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Xu X, Han L, Zheng Z, Zhao R, Li L, Shao X, Li G. Composite Multidimensional Ion Mobility-Mass Spectrometry for Improved Differentiation of Stereochemical Modifications. Anal Chem 2023; 95:2221-2228. [PMID: 36635260 DOI: 10.1021/acs.analchem.2c03522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Stereochemical modifications (SCMs), mostly present in the form of d-amino acid substitution, have been increasingly identified from a wide range of neuropeptides and disease-associated biomarker proteins. Traditional mass spectrometry-based SCM identification has been effectively enhanced with technological and strategic advancements in ion mobility spectrometry. With the additional separation provided by ion mobility, SCM-induced structural changes can be probed both in theory and in practice, although the structural resolution for low-abundance SCMs still requires further improvement to enable accurate quantification or unambiguous identification of stereoisomers. Herein, we present a multi-component-enabled multidimensional ion mobility-mass spectrometry (3M-IM-MS) analytical workflow, based upon the metal-enhanced chiral amplification strategy we proposed previously (Nat. Commun., 2019, 5038). Notably, the 3M-IM-MS strategy comprises and features the powerful mathematical tools of continuous wavelet transform and Gaussian fitting-enabled peak splitting. Consequently, the resolving capability of ion mobility spectrometry for SCM analysis has been significantly enhanced, providing mobility profiles with baseline separation and more than fivefold improvement in resolving power and overall resolution. This study represents an alternative toward ultrahigh-resolution structural interrogation of mixtures with very small differences, featuring an important and long-lasting topic in chemical measurement.
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Affiliation(s)
- Xia Xu
- Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Science, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Li Han
- Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Science, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Zhen Zheng
- School of Pharmacy, Tianjin Medical University, Tianjin 300070, China
| | - Rui Zhao
- Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Science, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Lingjun Li
- School of Pharmacy and Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Xueguang Shao
- Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Science, College of Chemistry, Nankai University, Tianjin 300071, China.,Haihe Laboratory of Sustainable Chemical Transformations, Tianjin 300192, China
| | - Gongyu Li
- Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Science, College of Chemistry, Nankai University, Tianjin 300071, China.,Haihe Laboratory of Sustainable Chemical Transformations, Tianjin 300192, China
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A benzodiazepine activator locks K v7.1 channels open by electro-mechanical uncoupling. Commun Biol 2022; 5:301. [PMID: 35365746 PMCID: PMC8976019 DOI: 10.1038/s42003-022-03229-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 02/22/2022] [Indexed: 01/18/2023] Open
Abstract
Loss-of-function mutations in Kv7.1 often lead to long QT syndrome (LQTS), a cardiac repolarization disorder associated with arrhythmia and subsequent sudden cardiac death. The discovery of agonistic IKs modulators may offer a new potential strategy in pharmacological treatment of this disorder. The benzodiazepine derivative (R)-L3 potently activates Kv7.1 channels and shortens action potential duration, thus may represent a starting point for drug development. However, the molecular mechanisms underlying modulation by (R)-L3 are still unknown. By combining alanine scanning mutagenesis, non-canonical amino acid incorporation, voltage-clamp electrophysiology and fluorometry, and in silico protein modelling, we show that (R)-L3 not only stimulates currents by allosteric modulation of the pore domain but also alters the kinetics independently from the pore domain effects. We identify novel (R)-L3-interacting key residues in the lower S4-segment of Kv7.1 and observed an uncoupling of the outer S4 segment with the inner S5, S6 and selectivity filter segments.
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Dilger JM, Martin TM, Wilkins BP, Bohrer BC, Thoreson KM, Fedick PW. Detection and toxicity modeling of anthraquinone dyes and chlorinated side products from a colored smoke pyrotechnic reaction. CHEMOSPHERE 2022; 287:131845. [PMID: 34523441 PMCID: PMC10058345 DOI: 10.1016/j.chemosphere.2021.131845] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 08/05/2021] [Accepted: 08/06/2021] [Indexed: 05/20/2023]
Abstract
"Green" pyrotechnics seek to remove known environmental pollutants and health hazards from their formulations. This chemical engineering approach often focuses on maintaining performance effects upon replacement of objectionable ingredients, yet neglects the chemical products formed by the exothermic reaction. In this work, milligram quantities of a lab-scale pyrotechnic red smoke composition were functioned within a thermal probe for product identification by pyrolysis-gas chromatography-mass spectrometry. Thermally decomposed ingredients and new side product derivatives were identified at lower relative abundances to the intact organic dye (as the engineered sublimation product). Side products included chlorination of the organic dye donated by the chlorate oxidizer. Machine learning quantitative structure-activity relationship models computed impacts to health and environmental hazards. High to very high toxicities were predicted for inhalation, mutagenicity, developmental, and endocrine disruption for common military pyrotechnic dyes and their analogous chlorinated side products. These results underscore the need to revise objectives of "green" pyrotechnic engineering.
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Affiliation(s)
- Jonathan M Dilger
- Naval Surface Warfare Center, Crane Division, 300 Highway 361, Crane, IN, 47522, USA.
| | - Todd M Martin
- Center for Computational Toxicology and Exposure, U.S. Environmental Protection Agency, 26 W. Martin Luther King Dr., Cincinnati, OH, 45268, USA
| | - Benjamin P Wilkins
- Naval Surface Warfare Center, Crane Division, 300 Highway 361, Crane, IN, 47522, USA
| | - Brian C Bohrer
- Department of Chemistry, University of Southern Indiana, 8600 University Blvd., Evansville, IN, 47712, USA
| | - Kelly M Thoreson
- Naval Surface Warfare Center, Crane Division, 300 Highway 361, Crane, IN, 47522, USA
| | - Patrick W Fedick
- Naval Air Warfare Center Weapons Division, 1900 N. Knox Road, China Lake, CA, 93555, USA
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Rivera ES, Djambazova KV, Neumann EK, Caprioli RM, Spraggins JM. Integrating ion mobility and imaging mass spectrometry for comprehensive analysis of biological tissues: A brief review and perspective. JOURNAL OF MASS SPECTROMETRY : JMS 2020; 55:e4614. [PMID: 32955134 PMCID: PMC8211109 DOI: 10.1002/jms.4614] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 06/27/2020] [Accepted: 07/02/2020] [Indexed: 05/02/2023]
Abstract
Imaging mass spectrometry (IMS) technologies are capable of mapping a wide array of biomolecules in diverse cellular and tissue environments. IMS has emerged as an essential tool for providing spatially targeted molecular information due to its high sensitivity, wide molecular coverage, and chemical specificity. One of the major challenges for mapping the complex cellular milieu is the presence of many isomers and isobars in these samples. This challenge is traditionally addressed using orthogonal liquid chromatography (LC)-based analysis, though, common approaches such as chromatography and electrophoresis are not able to be performed at timescales that are compatible with most imaging applications. Ion mobility offers rapid, gas-phase separations that are readily integrated with IMS workflows in order to provide additional data dimensionality that can improve signal-to-noise, dynamic range, and specificity. Here, we highlight recent examples of ion mobility coupled to IMS and highlight their importance to the field.
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Key Words
- IMS
- desorption electrospray ionization, DESI
- drift tube ion mobility spectrometry, DTIMS
- high-field asymmetric waveform ion mobility, FAIMS
- imaging mass spectrometry
- infrared matrix-assisted laser desorption electrospray ionization, IR-MALDESI
- ion mobility
- laser ablation electrospray ionization, LAESI
- lipids
- liquid extraction surface analysis, LESA
- liquid microjunction, (LMJ)
- matrix-assisted laser desorption electrospray ionization, MALDI
- metabolites
- proteins
- tissue analysis
- trapped ion mobility spectrometry, TIMS
- travelling wave ion mobility spectrometry, TWIMS
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Affiliation(s)
- Emilio S. Rivera
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, TN 37205, USA
- Mass Spectrometry Research Center, Vanderbilt University, 465 21 Ave S #9160, Nashville, TN 37235, USA
| | - Katerina V. Djambazova
- Mass Spectrometry Research Center, Vanderbilt University, 465 21 Ave S #9160, Nashville, TN 37235, USA
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, TN 37235, USA
| | - Elizabeth K. Neumann
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, TN 37205, USA
- Mass Spectrometry Research Center, Vanderbilt University, 465 21 Ave S #9160, Nashville, TN 37235, USA
| | - Richard M. Caprioli
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, TN 37205, USA
- Mass Spectrometry Research Center, Vanderbilt University, 465 21 Ave S #9160, Nashville, TN 37235, USA
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, TN 37235, USA
- Department of Pharmacology, Vanderbilt University, 2220 Pierce Avenue, Nashville, TN 37232, USA
- Department of Medicine, Vanderbilt University, 465 21 Ave S #9160, Nashville, TN 37235, USA
| | - Jeffrey M. Spraggins
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, TN 37205, USA
- Mass Spectrometry Research Center, Vanderbilt University, 465 21 Ave S #9160, Nashville, TN 37235, USA
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, TN 37235, USA
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Toropova AP, Toropov AA. Application of the Monte Carlo Method for the Prediction of Behavior of Peptides. Curr Protein Pept Sci 2019; 20:1151-1157. [DOI: 10.2174/1389203720666190123163907] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 12/17/2018] [Accepted: 12/20/2018] [Indexed: 12/26/2022]
Abstract
Prediction of physicochemical and biochemical behavior of peptides is an important and attractive
task of the modern natural sciences, since these substances have a key role in life processes. The
Monte Carlo technique is a possible way to solve the above task. The Monte Carlo method is a tool with
different applications relative to the study of peptides: (i) analysis of the 3D configurations (conformers);
(ii) establishment of quantitative structure – property / activity relationships (QSPRs/QSARs); and (iii)
development of databases on the biopolymers. Current ideas related to application of the Monte Carlo
technique for studying peptides and biopolymers have been discussed in this review.
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Affiliation(s)
- Alla P. Toropova
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Via La Masa 19, 20156 Milano, Italy
| | - Andrey A. Toropov
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Via La Masa 19, 20156 Milano, Italy
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Molecular basis for chirality-regulated Aβ self-assembly and receptor recognition revealed by ion mobility-mass spectrometry. Nat Commun 2019; 10:5038. [PMID: 31695027 PMCID: PMC6834639 DOI: 10.1038/s41467-019-12346-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Accepted: 09/02/2019] [Indexed: 12/22/2022] Open
Abstract
Despite extensive efforts on probing the mechanism of Alzheimer’s disease (AD) and enormous investments into AD drug development, the lack of effective disease-modifying therapeutics and the complexity of the AD pathogenesis process suggest a great need for further insights into alternative AD drug targets. Herein, we focus on the chiral effects of truncated amyloid beta (Aβ) and offer further structural and molecular evidence for epitope region-specific, chirality-regulated Aβ fragment self-assembly and its potential impact on receptor-recognition. A multidimensional ion mobility-mass spectrometry (IM-MS) analytical platform and in-solution kinetics analysis reveal the comprehensive structural and molecular basis for differential Aβ fragment chiral chemistry, including the differential and cooperative roles of chiral Aβ N-terminal and C-terminal fragments in receptor recognition. Our method is applicable to many other systems and the results may shed light on the potential development of novel AD therapeutic strategies based on targeting the D-isomerized Aβ, rather than natural L-Aβ. Chiral inversion of amino acids is thought to modulate the structure and function of amyloid beta (Aβ) but these processes are poorly understood. Here, the authors develop an ion mobility-mass spectrometry based approach to study chirality-regulated structural features of Aβ fragments and their influence on receptor recognition.
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Tro MJ, Charest N, Taitz Z, Shea JE, Bowers MT. The Classifying Autoencoder: Gaining Insight into Amyloid Assembly of Peptides and Proteins. J Phys Chem B 2019; 123:5256-5264. [DOI: 10.1021/acs.jpcb.9b03415] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Michael J. Tro
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106-9510, United States
| | - Nathaniel Charest
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106-9510, United States
| | - Zachary Taitz
- Department of Chemistry, Yale University, PO Box 208107, New Haven Connecticut 06520 8107, United States
| | - Joan-Emma Shea
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106-9510, United States
| | - Michael T. Bowers
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106-9510, United States
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Zheng X, Aly NA, Zhou Y, Dupuis KT, Bilbao A, Paurus VL, Orton DJ, Wilson R, Payne SH, Smith RD, Baker ES. A structural examination and collision cross section database for over 500 metabolites and xenobiotics using drift tube ion mobility spectrometry. Chem Sci 2017; 8:7724-7736. [PMID: 29568436 PMCID: PMC5853271 DOI: 10.1039/c7sc03464d] [Citation(s) in RCA: 138] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 09/21/2017] [Indexed: 12/19/2022] Open
Abstract
The confident identification of metabolites and xenobiotics in biological and environmental studies is an analytical challenge due to their immense dynamic range, vast chemical space and structural diversity. Ion mobility spectrometry (IMS) is widely used for small molecule analyses since it can separate isomeric species and be easily coupled with front end separations and mass spectrometry for multidimensional characterizations. However, to date IMS metabolomic and exposomic studies have been limited by an inadequate number of accurate collision cross section (CCS) values for small molecules, causing features to be detected but not confidently identified. In this work, we utilized drift tube IMS (DTIMS) to directly measure CCS values for over 500 small molecules including primary metabolites, secondary metabolites and xenobiotics. Since DTIMS measurements do not need calibrant ions or calibration like some other IMS techniques, they avoid calibration errors which can cause problems in distinguishing structurally similar molecules. All measurements were performed in triplicate in both positive and negative polarities with nitrogen gas and seven different electric fields, so that relative standard deviations (RSD) could be assessed for each molecule and structural differences studied. The primary metabolites analyzed to date have come from key metabolism pathways such as glycolysis, the pentose phosphate pathway and the tricarboxylic acid cycle, while the secondary metabolites consisted of classes such as terpenes and flavonoids, and the xenobiotics represented a range of molecules from antibiotics to polycyclic aromatic hydrocarbons. Different CCS trends were observed for several of the diverse small molecule classes and when urine features were matched to the database, the addition of the IMS dimension greatly reduced the possible number of candidate molecules. This CCS database and structural information are freely available for download at http://panomics.pnnl.gov/metabolites/ with new molecules being added frequently.
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Affiliation(s)
- Xueyun Zheng
- Biological Sciences Division , Pacific Northwest National Laboratory , 902 Battelle Blvd, P.O. Box 999, MSIN K8-98 , Richland , WA 99352 , USA . ; Tel: +1-509-371-6219
| | - Noor A Aly
- Biological Sciences Division , Pacific Northwest National Laboratory , 902 Battelle Blvd, P.O. Box 999, MSIN K8-98 , Richland , WA 99352 , USA . ; Tel: +1-509-371-6219
| | - Yuxuan Zhou
- Biological Sciences Division , Pacific Northwest National Laboratory , 902 Battelle Blvd, P.O. Box 999, MSIN K8-98 , Richland , WA 99352 , USA . ; Tel: +1-509-371-6219
| | - Kevin T Dupuis
- Biological Sciences Division , Pacific Northwest National Laboratory , 902 Battelle Blvd, P.O. Box 999, MSIN K8-98 , Richland , WA 99352 , USA . ; Tel: +1-509-371-6219
| | - Aivett Bilbao
- Biological Sciences Division , Pacific Northwest National Laboratory , 902 Battelle Blvd, P.O. Box 999, MSIN K8-98 , Richland , WA 99352 , USA . ; Tel: +1-509-371-6219
| | - Vanessa L Paurus
- Biological Sciences Division , Pacific Northwest National Laboratory , 902 Battelle Blvd, P.O. Box 999, MSIN K8-98 , Richland , WA 99352 , USA . ; Tel: +1-509-371-6219
| | - Daniel J Orton
- Biological Sciences Division , Pacific Northwest National Laboratory , 902 Battelle Blvd, P.O. Box 999, MSIN K8-98 , Richland , WA 99352 , USA . ; Tel: +1-509-371-6219
| | - Ryan Wilson
- Biological Sciences Division , Pacific Northwest National Laboratory , 902 Battelle Blvd, P.O. Box 999, MSIN K8-98 , Richland , WA 99352 , USA . ; Tel: +1-509-371-6219
| | - Samuel H Payne
- Biological Sciences Division , Pacific Northwest National Laboratory , 902 Battelle Blvd, P.O. Box 999, MSIN K8-98 , Richland , WA 99352 , USA . ; Tel: +1-509-371-6219
| | - Richard D Smith
- Biological Sciences Division , Pacific Northwest National Laboratory , 902 Battelle Blvd, P.O. Box 999, MSIN K8-98 , Richland , WA 99352 , USA . ; Tel: +1-509-371-6219
| | - Erin S Baker
- Biological Sciences Division , Pacific Northwest National Laboratory , 902 Battelle Blvd, P.O. Box 999, MSIN K8-98 , Richland , WA 99352 , USA . ; Tel: +1-509-371-6219
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