1
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Deigin V, Linkova N, Vinogradova J, Vinogradov D, Polyakova V, Medvedev D, Krasichkov A, Volpina O. The First Reciprocal Activities of Chiral Peptide Pharmaceuticals: Thymogen and Thymodepressin, as Examples. Int J Mol Sci 2024; 25:5042. [PMID: 38732260 PMCID: PMC11084461 DOI: 10.3390/ijms25095042] [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: 03/15/2024] [Revised: 05/03/2024] [Accepted: 05/03/2024] [Indexed: 05/13/2024] Open
Abstract
Peptides show high promise in the targeting and intracellular delivery of next-generation biotherapeutics. The main limitation is peptides' susceptibility to proteolysis in biological systems. Numerous strategies have been developed to overcome this challenge by chemically enhancing the resistance to proteolysis. In nature, amino acids, except glycine, are found in L- and D-enantiomers. The change from one form to the other will change the primary structure of polypeptides and proteins and may affect their function and biological activity. Given the inherent chiral nature of biological systems and their high enantiomeric selectivity, there is rising interest in manipulating the chirality of polypeptides to enhance their biomolecular interactions. In this review, we discuss the first examples of up-and-down homeostasis regulation by two enantiomeric drugs: immunostimulant Thymogen (L-Glu-L-Trp) and immunosuppressor Thymodepressin (D-Glu(D-Trp)). This study shows the perspective of exploring chirality to remove the chiral wall between L- and D-biomolecules. The selected clinical result will be discussed.
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Affiliation(s)
- Vladislav Deigin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya St., 16/10, Moscow 117997, Russia; (V.D.); (O.V.)
| | - Natalia Linkova
- St. Petersburg Research Institute of Phthisiopulmonology, Ligovskii Prospect, 2-4, St. Petersburg 191036, Russia;
- St. Petersburg Institute of Bioregulation and Gerontology, 3 Dynamo Ave., St. Petersburg 197110, Russia
| | - Julia Vinogradova
- The Department of Hospital Therapy No. 2, I.M. Sechenov First Moscow State Medical University, 8 Trubetskaya Str., Building 2, Moscow 119991, Russia; (J.V.); (D.V.)
| | - Dmitrii Vinogradov
- The Department of Hospital Therapy No. 2, I.M. Sechenov First Moscow State Medical University, 8 Trubetskaya Str., Building 2, Moscow 119991, Russia; (J.V.); (D.V.)
| | - Victoria Polyakova
- St. Petersburg Research Institute of Phthisiopulmonology, Ligovskii Prospect, 2-4, St. Petersburg 191036, Russia;
- St. Petersburg Institute of Bioregulation and Gerontology, 3 Dynamo Ave., St. Petersburg 197110, Russia
| | - Dmitrii Medvedev
- St. Petersburg Institute of Bioregulation and Gerontology, 3 Dynamo Ave., St. Petersburg 197110, Russia
- The Department of Social Rehabilitation and Occupational Therapy of the St. Petersburg Medical and Social Institute, Kondratievsky St., 72A, St. Petersburg 195271, Russia
| | - Alexander Krasichkov
- Department of Radio Engineering Systems, Saint Petersburg Electrotechnical University ‘LETI’, St. Petersburg 197376, Russia
| | - Olga Volpina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya St., 16/10, Moscow 117997, Russia; (V.D.); (O.V.)
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2
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Zhang M, Rottschäfer V, C M de Lange E. The potential impact of CYP and UGT drug-metabolizing enzymes on brain target site drug exposure. Drug Metab Rev 2024; 56:1-30. [PMID: 38126313 DOI: 10.1080/03602532.2023.2297154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 12/15/2023] [Indexed: 12/23/2023]
Abstract
Drug metabolism is one of the critical determinants of drug disposition throughout the body. While traditionally associated with the liver, recent research has unveiled the presence and functional significance of drug-metabolizing enzymes (DMEs) within the brain. Specifically, cytochrome P-450 enzymes (CYPs) and UDP-glucuronosyltransferases (UGTs) enzymes have emerged as key players in drug biotransformation within the central nervous system (CNS). This comprehensive review explores the cellular and subcellular distribution of CYPs and UGTs within the CNS, emphasizing regional expression and contrasting profiles between the liver and brain, humans and rats. Moreover, we discuss the impact of species and sex differences on CYPs and UGTs within the CNS. This review also provides an overview of methodologies for identifying and quantifying enzyme activities in the brain. Additionally, we present factors influencing CYPs and UGTs activities in the brain, including genetic polymorphisms, physiological variables, pathophysiological conditions, and environmental factors. Examples of CYP- and UGT-mediated drug metabolism within the brain are presented at the end, illustrating the pivotal role of these enzymes in drug therapy and potential toxicity. In conclusion, this review enhances our understanding of drug metabolism's significance in the brain, with a specific focus on CYPs and UGTs. Insights into the expression, activity, and influential factors of these enzymes within the CNS have crucial implications for drug development, the design of safe drug treatment strategies, and the comprehension of drug actions within the CNS. To that end, CNS pharmacokinetic (PK) models can be improved to further advance drug development and personalized therapy.
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Affiliation(s)
- Mengxu Zhang
- Division of Systems Pharmacology and Pharmacy, Predictive Pharmacology Group, Leiden Academic Centre of Drug Research, Leiden University, Leiden, The Netherlands
| | - Vivi Rottschäfer
- Mathematical Institute, Leiden University, Leiden, The Netherlands
- Korteweg-de Vries Institute for Mathematics, University of Amsterdam, Amsterdam, The Netherlands
| | - Elizabeth C M de Lange
- Division of Systems Pharmacology and Pharmacy, Predictive Pharmacology Group, Leiden Academic Centre of Drug Research, Leiden University, Leiden, The Netherlands
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3
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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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4
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Okyem S, Romanova EV, Tai HC, Checco JW, Sweedler JV. Nontargeted Identification of D-Amino Acid-Containing Peptides Through Enzymatic Screening, Chiral Amino Acid Analysis, and LC-MS. Methods Mol Biol 2024; 2758:227-240. [PMID: 38549017 PMCID: PMC11034756 DOI: 10.1007/978-1-0716-3646-6_12] [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: 04/02/2024]
Abstract
D-amino acid-containing peptides (DAACPs) in animals are a class of bioactive molecules formed via the posttranslational modification of peptides consisting of all-L-amino acid residues. Amino acid residue isomerization greatly impacts the function of the resulting DAACP. However, because isomerization does not change the peptide's mass, this modification is difficult to detect by most mass spectrometry-based peptidomic approaches. Here we describe a method for the identification of DAACPs that can be used to systematically survey peptides extracted from a tissue sample in a nontargeted manner.
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Affiliation(s)
- Samuel Okyem
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Elena V Romanova
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Hua-Chia Tai
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - James W Checco
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, USA
- The Nebraska Center for Integrated Biomolecular Communication (NCIBC), University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Jonathan V Sweedler
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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5
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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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6
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Sivanesan I, Gopal J, Hasan N, Muthu M. A systematic assessment of matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) application for rapid identification of pathogenic microbes that affect food crops: delivered and future deliverables. RSC Adv 2023; 13:17297-17314. [PMID: 37304772 PMCID: PMC10251190 DOI: 10.1039/d3ra01633a] [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: 03/13/2023] [Accepted: 05/20/2023] [Indexed: 06/13/2023] Open
Abstract
MALDI-TOF MS has decades of experience in the detection and identification of microbial pathogens. This has now become a valuable analytical tool when it comes to the identification and detection of clinical microbial pathogens. This review gives a brief synopsis of what has been achieved using MALDI-TOF MS in clinical microbiology. The major focus, however, is on summarizing and highlighting the effectiveness of MALDI-TOF MS as a novel tool for rapid identification of food crop microbial pathogens. The methods used and the sample preparation methodologies reported thus far have been highlighted and the challenges and gaps and recommendations for fine tuning the technique have been put forth. In an era where anything close to the health and welfare of humanity has been considered as the top priority, this review pitches on one such relevant research topics.
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Affiliation(s)
- Iyyakkannu Sivanesan
- Department of Bioresources and Food Science, Institute of Natural Science and Agriculture, Konkuk University 1 Hwayang-dong, Gwangjin-gu Seoul 05029 Korea
| | - Judy Gopal
- Department of Research and Innovation, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences (SIMATS) Thandalam Chennai 602105 Tamil Nadu India +91 44 2681 1009 +91 44 66726677
| | - Nazim Hasan
- Department of Chemistry, Faculty of Science, Jazan University P.O. Box 114 Jazan Saudi Arabia
| | - Manikandan Muthu
- Department of Research and Innovation, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences (SIMATS) Thandalam Chennai 602105 Tamil Nadu India +91 44 2681 1009 +91 44 66726677
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7
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Applications of MALDI-MS/MS-Based Proteomics in Biomedical Research. Molecules 2022; 27:molecules27196196. [PMID: 36234736 PMCID: PMC9570737 DOI: 10.3390/molecules27196196] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/14/2022] [Accepted: 09/15/2022] [Indexed: 11/22/2022] Open
Abstract
Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) is one of the most widely used techniques in proteomics to achieve structural identification and characterization of proteins and peptides, including their variety of proteoforms due to post-translational modifications (PTMs) or protein–protein interactions (PPIs). MALDI-MS and MALDI tandem mass spectrometry (MS/MS) have been developed as analytical techniques to study small and large molecules, offering picomole to femtomole sensitivity and enabling the direct analysis of biological samples, such as biofluids, solid tissues, tissue/cell homogenates, and cell culture lysates, with a minimized procedure of sample preparation. In the last decades, structural identification of peptides and proteins achieved by MALDI-MS/MS helped researchers and clinicians to decipher molecular function, biological process, cellular component, and related pathways of the gene products as well as their involvement in pathogenesis of diseases. In this review, we highlight the applications of MALDI ionization source and tandem approaches for MS for analyzing biomedical relevant peptides and proteins. Furthermore, one of the most relevant applications of MALDI-MS/MS is to provide “molecular pictures”, which offer in situ information about molecular weight proteins without labeling of potential targets. Histology-directed MALDI-mass spectrometry imaging (MSI) uses MALDI-ToF/ToF or other MALDI tandem mass spectrometers for accurate sequence analysis of peptide biomarkers and biological active compounds directly in tissues, to assure complementary and essential spatial data compared with those obtained by LC-ESI-MS/MS technique.
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8
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Chirality in Organic and Mineral Systems: A Review of Reactivity and Alteration Processes Relevant to Prebiotic Chemistry and Life Detection Missions. Symmetry (Basel) 2022. [DOI: 10.3390/sym14030460] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Chirality is a central feature in the evolution of biological systems, but the reason for biology’s strong preference for specific chiralities of amino acids, sugars, and other molecules remains a controversial and unanswered question in origins of life research. Biological polymers tend toward homochiral systems, which favor the incorporation of a single enantiomer (molecules with a specific chiral configuration) over the other. There have been numerous investigations into the processes that preferentially enrich one enantiomer to understand the evolution of an early, racemic, prebiotic organic world. Chirality can also be a property of minerals; their interaction with chiral organics is important for assessing how post-depositional alteration processes could affect the stereochemical configuration of simple and complex organic molecules. In this paper, we review the properties of organic compounds and minerals as well as the physical, chemical, and geological processes that affect organic and mineral chirality during the preservation and detection of organic compounds. We provide perspectives and discussions on the reactions and analytical techniques that can be performed in the laboratory, and comment on the state of knowledge of flight-capable technologies in current and future planetary missions, with a focus on organics analysis and life detection.
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9
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Yussif BM, Checco JW. Evaluation of endogenous peptide stereochemistry using liquid chromatography-mass spectrometry-based spiking experiments. Methods Enzymol 2022; 663:205-234. [DOI: 10.1016/bs.mie.2021.10.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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10
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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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11
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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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12
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Moyer TB, Parsley NC, Sadecki PW, Schug WJ, Hicks LM. Leveraging orthogonal mass spectrometry based strategies for comprehensive sequencing and characterization of ribosomal antimicrobial peptide natural products. Nat Prod Rep 2021; 38:489-509. [PMID: 32929442 PMCID: PMC7956910 DOI: 10.1039/d0np00046a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Covering: Up to July 2020Ribosomal antimicrobial peptide (AMP) natural products, also known as ribosomally synthesized and post-translationally modified peptides (RiPPs) or host defense peptides, demonstrate potent bioactivities and impressive complexity that complicate molecular and biological characterization. Tandem mass spectrometry (MS) has rapidly accelerated bioactive peptide sequencing efforts, yet standard workflows insufficiently address intrinsic AMP diversity. Herein, orthogonal approaches to accelerate comprehensive and accurate molecular characterization without the need for prior isolation are reviewed. Chemical derivatization, proteolysis (enzymatic and chemical cleavage), multistage MS fragmentation, and separation (liquid chromatography and ion mobility) strategies can provide complementary amino acid composition and post-translational modification data to constrain sequence solutions. Examination of two complex case studies, gomesin and styelin D, highlights the practical implementation of the proposed approaches. Finally, we emphasize the importance of heterogeneous AMP peptidoforms that confer varying biological function, an area that warrants significant further development.
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Affiliation(s)
- Tessa B Moyer
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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13
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Sato H, Shimizu M, Watanabe K, Yoshida J, Kawamura I, Koshoubu J. Multidimensional Vibrational Circular Dichroism Apparatus Equipped with Quantum Cascade Laser and Its Use for Investigating Some Peptide Systems Containing d-Amino Acids. Anal Chem 2021; 93:2742-2748. [DOI: 10.1021/acs.analchem.0c02990] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Hisako Sato
- Graduate School of Science and Engineering, Ehime University, Matsuyama 790-8577, Japan
| | - Masaru Shimizu
- JASCO Corporation, Ishikawa 2967-5, Hachioji, Tokyo 192-8537, Japan
| | - Keisuke Watanabe
- JASCO Corporation, Ishikawa 2967-5, Hachioji, Tokyo 192-8537, Japan
| | - Jun Yoshida
- Department of Chemistry, School of Science, Kitasato University, Kitasato 1-15-1, Sagamihara 252-0373, Japan
| | - Izuru Kawamura
- Graduate School of Engineering Science, Yokohama National University, Hodogaya-ku, Yokohama 240-8501, Japan
| | - Jun Koshoubu
- JASCO Corporation, Ishikawa 2967-5, Hachioji, Tokyo 192-8537, Japan
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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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Jimenez EC. D-Amino Acids in Peptides from Animals, Including Human: Occurrence, Structure, Bioactivity and Pharmacology. Curr Protein Pept Sci 2020; 21:622-637. [PMID: 32338216 DOI: 10.2174/1389203721666200426233758] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 02/06/2020] [Accepted: 02/13/2020] [Indexed: 11/22/2022]
Abstract
All life forms typically possess homochirality, with rare exceptions. In the case of peptides and proteins, only L-amino acids are known to be encoded by genes. Nevertheless, D-amino acids have been identified in a variety of peptides, synthesized by animal cells. They include neuroexcitatory and neuroprotective peptides, cardioexcitatory peptides, hyperglycemic hormones, opioid peptides, antimicrobial peptides, natriuretic and defensin-like peptides, and fibrinopeptides. This article is a review of their occurrence, structure and bioactivity. It further explores the pharmacology and potential medical applications of some of the peptides.
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Affiliation(s)
- Elsie C Jimenez
- Department of Physical Sciences, College of Science, University of the Philippines Baguio, Baguio City 2600, Philippines
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16
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Separation of D-amino acid-containing peptide phenylseptin using 3,3'-phenyl-1,1'-binaphthyl-18-crown-6-ether columns. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1868:140429. [PMID: 32298805 DOI: 10.1016/j.bbapap.2020.140429] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 03/05/2020] [Accepted: 04/09/2020] [Indexed: 12/19/2022]
Abstract
Several D-amino acid-containing peptides (DAACPs) with antimicrobial, cardio-excitatory, or neuronal activities have been found in several species. Here, we demonstrated the chiral separation of the antimicrobial peptide diastereomers, D-phenylseptin and L-phenylseptin using (S) and (R) 3,3'-phenyl-1,1'-binaphthyl-18-crown-6-ether columns (CR-I (+) and CR-I (-), respectively) and also investigated the underlying mechanism. First, using D-amino acid-containing tripeptide Phe-Phe-Phe-OH, we found that CR-I (+) could be used to recognize diastereomeric tripeptides containing an L-amino acid as the first residue. On the contrary, CR-I (-) enabled separation of a series of diastereomers with D-amino acid as the first residue. Therefore, we achieved separation of the stereoisomers using the chiral columns depending on the position of the D- amino acid in the peptide and demonstrated the orthogonality of separations of the chiral columns. Then, using CR-I (+), we separated amphibian antimicrobial peptide diastereomers, L- and D-phenylseptin, which have the sequences, L-Phe-L-Phe-L-Phe and L-Phe-D-Phe-L-Phe at their N-termini, respectively. In order to understand the host-guest interactions, we performed molecular dynamics simulations for L-Phe-L-Phe-L-Phe tripeptide-CR-I molecule complex systems. Three hydrogen bonds between the N-terminal amine group -NH3+ and the crown ether oxygens were the dominant interactions. The hydrophobic interactions between phenyl-rings in the chiral selector unit of CR-I (+) and the side chains of 2nd and 3rd residues of the peptide also contributed to the affinity. Our results show that the CR-I (+)-column can be applied for the separation of endogenous DAACPs generated by the post-translational modification.
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17
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Liu Y, Sun Y, Li S, Liu M, Qin X, Chen X, Lin Y. Tetrahedral Framework Nucleic Acids Deliver Antimicrobial Peptides with Improved Effects and Less Susceptibility to Bacterial Degradation. NANO LETTERS 2020; 20:3602-3610. [PMID: 32272018 DOI: 10.1021/acs.nanolett.0c00529] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Yuhao Liu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yue Sun
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Songhang Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Mengting Liu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Xin Qin
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Xingyu Chen
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yunfeng Lin
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
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18
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Li G, Delafield DG, Li L. Improved structural elucidation of peptide isomers and their receptors using advanced ion mobility-mass spectrometry. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2019.05.048] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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19
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Cheng S, Tu M, Liu H, Zhao G, Du M. Food-derived antithrombotic peptides: Preparation, identification, and interactions with thrombin. Crit Rev Food Sci Nutr 2019; 59:S81-S95. [PMID: 30740983 DOI: 10.1080/10408398.2018.1524363] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Thromboembolism and its sequelae have been the leading causes of morbidity and mortality throughout the world. Food-derived antithrombotic peptides, as potential ingredients in health-promoting functional foods targeting thrombus, have attracted increasing attention because of their high biological activities, low toxicity, and ease of metabolism in the human body. This review presents the conventional workflow of preparation, isolation and identification of antithrombotic peptides from various kinds of food materials. More importantly, to analyze the antithrombotic effects and mechanism of antithrombotic peptides, methods for interaction of anticoagulant peptides and thrombin, the main participant in thrombosis, were analyzed from biochemistry, solution chemistry and crystal chemistry. The present study is intended to highlight the recent advances in research of food-derived antithrombotic peptide as a novel vehicle in the field of food science and nutrition. Future outlooks are highlighted with the aim to suggest a research line to be followed in further studies with the introduced research approach.
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Affiliation(s)
- Shuzheng Cheng
- a School of Food Science and Technology, National Engineering Research Center of Seafood , Dalian Polytechnic University , Dalian , Liaoning , China.,b Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering , China Agricultural University , Beijing , China
| | - Maolin Tu
- c Department of Food Science and Engineering , Harbin Institute of Technology , Harbin , Heilongjiang , China
| | - Hanxiong Liu
- a School of Food Science and Technology, National Engineering Research Center of Seafood , Dalian Polytechnic University , Dalian , Liaoning , China
| | - Guanghua Zhao
- b Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering , China Agricultural University , Beijing , China
| | - Ming Du
- a School of Food Science and Technology, National Engineering Research Center of Seafood , Dalian Polytechnic University , Dalian , Liaoning , China
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Ou Y, Wilson RE, Weber SG. Methods of Measuring Enzyme Activity Ex Vivo and In Vivo. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2018; 11:509-533. [PMID: 29505726 PMCID: PMC6147230 DOI: 10.1146/annurev-anchem-061417-125619] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Enzymes catalyze a variety of biochemical reactions in the body and, in conjunction with transporters and receptors, control virtually all physiological processes. There is great value in measuring enzyme activity ex vivo and in vivo. Spatial and temporal differences or changes in enzyme activity can be related to a variety of natural and pathological processes. Several analytical approaches have been developed to meet this need. They can be classified broadly as methods either based on artificial substrates, with the goal of creating images of diseased tissue, or based on natural substrates, with the goal of understanding natural processes. This review covers a selection of these methods, including optical, magnetic resonance, mass spectrometry, and physical sampling approaches, with a focus on creative chemistry and method development that make ex vivo and in vivo measurements of enzyme activity possible.
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Affiliation(s)
| | - Rachael E Wilson
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA;
| | - Stephen G Weber
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA;
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Tai HC, Checco JW, Sweedler JV. Non-targeted Identification of D-Amino Acid-Containing Peptides Through Enzymatic Screening, Chiral Amino Acid Analysis, and LC-MS. Methods Mol Biol 2018; 1719:107-118. [PMID: 29476507 DOI: 10.1007/978-1-4939-7537-2_7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
D-Amino acid-containing peptides (DAACPs) in animals are a class of bioactive molecules formed via the posttranslational modification of peptides consisting of all-L-amino acid residues. Amino acid residue isomerization greatly impacts the function of the resulting DAACP. However, because isomerization does not change the peptide's mass, this modification is difficult to detect by most mass spectrometry-based peptidomic approaches. Here we describe a method for the identification of DAACPs that can be used to systematically survey peptides extracted from a tissue sample in a non-targeted manner.
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Affiliation(s)
- Hua-Chia Tai
- Department of Chemistry, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - James W Checco
- Department of Chemistry, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Jonathan V Sweedler
- Department of Chemistry, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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22
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Miyamoto T, Homma H. Detection and quantification of d-amino acid residues in peptides and proteins using acid hydrolysis. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1866:775-782. [PMID: 29292238 DOI: 10.1016/j.bbapap.2017.12.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 12/04/2017] [Accepted: 12/19/2017] [Indexed: 12/14/2022]
Abstract
Biomolecular homochirality refers to the assumption that amino acids in all living organisms were believed to be of the l-configuration. However, free d-amino acids are present in a wide variety of organisms and d-amino acid residues are also found in various peptides and proteins, being generated by enzymatic or non-enzymatic isomerization. In mammals, peptides and proteins containing d-amino acids have been linked to various diseases, and they act as novel disease biomarkers. Analytical methods capable of precisely detecting and quantifying d-amino acids in peptides and proteins are therefore important and useful, albeit their difficulty and complexity. Herein, we reviewed conventional analytical methods, especially 0h extrapolating method, and the problems of this method. For the solution of these problems, we furthermore described our recently developed, sensitive method, deuterium-hydrogen exchange method, to detect innate d-amino acid residues in peptides and proteins, and its applications to sample ovalbumin. This article is part of a Special Issue entitled: d-Amino acids: biology in the mirror, edited by Dr. Loredano Pollegioni, Dr. Jean-Pierre Mothet and Dr. Molla Gianluca.
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Affiliation(s)
- Tetsuya Miyamoto
- Graduate School of Pharmaceutical Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Hiroshi Homma
- Graduate School of Pharmaceutical Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan.
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23
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Jansson ET. Strategies for analysis of isomeric peptides. J Sep Sci 2017; 41:385-397. [PMID: 28922569 DOI: 10.1002/jssc.201700852] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Revised: 09/06/2017] [Accepted: 09/06/2017] [Indexed: 01/09/2023]
Abstract
This review presents an overview and recent progress of strategies for detecting isomerism in peptides, with focus on d/l epimerization and the various isomers that the presence of an aspartic acid residue may yield in a protein or peptide. While mass spectrometry has become a majorly used method of choice within proteomics, isomerism is inherently difficult to analyze because it is a modification that does not yield any change in mass of the analyte. Here, several techniques used for analysis of peptide isomerism are discussed, including enzymatic assays, liquid chromatography, and capillary electrophoresis. Recent progress in method development using mass spectrometry is also discussed, including labeling strategies, fragmentation techniques, and ion-mobility spectrometry.
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Affiliation(s)
- Erik T Jansson
- Department of Chemistry-BMC, Uppsala University, Uppsala, Sweden
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24
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Robinson SD, Undheim EAB, Ueberheide B, King GF. Venom peptides as therapeutics: advances, challenges and the future of venom-peptide discovery. Expert Rev Proteomics 2017; 14:931-939. [DOI: 10.1080/14789450.2017.1377613] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Samuel D. Robinson
- Institute for Molecular Bioscience, University of Queensland, St Lucia, Australia
- Centre for Advanced Imaging, University of Queensland, St Lucia, Australia
| | | | | | - Glenn F. King
- Institute for Molecular Bioscience, University of Queensland, St Lucia, Australia
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Abstract
More than half a century ago researchers thought that D-amino acids had a minor function compared to L-enantiomers in biological processes. Many evidences have shown that D-amino acids are present in high concentration in microorganisms, plants, mammals and humans and fulfil specific biological functions. In the brain of mammals, D-serine (D-Ser) acts as a co-agonist of the N-methyl-D-aspartate (NMDA)-type glutamate receptors, responsible for learning, memory and behaviour. D-Ser metabolism is relevant for disorders associated with an altered function of the NMDA receptor, such as schizophrenia, ischemia, epilepsy and neurodegenerative disorders. On the other hand, D-aspartate (D-Asp) is one of the major regulators of adult neurogenesis and plays an important role in the development of endocrine function. D-Asp is present in the neuroendocrine and endocrine tissues and testes, and regulates the synthesis and secretion of hormones and spermatogenesis. Also food proteins contain D-amino acids that are naturally originated or processing-induced under conditions such as high temperatures, acid and alkali treatments and fermentation processes. The presence of D-amino acids in dairy products denotes thermal and alkaline treatments and microbial contamination. Two enzymes are involved in the metabolism of D-amino acids: amino acid racemase in the synthesis and D-amino acid oxidase in the degradation.
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26
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Sato H, Kawamura I, Yamagishi A, Sato F. Solid-state Vibrational Circular Dichroism Spectra of Isoleucine and Its Related Compounds: Effects of Interplay between Two Chiral Centers. CHEM LETT 2017. [DOI: 10.1246/cl.161043] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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27
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Weiss RM, Li J, Liu HH, Washington MA, Giesen JA, Grayson SM, Meyer TY. Determining Sequence Fidelity in Repeating Sequence Poly(lactic-co-glycolic acid)s. Macromolecules 2017. [DOI: 10.1021/acs.macromol.6b02202] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Ryan M. Weiss
- Department
of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
| | - Jian Li
- Department
of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
| | - Han H. Liu
- Department
of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
| | - Michael A. Washington
- Department
of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
| | - Joseph A. Giesen
- Department
of Chemistry, Tulane University, New Orleans, Louisiana 70118, United States
| | - Scott M. Grayson
- Department
of Chemistry, Tulane University, New Orleans, Louisiana 70118, United States
| | - Tara Y. Meyer
- Department
of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
- McGowan
Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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28
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Livnat I, Tai HC, Jansson ET, Bai L, Romanova EV, Chen TT, Yu K, Chen SA, Zhang Y, Wang ZY, Liu DD, Weiss KR, Jing J, Sweedler JV. A d-Amino Acid-Containing Neuropeptide Discovery Funnel. Anal Chem 2016; 88:11868-11876. [PMID: 27788334 PMCID: PMC5144109 DOI: 10.1021/acs.analchem.6b03658] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
![]()
A receptor binding
class of d-amino acid-containing peptides
(DAACPs) is formed in animals from an enzymatically mediated post-translational
modification of ribosomally translated all-l-amino acid peptides.
Although this modification can be required for biological actions,
detecting it is challenging because DAACPs have the same mass as their
all-l-amino acid counterparts. We developed a suite of mass
spectrometry (MS) protocols for the nontargeted discovery of DAACPs
and validated their effectiveness using neurons from Aplysia
californica. The approach involves the following three steps,
with each confirming and refining the hits found in the prior step.
The first step is screening for peptides resistant to digestion by
aminopeptidase M. The second verifies the presence of a chiral amino
acid via acid hydrolysis in deuterium chloride, labeling with Marfey’s
reagent, and liquid chromatography–mass spectrometry to determine
the chirality of each amino acid. The third involves synthesizing
the putative DAACPs and comparing them to the endogenous standards.
Advantages of the method, the d-amino acid-containing neuropeptide
discovery funnel, are that it is capable of detecting the d-form of any common chiral amino acid, and the first two steps do
not require peptide standards. Using these protocols, we report that
two peptides from the Aplysia achatin-like neuropeptide
precursor exist as GdYFD and SdYADSKDEESNAALSDFA.
Interestingly, GdYFD was bioactive in the Aplysia feeding and locomotor circuits but SdYADSKDEESNAALSDFA
was not. The discovery funnel provides an effective means to characterize
DAACPs in the nervous systems of animals in a nontargeted manner.
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Affiliation(s)
| | | | | | | | | | - Ting-Ting Chen
- State Key Laboratory of Pharmaceutical Biotechnology, Collaborative Innovation Center of Chemistry for Life Sciences, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Advanced Institute for Life Sciences, School of Life Sciences, Nanjing University , Nanjing, Jiangsu 210046, China
| | - Ke Yu
- State Key Laboratory of Pharmaceutical Biotechnology, Collaborative Innovation Center of Chemistry for Life Sciences, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Advanced Institute for Life Sciences, School of Life Sciences, Nanjing University , Nanjing, Jiangsu 210046, China
| | - Song-An Chen
- State Key Laboratory of Pharmaceutical Biotechnology, Collaborative Innovation Center of Chemistry for Life Sciences, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Advanced Institute for Life Sciences, School of Life Sciences, Nanjing University , Nanjing, Jiangsu 210046, China
| | - Yan Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, Collaborative Innovation Center of Chemistry for Life Sciences, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Advanced Institute for Life Sciences, School of Life Sciences, Nanjing University , Nanjing, Jiangsu 210046, China
| | - Zheng-Yang Wang
- State Key Laboratory of Pharmaceutical Biotechnology, Collaborative Innovation Center of Chemistry for Life Sciences, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Advanced Institute for Life Sciences, School of Life Sciences, Nanjing University , Nanjing, Jiangsu 210046, China
| | - Dan-Dan Liu
- State Key Laboratory of Pharmaceutical Biotechnology, Collaborative Innovation Center of Chemistry for Life Sciences, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Advanced Institute for Life Sciences, School of Life Sciences, Nanjing University , Nanjing, Jiangsu 210046, China
| | - Klaudiusz R Weiss
- Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai , New York, New York 10029, United States
| | - Jian Jing
- State Key Laboratory of Pharmaceutical Biotechnology, Collaborative Innovation Center of Chemistry for Life Sciences, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Advanced Institute for Life Sciences, School of Life Sciences, Nanjing University , Nanjing, Jiangsu 210046, China.,Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai , New York, New York 10029, United States
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