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Pham TK, Buczek WA, Mead RJ, Shaw PJ, Collins MO. Proteomic Approaches to Study Cysteine Oxidation: Applications in Neurodegenerative Diseases. Front Mol Neurosci 2021; 14:678837. [PMID: 34177463 PMCID: PMC8219902 DOI: 10.3389/fnmol.2021.678837] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 05/03/2021] [Indexed: 11/15/2022] Open
Abstract
Oxidative stress appears to be a key feature of many neurodegenerative diseases either as a cause or consequence of disease. A range of molecules are subject to oxidation, but in particular, proteins are an important target and measure of oxidative stress. Proteins are subject to a range of oxidative modifications at reactive cysteine residues, and depending on the level of oxidative stress, these modifications may be reversible or irreversible. A range of experimental approaches has been developed to characterize cysteine oxidation of proteins. In particular, mass spectrometry-based proteomic methods have emerged as a powerful means to identify and quantify cysteine oxidation sites on a proteome scale; however, their application to study neurodegenerative diseases is limited to date. Here we provide a guide to these approaches and highlight the under-exploited utility of these methods to measure oxidative stress in neurodegenerative diseases for biomarker discovery, target engagement and to understand disease mechanisms.
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Affiliation(s)
- Trong Khoa Pham
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, United Kingdom
- Department of Biomedical Science, University of Sheffield, Sheffield, United Kingdom
| | - Weronika A. Buczek
- Department of Biomedical Science, University of Sheffield, Sheffield, United Kingdom
| | - Richard J. Mead
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, United Kingdom
| | - Pamela J. Shaw
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, United Kingdom
| | - Mark O. Collins
- Department of Biomedical Science, University of Sheffield, Sheffield, United Kingdom
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Theisen A, Yan B, Brown JM, Morris M, Bellina B, Barran PE. Use of Ultraviolet Photodissociation Coupled with Ion Mobility Mass Spectrometry To Determine Structure and Sequence from Drift Time Selected Peptides and Proteins. Anal Chem 2016; 88:9964-9971. [DOI: 10.1021/acs.analchem.6b01705] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Alina Theisen
- Michael
Barber Centre for Collaborative Mass Spectrometry, Manchester Institute
of Biotechnology, and Photon Science Insitute, University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Bin Yan
- Michael
Barber Centre for Collaborative Mass Spectrometry, Manchester Institute
of Biotechnology, and Photon Science Insitute, University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Jeffery M. Brown
- Waters Corporation, Stamford
Avenue, Altrincham Road, Wilmslow, SK9 4AX, United Kingdom
| | - Michael Morris
- Waters Corporation, Stamford
Avenue, Altrincham Road, Wilmslow, SK9 4AX, United Kingdom
| | - Bruno Bellina
- Michael
Barber Centre for Collaborative Mass Spectrometry, Manchester Institute
of Biotechnology, and Photon Science Insitute, University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Perdita E. Barran
- Michael
Barber Centre for Collaborative Mass Spectrometry, Manchester Institute
of Biotechnology, and Photon Science Insitute, University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
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Kintzing JR, Cochran JR. Engineered knottin peptides as diagnostics, therapeutics, and drug delivery vehicles. Curr Opin Chem Biol 2016; 34:143-150. [PMID: 27642714 DOI: 10.1016/j.cbpa.2016.08.022] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 08/24/2016] [Accepted: 08/25/2016] [Indexed: 12/18/2022]
Abstract
Inhibitor cystine-knots, also known as knottins, are a structural family of ultra-stable peptides with diverse functions. Knottins and related backbone-cyclized peptides called cyclotides contain three disulfide bonds connected in a particular arrangement that endows these peptides with high thermal, proteolytic, and chemical stability. Knottins have gained interest as candidates for non-invasive molecular imaging and for drug development as they can possess the pharmacological properties of small molecules and the target affinity and selectively of protein biologics. Naturally occurring knottins are clinically approved for treating chronic pain and GI disorders. Combinatorial methods are being used to engineer knottins that can bind to other clinically relevant targets in cancer, and inflammatory and cardiac disease. This review details recent examples of engineered knottin peptides; their use as molecular imaging agents, therapeutics, and drug delivery vehicles; modifications that can be introduced to improve peptide folding and bioactivity; and future perspectives and challenges in the field.
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Affiliation(s)
- James R Kintzing
- Department of Bioengineering, Stanford University, United States
| | - Jennifer R Cochran
- Department of Bioengineering, Stanford University, United States; Department of Chemical Engineering, Stanford University, United States.
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Simon MD, Maki Y, Vinogradov AA, Zhang C, Yu H, Lin YS, Kajihara Y, Pentelute BL. d-Amino Acid Scan of Two Small Proteins. J Am Chem Soc 2016; 138:12099-111. [DOI: 10.1021/jacs.6b03765] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Mark D. Simon
- Department
of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts
Avenue, Cambridge, Massachusetts 02139, United States
| | - Yuta Maki
- Department
of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts
Avenue, Cambridge, Massachusetts 02139, United States
- Department
of Chemistry, Graduate School of Science, Osaka University, 1-1,
Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
| | - Alexander A. Vinogradov
- Department
of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts
Avenue, Cambridge, Massachusetts 02139, United States
| | - Chi Zhang
- Department
of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts
Avenue, Cambridge, Massachusetts 02139, United States
| | - Hongtao Yu
- Department
of Chemistry, Tufts University, 62 Talbot Avenue, Medford, Massachusetts 02155, United States
| | - Yu-Shan Lin
- Department
of Chemistry, Tufts University, 62 Talbot Avenue, Medford, Massachusetts 02155, United States
| | - Yasuhiro Kajihara
- Department
of Chemistry, Graduate School of Science, Osaka University, 1-1,
Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
| | - Bradley L. Pentelute
- Department
of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts
Avenue, Cambridge, Massachusetts 02139, United States
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