1
|
Osho KE, Kunwor K, Borotto NB. Ion Mobility-Assisted Free Radical-Initiated Peptide Sequencing. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2025; 508:117396. [PMID: 39830974 PMCID: PMC11737517 DOI: 10.1016/j.ijms.2024.117396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2025]
Abstract
Free radical-initiated peptide sequencing (FRIPS) is a tandem mass spectrometry technique (MS/MS) that enables radical-based dissociation on instruments only capable of collisional activation. In FRIPS, peptides are chemically-derivatized with a compound that undergoes homolytic cleavage and generates radicals upon collisional activation. These radicals then propagate through the peptide backbone enabling the sequencing of peptide ions. This MS/MS technique has shown promise in sequencing post-translationally modified peptides, but it is typically performed in an MS3 workflow and single-step MS/MS approaches result in the generation of both collisional- and radical-driven dissociation products and highly complex spectra. Recently, our group developed a method to dissociate peptide ions prior to ion mobility analysis within a trapped-ion mobility spectrometry (TIMS) device. In this work, we examine if this "CIDtims" technique can initiate the homolytic cleavage of the FRIPS precursor. We then examine if the resultant ion mobility separation results in additional assignments of product ions and improved sequence coverage. We demonstrate that activation within the TIMS device does indeed promote robust radical initiation and fragmentation of peptide cations and that the generated product ions are mobility separated enabling facile assignment and increased sequence coverage.
Collapse
Affiliation(s)
- Kemi E. Osho
- Department of Chemistry, University of Nevada, 1664 N. Virginia Street,
Reno, Nevada 89557, United States
| | - Keshari Kunwor
- Department of Chemistry, University of Nevada, 1664 N. Virginia Street,
Reno, Nevada 89557, United States
| | - Nicholas B. Borotto
- Department of Chemistry, University of Nevada, 1664 N. Virginia Street,
Reno, Nevada 89557, United States
| |
Collapse
|
2
|
Deng L, May JC, McBee JK, Rosen A, Rorrer LC, Clingman R, Fico M, McLean JA, DeBord D. Rounded Turn SLIM Design for High-Resolution Ion Mobility Mass Spectrometry Analysis of Small Molecules. Anal Chem 2024; 96:20179-20188. [PMID: 39661157 DOI: 10.1021/acs.analchem.4c03808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2024]
Abstract
Various rounded turn designs in Structures for Lossless Ion Manipulation (SLIM) were explored via ion trajectory simulations. The optimized design was integrated into a SLIM ion mobility (IM) system coupled with a time-of-flight (TOF) mass spectrometer (MS) for further experimental investigation. The SLIM-TOF IM-MS system was assessed for IM resolution and ion transmission efficiency across a wide m/z range using various RF frequencies and buffer gas combinations. High ion transmission efficiency and high resolution ion mobility (HRIM) separation were achieved for Agilent tune mix ions through a ∼12.8 m serpentine separation path in both nitrogen and helium. In helium, ion transmission for low m/z ions was enhanced at higher RF trapping frequency, enabling the detection of ions with m/z below 50 and all 17 amino acids from a standard mixture. Lossless ion transmission was observed for glycine (m/z 76) in both passthrough and HRIM modes. HRIM resolution was benchmarked using L-isoleucine, L-leucine, and various other isobaric and isomeric metabolites with m/z values of 60-89. This work demonstrates a rounded turn SLIM design that enables HRIM measurements for small molecule analytes, with a particular focus on metabolomics, where IM offers a means to enhance the speed, robustness, and specificity of analytical workflows.
Collapse
Affiliation(s)
- Liulin Deng
- MOBILion Systems, Inc., 4 Hillman Drive, Suite 130, Chadds Ford, Pennsylvania 19317, United States
| | - Jody C May
- Center for Innovative Technology, Department of Chemistry, Vanderbilt Institute of Chemical Biology, Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Joshua K McBee
- MOBILion Systems, Inc., 4 Hillman Drive, Suite 130, Chadds Ford, Pennsylvania 19317, United States
| | - Adam Rosen
- MOBILion Systems, Inc., 4 Hillman Drive, Suite 130, Chadds Ford, Pennsylvania 19317, United States
| | - Leonard C Rorrer
- MOBILion Systems, Inc., 4 Hillman Drive, Suite 130, Chadds Ford, Pennsylvania 19317, United States
| | - Ryan Clingman
- MOBILion Systems, Inc., 4 Hillman Drive, Suite 130, Chadds Ford, Pennsylvania 19317, United States
| | - Miriam Fico
- MOBILion Systems, Inc., 4 Hillman Drive, Suite 130, Chadds Ford, Pennsylvania 19317, United States
| | - John A McLean
- Center for Innovative Technology, Department of Chemistry, Vanderbilt Institute of Chemical Biology, Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Daniel DeBord
- MOBILion Systems, Inc., 4 Hillman Drive, Suite 130, Chadds Ford, Pennsylvania 19317, United States
| |
Collapse
|
3
|
Oppenländer T, Gross JH. Collision cross sections of large positive fullerene molecular ions and their use as ion mobility calibrants in trapped ion mobility mass spectrometry. Anal Bioanal Chem 2024; 416:6187-6197. [PMID: 39384572 PMCID: PMC11541393 DOI: 10.1007/s00216-024-05579-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2024] [Revised: 09/23/2024] [Accepted: 09/27/2024] [Indexed: 10/11/2024]
Abstract
Positive-ion laser desorption/ionization (LDI) of fullerenes contained in soot as produced by the Krätschmer-Huffman process delivers a wide range of fullerene molecular ions from C56+• to above C300+•. Here, the collision cross section (CCS) values of those fullerene molecular ions are determined using a trapped ion mobility-quadrupole-time-of-flight (TIMS-Q-TOF) instrument. While CCS values in the range from C60+• to C96+• are already known with high accuracy, those of ions from C98+• onward had yet to be determined. The fullerene molecular ions covered in this work have CCS values from about 200 to 440 Å2. The fullerene molecular ion series is evenly spaced at C2 differences in composition, and thus, small CCS differences of just 2.2-3.5 Å2 were determined across the entire range. Fullerene M+• ions may be employed as mobility calibrants, in particular, when very narrow 1/K0 ranges are being analyzed to achieve high TIMS resolving power. In addition, due to the simple elemental composition, M+• ions of fullerenes could also serve for mass calibration. This study describes the determination of CCS values of fullerene molecular ions from C56+• to C240+• and the application of ions from C56+• to C220+• to calibrate the ion mobility scale of a Bruker timsTOFflex instrument in any combination of LDI, matrix-assisted laser desorption/ionization (MALDI), and electrospray ionization (ESI) modes in the CCS range from about 200 to 420 Å2. This use was exemplified along with ions from Agilent Tune Mix, leucine-enkephalin, angiotensin I, angiotensin II, and substance P.
Collapse
Affiliation(s)
- Tobias Oppenländer
- Institute of Organic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany
| | - Jürgen H Gross
- Institute of Organic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany.
| |
Collapse
|
4
|
McDowell CT, Lu X, Mehta AS, Angel PM, Drake RR. Applications and continued evolution of glycan imaging mass spectrometry. MASS SPECTROMETRY REVIEWS 2023; 42:674-705. [PMID: 34392557 PMCID: PMC8946722 DOI: 10.1002/mas.21725] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 07/16/2021] [Accepted: 08/03/2021] [Indexed: 05/03/2023]
Abstract
Glycosylation is an important posttranslational modifier of proteins and lipid conjugates critical for the stability and function of these macromolecules. Particularly important are N-linked glycans attached to asparagine residues in proteins. N-glycans have well-defined roles in protein folding, cellular trafficking and signal transduction, and alterations to them are implicated in a variety of diseases. However, the non-template driven biosynthesis of these N-glycans leads to significant structural diversity, making it challenging to identify the most biologically and clinically relevant species using conventional analyses. Advances in mass spectrometry instrumentation and data acquisition, as well as in enzymatic and chemical sample preparation strategies, have positioned mass spectrometry approaches as powerful analytical tools for the characterization of glycosylation in health and disease. Imaging mass spectrometry expands upon these strategies by capturing the spatial component of a glycan's distribution in-situ, lending additional insight into the organization and function of these molecules. Herein we review the ongoing evolution of glycan imaging mass spectrometry beginning with widely adopted tissue imaging approaches and expanding to other matrices and sample types with potential research and clinical implications. Adaptations of these techniques, along with their applications to various states of disease, are discussed. Collectively, glycan imaging mass spectrometry analyses broaden our understanding of the biological and clinical relevance of N-glycosylation to human disease.
Collapse
Affiliation(s)
- Colin T. McDowell
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Xiaowei Lu
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Anand S. Mehta
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Peggi M. Angel
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Richard R. Drake
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC, 29425, USA
| |
Collapse
|
5
|
Blaschke CRK, McDowell CT, Black AP, Mehta AS, Angel PM, Drake RR. Glycan Imaging Mass Spectrometry: Progress in Developing Clinical Diagnostic Assays for Tissues, Biofluids, and Cells. Clin Lab Med 2021; 41:247-266. [PMID: 34020762 PMCID: PMC8862151 DOI: 10.1016/j.cll.2021.03.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
N-glycan imaging mass spectrometry (IMS) can rapidly and reproducibly identify changes in disease-associated N-linked glycosylation that are linked with histopathology features in standard formalin-fixed paraffin-embedded tissue samples. It can detect multiple N-glycans simultaneously and has been used to identify specific N-glycans and carbohydrate structural motifs as possible cancer biomarkers. Recent advancements in instrumentation and sample preparation are also discussed. The tissue N-glycan IMS workflow has been adapted to new glass slide-based assays for effective and rapid analysis of clinical biofluids, cultured cells, and immunoarray-captured glycoproteins for detection of changes in glycosylation associated with disease.
Collapse
Affiliation(s)
- Calvin R K Blaschke
- Department of Cell and Molecular Pharmacology, Medical University of South Carolina, 173 Ashley Avenue, BSB 358, Charleston, SC 29425, USA
| | - Colin T McDowell
- Department of Cell and Molecular Pharmacology, Medical University of South Carolina, 173 Ashley Avenue, BSB 358, Charleston, SC 29425, USA
| | - Alyson P Black
- Department of Cell and Molecular Pharmacology, Medical University of South Carolina, 173 Ashley Avenue, BSB 358, Charleston, SC 29425, USA
| | - Anand S Mehta
- Department of Cell and Molecular Pharmacology, Medical University of South Carolina, 173 Ashley Avenue, BSB 358, Charleston, SC 29425, USA
| | - Peggi M Angel
- Department of Cell and Molecular Pharmacology, Medical University of South Carolina, 173 Ashley Avenue, BSB 358, Charleston, SC 29425, USA
| | - Richard R Drake
- Department of Cell and Molecular Pharmacology, Medical University of South Carolina, 173 Ashley Avenue, BSB 358, Charleston, SC 29425, USA.
| |
Collapse
|
6
|
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.
Collapse
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
| |
Collapse
|
7
|
Rüger CP, Maillard J, Le Maître J, Ridgeway M, Thompson CJ, Schmitz-Afonso I, Gautier T, Carrasco N, Park MA, Giusti P, Afonso C. Structural Study of Analogues of Titan's Haze by Trapped Ion Mobility Coupled with a Fourier Transform Ion Cyclotron Mass Spectrometer. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:1169-1173. [PMID: 31066005 DOI: 10.1007/s13361-019-02205-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 03/27/2019] [Accepted: 03/29/2019] [Indexed: 06/09/2023]
Abstract
The aerosols present in the atmosphere of the Saturn's moon Titan are of particular planetary science interest and several spacecraft missions are already allowed to gather spectroscopic data. Titan haze's analogs, so-called tholins, were produced on earth to push forward the comprehension of their formation and properties. In this study, this highly complex mixture was analyzed here for the first time by trapped ion mobility spectrometry coupled to ultra-high resolution mass spectrometry (FTICR MS). Electrospray ionization revealed the characteristic CHNx-class components, with CHN5-6 and DBE 6-7 most abundant. Deploying specialized visualization, enabled by accurate mass measurements and elemental composition assignments, the adapted Kendrick mass defect analysis highlights the C2H3N homolog series, whereas the nitrogen-modified van Krevelen diagram exhibits a clear trend towards H/C 1.5 and N/C 0.5. More interestingly, the representation of m/z versus collision cross section (CCS) allowed hypothesizing a ramified N-PAH structural motif. State-of-the-art IMS is currently not able to resolve the isomeric continuum of ultra-complex mixtures; thus, peak parameters other than the CCS value are explored. As such, analyzing the mobility peak width versus m/z shows a linear increase in isomeric diversity between m/z 170 and 350 and a near plateau in diversity at higher m/z for the N-PAH-like structure. Due to the high complexity of the sample, these structural insights are only to be revealed by TIMS-FTICR MS.
Collapse
Affiliation(s)
- Christopher P Rüger
- CNRS/Université de Rouen, UMR 6014 COBRA, 1 rue Tesnière, 76821, Mont Saint Aignan Cedex, France.
| | - Julien Maillard
- CNRS/Université de Rouen, UMR 6014 COBRA, 1 rue Tesnière, 76821, Mont Saint Aignan Cedex, France
- LATMOS/IPSL, Université Versailles St Quentin, UPMC Université Paris 06, CNRS, 11 blvd d'Alembert, 78280 Guyancourt, France
| | - Johann Le Maître
- CNRS/Université de Rouen, UMR 6014 COBRA, 1 rue Tesnière, 76821, Mont Saint Aignan Cedex, France
- TOTAL Refining and Chemicals, Total Research and Technologies Gonfreville, 76700 Harfleur, France
| | | | | | - Isabelle Schmitz-Afonso
- CNRS/Université de Rouen, UMR 6014 COBRA, 1 rue Tesnière, 76821, Mont Saint Aignan Cedex, France
| | - Thomas Gautier
- LATMOS/IPSL, Université Versailles St Quentin, UPMC Université Paris 06, CNRS, 11 blvd d'Alembert, 78280 Guyancourt, France
| | - Nathalie Carrasco
- LATMOS/IPSL, Université Versailles St Quentin, UPMC Université Paris 06, CNRS, 11 blvd d'Alembert, 78280 Guyancourt, France
| | | | - Pierre Giusti
- TOTAL Refining and Chemicals, Total Research and Technologies Gonfreville, 76700 Harfleur, France
| | - Carlos Afonso
- CNRS/Université de Rouen, UMR 6014 COBRA, 1 rue Tesnière, 76821, Mont Saint Aignan Cedex, France
| |
Collapse
|
8
|
Butcher D, Miksovska J, Ridgeway ME, Park MA, Fernandez-Lima F. The effects of solution additives and gas-phase modifiers on the molecular environment and conformational space of common heme proteins. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2019; 33:399-404. [PMID: 30421840 DOI: 10.1002/rcm.8347] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 10/23/2018] [Accepted: 11/05/2018] [Indexed: 06/09/2023]
Abstract
RATIONALE The molecular environment is known to impact the secondary and tertiary structures of biomolecules both in solution and in the gas phase, shifting the equilibrium between different conformational and oligomerization states. However, there is a lack of studies monitoring the impacts of solution additives and gas-phase modifiers on biomolecules characterized using ion mobility techniques. METHODS The effect of solution additives and gas-phase modifiers on the molecular environment of two common heme proteins, bovine cytochrome c and equine myoglobin, is investigated as a function of the time after desolvation (e.g., 100-500 ms) using nanoelectrospray ionization coupled to trapped ion mobility spectrometry with detection by time-of-flight mass spectrometry. Organic compounds used as additives/modifiers (methanol, acetonitrile, acetone) were either added to the aqueous protein solution before ionization or added to the ion mobility bath gas by nebulization. RESULTS Changes in the mobility profiles are observed depending on the starting solution composition (i.e., in aqueous solution at neutral pH or in the presence of organic content: methanol, acetone, or acetonitrile) and the protein. In the presence of gas-phase modifiers (i.e., N2 doped with methanol, acetone, or acetonitrile), a shift in the mobility profiles driven by the gas-modifier mass and size and changes in the relative abundances and number of IMS bands are observed. CONCLUSIONS We attribute the observed changes in the mobility profiles in the presence of gas-phase modifiers to a clustering/declustering mechanism by which organic molecules adsorb to the protein ion surface and lower energetic barriers for interconversion between conformational states, thus redefining the free energy landscape and equilibria between conformers. These structural biology experiments open new avenues for manipulation and interrogation of biomolecules in the gas phase with the potential to emulate a large suite of solution conditions, ultimately including conditions that more accurately reflect a variety of intracellular environments.
Collapse
Affiliation(s)
- David Butcher
- Department of Chemistry & Biochemistry, Florida International University, Miami, FL, USA
| | - Jaroslava Miksovska
- Department of Chemistry & Biochemistry, Florida International University, Miami, FL, USA
- Biomolecular Sciences Institute, Florida International University, Miami, FL, USA
| | | | | | - Francisco Fernandez-Lima
- Department of Chemistry & Biochemistry, Florida International University, Miami, FL, USA
- Biomolecular Sciences Institute, Florida International University, Miami, FL, USA
| |
Collapse
|
9
|
Chouinard CD, Nagy G, Smith RD, Baker ES. Ion Mobility-Mass Spectrometry in Metabolomic, Lipidomic, and Proteomic Analyses. ADVANCES IN ION MOBILITY-MASS SPECTROMETRY: FUNDAMENTALS, INSTRUMENTATION AND APPLICATIONS 2019. [DOI: 10.1016/bs.coac.2018.11.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
|
10
|
Butcher D, Chapagain P, Leng F, Fernandez-Lima F. Differentiating Parallel and Antiparallel DNA Duplexes in the Gas Phase Using Trapped Ion Mobility Spectrometry. J Phys Chem B 2018; 122:6855-6861. [PMID: 29886735 DOI: 10.1021/acs.jpcb.7b12544] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Deoxyribonucleic acids can form a wide variety of structural motifs which differ greatly from the typical antiparallel duplex stabilized by Watson-Crick base pairing. Many of these structures are thought to occur in vivo and may have essential roles in the biology of the cell. Among these is the parallel-stranded duplex-a structural motif in which DNA strands associate in a head-to-head fashion with the 5' ends at the same end of the duplex-which is stabilized by reverse Watson-Crick base pairing. In this study, parallel- and antiparallel-stranded DNA duplexes formed from two different 12-mer oligonucleotides were studied using native electrospray ionization combined with trapped ion mobility spectrometry and mass spectrometry. The DNA duplex charge plays an important role in the gas-phase mobility profile, with a more compact form in negative mode than in positive mode (ΔΩ ≈ 100 Å2 between -4 and +4). Despite sequence mismatches, homo- and hetero-DNA duplexes were formed in solution and transfer to the gas phase, where a more compact structure was observed for the parallel compared to the antiparallel duplexes (ΔΩ ≈ 50 Å2), in good agreement with theoretical calculations. Theoretical studies suggest that a reduction (or compaction) along the helical axis of the parallel and antiparallel DNA duplexes is observed upon transfer to the gas phase.
Collapse
|
11
|
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: 3.8] [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.
Collapse
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
| |
Collapse
|