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Miller SA, Jeanne Dit Fouque K, Mebel AM, Chandler KB, Fernandez-Lima F. Gas-Phase Structures of Fucosylated Oligosaccharides: Alkali Metal and Halogen Influences. J Phys Chem B 2024; 128:8869-8877. [PMID: 39226480 PMCID: PMC11421426 DOI: 10.1021/acs.jpcb.4c02696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
Fucosylated carbohydrate antigens play critical roles in physiology and pathology with function linked to their structural details. However, the separation and structural characterization of isomeric fucosylated epitopes remain challenging analytically. Here, we report for the first time the influence of alkali metal cations (Li+, Na+, K+, Rb+, and Cs+) and halogen anions (Cl-, Br-, and I-) on the gas-phase conformational landscapes of common fucosylated trisaccharides (Lewis A, X, and H types 1 and 2) and tetrasaccharides (Lewis B and Y) using trapped ion mobility spectrometry coupled to mass spectrometry and theoretical calculations. Inspection of the mobility profiles of individual standards showed a dependence on the number of mobility bands with the oligosaccharide and the alkali metal and halogen; collision cross sections are reported for all of the observed species. Results showed that trisaccharides (Lewis A, X, and H types 1 and 2) can be best mobility resolved in the positive mode using the [M + Li]+ molecular ion form (baseline resolution r ≈ 2.88 between Lewis X and A); tetrasaccharides can be best mobility resolved in the negative mode using the [M + I]- molecular ion form (baseline separation r ≈ 1.35 between Lewis B and Y). The correlation between the number of oligosaccharide conformers as a function of the molecular ion adduct was studied using density functional theory. Theoretical calculations revealed that smaller cations can form more stable structures based on the number of coordinations, while larger cations induced greater oligosaccharide reorganizations; candidate structures are proposed to better understand the gas-phase oligosaccharide rearrangement trends. Inspection of the candidate structures suggests that the interplay between ion size/charge density and molecular structure dictated the conformational preferences and, consequently, the number of mobility bands and the mobility separation across isomers. This work provides a fundamental understanding of the gas-phase structural dynamics of fucosylated oligosaccharides and their interaction with alkali metals and halogens.
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Affiliation(s)
- Samuel A Miller
- Department of Chemistry and Biochemistry and Biomolecular Sciences Institute, Florida International University, 11200 SW Eighth Street, Miami, Florida 33199, United States
| | - Kevin Jeanne Dit Fouque
- Department of Chemistry and Biochemistry and Biomolecular Sciences Institute, Florida International University, 11200 SW Eighth Street, Miami, Florida 33199, United States
| | - Alexander M Mebel
- Department of Chemistry and Biochemistry and Biomolecular Sciences Institute, Florida International University, 11200 SW Eighth Street, Miami, Florida 33199, United States
| | - Kevin Brown Chandler
- Translational Glycobiology Institute, Department of Translational Medicine, Herbert Wertheim College of Medicine, Florida International University, 11200 SW Eighth Street, Miami, Florida 33199, United States
- Biomolecular Sciences Institute, Florida International University, 11200 SW Eighth Street, Miami, Florida 33199, United States
| | - Francisco Fernandez-Lima
- Department of Chemistry and Biochemistry and Biomolecular Sciences Institute, Florida International University, 11200 SW Eighth Street, Miami, Florida 33199, United States
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2
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Jeanne Dit Fouque K, Molano-Arevalo JC, Leng F, Fernandez-Lima F. Conformational and Structural Characterization of Knotted Proteins. Biochemistry 2024; 63:2293-2299. [PMID: 39189377 DOI: 10.1021/acs.biochem.4c00218] [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: 08/28/2024]
Abstract
Knotted proteins are fascinating natural biomolecules whose backbones entangle themselves in a knot. Their particular knotted configurations provide them with a wide range of topological features. However, their folding/unfolding mechanisms, stability, and function are poorly understood. In the present work, native trapped ion mobility spectrometry-mass spectrometry (TIMS-MS) was used for characterizing structural features of two model knotted proteins: a Gordian 52 knot ubiquitin C-terminal hydrolase (UCH) and a Stevedore 61 knot (α-haloacid dehalogenase, DehI). Experimental results showed structural transitions of UCH and DehI as a function of solution composition (0-50% MeOH) and temperature (T ∼20-95 °C). An increase in the protein charge states and collision cross sections (∼2750-8750 Å2 and ∼3250-15,385 Å2 for UCH and DehI, respectively) with the solution organic content (OC) and temperature suggested a three-step unfolding pathway with at least four structural transitions. Results also showed that the integrity of the UCH knot core was more resistant to thermal unfolding when compared to DehI; however, both knot cores can be disrupted with the increase in the solution OC. Additional enzymatic digestion experiments using carboxypeptidase Y combined with molecular dynamics simulations showed that the knot core was preserved between Glu20 and Glu188 and Arg89 and His304 residues for UCH and DehI, respectively, where disruption of the knot core led to structural collapse followed by unfolding events. This work highlights the potential of solution OC and temperature studies combined with native TIMS-MS for the comprehensive characterization of knotted proteins to gain a better understanding of their structural transitions.
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Affiliation(s)
- Kevin Jeanne Dit Fouque
- Department of Chemistry and Biochemistry and Biomolecular Sciences Institute, Florida International University, Miami, Florida, 33199, United States
| | - Juan Camilo Molano-Arevalo
- Department of Chemistry and Biochemistry and Biomolecular Sciences Institute, Florida International University, Miami, Florida, 33199, United States
| | - Fenfei Leng
- 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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3
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Yang HC, Scruggs SS, Chai M, Mathai G, Taylor JS, Gross ML. Distinguishing Isomeric Cyclobutane Thymidine Dimers by Ion Mobility and Tandem Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:1768-1774. [PMID: 38952267 PMCID: PMC11305913 DOI: 10.1021/jasms.4c00133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/03/2024]
Abstract
Irradiation of the major conformation of duplex DNA found in cells (B form) produces cyclobutane pyrimidine dimers (CPDs) from adjacent pyrimidines in a head-to-head orientation (syn) with the C5 substituents in a cis stereochemistry. These CPDs have crucial implications in skin cancer. Irradiation of G-quadruplexes and other non-B DNA conformations in vitro produces, however, CPDs between nonadjacent pyrimidines in nearby loops with syn and head-to-tail orientations (anti) with both cis and trans stereochemistry to yield a mixture of six possible isomers of the T=T dimer. This outcome is further complicated by formation of mixtures of nonadjacent CPDs of C=T, T=C, and C=C, and successful analysis depends on development of specific and sensitive methods. Toward meeting this need, we investigated whether ion mobility mass spectrometry (IMMS) and MS/MS can distinguish the cis,syn and trans,anti T=T CPDs. Ion mobility can afford baseline separation and give relative mobilities that are in accord with predicted cross sections. Complementing this ability to distinguish isomers is MS/MS collisional activation where fragmentation also distinguishes the two isomers and confirms conclusions drawn from ion mobility analysis. The observations offer early support that ion mobility and MS/MS can enable the distinction of DNA photoproduct isomers.
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Affiliation(s)
- Hsin-Chieh Yang
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130
| | - Savannah S. Scruggs
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130
| | - Mengqi Chai
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130
| | - George Mathai
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130
| | - John-Stephen Taylor
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130
| | - Michael L. Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130
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4
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Xu S, Zhu Z, Delafield DG, Rigby MJ, Lu G, Braun M, Puglielli L, Li L. Spatially and temporally probing distinctive glycerophospholipid alterations in Alzheimer's disease mouse brain via high-resolution ion mobility-enabled sn-position resolved lipidomics. Nat Commun 2024; 15:6252. [PMID: 39048572 PMCID: PMC11269705 DOI: 10.1038/s41467-024-50299-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 07/08/2024] [Indexed: 07/27/2024] Open
Abstract
Dysregulated glycerophospholipid (GP) metabolism in the brain is associated with the progression of neurodegenerative diseases including Alzheimer's disease (AD). Routine liquid chromatography-mass spectrometry (LC-MS)-based large-scale lipidomic methods often fail to elucidate subtle yet important structural features such as sn-position, hindering the precise interrogation of GP molecules. Leveraging high-resolution demultiplexing (HRdm) ion mobility spectrometry (IMS), we develop a four-dimensional (4D) lipidomic strategy to resolve GP sn-position isomers. We further construct a comprehensive experimental 4D GP database of 498 GPs identified from the mouse brain and an in-depth extended 4D library of 2500 GPs predicted by machine learning, enabling automated profiling of GPs with detailed acyl chain sn-position assignment. Analyzing three mouse brain regions (hippocampus, cerebellum, and cortex), we successfully identify a total of 592 GPs including 130 pairs of sn-position isomers. Further temporal GPs analysis in the three functional brain regions illustrates their metabolic alterations in AD progression.
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Affiliation(s)
- Shuling Xu
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Zhijun Zhu
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Daniel G Delafield
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Michael J Rigby
- Department of Medicine, University of Wisconsin-Madison, Madison, WI, 53705, USA
- Waisman Center, University of Wisconsin-Madison, Madison, WI, 53705, USA
- Neuroscience Training Program, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Gaoyuan Lu
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Megan Braun
- Department of Medicine, University of Wisconsin-Madison, Madison, WI, 53705, USA
- Waisman Center, University of Wisconsin-Madison, Madison, WI, 53705, USA
- Neuroscience Training Program, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Luigi Puglielli
- Department of Medicine, University of Wisconsin-Madison, Madison, WI, 53705, USA
- Waisman Center, University of Wisconsin-Madison, Madison, WI, 53705, USA
- Geriatric Research Education Clinical Center, Veterans Affairs Medical Center, Madison, WI, 53705, USA
| | - Lingjun Li
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, USA.
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA.
- Lachman Institute for Pharmaceutical Development, School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, USA.
- Wisconsin Center for NanoBioSystems, School of Pharmacy, University of Wisconsin- Madison, Madison, WI, 53705, USA.
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5
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Ross DH, Bhotika H, Zheng X, Smith RD, Burnum-Johnson KE, Bilbao A. Computational tools and algorithms for ion mobility spectrometry-mass spectrometry. Proteomics 2024; 24:e2200436. [PMID: 38438732 DOI: 10.1002/pmic.202200436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 02/12/2024] [Accepted: 02/14/2024] [Indexed: 03/06/2024]
Abstract
Ion mobility spectrometry-mass spectrometry (IMS-MS or IM-MS) is a powerful analytical technique that combines the gas-phase separation capabilities of IM with the identification and quantification capabilities of MS. IM-MS can differentiate molecules with indistinguishable masses but different structures (e.g., isomers, isobars, molecular classes, and contaminant ions). The importance of this analytical technique is reflected by a staged increase in the number of applications for molecular characterization across a variety of fields, from different MS-based omics (proteomics, metabolomics, lipidomics, etc.) to the structural characterization of glycans, organic matter, proteins, and macromolecular complexes. With the increasing application of IM-MS there is a pressing need for effective and accessible computational tools. This article presents an overview of the most recent free and open-source software tools specifically tailored for the analysis and interpretation of data derived from IM-MS instrumentation. This review enumerates these tools and outlines their main algorithmic approaches, while highlighting representative applications across different fields. Finally, a discussion of current limitations and expectable improvements is presented.
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Affiliation(s)
- Dylan H Ross
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Harsh Bhotika
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Xueyun Zheng
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Kristin E Burnum-Johnson
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Aivett Bilbao
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA
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Chakraborty P, Malola S, Weis P, Neumaier M, Schneider EK, Häkkinen H, Kappes MM. Tailoring Vacancy Defects in Isolated Atomically Precise Silver Clusters through Mercury-Doped Intermediates. J Phys Chem Lett 2023; 14:11659-11664. [PMID: 38109267 DOI: 10.1021/acs.jpclett.3c02866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2023]
Abstract
Vacancy defects are known to have significant effects on the physical and chemical properties of nanomaterials. However, the formation and structural dynamics of vacancy defects in atomically precise coinage metal clusters have hardly been explored due to the challenges associated with isolation of such defected clusters. Herein, we isolate [Ag28(BDT)12]2- (BDT is 1,3-benzenedithiol), a cluster with a "missing atom" site compared to [Ag29(BDT)12]3-, whose precise structure is known from X-ray diffraction. [Ag28(BDT)12]2- was formed in the gas-phase by collisional heating of [Ag28Hg(BDT)12]2-, a Hg-doped analogue of the parent cluster. The structural changes resulting from the loss of the Hg heteroatom were investigated by trapped ion mobility mass spectrometry. Density functional theory calculations were performed to provide further insights into the defect structures, and molecular dynamics simulations revealed defect site-dependent structural relaxation processes.
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Affiliation(s)
- Papri Chakraborty
- Institute of Nanotechnology, Karlsruhe Institute of Technology, 76344 Eggenstein-Leopoldshafen, Germany
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Sami Malola
- Department of Physics, Nanoscience Center, University of Jyväskylä, 40014 Jyväskylä, Finland
| | - Patrick Weis
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Marco Neumaier
- Institute of Nanotechnology, Karlsruhe Institute of Technology, 76344 Eggenstein-Leopoldshafen, Germany
| | - Erik Karsten Schneider
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Hannu Häkkinen
- Department of Physics, Nanoscience Center, University of Jyväskylä, 40014 Jyväskylä, Finland
- Department of Chemistry, Nanoscience Center, University of Jyväskylä, 40014 Jyväskylä, Finland
| | - Manfred M Kappes
- Institute of Nanotechnology, Karlsruhe Institute of Technology, 76344 Eggenstein-Leopoldshafen, Germany
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
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7
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Bonnet V, Clodic G, Sonnendecker C, Zimmermann W, Przybylski C. Ion mobility mass spectrometry enables the discrimination of positional isomers and the detection of conformers from cyclic oligosaccharides-metals supramolecular complexes. Carbohydr Polym 2023; 320:121205. [PMID: 37659808 DOI: 10.1016/j.carbpol.2023.121205] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 07/07/2023] [Accepted: 07/12/2023] [Indexed: 09/04/2023]
Abstract
Cyclic oligosaccharides are well known to interact with various metals, able to form supramolecular complexes with distinct sizes and shapes. However, the presence of various isomers in a sample, including positional isomers and conformers, can significantly impact molecular recognition, encapsulation ability and chemical reactivity. Therefore, it is crucial to have tools for deep samples probing and correlation establishments. The emerging ion mobility mass spectrometry (IM-MS) has the advantages to be rapid and sensitive, but is still in its infancy for the investigation of supramolecular assemblies. In the herein study, it was demonstrated that IM-MS is suitable to discriminate several isomers of cyclodextrins (CD)-metals complexes, used as cyclic oligosaccharide models. In this sense, we investigated branched 6-O-α-glucosyl- or 6-O-α-maltosyl-β-cyclodextrins (G1-β-CD and G2-β-CD) and their purely cyclic isomers: CD8 (γ-CD) and CD9 (δ-CD). The corresponding collision cross section (CCS) values were deducted for the main positive singly and doubly charged species. Experimental CCS values were matched with models obtained from molecular modelling. The high mobility resolving power and resolution enabled discrimination of positional isomers, identification of various conformers and accurate relative content estimation. These results represent a milestone in the identification of carbohydrate conformers that cannot be easily reached by other approaches.
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Affiliation(s)
- Véronique Bonnet
- Laboratoire de Glycochimie, des Antimicrobiens et des Agroressources, Université de Picardie Jules Verne, 80039 Amiens, France
| | - Gilles Clodic
- Sorbonne Université, Mass Spectrometry Sciences Sorbonne University, MS3U Platform, UFR 926, UFR 927, Paris, France
| | | | - Wolfgang Zimmermann
- Institute of Analytical Chemistry, Leipzig University, 04103 Leipzig, Germany
| | - Cédric Przybylski
- Sorbonne Université, CNRS, Institut Parisien de Chimie Moléculaire, IPCM, 4 Place Jussieu, 75005 Paris, France; Université Paris-Saclay, Univ Evry, CNRS, LAMBE, Evry-Courcouronnes 91000, France.
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8
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Schramm HM, Tamadate T, Hogan CJ, Clowers BH. Evaluation of Hydrogen-Deuterium Exchange during Transient Vapor Binding of MeOD with Model Peptide Systems Angiotensin II and Bradykinin. J Phys Chem A 2023; 127:8849-8861. [PMID: 37827113 DOI: 10.1021/acs.jpca.3c04608] [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: 10/14/2023]
Abstract
The advancement of hybrid mass spectrometric tools as an indirect probe of molecular structure and dynamics relies heavily upon a clear understanding between gas-phase ion reactivity and ion structural characteristics. This work provides new insights into gas-phase ion-neutral reactions of the model peptides (i.e., angiotensin II and bradykinin) on a per-residue basis by integrating hydrogen/deuterium exchange, ion mobility, tandem mass spectrometry, selective vapor binding, and molecular dynamics simulations. By comparing fragmentation patterns with simulated probabilities of vapor uptake, a clear link between gas-phase hydrogen/deuterium exchange and the probabilities of localized vapor association is established. The observed molecular dynamics trends related to the sites and duration of vapor binding track closely with experimental observation. Additionally, the influence of additional charges and structural characteristics on exchange kinetics and ion-neutral cluster formation is examined. These data provide a foundation for the analysis of solvation dynamics of larger, native-like conformations of proteins in the gas phase.
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Affiliation(s)
- Haley M Schramm
- Department of Chemistry, Washington State University, Pullman, Washington 99163, United States
| | - Tomoya Tamadate
- Department of Mechanical Engineering, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Christopher J Hogan
- Department of Mechanical Engineering, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Brian H Clowers
- Department of Chemistry, Washington State University, Pullman, Washington 99163, United States
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9
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Rajkovic M, Benter T, Wißdorf W. Molecular Dynamics-Based Modeling of Ion-Neutral Collisions in an Open Ion Trajectory Simulation Framework. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:2156-2165. [PMID: 37703916 DOI: 10.1021/jasms.3c00139] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/15/2023]
Abstract
Ion mobility spectrometry (IMS) and ion mobility mass spectrometry (IMS-MS) methods have become increasingly popular and are important analytical techniques to determine information about the structural parameters of gas-phase analytes. The accurate description of the interaction between molecular ions and neutral background gas particles is an essential part of high-quality simulations of such modern mass- and ion-mobility-spectrometric systems. Established ion-neutral collision models (Hard-sphere collision modeling and statistical diffusion simulations) in common ion-trajectory simulation systems like SIMION use strongly simplified assumptions and are thus limited in their predictive ability. In contrast, collision cross-section (CCS) modeling programs (e.g., MOBCAL, IMoS, and Colloidoscope) allow high-quality ion mobility predictions for low-field equilibrium conditions using explicit scattering processes with a molecular dynamics-based trajectory method but cannot be used for nonequilibrium collision modeling in an ion trajectory simulation. This work presents an extension to the open-source Ion Dynamics Simulation Framework (IDSimF), which allows the simulation of ion dynamics under arbitrary and even nonequilibrium conditions. It was extended by an advanced collision model employing the molecular dynamics trajectory method for a detailed microscopic description of ion-neutral collisions within ion-trajectory simulations. We used drift tube ion mobility spectrometry (DT-IMS) to validate the predictive abilities of the model and to estimate the runtime requirements for productive simulations. Simulated high-field ion mobilities for small ion systems in a drift tube IMS are compared to experimental values from the literature and an implementation of a hard-sphere model in IDSimF for helium and argon as background gas particles. Significant improvements in ion mobility predictions using the molecular dynamics trajectory approach are obtained with deviations of only a few percent from experimental values. Therefore, the established and publicly available MD collision model will serve as foundation for nonequilibrium ion dynamics simulations and the development of improved ion dynamics modeling methods.
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Affiliation(s)
- Michelle Rajkovic
- Department of Physical and Theoretical Chemistry, University of Wuppertal, Gaussstraße 20, 42119 Wuppertal, Germany
| | - Thorsten Benter
- Department of Physical and Theoretical Chemistry, University of Wuppertal, Gaussstraße 20, 42119 Wuppertal, Germany
| | - Walter Wißdorf
- Department of Physical and Theoretical Chemistry, University of Wuppertal, Gaussstraße 20, 42119 Wuppertal, Germany
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10
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Campuzano IDG. A Research Journey: Over a Decade of Denaturing and Native-MS Analyses of Hydrophobic and Membrane Proteins in Amgen Therapeutic Discovery. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:2413-2431. [PMID: 37643331 DOI: 10.1021/jasms.3c00175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Membrane proteins and associated complexes currently comprise the majority of therapeutic targets and remain among the most challenging classes of proteins for analytical characterization. Through long-term strategic collaborations forged between industrial and academic research groups, there has been tremendous progress in advancing membrane protein mass spectrometry (MS) analytical methods and their concomitant application to Amgen therapeutic project progression. Herein, I will describe a detailed and personal account of how electrospray ionization (ESI) native mass spectrometry (nMS), ion mobility-MS (IM-MS), reversed phase liquid chromatographic mass spectrometry (RPLC-MS), high-throughput solid phase extraction mass spectrometry, and matrix-assisted laser desorption ionization mass spectrometry methods were developed, optimized, and validated within Amgen Research, and importantly, how these analytical methods were applied for membrane and hydrophobic protein analyses and ultimately therapeutic project support and progression. Additionally, I will discuss all the highly important and productive collaborative efforts, both internal Amgen and external academic, which were key in generating the samples, methods, and associated data described herein. I will also describe some early and previously unpublished nano-ESI (nESI) native-MS data from Amgen Research and the highly productive University of California Los Angeles (UCLA) collaboration. I will also present previously unpublished examples of real-life Amgen biotherapeutic membrane protein projects that were supported by all the MS (and IM) analytical techniques described herein. I will start by describing the initial nESI nMS experiments performed at Amgen in 2011 on empty nanodisc molecules, using a quadrupole time-of-flight MS, and how these experiments progressed on to the 15 Tesla Fourier transform ion cyclotron resonance MS at UCLA. Then described are monomeric and multimeric membrane protein data acquired in both nESI nMS and tandem-MS modes, using multiple methods of ion activation, resulting in dramatic spectral simplification. Also described is how we investigated the far less established and less published subject, that is denaturing RPLC-MS analysis of membrane proteins, and how we developed a highly robust and reproducible RPLC-MS method capable of effective separation of membrane proteins differing in only the presence or absence of an N-terminal post translational modification. Also described is the evolution of the aforementioned RPLC-MS method into a high-throughput solid phase extraction MS method. Finally, I will give my opinion on key developments and how the area of nMS of membrane proteins needs to evolve to a state where it can be applied within the biopharmaceutical research environment for routine therapeutic project support.
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Affiliation(s)
- Iain D G Campuzano
- Amgen Research, Center for Research Acceleration by Digital Innovation, Molecular Analytics, Thousand Oaks, California 91320, United States
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11
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Liu Z, Roy M, DeYonker NJ, Gopalakrishnan R. Neutral gas pressure dependence of ion-ion mutual neutralization rate constants using Landau-Zener theory coupled with trajectory simulations. J Chem Phys 2023; 159:114111. [PMID: 37724728 DOI: 10.1063/5.0168609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 08/28/2023] [Indexed: 09/21/2023] Open
Abstract
In this computational study, we describe a self-consistent trajectory simulation approach to capture the effect of neutral gas pressure on ion-ion mutual neutralization (MN) reactions. The electron transfer probability estimated using Landau-Zener (LZ) transition state theory is incorporated into classical trajectory simulations to elicit predictions of MN cross sections in vacuum and rate constants at finite neutral gas pressures. Electronic structure calculations with multireference configuration interaction and large correlation consistent basis sets are used to derive inputs to the LZ theory. The key advance of our trajectory simulation approach is the inclusion of the effect of ion-neutral interactions on MN using a Langevin representation of the effect of background gas on ion transport. For H+ - H- and Li+ - H(D)-, our approach quantitatively agrees with measured speed-dependent cross sections for up to ∼105 m/s. For the ion pair Ne+ - Cl-, our predictions of the MN rate constant at ∼1 Torr are a factor of ∼2 to 3 higher than the experimentally measured value. Similarly, for Xe+ - F- in the pressure range of ∼20 000-80 000 Pa, our predictions of the MN rate constant are ∼20% lower but are in excellent qualitative agreement with experimental data. The paradigm of using trajectory simulations to self-consistently capture the effect of gas pressure on MN reactions advanced here provides avenues for the inclusion of additional nonclassical effects in future work.
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Affiliation(s)
- Zhibo Liu
- Department of Mechanical Engineering, The University of Memphis, Memphis, Tennessee 38152, USA
| | - Mrittika Roy
- Department of Mechanical Engineering, The University of Memphis, Memphis, Tennessee 38152, USA
| | - Nathan J DeYonker
- Department of Chemistry, The University of Memphis, Memphis, Tennessee 38152, USA
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12
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Kartowikromo KY, Olajide OE, Hamid AM. Collision cross section measurement and prediction methods in omics. JOURNAL OF MASS SPECTROMETRY : JMS 2023; 58:e4973. [PMID: 37620034 PMCID: PMC10530098 DOI: 10.1002/jms.4973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 06/26/2023] [Accepted: 07/20/2023] [Indexed: 08/26/2023]
Abstract
Omics studies such as metabolomics, lipidomics, and proteomics have become important for understanding the mechanisms in living organisms. However, the compounds detected are structurally different and contain isomers, with each structure or isomer leading to a different result in terms of the role they play in the cell or tissue in the organism. Therefore, it is important to detect, characterize, and elucidate the structures of these compounds. Liquid chromatography and mass spectrometry have been utilized for decades in the structure elucidation of key compounds. While prediction models of parameters (such as retention time and fragmentation pattern) have also been developed for these separation techniques, they have some limitations. Moreover, ion mobility has become one of the most promising techniques to give a fingerprint to these compounds by determining their collision cross section (CCS) values, which reflect their shape and size. Obtaining accurate CCS enables its use as a filter for potential analyte structures. These CCS values can be measured experimentally using calibrant-independent and calibrant-dependent approaches. Identification of compounds based on experimental CCS values in untargeted analysis typically requires CCS references from standards, which are currently limited and, if available, would require a large amount of time for experimental measurements. Therefore, researchers use theoretical tools to predict CCS values for untargeted and targeted analysis. In this review, an overview of the different methods for the experimental and theoretical estimation of CCS values is given where theoretical prediction tools include computational and machine modeling type approaches. Moreover, the limitations of the current experimental and theoretical approaches and their potential mitigation methods were discussed.
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Affiliation(s)
| | - Orobola E Olajide
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama, USA
| | - Ahmed M Hamid
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama, USA
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13
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Cajahuaringa S, Caetano DLZ, Zanotto LN, Araujo G, Skaf MS. MassCCS: A High-Performance Collision Cross-Section Software for Large Macromolecular Assemblies. J Chem Inf Model 2023; 63:3557-3566. [PMID: 37184925 PMCID: PMC10269586 DOI: 10.1021/acs.jcim.3c00405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Indexed: 05/16/2023]
Abstract
Ion mobility mass spectrometry (IM-MS) techniques have become highly valued as a tool for structural characterization of biomolecular systems since they yield accurate measurements of the rotationally averaged collision cross-section (CCS) against a buffer gas. Despite its enormous potential, IM-MS data interpretation is often challenging due to the conformational isomerism of metabolites, lipids, proteins, and other biomolecules in the gas phase. Therefore, reliable and fast CCS calculations are needed to help interpret IM-MS data. In this work, we present MassCCS, a parallelized open-source code for computing CCS of molecules ranging from small organic compounds to massive protein assemblies at the trajectory method level of description using atomic and molecular buffer gas particles. The performance of the code is comparable to other available software for small molecules and proteins but is significantly faster for larger macromolecular assemblies. We performed extensive tests regarding accuracy, performance, and scalability with system size and number of CPU cores. MassCCS has proven highly accurate and efficient, with execution times under a few minutes, even for large (84.87 MDa) virus capsid assemblies with very modest computational resources. MassCCS is freely available at https://github.com/cces-cepid/massccs.
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Affiliation(s)
- Samuel Cajahuaringa
- Institute
of Computing, University of Campinas, Campinas, São Paulo 13083-852, Brazil
- Center
for Computing in Engineering & Sciences, University of Campinas, Campinas, São Paulo 13083-861, Brazil
| | - Daniel L. Z. Caetano
- Center
for Computing in Engineering & Sciences, University of Campinas, Campinas, São Paulo 13083-861, Brazil
- Institute
of Chemistry, University of Campinas, Campinas, São Paulo 13083-970, Brazil
| | - Leandro N. Zanotto
- Institute
of Computing, University of Campinas, Campinas, São Paulo 13083-852, Brazil
- Center
for Computing in Engineering & Sciences, University of Campinas, Campinas, São Paulo 13083-861, Brazil
| | - Guido Araujo
- Institute
of Computing, University of Campinas, Campinas, São Paulo 13083-852, Brazil
- Center
for Computing in Engineering & Sciences, University of Campinas, Campinas, São Paulo 13083-861, Brazil
| | - Munir S. Skaf
- Center
for Computing in Engineering & Sciences, University of Campinas, Campinas, São Paulo 13083-861, Brazil
- Institute
of Chemistry, University of Campinas, Campinas, São Paulo 13083-970, Brazil
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14
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Chakraborty P, Neumaier M, Weis P, Kappes MM. Exploring Isomerism in Isolated Cyclodextrin Oligomers through Trapped Ion Mobility Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:676-684. [PMID: 36952473 DOI: 10.1021/jasms.2c00351] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Cyclodextrin (CD) macrocycles are used to create a wide range of supramolecular architectures which are also of interest in applications such as selective gas adsorption, drug delivery, and catalysis. However, predicting their assemblies and identifying the possible isomers in CD oligomers have always remained challenging due to their dynamic nature. Herein, we interacted CDs (α, β, and γ) with a divalent metal ion, Cu2+, to create a series of Cu2+-linked CD oligomers, from dimers to pentamers. We characterized these oligomers using electrospray ionization mass spectrometry and probed isomerism in each of these isolated oligomers using high resolution trapped ion mobility spectrometry. Using this technique, we separated multiple isomers for each of the Cu2+-interlinked CD oligomers and estimated their relative population, which was not accessible previously using other characterization techniques. We further carried out structural analysis of the observed isomers by comparing the experimental collision cross sections (CCSs) to that of modeled structures. We infer that the isomeric heterogeneity reflects size-specific packing patterns of individual CDs (e.g., close-packed/linear). In some cases, we also reveal the existence of kinetically trapped structures in the gas phase and study their transformation to thermodynamically controlled forms by examining the influence of activation of the ions on isomer interconversion.
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Affiliation(s)
- Papri Chakraborty
- Institute of Nanotechnology, Karlsruhe Institute of Technology, 76344 Eggenstein-Leopoldshafen, Germany
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Marco Neumaier
- Institute of Nanotechnology, Karlsruhe Institute of Technology, 76344 Eggenstein-Leopoldshafen, Germany
| | - Patrick Weis
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Manfred M Kappes
- Institute of Nanotechnology, Karlsruhe Institute of Technology, 76344 Eggenstein-Leopoldshafen, Germany
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
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15
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Christofi E, Barran P. Ion Mobility Mass Spectrometry (IM-MS) for Structural Biology: Insights Gained by Measuring Mass, Charge, and Collision Cross Section. Chem Rev 2023; 123:2902-2949. [PMID: 36827511 PMCID: PMC10037255 DOI: 10.1021/acs.chemrev.2c00600] [Citation(s) in RCA: 43] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Indexed: 02/26/2023]
Abstract
The investigation of macromolecular biomolecules with ion mobility mass spectrometry (IM-MS) techniques has provided substantial insights into the field of structural biology over the past two decades. An IM-MS workflow applied to a given target analyte provides mass, charge, and conformation, and all three of these can be used to discern structural information. While mass and charge are determined in mass spectrometry (MS), it is the addition of ion mobility that enables the separation of isomeric and isobaric ions and the direct elucidation of conformation, which has reaped huge benefits for structural biology. In this review, where we focus on the analysis of proteins and their complexes, we outline the typical features of an IM-MS experiment from the preparation of samples, the creation of ions, and their separation in different mobility and mass spectrometers. We describe the interpretation of ion mobility data in terms of protein conformation and how the data can be compared with data from other sources with the use of computational tools. The benefit of coupling mobility analysis to activation via collisions with gas or surfaces or photons photoactivation is detailed with reference to recent examples. And finally, we focus on insights afforded by IM-MS experiments when applied to the study of conformationally dynamic and intrinsically disordered proteins.
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Affiliation(s)
- Emilia Christofi
- Michael Barber Centre for Collaborative
Mass Spectrometry, Manchester Institute of Biotechnology, University of Manchester, Princess Street, Manchester M1 7DN, United Kingdom
| | - Perdita Barran
- Michael Barber Centre for Collaborative
Mass Spectrometry, Manchester Institute of Biotechnology, University of Manchester, Princess Street, Manchester M1 7DN, United Kingdom
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16
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Fu D, Habtegabir SG, Wang H, Feng S, Han Y. Understanding of protomers/deprotomers by combining mass spectrometry and computation. Anal Bioanal Chem 2023:10.1007/s00216-023-04574-1. [PMID: 36737499 DOI: 10.1007/s00216-023-04574-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 01/19/2023] [Accepted: 01/27/2023] [Indexed: 02/05/2023]
Abstract
Multifunctional compounds may form different prototropic isomers under different conditions, which are known as protomers/deprotomers. In biological systems, these protomer/deprotomer isomers affect the interaction modes and conformational landscape between compounds and enzymes and thus present different biological activities. Study on protomers/deprotomers is essentially the study on the acidity/basicity of each intramolecular functional group and its effect on molecular structure. In recent years, the combination of mass spectrometry (MS) and computational chemistry has been proven to be a powerful and effective means to study prototropic isomers. MS-based technologies are developed to discriminate and characterize protomers/deprotomers to provide structural information and monitor transformations, showing great superiority than other experimental methods. Computational chemistry is used to predict the thermodynamic stability of protomers/deprotomers, provide the simulated MS/MS spectra, infrared spectra, and calculate collision cross-section values. By comparing the theoretical data with the corresponding experimental results, the researchers can not only determine the protomer/deprotomer structure, but also investigate the structure-activity relationship in a given system. This review covers various MS methods and theoretical calculations and their devotion to isomer discrimination, structure identification, conformational transformation, and phase transition investigation of protomers/deprotomers.
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Affiliation(s)
- Dali Fu
- State Key Laboratory of Heavy Oil Processing, College of Chemical Engineering and Environment, China University of Petroleum-Beijing, Beijing, 102249, People's Republic of China
| | - Sara Girmay Habtegabir
- State Key Laboratory of Heavy Oil Processing, College of Chemical Engineering and Environment, China University of Petroleum-Beijing, Beijing, 102249, People's Republic of China
| | - Haodong Wang
- State Key Laboratory of Heavy Oil Processing, College of Chemical Engineering and Environment, China University of Petroleum-Beijing, Beijing, 102249, People's Republic of China
| | - Shijie Feng
- State Key Laboratory of Heavy Oil Processing, College of Chemical Engineering and Environment, China University of Petroleum-Beijing, Beijing, 102249, People's Republic of China
| | - Yehua Han
- State Key Laboratory of Heavy Oil Processing, College of Chemical Engineering and Environment, China University of Petroleum-Beijing, Beijing, 102249, People's Republic of China.
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17
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Naylor CN, Schaefer C, Kirk AT, Zimmermann S. The origin of isomerization of aniline revealed by high kinetic energy ion mobility spectrometry (HiKE-IMS). Phys Chem Chem Phys 2023; 25:1139-1152. [PMID: 36515135 DOI: 10.1039/d2cp01994a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Although aniline is a relatively simple small molecule, the origin of its two peaks observed in ion mobility spectrometry (IMS) has remained under debate for at least 30 years. First hypothesized as a difference in protonation site (amine vs. benzene ring), each ion mobility peak differs by one Dalton when coupled with mass spectrometry where the faster mobility peak is the molecular ion peak, and the slower mobility peak is protonated. To complicate the deconvolution of structures, some previous literature shows the peaks as unresolved and thus proposes these species exist in equilibrium. In this work, we show that when measured with high kinetic energy ion mobility spectrometry (HiKE-IMS), the two peaks observed in spectra of both aniline and all n-fluoroanilines are fully separated (chromatographic resolution from 2-7, Rp > 110) and therefore not in equilibrium. The HiKE-IMS is capable of changing ionization conditions independently of drift region conditions, and our results agree with previous literature showing that ionization source settings (including possible fragmentation at this stage) are the only influence determining the speciation of the two aniline peaks. Finally, when the drift and reactant gas are changed to nitrogen, a third peak appears at high E/N for 2-fluoroaniline and 4-fluoroaniline for the first time in reported literature. As observed by HiKE-IMS-MS, the new third peak is also protonated showing that the para-protonated aniline and resulting fragment ion, molecular ion aniline, can be fully separated in the mobility domain for the first time. The appearance of the third peak is only possible due to the increased separation of the other two peaks within the HiKE-IMS.
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Affiliation(s)
- Cameron N Naylor
- Leibniz University Hannover, Institute of Electrical Engineering and Measurement Technology, Department of Sensors and Measurement Technology, 30167 Hannover, Germany.
| | - Christoph Schaefer
- Leibniz University Hannover, Institute of Electrical Engineering and Measurement Technology, Department of Sensors and Measurement Technology, 30167 Hannover, Germany.
| | - Ansgar T Kirk
- Leibniz University Hannover, Institute of Electrical Engineering and Measurement Technology, Department of Sensors and Measurement Technology, 30167 Hannover, Germany.
| | - Stefan Zimmermann
- Leibniz University Hannover, Institute of Electrical Engineering and Measurement Technology, Department of Sensors and Measurement Technology, 30167 Hannover, Germany.
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18
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Cowart A, Brük ML, Žoglo N, Roithmeyer H, Uudsemaa M, Trummal A, Selke K, Aav R, Kalenius E, Adamson J. Solution- and gas-phase study of binding of ammonium and bisammonium hydrocarbons to oxacalix[4]arene carboxylate. RSC Adv 2023; 13:1041-1048. [PMID: 36686943 PMCID: PMC9812018 DOI: 10.1039/d2ra07614d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 12/19/2022] [Indexed: 01/06/2023] Open
Abstract
Oxacalixarenes represent a distinctive class of macrocyclic compounds, which are closely related to the parent calixarene family, offering binding motifs characteristic of calixarenes and crown ethers. Nevertheless, they still lack extensive characterization in terms of molecular recognition properties and the subsequent practical applicability. We present here the results of binding studies of an oxacalix[4]arene carboxylate macrocycle toward a variety of organic ammonium cationic species. Our results show that the substituents attached to the guest ammonium compound largely influence the binding strengths of the host. Furthermore, we show that the characteristic binding pattern changes upon transition from the gas phase to solution in terms of the governing intermolecular interactions. We identify the key factors affecting host-guest binding efficacy and suggest rules for the important molecular structural motifs of the interacting parts of ammonium guest species and the macrocycle to facilitate sensing of ammonium cations.
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Affiliation(s)
- Anna Cowart
- Laboratory of Chemical Physics, National Institute of Chemical Physics and BiophysicsAkadeemia Tee 2312618 TallinnEstonia,Department of Chemistry and Biotechnology, Tallinn University of TechnologyAkadeemia Tee 1512618 TallinnEstonia
| | - Mari-Liis Brük
- Laboratory of Chemical Physics, National Institute of Chemical Physics and BiophysicsAkadeemia Tee 2312618 TallinnEstonia,Department of Chemistry and Biotechnology, Tallinn University of TechnologyAkadeemia Tee 1512618 TallinnEstonia
| | - Nikita Žoglo
- Laboratory of Chemical Physics, National Institute of Chemical Physics and BiophysicsAkadeemia Tee 2312618 TallinnEstonia
| | - Helena Roithmeyer
- Laboratory of Chemical Physics, National Institute of Chemical Physics and BiophysicsAkadeemia Tee 2312618 TallinnEstonia
| | - Merle Uudsemaa
- Laboratory of Chemical Physics, National Institute of Chemical Physics and BiophysicsAkadeemia Tee 2312618 TallinnEstonia
| | - Aleksander Trummal
- Laboratory of Chemical Physics, National Institute of Chemical Physics and BiophysicsAkadeemia Tee 2312618 TallinnEstonia
| | - Kaspar Selke
- Laboratory of Chemical Physics, National Institute of Chemical Physics and BiophysicsAkadeemia Tee 2312618 TallinnEstonia
| | - Riina Aav
- Department of Chemistry and Biotechnology, Tallinn University of TechnologyAkadeemia Tee 1512618 TallinnEstonia
| | - Elina Kalenius
- Department of Chemistry, NanoScience Center, University of JyväskyläSurvontie 9BFI-40014 JYFinland
| | - Jasper Adamson
- Laboratory of Chemical Physics, National Institute of Chemical Physics and BiophysicsAkadeemia Tee 2312618 TallinnEstonia
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19
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Przybylski C, Bonnet V. Probing topology of supramolecular complexes between cyclodextrins and alkali metals by ion mobility-mass spectrometry. Carbohydr Polym 2022; 297:120019. [DOI: 10.1016/j.carbpol.2022.120019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/19/2022] [Accepted: 08/19/2022] [Indexed: 11/16/2022]
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20
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Lebedev AV, Kolbinev SS. The $${\text{NH}}_{4}^{ + }$$(H2O)n Reagent Ion: Calculations of the Structure, Thermodynamic Parameters of Hydration, Equilibrium Composition, and Mobility. JOURNAL OF ANALYTICAL CHEMISTRY 2022. [DOI: 10.1134/s1061934822140039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
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21
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Cheung See Kit M, Webb IK. Application of Multiple Length Cross-linkers to the Characterization of Gaseous Protein Structure. Anal Chem 2022; 94:13301-13310. [PMID: 36100581 PMCID: PMC9532380 DOI: 10.1021/acs.analchem.2c03044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The speed, sensitivity, and tolerance of heterogeneity, as well as the kinetic trapping of solution-like states during electrospray, make native mass spectrometry an attractive method to study protein structure. Increases in the resolution of ion mobility measurements and in mass resolving power and range are leading to the increase of the information content of intact protein measurements and an expanded role of mass spectrometry in structural biology. Herein, a suite of different length noncovalent (sulfonate to positively charged side chain) cross-linkers was introduced via gas-phase ion/ion chemistry and used to determine distance restraints of kinetically trapped gas-phase structures of native-like cytochrome c ions. Electron capture dissociation allowed for the identification of cross-linked sites. Different length linkers resulted in distinct pairs of side chains being linked, supporting the ability of gas-phase cross-linking to be structurally specific. The gas-phase lengths of the cross-linkers were determined by conformational searches and density functional theory, allowing for the interpretation of the cross-links as distance restraints. These distance restraints were used to model gas-phase structures with molecular dynamics simulations, revealing a mixture of structures with similar overall shape/size but distinct features, thereby illustrating the kinetic trapping of multiple native-like solution structures in the gas phase.
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Affiliation(s)
- Melanie Cheung See Kit
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, Indianapolis, Indiana 46202, USA
| | - Ian K. Webb
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, Indianapolis, Indiana 46202, USA
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
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22
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Ieritano C, Hopkins WS. The hitchhiker's guide to dynamic ion-solvent clustering: applications in differential ion mobility spectrometry. Phys Chem Chem Phys 2022; 24:20594-20615. [PMID: 36000315 DOI: 10.1039/d2cp02540j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This article highlights the fundamentals of ion-solvent clustering processes that are pertinent to understanding an ion's behaviour during differential mobility spectrometry (DMS) experiments. We contrast DMS with static-field ion mobility, where separation is affected by mobility differences under the high-field and low-field conditions of an asymmetric oscillating electric field. Although commonly used in mass spectrometric (MS) workflows to enhance signal-to-noise ratios and remove isobaric contaminants, the chemistry and physics that underpins the phenomenon of differential mobility has yet to be fully fleshed out. Moreover, we are just now making progress towards understanding how the DMS separation waveform creates a dynamic clustering environment when the carrier gas is seeded with the vapour of a volatile solvent molecule (e.g., methanol). Interestingly, one can correlate the dynamic clustering behaviour observed in DMS experiments with gas-phase and solution-phase molecular properties such as hydrophobicity, acidity, and solubility. However, to create a generalized, global model for property determination using DMS data one must employ machine learning. In this article, we provide a first-principles description of differential ion mobility in a dynamic clustering environment. We then discuss the correlation between dynamic clustering propensity and analyte physicochemical properties and demonstrate that analytes exhibiting similar ion-solvent interactions (e.g., charge-dipole) follow well-defined trends with respect to DMS clustering behaviour. Finally, we describe how supervised machine learning can be used to create predictive models of molecular properties using DMS data. We additionally highlight open questions in the field and provide our perspective on future directions that can be explored.
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Affiliation(s)
- Christian Ieritano
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada. .,Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada.,Watermine Innovation, Waterloo, Ontario, N0B 2T0, Canada
| | - W Scott Hopkins
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada. .,Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada.,Watermine Innovation, Waterloo, Ontario, N0B 2T0, Canada.,Centre for Eye and Vision Research, 17W Hong Kong Science Park, New Territories, 999077, Hong Kong
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23
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Quesada JV, Chmela J, Greisch JF, Klopper W, Harding ME. A litmus test for the balanced description of dispersion interactions and coordination chemistry of lanthanoids. Phys Chem Chem Phys 2022; 24:25106-25117. [PMID: 35920212 DOI: 10.1039/d2cp01414a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The influence of long-range interactions on the structure of complexes of Eu(III) with four 9-hydroxy-phenalen-1-one ligands (HPLN) and one alkaline earth metal dication [Eu(PLN)4AE]+ (AE: Mg, Ca, Sr, and Ba) is analyzed. Through the [Eu(PLN)4Ca]+ complex, which is a charged complex with two metals-one of them a lanthanoid-and with four relatively fluxional π-ligands, the difficulties of describing such systems are identified. The inclusion of the D3(BJ) or D4 corrections to different density functionals introduces significant changes in the structure, which are shown to stem from the interaction between pairs of PLN ligands. This interaction is studied further with a variety of density functionals, wave-function based methods, and by means of the random phase approximation. By comparing the computed results with those from experimental evidence of gas-phase photoluminescence and ion mobility measurements it is concluded that the inclusion of dispersion corrections does not always yield structures that are in agreement with the experimental findings.
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Affiliation(s)
- Juana Vázquez Quesada
- Institut für Physikalische Chemie, Karlsruher Institut für Technologie (KIT), Campus Süd, Postfach 6980, D-76049 Karlsruhe, Germany.
| | - Jiří Chmela
- Institut für Physikalische Chemie, Karlsruher Institut für Technologie (KIT), Campus Süd, Postfach 6980, D-76049 Karlsruhe, Germany.
| | - Jean-François Greisch
- Institut für Nanotechnologie, Karlsruher Institut für Technologie (KIT), Campus Nord, Postfach 3640, D-76021 Karlsruhe, Germany.
| | - Wim Klopper
- Institut für Physikalische Chemie, Karlsruher Institut für Technologie (KIT), Campus Süd, Postfach 6980, D-76049 Karlsruhe, Germany. .,Institut für Nanotechnologie, Karlsruher Institut für Technologie (KIT), Campus Nord, Postfach 3640, D-76021 Karlsruhe, Germany.
| | - Michael E Harding
- Institut für Nanotechnologie, Karlsruher Institut für Technologie (KIT), Campus Nord, Postfach 3640, D-76021 Karlsruhe, Germany.
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24
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Alam MS, Azam S, Pham K, Leyva D, Fouque KJD, Fernandez-Lima F, Miksovska J. Nanomolar affinity of EF-hands in neuronal calcium sensor 1 for bivalent cations Pb2+, Mn2+ and Hg2. Metallomics 2022; 14:6601456. [PMID: 35657675 DOI: 10.1093/mtomcs/mfac039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 05/31/2022] [Indexed: 11/12/2022]
Abstract
Abiogenic metals Pb and Hg are highly toxic since chronic and/or acute exposure often leads to severe neuropathologies. Mn2+ is an essential metal ion but in excess can impair neuronal function. In this study, we address in vitro the interactions between neuronal calcium sensor 1 (NCS1) and divalent cations. Results showed that non-physiological ions (Pb2+, Mn2+ and Hg2+) bind to EF-hands in NCS1 with nanomolar affinity and lower equilibrium dissociation constant than the physiological Ca2+ ion. (Kd,Pb2+ = 7.0±1.0 nM; Kd,Mn2+ = 34.0±6.0 nM; Kd, Hg2+ = 0.5±0.1 nM and 27.0±13.0 nM and Kd,Ca2+ = 96.0±48.0 nM). Native ultra-high resolution mass spectrometry (FT-ICR MS) and trapped ion mobility spectrometry - mass spectrometry (nESI-TIMS-MS) studies provided the NCS1-metal complex compositions - up to four Ca2+ or Mn2+ ions and three Pb2+ ions (M⋅Pb1-3Ca1-3, M⋅Mn1-4Ca1-2, and M⋅Ca1-4) were observed in complex - and similarity across the mobility profiles suggests that the overall native structure is preserved regardless of the number and type of cations. However, the non-physiological metal ions (Pb2+, Mn2+, and Hg2+) binding to NCS1 leads to more efficient quenching of Trp emission and a decrease in W30 and W103 solvent exposure compared to the apo and Ca2+ bound form, although the secondary structural rearrangement and exposure of hydrophobic sites are analogous to those for Ca2+ bound protein. Only Pb2+ and Hg2+ binding to EF-hands leads to the NCS1 dimerization whereas Mn2+ bound NCS1 remains in the monomeric form, suggesting that other factors in addition to metal ion coordination, are required for protein dimerization.
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Affiliation(s)
- Md Shofiul Alam
- Department of Chemistry and Biochemistry, Florida International University, Miami FL 33199USA
| | - Samiol Azam
- Department of Chemistry and Biochemistry, Florida International University, Miami FL 33199USA
| | - Khoa Pham
- Department of Chemistry and Biochemistry, Florida International University, Miami FL 33199USA
| | - Dennys Leyva
- Department of Chemistry and Biochemistry, Florida International University, Miami FL 33199USA
| | - Kevin Jeanne Dit Fouque
- Department of Chemistry and Biochemistry, Florida International University, Miami FL 33199USA.,Biomolecular Sciences Institute, Florida International University, Miami, 33199USA
| | - Francisco Fernandez-Lima
- Department of Chemistry and Biochemistry, Florida International University, Miami FL 33199USA.,Biomolecular Sciences Institute, Florida International University, Miami, 33199USA
| | - Jaroslava Miksovska
- Department of Chemistry and Biochemistry, Florida International University, Miami FL 33199USA.,Biomolecular Sciences Institute, Florida International University, Miami, 33199USA
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25
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Yang H, Ding D, Skyttä A, Cai R, Kulmala M, Kangasluoma J. Electrical Mobility as an Indicator for Flexibly Deducing the Kinetics of Nanoparticle Evaporation. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2022; 126:8794-8800. [PMID: 35655937 PMCID: PMC9150095 DOI: 10.1021/acs.jpcc.2c02858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 04/30/2022] [Indexed: 06/15/2023]
Abstract
Condensation and evaporation of vapor species on nanoparticle surfaces drive the aerosol evolution in various industrial/atmospheric systems, but probing these transient processes is challenging due to related time and length scales. Herein, we present a novel methodology for deducing nanoparticle evaporation kinetics using electrical mobility as a natural size indicator. Monodispersed nanoparticles are fed to a differential mobility analyzer which serves simultaneously as an evaporation flowtube and an instrument for measuring the electrical mobility, realizing measurements of evaporation processes with time scales comparable to the instrument response time. A theoretical framework is derived for deducing the evaporation kinetics from instrument responses through analyzing the nanoparticle trajectory and size-mobility relationship, which considers the coupled mass and heat transfer effect and is applicable to the whole Knudsen number range. The methodology is demonstrated against evaporation but can potentially be extended to condensation and other industrial/atmospheric processes involving rapid size change of nanoparticles.
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Grabarics M, Lettow M, Kirschbaum C, Greis K, Manz C, Pagel K. Mass Spectrometry-Based Techniques to Elucidate the Sugar Code. Chem Rev 2022; 122:7840-7908. [PMID: 34491038 PMCID: PMC9052437 DOI: 10.1021/acs.chemrev.1c00380] [Citation(s) in RCA: 61] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Indexed: 12/22/2022]
Abstract
Cells encode information in the sequence of biopolymers, such as nucleic acids, proteins, and glycans. Although glycans are essential to all living organisms, surprisingly little is known about the "sugar code" and the biological roles of these molecules. The reason glycobiology lags behind its counterparts dealing with nucleic acids and proteins lies in the complexity of carbohydrate structures, which renders their analysis extremely challenging. Building blocks that may differ only in the configuration of a single stereocenter, combined with the vast possibilities to connect monosaccharide units, lead to an immense variety of isomers, which poses a formidable challenge to conventional mass spectrometry. In recent years, however, a combination of innovative ion activation methods, commercialization of ion mobility-mass spectrometry, progress in gas-phase ion spectroscopy, and advances in computational chemistry have led to a revolution in mass spectrometry-based glycan analysis. The present review focuses on the above techniques that expanded the traditional glycomics toolkit and provided spectacular insight into the structure of these fascinating biomolecules. To emphasize the specific challenges associated with them, major classes of mammalian glycans are discussed in separate sections. By doing so, we aim to put the spotlight on the most important element of glycobiology: the glycans themselves.
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Affiliation(s)
- Márkó Grabarics
- Institute
of Chemistry and Biochemistry, Freie Universität
Berlin, Arnimallee 22, 14195 Berlin, Germany
- Department
of Molecular Physics, Fritz Haber Institute
of the Max Planck Society, Faradayweg 4−6, 14195 Berlin, Germany
| | - Maike Lettow
- Institute
of Chemistry and Biochemistry, Freie Universität
Berlin, Arnimallee 22, 14195 Berlin, Germany
- Department
of Molecular Physics, Fritz Haber Institute
of the Max Planck Society, Faradayweg 4−6, 14195 Berlin, Germany
| | - Carla Kirschbaum
- Institute
of Chemistry and Biochemistry, Freie Universität
Berlin, Arnimallee 22, 14195 Berlin, Germany
- Department
of Molecular Physics, Fritz Haber Institute
of the Max Planck Society, Faradayweg 4−6, 14195 Berlin, Germany
| | - Kim Greis
- Institute
of Chemistry and Biochemistry, Freie Universität
Berlin, Arnimallee 22, 14195 Berlin, Germany
- Department
of Molecular Physics, Fritz Haber Institute
of the Max Planck Society, Faradayweg 4−6, 14195 Berlin, Germany
| | - Christian Manz
- Institute
of Chemistry and Biochemistry, Freie Universität
Berlin, Arnimallee 22, 14195 Berlin, Germany
- Department
of Molecular Physics, Fritz Haber Institute
of the Max Planck Society, Faradayweg 4−6, 14195 Berlin, Germany
| | - Kevin Pagel
- Institute
of Chemistry and Biochemistry, Freie Universität
Berlin, Arnimallee 22, 14195 Berlin, Germany
- Department
of Molecular Physics, Fritz Haber Institute
of the Max Planck Society, Faradayweg 4−6, 14195 Berlin, Germany
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27
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Schäfer A, Vetsova VA, Schneider EK, Kappes M, Seitz M, Daumann LJ, Weis P. Ion Mobility Studies of Pyrroloquinoline Quinone Aza-Crown Ether-Lanthanide Complexes. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:722-730. [PMID: 35300493 DOI: 10.1021/jasms.2c00023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Lanthanide-dependent enzymes and their biomimetic complexes have arisen as an interesting target of research in the past decade. These enzymes, specifically, pyrroloquinoline quinone (PQQ)-bearing methanol dehydrogenases, efficiently convert alcohols to the respective aldehydes. To rationally design bioinspired alcohol dehydrogenation catalysts, it is imperative to understand the species involved in catalysis. However, given the extremely flexible coordination sphere of lanthanides, it is often difficult to assess the number and nature of the active species. Here, we show how such questions can be addressed by using a combination of ion mobility spectrometry, mass spectrometry, and quantum-chemical calculations to study the test systems PQQ and lanthanide-PQQ-crown ether ligand complexes. Specifically, we determine the gas-phase structures of [PQQH2]-, [PQQH2+H2O]-, [PQQH2+MeOH]-, [PQQ-15c5+H]+, and [PQQ-15c5+Ln+NO3]2+ (Ln = La to Lu, except Pm). In the latter case, a trend to smaller collision cross sections across the lanthanide series is clearly observable, in line with the well-known lanthanide contraction. We hope that in the future such investigations will help to guide the design and understanding of lanthanide-based biomimetic complexes optimized for catalytic function.
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Affiliation(s)
- Alexander Schäfer
- Karlsruhe Institute of Technology Institute of Physical Chemistry Fritz-Haber-Weg 2, 76128 Karlsruhe, Germany
| | - Violeta A Vetsova
- Department of Chemistry Ludwig Maximilian University of Munich Butenandtstraße 5-13, 81377 Munich, Germany
| | - Erik K Schneider
- Karlsruhe Institute of Technology Institute of Physical Chemistry Fritz-Haber-Weg 2, 76128 Karlsruhe, Germany
| | - Manfred Kappes
- Karlsruhe Institute of Technology Institute of Physical Chemistry Fritz-Haber-Weg 2, 76128 Karlsruhe, Germany
- Karlsruhe Institute of Technology Institute of Nanotechnology Hermann von Helmholtz Pl 1,76344 Eggenstein Leopoldshafen, Germany
| | - Michael Seitz
- University of Tübingen Institute of Inorganic Chemistry Auf der Morgenstelle 18, 72076 Tübingen, Germany
| | - Lena J Daumann
- Department of Chemistry Ludwig Maximilian University of Munich Butenandtstraße 5-13, 81377 Munich, Germany
| | - Patrick Weis
- Karlsruhe Institute of Technology Institute of Physical Chemistry Fritz-Haber-Weg 2, 76128 Karlsruhe, Germany
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28
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Schneider EK, Weis P, Münzfeld L, Roesky PW, Kappes MM. Anionic Stacks of Alkali-Interlinked Yttrium and Dysprosium Bicyclooctatetraenes in Isolation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:695-703. [PMID: 35298159 DOI: 10.1021/jasms.1c00378] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Electrospray ionization of THF solutions of preformed [K(18-c-6)][M(COT)2] (M = Dy(III), Y(III); COT = C8H82-,18-c-6 = C12H24O6) yields the isolated species [(M(COT)2)n+1 + nK]- with n = 0-3. High-resolution ion mobility spectrometry combined with density functional theory calculations performed for the n = 0-2 aggregates indicate that anionic multidecker stacks interlinked by potassium cations are formed. The alternating metal ions are aligned linearly: COT2--M3+-COT2--K+-COT2--M3+-COT2-. The different M3+ ionic radii lead to slight but resolvable changes in mobility and thus collision cross sections indicative of different overall heights of the multidecker stacks. CID measurements show that the aggregates fragment by cleavage at the K+ interconnections.
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Affiliation(s)
- Erik K Schneider
- Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber Weg 2, 76131 Karlsruhe, Germany
| | - Patrick Weis
- Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber Weg 2, 76131 Karlsruhe, Germany
| | - Luca Münzfeld
- Institute of Inorganic Chemistry, Karlsruhe Institute of Technology (KIT), Engesserstrasse 12, 76131 Karlsruhe, Germany
| | - Peter W Roesky
- Institute of Inorganic Chemistry, Karlsruhe Institute of Technology (KIT), Engesserstrasse 12, 76131 Karlsruhe, Germany
| | - Manfred M Kappes
- Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber Weg 2, 76131 Karlsruhe, Germany
- Institute of Nanotechnology, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
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29
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Bianco A, Neefjes I, Alfaouri D, Vehkamäki H, Kurtén T, Ahonen L, Passananti M, Kangasluoma J. Separation of isomers using a differential mobility analyser (DMA): Comparison of experimental vs modelled ion mobility. Talanta 2022; 243:123339. [DOI: 10.1016/j.talanta.2022.123339] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 02/24/2022] [Accepted: 02/26/2022] [Indexed: 01/01/2023]
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Rolland AD, Biberic LS, Prell JS. Investigation of Charge-State-Dependent Compaction of Protein Ions with Native Ion Mobility-Mass Spectrometry and Theory. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:369-381. [PMID: 35073092 PMCID: PMC11404549 DOI: 10.1021/jasms.1c00351] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The precise relationship between native gas-phase protein ion structure, charge, desolvation, and activation remains elusive. Much evidence supports the Charge Residue Model for native protein ions formed by electrospray ionization, but scaling laws derived from it relate only to overall ion size. Closer examination of drift tube CCSs across individual native protein ion charge state distributions (CSDs) reveals deviations from global trends. To investigate whether this is due to structure variation across CSDs or contributions of long-range charge-dipole interactions, we performed in vacuo force field molecular dynamics (MD) simulations of multiple charge conformers of three proteins representing a variety of physical and structural features: β-lactoglobulin, concanavalin A, and glutamate dehydrogenase. Results from these simulated ions indicate subtle structure variation across their native CSDs, although effects of these structural differences and long-range charge-dependent interactions on CCS are small. The structure and CCS of smaller proteins may be more sensitive to charge due to their low surface-to-volume ratios and reduced capacity to compact. Secondary and higher order structure from condensed-phase structures is largely retained in these simulations, supporting the use of the term "native-like" to describe results from native ion mobility-mass spectrometry experiments, although, notably, the most compact structure can be the most different from the condensed-phase structure. Collapse of surface side chains to self-solvate through formation of new hydrogen bonds is a major feature of gas-phase compaction and likely occurs during the desolvation process. Results from these MD simulations provide new insight into the relationship of gas-phase protein ion structure, charge, and CCS.
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Affiliation(s)
- Amber D Rolland
- Department of Chemistry and Biochemistry, University of Oregon, 1253 University of Oregon, Eugene, Oregon 97403-1253, United States
| | - Lejla S Biberic
- Department of Chemistry and Biochemistry, University of Oregon, 1253 University of Oregon, Eugene, Oregon 97403-1253, United States
| | - James S Prell
- Department of Chemistry and Biochemistry, University of Oregon, 1253 University of Oregon, Eugene, Oregon 97403-1253, United States
- Materials Science Institute, University of Oregon, 1252 University of Oregon, Eugene, Oregon 97403-1252, United States
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31
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Garabedian A, Jeanne Dit Fouque K, Chapagain PP, Leng F, Fernandez-Lima F. OUP accepted manuscript. Nucleic Acids Res 2022; 50:2431-2439. [PMID: 35212375 PMCID: PMC8934665 DOI: 10.1093/nar/gkac115] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 12/30/2021] [Accepted: 02/08/2022] [Indexed: 11/25/2022] Open
Abstract
The mammalian high mobility group protein AT-hook 2 (HMGA2) houses three motifs that preferentially bind short stretches of AT-rich DNA regions. These DNA binding motifs, known as ‘AT-hooks’, are traditionally characterized as being unstructured. Upon binding to AT-rich DNA, they form ordered assemblies. It is this disordered-to-ordered transition that has implicated HMGA2 as a protein actively involved in many biological processes, with abnormal HMGA expression linked to a variety of health problems including diabetes, obesity, and oncogenesis. In the current work, the solution binding dynamics of the three ‘AT-hook’ peptides (ATHPs) with AT-rich DNA hairpin substrates were studied using DNA UV melting studies, fluorescence spectroscopy, native ion mobility spectrometry-mass spectrometry (IMS-MS), solution isothermal titration calorimetry (ITC) and molecular modeling. Results showed that the ATHPs bind to the DNA to form a single, 1:1 and 2:1, ‘key-locked’ conformational ensemble. The molecular models showed that 1:1 and 2:1 complex formation is driven by the capacity of the ATHPs to bind to the minor and major grooves of the AT-rich DNA oligomers. Complementary solution ITC results confirmed that the 2:1 stoichiometry of ATHP: DNA is originated under native conditions in solution.
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Affiliation(s)
- Alyssa Garabedian
- Department of Chemistry and Biochemistry, Florida International University, Miami, 33199, USA
| | - Kevin Jeanne Dit Fouque
- Department of Chemistry and Biochemistry, Florida International University, Miami, 33199, USA
- Biomolecular Sciences Institute, Florida International University, Miami, 33199, USA
| | - Prem P Chapagain
- Department of Physics, Florida International University, Miami, 33199, USA
- Biomolecular Sciences Institute, Florida International University, Miami, 33199, USA
| | - Fenfei Leng
- Department of Chemistry and Biochemistry, Florida International University, Miami, 33199, USA
- Biomolecular Sciences Institute, Florida International University, Miami, 33199, USA
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32
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Lebedev AV. Peculiarities of 2,6-Di-tert-butylpyridine Protonation: Mobility of Protonated Molecules. JOURNAL OF ANALYTICAL CHEMISTRY 2021. [DOI: 10.1134/s1061934821130074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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33
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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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34
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Edwards AN, Tran HM, Gallagher ES. Propagating Error through Traveling-Wave Ion Mobility Calibration. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:2621-2630. [PMID: 34662111 DOI: 10.1021/jasms.1c00144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Native mass spectrometry (MS) is used to elucidate the stoichiometry of protein complexes and quantify binding interactions by maintaining native-like, noncovalent interactions in the gas phase. However, ionization forces proteins into specific conformations, losing the solution-phase dynamics associated with solvated protein structures. Comparison of gas-phase structures to those in solution, or to other gas-phase ion populations, has many biological implications. For one, analyzing the variety of conformations that are maintained in the gas-phase can provide insight into a protein's solution-phase energy landscape. The gas-phase conformations of proteins and complexes can be investigated using ion mobility (IM) spectrometry. Specifically, drift tube (DT)-IM utilizes uniform electric fields to propel a population of gas-phase ions through a region containing a neutral gas. By measuring the mobility (K) of gas-phase ions, users are able to calculate an average momentum transfer cross section (DTCCS), which provides structural information on the ion. Conversely, in traveling-wave ion mobility spectrometry (TWIMS), TWCCS values cannot be derived directly from an ion's mobility but must be determined following calibration. Though the required calibration adds uncertainty, it is common to report only an average and standard deviation of the calculated TWCCS, accounting for uncertainty associated with replicate measurements, which is a fraction of the overall uncertainty. Herein, we calibrate a TWIMS instrument and derive TWCCSN2 and TWCCSN2→He values for four proteins: cytochrome c, ubiquitin, apo-myoglobin, and holo-myoglobin. We show that compared to reporting only the standard deviation of TWCCS, propagating error through the calibration results in a significant increase in the number of calculated TWCCS values that agree within experimental error with literature values (DTCCS). Incorporating this additional uncertainty provides a more thorough assessment of a protein ion's gas-phase conformations, enabling the structures sampled by native IM-MS to be compared against other reported structures, both experimental and computational.
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Affiliation(s)
- Alexis N Edwards
- Department of Chemistry and Biochemistry, Baylor University, One Bear Place #97348, Waco, Texas 76798, United States
| | - Hien M Tran
- Department of Chemistry and Biochemistry, Baylor University, One Bear Place #97348, Waco, Texas 76798, United States
| | - Elyssia S Gallagher
- Department of Chemistry and Biochemistry, Baylor University, One Bear Place #97348, Waco, Texas 76798, United States
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Zippel C, Israil R, Schüssler L, Hassan Z, Schneider EK, Weis P, Nieger M, Bizzarri C, Kappes MM, Riehn C, Diller R, Bräse S. Metal-to-Metal Distance Modulated Au(I)/Ru(II) Cyclophanyl Complexes: Cooperative Effects in Photoredox Catalysis. Chemistry 2021; 27:15187-15200. [PMID: 34655123 PMCID: PMC8596992 DOI: 10.1002/chem.202102341] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Indexed: 12/13/2022]
Abstract
The modular synthesis of Au(I)/Ru(II) decorated mono- and heterobimetallic complexes with π-conjugated [2.2]paracyclophane is described. [2.2]Paracyclophane serves as a rigid spacer which holds the metal centers in precise spatial orientations and allows metal-to-metal distance modulation. A broad set of architectural arrangements of pseudo -geminal, -ortho, -meta, and -para substitution patterns were employed. Metal-to-metal distance modulation of Au(I)/Ru(II) heterobimetallic complexes and the innate transannular π-communication of the cyclophanyl scaffold provides a promising platform for the investigations of structure-activity relationship and cooperative effects. The Au(I)/Ru(II) heterobimetallic cyclophanyl complexes are stable, easily accessible, and exhibit promising catalytic activity in the visible-light promoted arylative Meyer-Schuster rearrangement.
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Affiliation(s)
- Christoph Zippel
- Institute of Organic Chemistry (IOC)Karlsruhe Institute of Technology (KIT)Fritz-Haber-Weg 676131KarlsruheGermany
| | - Roumany Israil
- Department of Chemistry, Technische Universität Kaiserslautern (TUK)Erwin-Schrödinger-Str. 5267663KaiserslauternGermany
| | - Lars Schüssler
- Department of Physics, Technische Universität Kaiserslautern (TUK)Erwin-Schrödinger-Str. 4667663KaiserslauternGermany
| | - Zahid Hassan
- Institute of Organic Chemistry (IOC)Karlsruhe Institute of Technology (KIT)Fritz-Haber-Weg 676131KarlsruheGermany
| | - Erik K. Schneider
- Institute of Physical ChemistryKarlsruhe Institute of Technology (KIT)Fritz-Haber Weg 276131KarlsruheGermany
| | - Patrick Weis
- Institute of Physical ChemistryKarlsruhe Institute of Technology (KIT)Fritz-Haber Weg 276131KarlsruheGermany
| | - Martin Nieger
- Department of ChemistryUniversity of HelsinkiP. O. Box 55Helsinki00014Finland
| | - Claudia Bizzarri
- Institute of Organic Chemistry (IOC)Karlsruhe Institute of Technology (KIT)Fritz-Haber-Weg 676131KarlsruheGermany
| | - Manfred M. Kappes
- Institute of Physical ChemistryKarlsruhe Institute of Technology (KIT)Fritz-Haber Weg 276131KarlsruheGermany
- Institute of NanotechnologyKarlsruhe Institute of TechnologyHerman-von Helmholtz-Platz 176344Eggenstein-LeopoldshafenGermany
| | - Christoph Riehn
- Department of Chemistry, Technische Universität Kaiserslautern (TUK)Erwin-Schrödinger-Str. 5267663KaiserslauternGermany
- Research Center OPTIMASErwin-Schrödinger-Str. 4667663KaiserslauternGermany
| | - Rolf Diller
- Department of Physics, Technische Universität Kaiserslautern (TUK)Erwin-Schrödinger-Str. 4667663KaiserslauternGermany
| | - Stefan Bräse
- Institute of Organic Chemistry (IOC)Karlsruhe Institute of Technology (KIT)Fritz-Haber-Weg 676131KarlsruheGermany
- Institute of Biological and Chemical SystemsFunctional Molecular Systems (IBCS-FMS) Karlsruhe Institute of Technology (KIT)Hermann-von-Helmholtz-Platz 176344Eggenstein-LeopoldshafenGermany
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36
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Zagorec-Marks W, Dodson LG, Weis P, Schneider EK, Kappes MM, Weber JM. Intrinsic Structure and Electronic Spectrum of Deprotonated Biliverdin: Cryogenic Ion Spectroscopy and Ion Mobility. J Am Chem Soc 2021; 143:17778-17785. [PMID: 34637616 DOI: 10.1021/jacs.1c08701] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We investigated the structural and spectroscopic properties of singly deprotonated biliverdin anions in vacuo, using a combination of cryogenic ion spectroscopy, ion mobility spectrometry, and density functional theory. The ion mobility results show that at least two conformers are populated, with the dominant conformer at 75-90% relative abundance. The vibrational NH stretching signatures are sensitive to the tetrapyrrole structure, and they indicate that the tetrapyrrole system is in a helical conformation, consistent with simulated ion mobility collision cross sections. The vibrational spectrum in the fingerprint region of this singly deprotonated species shows that the two propionate groups share the remaining acidic proton. The S1 band of the electronic spectrum in vacuo is broad, despite ion trap temperatures of 20 K during ion preparation, with a congested Franck-Condon envelope showing partially resolved vibrational features. The vertical transition exhibits a small solvatochromic red shift (-320 cm-1) in aqueous solution.
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Affiliation(s)
- Wyatt Zagorec-Marks
- JILA and Department of Chemistry, University of Colorado, 440 UCB, Boulder, Colorado 80309-0440, United States
| | - Leah G Dodson
- JILA and NIST, University of Colorado, 440 UCB, Boulder, Colorado 80309-0440, United States
| | - Patrick Weis
- Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 2, 76131 Karlsruhe, Germany
| | - Erik K Schneider
- Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 2, 76131 Karlsruhe, Germany
| | - Manfred M Kappes
- Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 2, 76131 Karlsruhe, Germany
| | - J Mathias Weber
- JILA and Department of Chemistry, University of Colorado, 440 UCB, Boulder, Colorado 80309-0440, United States
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37
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Largy E, König A, Ghosh A, Ghosh D, Benabou S, Rosu F, Gabelica V. Mass Spectrometry of Nucleic Acid Noncovalent Complexes. Chem Rev 2021; 122:7720-7839. [PMID: 34587741 DOI: 10.1021/acs.chemrev.1c00386] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Nucleic acids have been among the first targets for antitumor drugs and antibiotics. With the unveiling of new biological roles in regulation of gene expression, specific DNA and RNA structures have become very attractive targets, especially when the corresponding proteins are undruggable. Biophysical assays to assess target structure as well as ligand binding stoichiometry, affinity, specificity, and binding modes are part of the drug development process. Mass spectrometry offers unique advantages as a biophysical method owing to its ability to distinguish each stoichiometry present in a mixture. In addition, advanced mass spectrometry approaches (reactive probing, fragmentation techniques, ion mobility spectrometry, ion spectroscopy) provide more detailed information on the complexes. Here, we review the fundamentals of mass spectrometry and all its particularities when studying noncovalent nucleic acid structures, and then review what has been learned thanks to mass spectrometry on nucleic acid structures, self-assemblies (e.g., duplexes or G-quadruplexes), and their complexes with ligands.
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Affiliation(s)
- Eric Largy
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Alexander König
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Anirban Ghosh
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Debasmita Ghosh
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Sanae Benabou
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Frédéric Rosu
- Univ. Bordeaux, CNRS, INSERM, IECB, UMS 3033, F-33600 Pessac, France
| | - Valérie Gabelica
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
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38
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White N, Seelig JD, Loyalka SK. Computation of drag and diffusion coefficient for coronavirus: I. JOURNAL OF AEROSOL SCIENCE 2021; 157:105806. [PMID: 33976456 PMCID: PMC8103743 DOI: 10.1016/j.jaerosci.2021.105806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 04/23/2021] [Accepted: 04/27/2021] [Indexed: 06/12/2023]
Abstract
Monte Carlo simulations and integral equation techniques allow for the flexible and efficient computation of drag and diffusion coefficients for virus mimetic particles. We highlight a Monte Carlo method that is useful for computing the drag on biomimetic particles in the free-molecular regime and a numerical technique to solve a boundary integral equation (related to the Stokes equation) in the hydrodynamic limit. The free-molecular and the continuum results allow the construction of an approximation for the drag applicable over the full range of Knudsen numbers. Finally, we outline how this work will be useful in modeling viral transport in air and fluids and in viral morphology measurements and in viral separations via electrospray-differential mobility analyzers (ES-DMA).
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Affiliation(s)
- Nathan White
- Department of Mechanical & Aerospace Engineering, Lafferre Hall, University of Missouri, Columbia, MO, 65211, USA
| | | | - Sudarshan K Loyalka
- Department of Mechanical & Aerospace Engineering, Lafferre Hall, University of Missouri, Columbia, MO, 65211, USA
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39
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Ieritano C, Campbell JL, Hopkins WS. Predicting differential ion mobility behaviour in silico using machine learning. Analyst 2021; 146:4737-4743. [PMID: 34212943 DOI: 10.1039/d1an00557j] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Although there has been a surge in popularity of differential mobility spectrometry (DMS) within analytical workflows, determining separation conditions within the DMS parameter space still requires manual optimization. A means of accurately predicting differential ion mobility would benefit practitioners by significantly reducing the time associated with method development. Here, we report a machine learning (ML) approach that predicts dispersion curves in an N2 environment, which are the compensation voltages (CVs) required for optimal ion transmission across a range of separation voltages (SVs) between 1500 to 4000 V. After training a random-forest based model using the DMS information of 409 cationic analytes, dispersion curves were reproduced with a mean absolute error (MAE) of ≤ 2.4 V, approaching typical experimental peak FWHMs of ±1.5 V. The predictive ML model was trained using only m/z and ion-neutral collision cross section (CCS) as inputs, both of which can be obtained from experimental databases before being extensively validated. By updating the model via inclusion of two CV datapoints at lower SVs (1500 V and 2000 V) accuracy was further improved to MAE ≤ 1.2 V. This improvement stems from the ability of the "guided" ML routine to accurately capture Type A and B behaviour, which was exhibited by only 2% and 17% of ions, respectively, within the dataset. Dispersion curve predictions of the database's most common Type C ions (81%) using the unguided and guided approaches exhibited average errors of 0.6 V and 0.1 V, respectively.
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Affiliation(s)
- Christian Ieritano
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada. and Waterloo Institute for Nanotechnology, University of 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
| | - J Larry Campbell
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada. and WaterMine Innovation, Inc., Waterloo, Ontario N0B 2T0, Canada and Bedrock Scientific Inc., Milton, Ontario L6T 6J9, Canada
| | - W Scott Hopkins
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada. and Waterloo Institute for Nanotechnology, University of 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada and WaterMine Innovation, Inc., Waterloo, Ontario N0B 2T0, Canada and Centre for Eye and Vision Research, Hong Kong Science Park, New Territories, 999077, Hong Kong
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40
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Vicent C, Martinez‐Agramunt V, Gandhi V, Larriba‐Andaluz C, Gusev DG, Peris E. Ion Mobility Mass Spectrometry Uncovers Guest‐Induced Distortions in a Supramolecular Organometallic Metallosquare. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202100914] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Cristian Vicent
- Servei Central d'Instrumentació Científica (SCIC) Universitat Jaume I Avda. Sos Baynat s/n 12006 Castellón Spain
| | - Victor Martinez‐Agramunt
- Institute of Advanced Materials (INAM) Universitat Jaume I Av. Vicente Sos Baynat s/n 12071 Castellón Spain
| | - Viraj Gandhi
- Department of Mechanical and Energy Engineering IUPUI Indianapolis IN 46206 USA
| | | | - Dmitry G. Gusev
- Department of Chemistry and Biochemistry Wilfrid Laurier University 75 University Avenue West Waterloo Ontario N2L 3C5 Canada
| | - Eduardo Peris
- Institute of Advanced Materials (INAM) Universitat Jaume I Av. Vicente Sos Baynat s/n 12071 Castellón Spain
- Department of Mechanical and Energy Engineering IUPUI Indianapolis IN 46206 USA
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41
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Vicent C, Martinez‐Agramunt V, Gandhi V, Larriba‐Andaluz C, Gusev DG, Peris E. Ion Mobility Mass Spectrometry Uncovers Guest-Induced Distortions in a Supramolecular Organometallic Metallosquare. Angew Chem Int Ed Engl 2021; 60:15412-15417. [PMID: 33783064 PMCID: PMC8361979 DOI: 10.1002/anie.202100914] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Indexed: 12/21/2022]
Abstract
The encapsulation of the tetracationic palladium metallosquare with four pyrene-bis-imidazolylidene ligands [1]4+ with a series of organic molecules was studied by Electrospray ionization Travelling Wave Ion-Mobility Mass Spectrometry (ESI TWIM-MS). The method allowed to determine the Collision Cross Sections (CCSs), which were used to assess the size changes experienced by the host upon encapsulation of the guest molecules. When fullerenes were used as guests, the host is expanded ΔCCS 13 Å2 and 23 Å2 , for C60 or C70 , respectively. The metallorectangle [1]4+ was also used for the encapsulation of a series of polycyclic aromatic hydrocarbons (PAHs) and naphthalenetetracarboxylic diimide (NTCDI), to form complexes of formula [(NTCDI)2 (PAH)@1]4+ . For these host:guest adducts, the ESI IM-MS studies revealed that [1]4+ is expanded by 47-49 Å2 .. The energy-minimized structures of [1]4+ , [C60 @1]4+ , [C70 @1]4+ , [(NTCDI)2 (corannulene)@1]4+ in the gas phase were obtained by DFT calculations.Introduction.
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Affiliation(s)
- Cristian Vicent
- Servei Central d'Instrumentació Científica (SCIC)Universitat Jaume IAvda. Sos Baynat s/n12006CastellónSpain
| | - Victor Martinez‐Agramunt
- Institute of Advanced Materials (INAM)Universitat Jaume IAv. Vicente Sos Baynat s/n12071CastellónSpain
| | - Viraj Gandhi
- Department of Mechanical and Energy EngineeringIUPUIIndianapolisIN46206USA
| | | | - Dmitry G. Gusev
- Department of Chemistry and BiochemistryWilfrid Laurier University75 University Avenue WestWaterlooOntarioN2L 3C5Canada
| | - Eduardo Peris
- Institute of Advanced Materials (INAM)Universitat Jaume IAv. Vicente Sos Baynat s/n12071CastellónSpain
- Department of Mechanical and Energy EngineeringIUPUIIndianapolisIN46206USA
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42
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Abdelmouleh M, Lalande M, Nicol E, Frison G, van der Rest G, Poully JC. Chemical Processes Involving 18-Crown-6-Ether in Activated Noncovalent Complexes with Protonated Peptides. Chemphyschem 2021; 22:1243-1250. [PMID: 33881793 DOI: 10.1002/cphc.202100075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 04/07/2021] [Indexed: 11/10/2022]
Abstract
These last decades, it has been widely assumed that 18-crown-6-ether (CE) plays a spectator role during the chemical processes occurring in isolated host-guest complexes between peptides or proteins and CE after activation in mass spectrometers. Our present experimental and theoretical results challenge this hypothesis by showing that CE can abstract a proton or a protonated molecule from protonated peptides after activation by collisions in argon or electron capture/transfer. Furthermore, thanks to comparison between experimental and calculated values of collision cross-sections, we demonstrate that CE can change binding site after electron transfer. We also propose detailed mechanisms for these processes.
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Affiliation(s)
- Marwa Abdelmouleh
- CIMAP UMR 6252, CEA/CNRS/ENSICAEN/Université de Caen Normandie, Bd Becquerel, 14070, Caen, France
| | - Mathieu Lalande
- CIMAP UMR 6252, CEA/CNRS/ENSICAEN/Université de Caen Normandie, Bd Becquerel, 14070, Caen, France
| | - Edith Nicol
- Laboratoire de Chimie Moléculaire, Ecole Polytech, Inst Polytech Paris, CNRS, 91128, Palaiseau, France
| | - Gilles Frison
- Laboratoire de Chimie Moléculaire, Ecole Polytech, Inst Polytech Paris, CNRS, 91128, Palaiseau, France.,Laboratoire de Chimie Théorique, Sorbonne Université and CNRS, 75005, Paris, France
| | - Guillaume van der Rest
- Institut de Chimie Physique, Université Paris Saclay, CNRS, Bâtiment 349, 91405, Orsay, France
| | - Jean-Christophe Poully
- CIMAP UMR 6252, CEA/CNRS/ENSICAEN/Université de Caen Normandie, Bd Becquerel, 14070, Caen, France
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43
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Grabarics M, Lettow M, Kirk AT, von Helden G, Causon TJ, Pagel K. Plate-height model of ion mobility-mass spectrometry: Part 2-Peak-to-peak resolution and peak capacity. J Sep Sci 2021; 44:2798-2813. [PMID: 33945207 DOI: 10.1002/jssc.202100201] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 04/28/2021] [Accepted: 04/29/2021] [Indexed: 12/30/2022]
Abstract
In a previous work, we explored zone broadening and the achievable plate numbers in linear drift tube ion mobility-mass spectrometry through developing a plate-height model [1]. On the basis of these findings, the present theoretical study extends the model by exploring peak-to-peak resolution and peak capacity in ion mobility separations. The first part provides a critical overview of chromatography-influenced resolution equations, including refinement of existing formulae. Furthermore, we present exact resolution equations for drift tube ion mobility spectrometry based on first principles. Upon implementing simple modifications, these exact formulae could be readily extended to traveling wave ion mobility separations and to cases when ion mobility spectrometry is coupled to mass spectrometry. The second part focuses on peak capacity. The well-known assumptions of constant plate number and constant peak width form the basis of existing approximate solutions. To overcome their limitations, an exact peak capacity equation is derived for drift tube ion mobility spectrometry. This exact solution is rooted in a suitable physical model of peak broadening, accounting for the finite injection pulse and subsequent diffusional spreading. By borrowing concepts from the theoretical toolbox of chromatography, we believe that the present study will help in integrating ion mobility spectrometry into the unified language of separation science.
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Affiliation(s)
- Márkó Grabarics
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany.,Department of Molecular Physics, Fritz Haber Institute of the Max Planck Society, Berlin, Germany
| | - Maike Lettow
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany.,Department of Molecular Physics, Fritz Haber Institute of the Max Planck Society, Berlin, Germany
| | - Ansgar T Kirk
- Institute of Electrical Engineering and Measurement Technology, Leibniz Universität Hannover, Hannover, Germany
| | - Gert von Helden
- Department of Molecular Physics, Fritz Haber Institute of the Max Planck Society, Berlin, Germany
| | - Tim J Causon
- Institute of Analytical Chemistry, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Kevin Pagel
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany.,Department of Molecular Physics, Fritz Haber Institute of the Max Planck Society, Berlin, Germany
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44
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Vetsova VA, Fisher KR, Lumpe H, Schäfer A, Schneider EK, Weis P, Daumann LJ. Pyrroloquinoline Quinone Aza-Crown Ether Complexes as Biomimetics for Lanthanide and Calcium Dependent Alcohol Dehydrogenases*. Chemistry 2021; 27:10087-10098. [PMID: 33872420 PMCID: PMC8361747 DOI: 10.1002/chem.202100346] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Indexed: 12/23/2022]
Abstract
Understanding the role of metal ions in biology can lead to the development of new catalysts for several industrially important transformations. Lanthanides are the most recent group of metal ions that have been shown to be important in biology, that is, in quinone‐dependent methanol dehydrogenases (MDH). Here we evaluate a literature‐known pyrroloquinoline quinone (PQQ) and 1‐aza‐15‐crown‐5 based ligand platform as scaffold for Ca2+, Ba2+, La3+ and Lu3+ biomimetics of MDH and we evaluate the importance of ligand design, charge, size, counterions and base for the alcohol oxidation reaction using NMR spectroscopy. In addition, we report a new straightforward synthetic route (3 steps instead of 11 and 33 % instead of 0.6 % yield) for biomimetic ligands based on PQQ. We show that when studying biomimetics for MDH, larger metal ions and those with lower charge in this case promote the dehydrogenation reaction more effectively and that this is likely an effect of the ligand design which must be considered when studying biomimetics. To gain more information on the structures and impact of counterions of the complexes, we performed collision induced dissociation (CID) experiments and observe that the nitrates are more tightly bound than the triflates. To resolve the structure of the complexes in the gas phase we combined DFT‐calculations and ion mobility measurements (IMS). Furthermore, we characterized the obtained complexes and reaction mixtures using Electron Paramagnetic Resonance (EPR) spectroscopy and show the presence of a small amount of quinone‐based radical.
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Affiliation(s)
- Violeta A Vetsova
- Department of Chemistry, Ludwig Maximilian University of Munich, Butenandtstraße 5-13, 81377, Munich, Germany
| | - Katherine R Fisher
- Department of Chemistry, Ludwig Maximilian University of Munich, Butenandtstraße 5-13, 81377, Munich, Germany
| | - Henning Lumpe
- Department of Chemistry, Ludwig Maximilian University of Munich, Butenandtstraße 5-13, 81377, Munich, Germany
| | - Alexander Schäfer
- Karlsruhe Institute of Technology, Institute of Physical Chemistry, Fritz-Haber-Weg 2, 76128, Karlsruhe, Germany
| | - Erik K Schneider
- Karlsruhe Institute of Technology, Institute of Physical Chemistry, Fritz-Haber-Weg 2, 76128, Karlsruhe, Germany
| | - Patrick Weis
- Karlsruhe Institute of Technology, Institute of Physical Chemistry, Fritz-Haber-Weg 2, 76128, Karlsruhe, Germany
| | - Lena J Daumann
- Department of Chemistry, Ludwig Maximilian University of Munich, Butenandtstraße 5-13, 81377, Munich, Germany
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45
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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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46
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Ligare MR, Morrison KA, Hewitt MA, Reveles JU, Govind N, Hernandez H, Baker ES, Clowers BH, Laskin J, Johnson GE. Ion Mobility Spectrometry Characterization of the Intermediate Hydrogen-Containing Gold Cluster Au 7(PPh 3) 7H 52. J Phys Chem Lett 2021; 12:2502-2508. [PMID: 33667097 DOI: 10.1021/acs.jpclett.0c03664] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
We employ ion mobility spectrometry and density functional theory to determine the structure of Au7(PPh3)7H52+ (PPh3 = triphenylphosphine), which was recently identified by high mass resolution mass spectrometry. Experimental ion-neutral collision cross sections represent the momentum transfer between the ionic clusters and gas molecules averaged over the relative thermal velocities of the colliding pair, thereby providing structural insights. Theoretical calculations indicate the geometry of Au7(PPh3)7H52+ is similar to Au7(PPh3)7+, with three hydrogen atoms bridging two gold atoms and two hydrogen atoms forming single Au-H bonds. Collision-induced dissociation products observed during IMS experiments reveal that smaller hydrogen-containing clusters may be produced through fragmentation of Au7(PPh3)7H52+. Our findings indicate that hydrogen-containing species like Au7(PPh3)7H52+ act as intermediates in the formation of larger phosphine ligated gold clusters. These results advance the understanding and ability to control the mechanisms of size-selective cluster formation, which is necessary for scalable synthesis of clusters with tailored properties.
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Affiliation(s)
- Marshall R Ligare
- Physical Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, United States
| | - Kelsey A Morrison
- Department of Chemistry, Washington State University, P.O. Box 644630, Pullman, Washington 99164, United States
| | - Michael A Hewitt
- Department of Chemistry, Grinnell College, Grinnell, Iowa 50112, United States
| | - J Ulises Reveles
- Advanced Career Education (ACE) Center at Highland Springs, Highland Springs, Virginia 23075, United States
| | - Niranjan Govind
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99354, United States
| | - Heriberto Hernandez
- Department of Chemistry, Grinnell College, Grinnell, Iowa 50112, United States
| | - Erin S Baker
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Brian H Clowers
- Department of Chemistry, Washington State University, P.O. Box 644630, Pullman, Washington 99164, United States
| | - Julia Laskin
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Grant E Johnson
- Physical Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, United States
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47
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Naylor CN, Clowers BH. Reevaluating the Role of Polarizability in Ion Mobility Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:618-627. [PMID: 33533630 DOI: 10.1021/jasms.0c00338] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
With the expanding commercial availability of gas-phase separation systems that incorporate gas-phase mobility, there is a concurrent rise in efforts to cast the gas-phase mobility coefficient in terms of an ion-neutral collision cross-section (CCS). The motivating factors for this trend are varied, but many aim to complement experimental results with computationally generated CCS values from in silico structural approximations. Unfortunately, the current paradigm for relating experimental mobility results to computationally derived structures relies upon empirical approaches, including a myriad of variables that do not realistically bound the comparison. In this Critical Insight, we advocate for the development of a self-consistent experimental and computational framework that uses laboratory results to constrain the scope of the modeling effort. This paper aims to prompt discussion, challenge assumptions, and promote the development of more efficient, accurate computational techniques within the gas-phase ion measurement community. Specifically, we postulate whether experimental deviations from Langevin's polarization limit (Kpol) are suitable to estimate the relative contributions of hard-sphere collisions and long-range interactions within CCS values. Not surprisingly, different molecule classes exhibit different trends in the K/Kpol ratio when normalized for reduced mass, and the most common IMS calibrants (e.g., tune mix, polyalanine, tetraalkylammonium salts) follow different polarizability trends than many of the analytes probed in the literature. Succinctly, if gas-phase ion structure is largely invariant based upon the colliding neutral and newly developed experimental efforts can quantitatively capture ion polarizability, then modeling efforts describing a target analyte must be self-consistent as the collision neutral is changed in silico.
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Affiliation(s)
- Cameron N Naylor
- Department of Chemistry, Washington State University, Pullman, Washington 99164, United States
| | - Brian H Clowers
- Department of Chemistry, Washington State University, Pullman, Washington 99164, United States
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48
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Wu F, Yang S, Dai X, Gu L, Xu F, Fang X, Yu S, Ding CF. Discrimination of Aminobiphenyl Isomers in the Gas Phase and Investigation of Their Complex Conformations. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:716-724. [PMID: 33527834 DOI: 10.1021/jasms.0c00426] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The analysis of positional isomers is of great significance because their different chemical properties but similar structures make separation difficult. In this work, a simple method for simultaneously discriminating three positional isomers of 2-aminobiphenyl (2-ABP), 3-ABP, and 4-ABP was studied by ion mobility spectrometry (IMS) and quantum mechanical calculations at the molecular level. In the experiments, three ABP isomers were mixed with α-, β-, and γ-cyclodextrins (CD), and the IMS results show that the three ABP isomers were clearly recognized by the formed complex of [α-CD + ABP + H]+ via measuring their IMS, in which the different ion mobilities of 1.515, 1.544, 1.585 V·s·com-2 with the collision cross sections (CCS) of 307.3, 312.5, 320.8 Å2 were obtained for [α-CD + 2-ABP + H]+, [α-CD + 3-ABP + H]+, and [α-CD + 4-ABP + H]+, respectively. Collision induced dissociation analysis of the three [α-CD + ABP + H]+ isomer complexes were further studied, indicating that the same fragmentation process required different collisional energies, and the greater the CCS for the [α-CD + ABP + H]+ with looser structure and the smaller energy required. Besides, the favorable conformation and the CCS value of the different [CD + ABP + H]+ isomer complexes were measured via quantum mechanical calculations to detail their intermolecular interactions. It revealed that the intermolecular binding between 2-ABP and α-CD is different from that of 3- and 4-ABP, resulting in different molecular conformations and CCS, and the interaction modes of ABP with β-CD are similar to that with γ-CD, which are very consistent with the experimental observations. Finally, relative quantification of the method was performed, and satisfactory linearity with correlation coefficients (R2) greater than 0.99 was obtained. This method for isomer discrimination and conformation analysis possesses the advantages of simplicity, sensitivity, cost-effectiveness, and as such it may be widely applied in chemistry and pharmaceutical sciences.
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Affiliation(s)
- Fangling Wu
- Zhejiang Provincial Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China
- National Institute of Metrology, Beijing 100029, China
| | - Shutong Yang
- Zhejiang Provincial Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China
- National Institute of Metrology, Beijing 100029, China
| | - Xinhua Dai
- Zhejiang Provincial Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China
- National Institute of Metrology, Beijing 100029, China
| | - Liancheng Gu
- Zhejiang Provincial Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China
- National Institute of Metrology, Beijing 100029, China
| | - Fuxing Xu
- Zhejiang Provincial Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China
- National Institute of Metrology, Beijing 100029, China
| | - Xiang Fang
- Zhejiang Provincial Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China
- National Institute of Metrology, Beijing 100029, China
| | - Shaoning Yu
- Zhejiang Provincial Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China
- National Institute of Metrology, Beijing 100029, China
| | - Chuan-Fan Ding
- Zhejiang Provincial Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China
- National Institute of Metrology, Beijing 100029, China
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49
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Schissler C, Schneider EK, Felker B, Weis P, Nieger M, Kappes MM, Bräse S. A Synthetic Strategy for Cofacial Porphyrin-Based Homo- and Heterobimetallic Complexes. Chemistry 2021; 27:3047-3054. [PMID: 33459421 PMCID: PMC7898677 DOI: 10.1002/chem.202002394] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 11/16/2020] [Indexed: 12/20/2022]
Abstract
We present a straightforward and generally applicable synthesis route for cofacially linked homo- and heterobimetallic porphyrin complexes. The protocol allows the synthesis of unsymmetrical aryl-based meso-meso as well as β-meso-linked porphyrins. Our method significantly increases the overall yield for the published compound known as o-phenylene-bisporphyrin (OBBP) by a factor of 6.8. Besides the synthesis of 16 novel homobimetallic complexes containing MnIII , FeIII , NiII , CuII , ZnII , and PdII , we achieved the first single-crystal X-ray structure of an unsymmetrical cofacial benzene-linked porphyrin dimer containing both planar-chiral enantiomers of a NiII 2 complex. Additionally, this new methodology allows access to heterobimetallic complexes such as the FeIII -NiII containing carbon monoxide dehydrogenase active site analogue. The isolated species were investigated by various techniques, including ion mobility spectrometry, DFT calculations, and UV/Vis spectroscopy. This allowed us to probe the influence of interplane distance on Soret band splitting.
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Affiliation(s)
- Christoph Schissler
- Institute of Organic ChemistryKarlsruhe Institute of Technology (KIT)Fritz-Haber-Weg 676131KarlsruheGermany
| | - Erik K. Schneider
- Institute of Physical ChemistryKarlsruhe Institute of Technology (KIT)Fritz-Haber-Weg 276131KarlsruheGermany
| | - Benjamin Felker
- Institute of Organic ChemistryKarlsruhe Institute of Technology (KIT)Fritz-Haber-Weg 676131KarlsruheGermany
| | - Patrick Weis
- Institute of Physical ChemistryKarlsruhe Institute of Technology (KIT)Fritz-Haber-Weg 276131KarlsruheGermany
| | - Martin Nieger
- Department of ChemistryUniversity of HelsinkiP.O. Box 5500014HelsinkiFinland
| | - Manfred M. Kappes
- Institute of Physical ChemistryKarlsruhe Institute of Technology (KIT)Fritz-Haber-Weg 276131KarlsruheGermany
- Institute for NanotechnologyKarlsruhe Institute of Technology (KIT)Hermann-von-Helmholtz-Platz 176344Eggenstein-LeopoldshafenGermany
| | - Stefan Bräse
- Institute of Organic ChemistryKarlsruhe Institute of Technology (KIT)Fritz-Haber-Weg 676131KarlsruheGermany
- Institute for Biological and Chemical Systems—Functional Molecular, Systems, (IBCS-FMS)Karlsruhe Institute of Technology (KIT)Hermann-von-Helmholtz-Platz 176344Eggenstein-LeopoldshafenGermany
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Ross DH, Xu L. Determination of drugs and drug metabolites by ion mobility-mass spectrometry: A review. Anal Chim Acta 2021; 1154:338270. [PMID: 33736803 DOI: 10.1016/j.aca.2021.338270] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 01/25/2021] [Accepted: 01/27/2021] [Indexed: 01/04/2023]
Abstract
Ion mobility-mass spectrometry (IM-MS) has gained increased applications in the characterization and identification of drugs and drug metabolites, largely owning to the complementary separation of analyte ions based on their gas-phase size and shape in the IM dimension in addition to their mass-to-charge ratios. In this review, we discuss recent advances in such applications. We first introduce various types of IM techniques, focusing on those that allow the measurement of collision cross section (CCS), the physical property of an ion that reflects its gas-phase size and shape. Next, we discuss the IM-MS landscape of the large chemical space of drugs and multimodal distributions of certain drugs in IM separation due to the presence of protomers. We then review drug metabolism reactions and discuss the application of IM-MS in separation and identification of isomeric drug metabolites. Subsequently, we discuss various approaches to generate theoretical and predicted CCS data, including theory-based calculation methods and data-driven prediction models, and currently available resources on these approaches. Finally, current limitations and future directions of application of IM-MS are discussed.
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Affiliation(s)
- Dylan H Ross
- Department of Medicinal Chemistry, University of Washington, 1959, NE Pacific Street, HSB H-172, Seattle, WA, USA
| | - Libin Xu
- Department of Medicinal Chemistry, University of Washington, 1959, NE Pacific Street, HSB H-172, Seattle, WA, USA.
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