phase separation using a trapped ion mobility spectrometer. ACTA ACUST UNITED AC 2011; 14. [PMID: 24163587 DOI: 10.1007/s12127-011-0067-8] [Citation(s) in RCA: 212] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
In the present work we describe the principles of operation, versatility and applicability of a trapped ion mobility spectrometer (TIMS) analyzer for fast, gas-phase separation of molecular ions based on their size-to-charge ratio. Mobility-based separation using a TIMS device is shown for a series for isobar pairs. In a TIMS device, mobility resolution depends on the bath gas velocity and analysis scan speed, with the particularity that the mobility separation can be easily tuned from low to high resolution (R>50) in accordance with the analytical challenge. In contrast to traditional drift tube IMS analyzer, a TIMS device can be easily integrated in a mass spectrometer without a noticeable loss in ion transmission or sensitivity, thus providing a powerful separation platform prior to mass analysis.
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39
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Chen L, Shao Q, Gao YQ, Russell DH. Molecular Dynamics and Ion Mobility Spectrometry Study of Model β-Hairpin Peptide, Trpzip1. J Phys Chem A 2011; 115:4427-35. [DOI: 10.1021/jp110014j] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Liuxi Chen
- The Laboratory for Biological Mass Spectrometry, Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Qiang Shao
- The Laboratory for Biological Mass Spectrometry, Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Yi-Qin Gao
- The Laboratory for Biological Mass Spectrometry, Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - David H. Russell
- The Laboratory for Biological Mass Spectrometry, Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
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40
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Fernandez-Lima FA, Blase RC, Russell DH. A Study of Ion-Neutral Collision Cross Section Values for Low Charge States of Peptides, Proteins, and Peptide/Protein Complexes. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2010; 298:111-118. [PMID: 21503273 PMCID: PMC3077763 DOI: 10.1016/j.ijms.2009.10.009] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Here, we report ion-helium collision cross sections (CCS) for a number of peptide, small protein, and peptide/protein ionic complexes. The CCS values reported here are compared to previously reported results.[1, 2] We also compare values for low charge state species, i.e., [M + H](+) and [M + 2H](2+), formed by MALDI with values for high charge state species formed by ESI, and the measured CCSs are compared with predicted CCS for solid-state and solution phase structures and calculated structures obtained by using a protein-protein structure algorithm generator, based on a combined Biomolecular complex Generation with Global Evaluation and Ranking[3] and Multi Dimensional Scaling[4].
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41
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Ahmed A, Cho YJ, No MH, Koh J, Tomczyk N, Giles K, Yoo JS, Kim S. Application of the Mason−Schamp Equation and Ion Mobility Mass Spectrometry To Identify Structurally Related Compounds in Crude Oil. Anal Chem 2010; 83:77-83. [DOI: 10.1021/ac101934q] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Arif Ahmed
- Department of Chemistry, Kyungpook National University, Daegu, Korea, SK Energy Institute of Technology, Daejeon, Korea, Waters MS Technologies Centre, Manchester, United Kingdom, and Mass Spectrometry Group, Korean Basic Science Institute, Daejeon, Korea
| | - Yun Ju Cho
- Department of Chemistry, Kyungpook National University, Daegu, Korea, SK Energy Institute of Technology, Daejeon, Korea, Waters MS Technologies Centre, Manchester, United Kingdom, and Mass Spectrometry Group, Korean Basic Science Institute, Daejeon, Korea
| | - Myoung-han No
- Department of Chemistry, Kyungpook National University, Daegu, Korea, SK Energy Institute of Technology, Daejeon, Korea, Waters MS Technologies Centre, Manchester, United Kingdom, and Mass Spectrometry Group, Korean Basic Science Institute, Daejeon, Korea
| | - Jaesuk Koh
- Department of Chemistry, Kyungpook National University, Daegu, Korea, SK Energy Institute of Technology, Daejeon, Korea, Waters MS Technologies Centre, Manchester, United Kingdom, and Mass Spectrometry Group, Korean Basic Science Institute, Daejeon, Korea
| | - Nicholas Tomczyk
- Department of Chemistry, Kyungpook National University, Daegu, Korea, SK Energy Institute of Technology, Daejeon, Korea, Waters MS Technologies Centre, Manchester, United Kingdom, and Mass Spectrometry Group, Korean Basic Science Institute, Daejeon, Korea
| | - Kevin Giles
- Department of Chemistry, Kyungpook National University, Daegu, Korea, SK Energy Institute of Technology, Daejeon, Korea, Waters MS Technologies Centre, Manchester, United Kingdom, and Mass Spectrometry Group, Korean Basic Science Institute, Daejeon, Korea
| | - Jong Shin Yoo
- Department of Chemistry, Kyungpook National University, Daegu, Korea, SK Energy Institute of Technology, Daejeon, Korea, Waters MS Technologies Centre, Manchester, United Kingdom, and Mass Spectrometry Group, Korean Basic Science Institute, Daejeon, Korea
| | - Sunghwan Kim
- Department of Chemistry, Kyungpook National University, Daegu, Korea, SK Energy Institute of Technology, Daejeon, Korea, Waters MS Technologies Centre, Manchester, United Kingdom, and Mass Spectrometry Group, Korean Basic Science Institute, Daejeon, Korea
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42
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Pierson NA, Valentine SJ, Clemmer DE. Evidence for a quasi-equilibrium distribution of states for bradykinin [M + 3H]3+ ions in the gas phase. J Phys Chem B 2010; 114:7777-83. [PMID: 20469905 PMCID: PMC2922466 DOI: 10.1021/jp102478k] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Multidimensional ion mobility spectrometry coupled with mass spectrometry (IMS-IMS-MS) techniques are used to select and activate six different gas-phase conformations of bradykinin [M + 3H](3+) ions. Drift time distributions as a function of activation voltage show that at low voltages selected structures undergo conformational transitions in what appears to be a pathway dependent fashion. Over a relatively wide range of intermediate activation voltages a distribution of states that is independent of the initial conformation selected for activation (as well as the activation voltage in this intermediate region) is established. This distribution appears to represent an equilibrium distribution of gas-phase structures that is reached prior to the energy required for dissociation. Establishment of a quasi-equilibrium prior to dissociation results in identical dissociation patterns for different selected conformations. A discussion of the transition from solution-like to gas-phase structures is provided.
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Affiliation(s)
| | | | - David E. Clemmer
- Department of Chemistry, Indiana University, Bloomington, IN 47405
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43
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Albrieux F, Calvo F, Chirot F, Vorobyev A, Tsybin YO, Lepère V, Antoine R, Lemoine J, Dugourd P. Conformation of Polyalanine and Polyglycine Dications in the Gas Phase: Insight from Ion Mobility Spectrometry and Replica-Exchange Molecular Dynamics. J Phys Chem A 2010; 114:6888-96. [DOI: 10.1021/jp102621m] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Florian Albrieux
- Université de Lyon, F-69622, Lyon, France, Université Lyon 1, Villeurbanne, CNRS, UMR 5579, LASIM, UMR 5180, LSA, and Biomolecular Mass Spectrometry Laboratory, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Florent Calvo
- Université de Lyon, F-69622, Lyon, France, Université Lyon 1, Villeurbanne, CNRS, UMR 5579, LASIM, UMR 5180, LSA, and Biomolecular Mass Spectrometry Laboratory, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Fabien Chirot
- Université de Lyon, F-69622, Lyon, France, Université Lyon 1, Villeurbanne, CNRS, UMR 5579, LASIM, UMR 5180, LSA, and Biomolecular Mass Spectrometry Laboratory, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Aleksey Vorobyev
- Université de Lyon, F-69622, Lyon, France, Université Lyon 1, Villeurbanne, CNRS, UMR 5579, LASIM, UMR 5180, LSA, and Biomolecular Mass Spectrometry Laboratory, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Yury O. Tsybin
- Université de Lyon, F-69622, Lyon, France, Université Lyon 1, Villeurbanne, CNRS, UMR 5579, LASIM, UMR 5180, LSA, and Biomolecular Mass Spectrometry Laboratory, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Valéria Lepère
- Université de Lyon, F-69622, Lyon, France, Université Lyon 1, Villeurbanne, CNRS, UMR 5579, LASIM, UMR 5180, LSA, and Biomolecular Mass Spectrometry Laboratory, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Rodolphe Antoine
- Université de Lyon, F-69622, Lyon, France, Université Lyon 1, Villeurbanne, CNRS, UMR 5579, LASIM, UMR 5180, LSA, and Biomolecular Mass Spectrometry Laboratory, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Jérôme Lemoine
- Université de Lyon, F-69622, Lyon, France, Université Lyon 1, Villeurbanne, CNRS, UMR 5579, LASIM, UMR 5180, LSA, and Biomolecular Mass Spectrometry Laboratory, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Philippe Dugourd
- Université de Lyon, F-69622, Lyon, France, Université Lyon 1, Villeurbanne, CNRS, UMR 5579, LASIM, UMR 5180, LSA, and Biomolecular Mass Spectrometry Laboratory, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
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44
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Fernandez-Lima FA, Becker C, McKenna AM, Rodgers RP, Marshall AG, Russell DH. Petroleum Crude Oil Characterization by IMS-MS and FTICR MS. Anal Chem 2009; 81:9941-7. [DOI: 10.1021/ac901594f] [Citation(s) in RCA: 153] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Francisco A. Fernandez-Lima
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, Department of Chemistry, Baylor University, Waco, Texas 76706, Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, Florida State University, 1800 East Paul Dirac Drive, Tallahassee, Florida 32310-4005, and Department of Chemistry & Biochemistry, Florida State University, Tallahassee, Florida 32306
| | - Christopher Becker
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, Department of Chemistry, Baylor University, Waco, Texas 76706, Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, Florida State University, 1800 East Paul Dirac Drive, Tallahassee, Florida 32310-4005, and Department of Chemistry & Biochemistry, Florida State University, Tallahassee, Florida 32306
| | - Amy M. McKenna
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, Department of Chemistry, Baylor University, Waco, Texas 76706, Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, Florida State University, 1800 East Paul Dirac Drive, Tallahassee, Florida 32310-4005, and Department of Chemistry & Biochemistry, Florida State University, Tallahassee, Florida 32306
| | - Ryan P. Rodgers
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, Department of Chemistry, Baylor University, Waco, Texas 76706, Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, Florida State University, 1800 East Paul Dirac Drive, Tallahassee, Florida 32310-4005, and Department of Chemistry & Biochemistry, Florida State University, Tallahassee, Florida 32306
| | - Alan G. Marshall
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, Department of Chemistry, Baylor University, Waco, Texas 76706, Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, Florida State University, 1800 East Paul Dirac Drive, Tallahassee, Florida 32310-4005, and Department of Chemistry & Biochemistry, Florida State University, Tallahassee, Florida 32306
| | - David H. Russell
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, Department of Chemistry, Baylor University, Waco, Texas 76706, Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, Florida State University, 1800 East Paul Dirac Drive, Tallahassee, Florida 32310-4005, and Department of Chemistry & Biochemistry, Florida State University, Tallahassee, Florida 32306
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