1
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Chen J, Fasihianifard P, Raz AAP, Hickey BL, Moreno JL, Chang CEA, Hooley RJ, Zhong W. Selective recognition and discrimination of single isomeric changes in peptide strands with a host : guest sensing array. Chem Sci 2024; 15:1885-1893. [PMID: 38303931 PMCID: PMC10829040 DOI: 10.1039/d3sc06087j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 12/30/2023] [Indexed: 02/03/2024] Open
Abstract
An indirect competitive binding mechanism can be exploited to allow a combination of cationic fluorophores and water-soluble synthetic receptors to selectively recognize and discriminate peptide strands containing a single isomeric residue in the backbone. Peptide isomerization occurs in long-lived proteins and has been linked with diseases such as Alzheimer's, cataracts and cancer, so isomers are valuable yet underexplored targets for selective recognition. Planar cationic fluorophores can selectively bind hydrophobic, Trp-containing peptide strands in solution, and when paired with receptors that provide a competitive host for the fluorophore, can form a differential sensing array that enables selective discrimination of peptide isomers. Residue variations such as D- and L-Asp, D- and L-isoAsp, D-Ser and D-Glu can all be recognized, simply by their effects on the folded structure of the flexible peptide. Molecular dynamics simulations were applied to determine the most favorable conformation of the peptide : fluorophore conjugate, indicating that favorable π-stacking with internal tryptophan residues in a folded binding pocket enables micromolar binding affinity.
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Affiliation(s)
- Junyi Chen
- Environmental Toxicology Graduate Program, University of California-Riverside Riverside CA 92521 USA
| | - Parisa Fasihianifard
- Department of Chemistry, University of California-Riverside Riverside CA 92521 USA
| | - Alexie Andrea P Raz
- Department of Chemistry, University of California-Riverside Riverside CA 92521 USA
| | - Briana L Hickey
- Department of Chemistry, University of California-Riverside Riverside CA 92521 USA
| | - Jose L Moreno
- Department of Chemistry, University of California-Riverside Riverside CA 92521 USA
| | - Chia-En A Chang
- Department of Chemistry, University of California-Riverside Riverside CA 92521 USA
| | - Richard J Hooley
- Department of Chemistry, University of California-Riverside Riverside CA 92521 USA
- Environmental Toxicology Graduate Program, University of California-Riverside Riverside CA 92521 USA
| | - Wenwan Zhong
- Department of Chemistry, University of California-Riverside Riverside CA 92521 USA
- Environmental Toxicology Graduate Program, University of California-Riverside Riverside CA 92521 USA
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2
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Chen YC, Wu HY, Lin LC, Chang CW, Liao PC. Characterizing the D-Amino Acid Position in Peptide Epimers by Using Higher-Energy Collisional Dissociation Tandem Mass Spectrometry: A Case Study of Liraglutide. Int J Mol Sci 2024; 25:1379. [PMID: 38338662 PMCID: PMC10855602 DOI: 10.3390/ijms25031379] [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: 12/08/2023] [Revised: 01/19/2024] [Accepted: 01/20/2024] [Indexed: 02/12/2024] Open
Abstract
D-amino acid-containing peptides (DAACPs) occur in biological and artificial environments. Since the importance of DAACPs has been recognized, various mass spectrometry-based analytical approaches have been developed. However, the capability of higher-energy collisional dissociation (HCD) fragmentation to characterize DAACP sites has not been evaluated. In this study, we compared the normalized spectra intensity under different conditions of HCD and used liraglutide along with its DAACPs as examples. Our results indicated that the difference in the intensity of y ions between DAACPs and all-L liraglutide could not only distinguish them but also localize the sites of D-amino acids in the DAACPs. Our data demonstrate the potential of using HCD for the site characterization of DAACPs, which may have great impact in biological studies and peptide drug development.
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Affiliation(s)
- Yuan-Chih Chen
- Department of Environmental and Occupational Health, College of Medicine, National Cheng Kung University, Tainan 704, Taiwan
| | - Hsin-Yi Wu
- Instrumentation Center, National Taiwan University, Taipei 106, Taiwan
| | | | - Chih-Wei Chang
- Department of Environmental and Occupational Health, College of Medicine, National Cheng Kung University, Tainan 704, Taiwan
| | - Pao-Chi Liao
- Department of Environmental and Occupational Health, College of Medicine, National Cheng Kung University, Tainan 704, Taiwan
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3
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Abdulbagi M, Di B, Li B. Resolving D-Amino Acid Containing Peptides Using Ion Mobility-Mass Spectrometry: Challenges and Recent Developments. Crit Rev Anal Chem 2023:1-10. [PMID: 37975700 DOI: 10.1080/10408347.2023.2282510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
Peptides and proteins having D-amino acids in their sequences are now believed to be widespread among different living organisms. Their significance is attributed to the diverse functions of these molecules, such as having a certain pathological implication or enhancing biological activity. Indeed, some peptide molecules with D-amino acids in their structure have already found their way to clinical use such as the antibacterial gramicidin and the antidiabetic nateglinide. Ion mobility mass spectrometry (IM-MS) added an additional dimension of separation as it depends on ions mobility in the space, which is dependent on their shapes, and the shape depends on the orientation of atoms. Thus, D-amino acids containing peptides (DAACPs) will have different mobility and collision cross-section values than those with L-amino acids. Eventually, this will lead to baseline separation of the two peptides. Additionally, ion mobility can precisely locate the position of D-amino acids by analyzing the difference in the arrival times of the fragment ions. The importance of DAACPs, as well as the difficulties in discovering them, were addressed in this review. Similarly, we emphasized how recent developments in IM-MS have improved their detection and analysis. Consequently, the LC-IM-MS/MS platform appears to be promising in isomeric mixture analysis.
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Affiliation(s)
- Mohamed Abdulbagi
- Center Key Laboratory on Protein Chemistry and Structural Biology, China Pharmaceutical University, Nanjing, China
| | - Bin Di
- Center Key Laboratory on Protein Chemistry and Structural Biology, China Pharmaceutical University, Nanjing, China
- Key Laboratory of Drug Quality Control and Pharmacovigilance, China Pharmaceutical University, Nanjing, China
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing, China
| | - Bo Li
- Center Key Laboratory on Protein Chemistry and Structural Biology, China Pharmaceutical University, Nanjing, China
- Key Laboratory of Drug Quality Control and Pharmacovigilance, China Pharmaceutical University, Nanjing, China
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing, China
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4
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Li G, Jeon CK, Ma M, Jia Y, Zheng Z, Delafield DG, Lu G, Romanova EV, Sweedler JV, Ruotolo BT, Li L. Site-specific chirality-conferred structural compaction differentially mediates the cytotoxicity of Aβ42. Chem Sci 2023; 14:5936-5944. [PMID: 37293657 PMCID: PMC10246695 DOI: 10.1039/d3sc00678f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 05/06/2023] [Indexed: 06/10/2023] Open
Abstract
Growing evidence supports the confident association between distinct amyloid beta (Aβ) isoforms and Alzheimer's Disease (AD) pathogenesis. As such, critical investigations seeking to uncover the translational factors contributing to Aβ toxicity represent a venture of significant value. Herein, we comprehensively assess full-length Aβ42 stereochemistry, with a specific focus on models that consider naturally-occurring isomerization of Asp and Ser residues. We customize various forms of d-isomerized Aβ as natural mimics, ranging from fragments containing a single d residue to full length Aβ42 that includes multiple isomerized residues, systematically evaluating their cytotoxicity against a neuronal cell line. Combining multidimensional ion mobility-mass spectrometry experimental data with replica exchange molecular dynamics simulations, we confirm that co-d-epimerization at Asp and Ser residues within Aβ42 in both N-terminal and core regions effectively reduces its cytotoxicity. We provide evidence that this rescuing effect is associated with the differential and domain-specific compaction and remodeling of Aβ42 secondary structure.
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Affiliation(s)
- Gongyu Li
- State Key Laboratory of Pharmaceutical Chemical Biology, Research Center for Analytical Science and Tianjin Key Laboratory of Biosensing and Molecular Recognition, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University Tianjin 300071 China
- Haihe Laboratory of Sustainable Chemical Transformations Tianjin 300192 China
| | - Chae Kyung Jeon
- Department of Chemistry, University of Michigan Ann Arbor MI 48109 USA
| | - Min Ma
- School of Pharmacy and Department of Chemistry, University of Wisconsin-Madison 777 Highland Ave. Madison WI 53705 USA
| | - Yifei Jia
- State Key Laboratory of Pharmaceutical Chemical Biology, Research Center for Analytical Science and Tianjin Key Laboratory of Biosensing and Molecular Recognition, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University Tianjin 300071 China
| | - Zhen Zheng
- School of Pharmacy, Tianjin Medical University Tianjin 300070 China
| | - Daniel G Delafield
- School of Pharmacy and Department of Chemistry, University of Wisconsin-Madison 777 Highland Ave. Madison WI 53705 USA
| | - Gaoyuan Lu
- School of Pharmacy and Department of Chemistry, University of Wisconsin-Madison 777 Highland Ave. Madison WI 53705 USA
| | - Elena V Romanova
- Department of Chemistry and The Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign Urbana Illinois 61801 USA
| | - Jonathan V Sweedler
- Department of Chemistry and The Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign Urbana Illinois 61801 USA
| | - Brandon T Ruotolo
- Department of Chemistry, University of Michigan Ann Arbor MI 48109 USA
| | - Lingjun Li
- School of Pharmacy and Department of Chemistry, University of Wisconsin-Madison 777 Highland Ave. Madison WI 53705 USA
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5
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Phetsanthad A, Vu NQ, Yu Q, Buchberger AR, Chen Z, Keller C, Li L. Recent advances in mass spectrometry analysis of neuropeptides. MASS SPECTROMETRY REVIEWS 2023; 42:706-750. [PMID: 34558119 PMCID: PMC9067165 DOI: 10.1002/mas.21734] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 08/22/2021] [Accepted: 08/28/2021] [Indexed: 05/08/2023]
Abstract
Due to their involvement in numerous biochemical pathways, neuropeptides have been the focus of many recent research studies. Unfortunately, classic analytical methods, such as western blots and enzyme-linked immunosorbent assays, are extremely limited in terms of global investigations, leading researchers to search for more advanced techniques capable of probing the entire neuropeptidome of an organism. With recent technological advances, mass spectrometry (MS) has provided methodology to gain global knowledge of a neuropeptidome on a spatial, temporal, and quantitative level. This review will cover key considerations for the analysis of neuropeptides by MS, including sample preparation strategies, instrumental advances for identification, structural characterization, and imaging; insightful functional studies; and newly developed absolute and relative quantitation strategies. While many discoveries have been made with MS, the methodology is still in its infancy. Many of the current challenges and areas that need development will also be highlighted in this review.
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Affiliation(s)
- Ashley Phetsanthad
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Nhu Q. Vu
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Qing Yu
- School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53705, USA
| | - Amanda R. Buchberger
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Zhengwei Chen
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Caitlin Keller
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
- School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53705, USA
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6
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Liu L, Wang Z, Zhang Q, Mei Y, Li L, Liu H, Wang Z, Yang L. Ion Mobility Mass Spectrometry for the Separation and Characterization of Small Molecules. Anal Chem 2023; 95:134-151. [PMID: 36625109 DOI: 10.1021/acs.analchem.2c02866] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Longchan Liu
- The MOE Key Laboratory of Standardization of Chinese Medicines, The SATCM Key Laboratory of New Resources and Quality Evaluation of Chinese Medicines, The Shanghai Key Laboratory for Compound Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai201203, China
| | - Ziying Wang
- The MOE Key Laboratory of Standardization of Chinese Medicines, The SATCM Key Laboratory of New Resources and Quality Evaluation of Chinese Medicines, The Shanghai Key Laboratory for Compound Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai201203, China
| | - Qian Zhang
- The MOE Key Laboratory of Standardization of Chinese Medicines, The SATCM Key Laboratory of New Resources and Quality Evaluation of Chinese Medicines, The Shanghai Key Laboratory for Compound Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai201203, China
| | - Yuqi Mei
- The MOE Key Laboratory of Standardization of Chinese Medicines, The SATCM Key Laboratory of New Resources and Quality Evaluation of Chinese Medicines, The Shanghai Key Laboratory for Compound Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai201203, China
| | - Linnan Li
- The MOE Key Laboratory of Standardization of Chinese Medicines, The SATCM Key Laboratory of New Resources and Quality Evaluation of Chinese Medicines, The Shanghai Key Laboratory for Compound Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai201203, China
| | - Huwei Liu
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing100871, China
| | - Zhengtao Wang
- The MOE Key Laboratory of Standardization of Chinese Medicines, The SATCM Key Laboratory of New Resources and Quality Evaluation of Chinese Medicines, The Shanghai Key Laboratory for Compound Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai201203, China
| | - Li Yang
- The MOE Key Laboratory of Standardization of Chinese Medicines, The SATCM Key Laboratory of New Resources and Quality Evaluation of Chinese Medicines, The Shanghai Key Laboratory for Compound Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai201203, China.,Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai201203, China
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7
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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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8
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High-end ion mobility mass spectrometry: A current review of analytical capacity in omics applications and structural investigations. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116761] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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9
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Abdulbagi M, Wang L, Siddig O, Di B, Li B. D-Amino Acids and D-Amino Acid-Containing Peptides: Potential Disease Biomarkers and Therapeutic Targets? Biomolecules 2021; 11:1716. [PMID: 34827714 PMCID: PMC8615943 DOI: 10.3390/biom11111716] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 10/26/2021] [Accepted: 10/27/2021] [Indexed: 12/17/2022] Open
Abstract
In nature, amino acids are found in two forms, L and D enantiomers, except for glycine which does not have a chiral center. The change of one form to the other will lead to a change in the primary structure of proteins and hence may affect the function and biological activity of proteins. Indeed, several D-amino acid-containing peptides (DAACPs) were isolated from patients with cataracts, Alzheimer's and other diseases. Additionally, significant levels of free D-amino acids were found in several diseases, reflecting the disease conditions. Studying the molecular mechanisms of the DAACPs formation and the alteration in D-amino acids metabolism will certainly assist in understanding these diseases and finding new biomarkers and drug targets. In this review, the presence of DAACPs and free D-amino acids and their links with disease development and progress are summarized. Similarly, we highlight some recent advances in analytical techniques that led to improvement in the discovery and analysis of DAACPs and D-amino acids.
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Affiliation(s)
- Mohamed Abdulbagi
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing 210009, China; (M.A.); (L.W.); (O.S.)
| | - Liya Wang
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing 210009, China; (M.A.); (L.W.); (O.S.)
| | - Orwa Siddig
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing 210009, China; (M.A.); (L.W.); (O.S.)
| | - Bin Di
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing 210009, China; (M.A.); (L.W.); (O.S.)
- Center Key Laboratory on Protein Chemistry and Structural Biology, China Pharmaceutical University, Nanjing 210009, China
- MOE Key Laboratory of Drug Quality Control and Pharmacovigilance, China Pharmaceutical University, Nanjing 210009, China
| | - Bo Li
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing 210009, China; (M.A.); (L.W.); (O.S.)
- Center Key Laboratory on Protein Chemistry and Structural Biology, China Pharmaceutical University, Nanjing 210009, China
- MOE Key Laboratory of Drug Quality Control and Pharmacovigilance, China Pharmaceutical University, Nanjing 210009, China
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10
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Lian Z, Wang N, Tian Y, Huang L. Characterization of Synthetic Peptide Therapeutics Using Liquid Chromatography-Mass Spectrometry: Challenges, Solutions, Pitfalls, and Future Perspectives. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:1852-1860. [PMID: 34110145 DOI: 10.1021/jasms.0c00479] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Synthetic peptides represent an important and expanding class of therapeutics. Despite having a relatively small size as compared to monoclonal antibodies and other proteins, synthetic peptides are subject to many complex structural modifications originating from the starting materials, manufacturing process, and storage conditions. Although mass spectrometry has been increasingly used to characterize impurities of synthetic peptides, systematic review of this field is scarce. In this paper, an overview of the impurities in synthetic peptide therapeutics is provided in the context of how the knowledge from detailed characterization of the impurities using liquid chromatography-mass spectrometry (LC-MS) can be used to develop the manufacturing process and control strategy for synthetic peptide therapeutics following the critical quality attribute (CQA)-driven and risk-based approach. The thresholds for identifying and controlling the impurities are discussed based on currently available regulatory guidance. Specific LC-MS techniques for identification of various types of impurities based on their structural characteristics are discussed with the focus on structural isomers and stereoisomers (i.e., peptide epimers). Absolute and relative quantitation methods for the peptide impurities are critiqued. Potential pitfalls in characterization of synthetic peptide therapeutics using LC-MS are discussed. Finally, a systematic LC-MS workflow for characterizing the impurities in synthetic peptide therapeutics is proposed, and future perspectives on applying emerging LC-MS techniques to address the remaining challenges in the development of synthetic peptide therapeutics are presented.
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Affiliation(s)
- Zhirui Lian
- Bioproducts Research and Development, Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana 46285, United States
| | - Ning Wang
- Bioproducts Research and Development, Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana 46285, United States
| | - Yuwei Tian
- Bioproducts Research and Development, Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana 46285, United States
| | - Lihua Huang
- Bioproducts Research and Development, Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana 46285, United States
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11
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Miles HN, Delafield DG, Li L. Recent Developments and Applications of Quantitative Proteomics Strategies for High-Throughput Biomolecular Analyses in Cancer Research. RSC Chem Biol 2021; 4:1050-1072. [PMID: 34430874 PMCID: PMC8341969 DOI: 10.1039/d1cb00039j] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 05/18/2021] [Indexed: 12/28/2022] Open
Abstract
Innovations in medical technology and dedicated focus from the scientific community have inspired numerous treatment strategies for benign and invasive cancers. While these improvements often lend themselves to more positive prognoses and greater patient longevity, means for early detection and severity stratification have failed to keep pace. Detection and validation of cancer-specific biomarkers hinges on the ability to identify subtype-specific phenotypic and proteomic alterations and the systematic screening of diverse patient groups. For this reason, clinical and scientific research settings rely on high throughput and high sensitivity mass spectrometry methods to discover and quantify unique molecular perturbations in cancer patients. Discussed within is an overview of quantitative proteomics strategies and a summary of recent applications that enable revealing potential biomarkers and treatment targets in prostate, ovarian, breast, and pancreatic cancer in a high throughput manner.
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Affiliation(s)
- Hannah N. Miles
- School of Pharmacy, University of Wisconsin-Madison777 Highland AvenueMadisonWI53705-2222USA+1-608-262-5345+1-608-265-8491
| | | | - Lingjun Li
- School of Pharmacy, University of Wisconsin-Madison777 Highland AvenueMadisonWI53705-2222USA+1-608-262-5345+1-608-265-8491
- Department of Chemistry, University of Wisconsin-MadisonMadisonWI53706USA
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12
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Sauer CS, Phetsanthad A, Riusech OL, Li L. Developing mass spectrometry for the quantitative analysis of neuropeptides. Expert Rev Proteomics 2021; 18:607-621. [PMID: 34375152 PMCID: PMC8522511 DOI: 10.1080/14789450.2021.1967146] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 08/09/2021] [Indexed: 12/22/2022]
Abstract
INTRODUCTION Neuropeptides are signaling molecules originating in the neuroendocrine system that can act as neurotransmitters and hormones in many biochemical processes. Their exact function is difficult to characterize, however, due to dependence on concentration, post-translational modifications, and the presence of other comodulating neuropeptides. Mass spectrometry enables sensitive, accurate, and global peptidomic analyses that can profile neuropeptide expression changes to understand their roles in many biological problems, such as neurodegenerative disorders and metabolic function. AREAS COVERED We provide a brief overview of the fundamentals of neuropeptidomic research, limitations of existing methods, and recent progress in the field. This review is focused on developments in mass spectrometry and encompasses labeling strategies, post-translational modification analysis, mass spectrometry imaging, and integrated multi-omic workflows, with discussion emphasizing quantitative advancements. EXPERT OPINION Neuropeptidomics is critical for future clinical research with impacts in biomarker discovery, receptor identification, and drug design. While advancements are being made to improve sensitivity and accuracy, there is still room for improvement. Better quantitative strategies are required for clinical analyses, and these methods also need to be amenable to mass spectrometry imaging, post-translational modification analysis, and multi-omics to facilitate understanding and future treatment of many diseases.
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Affiliation(s)
- Christopher S. Sauer
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Ashley Phetsanthad
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Olga L. Riusech
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
- School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53075, USA
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13
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Mast DH, Liao HW, Romanova EV, Sweedler JV. Analysis of Peptide Stereochemistry in Single Cells by Capillary Electrophoresis-Trapped Ion Mobility Spectrometry Mass Spectrometry. Anal Chem 2021; 93:6205-6213. [PMID: 33825437 DOI: 10.1021/acs.analchem.1c00445] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Single cell analysis strives to probe molecular heterogeneity in morphologically similar cell populations through quantitative or qualitative measurements of genetic, proteomic, or metabolic products. Here, we applied mass analysis of single neurons to investigate cell-cell signaling peptides. The multiplicity of endogenous cell-cell signaling peptides is a common source of chemical diversity among cell populations. Certain peptides can undergo post-translational isomerization of select residues, which has important physiological consequences. The limited number of single cell analysis techniques that are sensitive to peptide stereochemistry make it challenging to study isomerization at the individual cell level. We performed capillary electrophoresis (CE) with mass spectrometry (MS) detection to characterize the peptide content of single cells. Using complementary trapped ion mobility spectrometry (TIMS) separations, we measured the stereochemical configurations of three neuropeptide gene products derived from the pleurin precursor in individual neurons (N = 3) isolated from the central nervous system of Aplysia californica. An analysis of the resultant mobility profiles indicated >98% of the detectable pleurin-derived peptides exist as the nonisomerized, all-l forms in individual neuron cell bodies. However, we observed 44% of the Plrn2 peptide from the pleurin precursor was present as the isomerized, d-residue-containing form in the nerve tissue. These findings demonstrate an unusual distribution of isomerized peptides in A. californica and establish CE-TIMS MS as a powerful analytical tool for investigating peptide stereochemistry at the single cell level.
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Affiliation(s)
- David H Mast
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,The Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Hsiao-Wei Liao
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Faculty of Pharmacy, National Yang-Ming University, No.155, Sec.2, Linong Street, Taipei 11221, Taiwan
| | - Elena V Romanova
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,The Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Jonathan V Sweedler
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,The Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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14
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Mast DH, Checco JW, Sweedler JV. Advancing d-amino acid-containing peptide discovery in the metazoan. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1869:140553. [PMID: 33002629 DOI: 10.1016/j.bbapap.2020.140553] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 09/01/2020] [Accepted: 09/25/2020] [Indexed: 12/12/2022]
Abstract
The discovery of enzyme-derived d-amino acid-containing peptides (DAACPs) that have physiological importance in the metazoan challenges previous assumptions about the homochirality of animal proteins while simultaneously revealing new analytical challenges in the structural and functional characterization of peptides. Most known DAACPs have been identified though laborious activity-guided purification studies or by homology to previously identified DAACPs. Peptide characterization experiments are increasingly dominated by high throughput mass spectrometry-based peptidomics, with stereochemistry rarely considered due to the technical challenges of identifying l/d isomerization. This review discusses the prevalence of enzyme-derived DAACPs among animals and the physiological consequences of peptide isomerization. Also highlighted are the analytical methods that have been applied for structural characterization/discovery of DAACPs, including results of several recent studies using non-targeted discovery methods for revealing novel DAACPs, strongly suggesting that more DAACPs remain to be uncovered.
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Affiliation(s)
- David H Mast
- Department of Chemistry and the Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - James W Checco
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, United States.
| | - Jonathan V Sweedler
- Department of Chemistry and the Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States.
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15
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Ying Y, Li H. Recent progress in the analysis of protein deamidation using mass spectrometry. Methods 2020; 200:42-57. [PMID: 32544593 DOI: 10.1016/j.ymeth.2020.06.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 05/15/2020] [Accepted: 06/11/2020] [Indexed: 02/06/2023] Open
Abstract
Deamidation is a nonenzymatic and spontaneous posttranslational modification (PTM) that introduces changes in both structure and charge of proteins, strongly associated with aging proteome instability and degenerative diseases. Deamidation is also a common PTM occurring in biopharmaceutical proteins, representing a major cause of degradation. Therefore, characterization of deamidation alongside its inter-related modifications, isomerization and racemization, is critically important to understand their roles in protein stability and diseases. Mass spectrometry (MS) has become an indispensable tool in site-specific identification of PTMs for proteomics and structural studies. In this review, we focus on the recent advances of MS analysis in protein deamidation. In particular, we provide an update on sample preparation, chromatographic separation, and MS technologies at multi-level scales, for accurate and reliable characterization of protein deamidation in both simple and complex biological samples, yielding important new insight on how deamidation together with isomerization and racemization occurs. These technological progresses will lead to a better understanding of how deamidation contributes to the pathology of aging and other degenerative diseases and the development of biopharmaceutical drugs.
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Affiliation(s)
- Yujia Ying
- School of Pharmaceutical Sciences, University of Sun Yat-sen University, No.132 Wai Huan Dong Lu, Guangzhou Higher Education Mega Center, Guangzhou 510006, China; School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, China
| | - Huilin Li
- School of Pharmaceutical Sciences, University of Sun Yat-sen University, No.132 Wai Huan Dong Lu, Guangzhou Higher Education Mega Center, Guangzhou 510006, China; Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, China.
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16
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Mast DH, Checco JW, Sweedler JV. Differential Post-Translational Amino Acid Isomerization Found among Neuropeptides in Aplysia californica. ACS Chem Biol 2020; 15:272-281. [PMID: 31877009 DOI: 10.1021/acschembio.9b00910] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
d-Amino acid-containing peptides (DAACPs) make up a class of post-translationally modified peptides in animals that play important roles as cell-to-cell signaling molecules. Despite the functional importance of l- to d-residue isomerization, little is known about its prevalence, mostly due to difficulties associated with detecting differences in peptide stereochemistry. Prior efforts to discover DAACPs have been largely focused on pursuing peptides based on homology to known DAACPs or DAACP-encoding precursors. Here, we used a combination of enzymatic screening, mass spectrometry, and chromatographic analysis to identify novel DAACPs in the central nervous system (CNS) of Aplysia californica. We identified five new DAACPs from the pleurin precursor and three DAACPs from previously uncharacterized proteins. In addition, two peptides from the pleurin precursor, Plrn2 and Plrn3, exist as DAACPs with the d-residue found at position 2 or 3. These differentially modified forms of Plrn2 and Plrn3 are located in specific regions of the animal's CNS. Plrn2 and Plrn3 appear to be the first animal DAACPs in which the d-residue is found at more than one position, and this suggests that l- to d-residue isomerization may be a more variable/dynamic modification than previously thought. Overall, this study demonstrates the utility of nontargeted DAACP discovery approaches for identifying new DAACPs and demonstrates that isomerization is prevalent throughout the CNS of A. californica.
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Affiliation(s)
- David H. Mast
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - James W. Checco
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Jonathan V. Sweedler
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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17
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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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