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Cobley JN. Exploring the unmapped cysteine redox proteoform landscape. Am J Physiol Cell Physiol 2024; 327:C844-C866. [PMID: 39099422 DOI: 10.1152/ajpcell.00152.2024] [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: 03/07/2024] [Revised: 07/16/2024] [Accepted: 07/16/2024] [Indexed: 08/06/2024]
Abstract
Cysteine redox proteoforms define the diverse molecular states that proteins with cysteine residues can adopt. A protein with one cysteine residue must adopt one of two binary proteoforms: reduced or oxidized. Their numbers scale: a protein with 10 cysteine residues must assume one of 1,024 proteoforms. Although they play pivotal biological roles, the vast cysteine redox proteoform landscape comprising vast numbers of theoretical proteoforms remains largely uncharted. Progress is hampered by a general underappreciation of cysteine redox proteoforms, their intricate complexity, and the formidable challenges that they pose to existing methods. The present review advances cysteine redox proteoform theory, scrutinizes methodological barriers, and elaborates innovative technologies for detecting unique residue-defined cysteine redox proteoforms. For example, chemistry-enabled hybrid approaches combining the strengths of top-down mass spectrometry (TD-MS) and bottom-up mass spectrometry (BU-MS) for systematically cataloguing cysteine redox proteoforms are delineated. These methods provide the technological means to map uncharted redox terrain. To unravel hidden redox regulatory mechanisms, discover new biomarkers, and pinpoint therapeutic targets by mining the theoretical cysteine redox proteoform space, a community-wide initiative termed the "Human Cysteine Redox Proteoform Project" is proposed. Exploring the cysteine redox proteoform landscape could transform current understanding of redox biology.
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Affiliation(s)
- James N Cobley
- School of Life Sciences, University of Dundee, Dundee, United Kingdom
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2
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Cobley JN, Margaritelis NV, Chatzinikolaou PN, Nikolaidis MG, Davison GW. Ten "Cheat Codes" for Measuring Oxidative Stress in Humans. Antioxidants (Basel) 2024; 13:877. [PMID: 39061945 PMCID: PMC11273696 DOI: 10.3390/antiox13070877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Revised: 07/17/2024] [Accepted: 07/18/2024] [Indexed: 07/28/2024] Open
Abstract
Formidable and often seemingly insurmountable conceptual, technical, and methodological challenges hamper the measurement of oxidative stress in humans. For instance, fraught and flawed methods, such as the thiobarbituric acid reactive substances assay kits for lipid peroxidation, rate-limit progress. To advance translational redox research, we present ten comprehensive "cheat codes" for measuring oxidative stress in humans. The cheat codes include analytical approaches to assess reactive oxygen species, antioxidants, oxidative damage, and redox regulation. They provide essential conceptual, technical, and methodological information inclusive of curated "do" and "don't" guidelines. Given the biochemical complexity of oxidative stress, we present a research question-grounded decision tree guide for selecting the most appropriate cheat code(s) to implement in a prospective human experiment. Worked examples demonstrate the benefits of the decision tree-based cheat code selection tool. The ten cheat codes define an invaluable resource for measuring oxidative stress in humans.
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Affiliation(s)
- James N. Cobley
- The University of Dundee, Dundee DD1 4HN, UK
- Ulster University, Belfast BT15 1ED, Northern Ireland, UK;
| | - Nikos V. Margaritelis
- Aristotle University of Thessaloniki, 62122 Serres, Greece; (N.V.M.); (P.N.C.); (M.G.N.)
| | | | - Michalis G. Nikolaidis
- Aristotle University of Thessaloniki, 62122 Serres, Greece; (N.V.M.); (P.N.C.); (M.G.N.)
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3
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Stair ER, Hicks LM. Recent advances in mass spectrometry-based methods to investigate reversible cysteine oxidation. Curr Opin Chem Biol 2023; 77:102389. [PMID: 37776664 DOI: 10.1016/j.cbpa.2023.102389] [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: 06/21/2023] [Revised: 08/10/2023] [Accepted: 08/31/2023] [Indexed: 10/02/2023]
Abstract
The post-translational modification of cysteine to diverse oxidative states is understood as a critical cellular mechanism to combat oxidative stress. To study the role of cysteine oxidation, cysteine enrichments and subsequent analysis via mass spectrometry are necessary. As such, technologies and methods are rapidly developing for sensitive and efficient enrichments of cysteines to further explore its role in signaling pathways. In this review, we analyze recent developments in methods to miniaturize cysteine enrichments, analyze the underexplored disulfide bound redoxome, and quantify site-specific cysteine oxidation. We predict that further development of these methods will improve cysteine coverage across more diverse organisms than those previously studied and elicit novel roles cysteines play in stress response.
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Affiliation(s)
- Evan R Stair
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Leslie M Hicks
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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Cobley JN. 50 shades of oxidative stress: A state-specific cysteine redox pattern hypothesis. Redox Biol 2023; 67:102936. [PMID: 37875063 PMCID: PMC10618833 DOI: 10.1016/j.redox.2023.102936] [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: 09/25/2023] [Revised: 10/12/2023] [Accepted: 10/16/2023] [Indexed: 10/26/2023] Open
Abstract
Oxidative stress is biochemically complex. Like primary colours, specific reactive oxygen species (ROS) and antioxidant inputs can be mixed to create unique "shades" of oxidative stress. Even a minimal redox module comprised of just 12 (ROS & antioxidant) inputs and 3 outputs (oxidative damage, cysteine-dependent redox-regulation, or both) yields over half a million "shades" of oxidative stress. The present paper proposes the novel hypothesis that: state-specific shades of oxidative stress, such as a discrete disease, are associated with distinct tell-tale cysteine oxidation patterns. The patterns are encoded by many parameters, from the identity of the oxidised proteins, the cysteine oxidation type, and magnitude. The hypothesis is conceptually grounded in distinct ROS and antioxidant inputs coalescing to produce unique cysteine oxidation outputs. And considers the potential biological significance of the holistic cysteine oxidation outputs. The literature supports the existence of state-specific cysteine oxidation patterns. Measuring and manipulating these patterns offer promising avenues for advancing oxidative stress research. The pattern inspired hypothesis provides a framework for understanding the complex biochemical nature of state-specific oxidative stress.
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Affiliation(s)
- James N Cobley
- Cysteine redox technology Group, Life Science Innovation Centre, University of the Highlands and Islands, Inverness, IV2 5NA, Scotland, UK.
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Tuncay A, Crabtree DR, Muggeridge DJ, Husi H, Cobley JN. Performance benchmarking microplate-immunoassays for quantifying target-specific cysteine oxidation reveals their potential for understanding redox-regulation and oxidative stress. Free Radic Biol Med 2023; 204:252-265. [PMID: 37192685 DOI: 10.1016/j.freeradbiomed.2023.05.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 04/24/2023] [Accepted: 05/05/2023] [Indexed: 05/18/2023]
Abstract
The antibody-linked oxi-state assay (ALISA) for quantifying target-specific cysteine oxidation can benefit specialist and non-specialist users. Specialists can benefit from time-efficient analysis and high-throughput target and/or sample n-plex capacities. The simple and accessible "off-the-shelf" nature of ALISA brings the benefits of oxidative damage assays to non-specialists studying redox-regulation. Until performance benchmarking establishes confidence in the "unseen" microplate results, ALISA is unlikely to be widely adopted. Here, we implemented pre-set pass/fail criteria to benchmark ALISA by evaluating immunoassay performance in diverse contexts. ELISA-mode ALISA assays were accurate, reliable, and sensitive. For example, the average inter-assay CV for detecting 20%- and 40%-oxidised PRDX2 or GAPDH standards was 4.6% (range: 3.6-7.4%). ALISA displayed target-specificity. Immunodepleting the target decreased the signal by ∼75%. Single-antibody formatted ALISA failed to quantify the matrix-facing alpha subunit of the mitochondrial ATP synthase. However, RedoxiFluor quantified the alpha subunit displaying exceptional performance in the single-antibody format. ALISA discovered that (1) monocyte-to-macrophage differentiation amplified PRDX2-oxidation in THP-1 cells and (2) exercise increased GAPDH-specific oxidation in human erythrocytes. The "unseen" microplate data were "seen-to-be-believed" via orthogonal visually displayed immunoassays like the dimer method. Finally, we established target (n = 3) and sample (n = 100) n-plex capacities in ∼4 h with 50-70 min hands-on time. Our work showcases the potential of ALISA to advance our understanding of redox-regulation and oxidative stress.
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Affiliation(s)
- Ahmet Tuncay
- Division of Biomedical Science, Life Science Innovation Centre, University of the Highlands and Islands, Inverness, IV2 5NA, Scotland, UK
| | - Daniel R Crabtree
- Division of Biomedical Science, Life Science Innovation Centre, University of the Highlands and Islands, Inverness, IV2 5NA, Scotland, UK
| | | | - Holger Husi
- Division of Biomedical Science, Life Science Innovation Centre, University of the Highlands and Islands, Inverness, IV2 5NA, Scotland, UK
| | - James N Cobley
- Division of Biomedical Science, Life Science Innovation Centre, University of the Highlands and Islands, Inverness, IV2 5NA, Scotland, UK; Cysteine Redox Technology Group, Life Science Innovation Centre, University of the Highlands and Islands, Inverness, IV2 5NA, Scotland, UK.
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Cobley JN. Oxiforms: Unique cysteine residue- and chemotype-specified chemical combinations can produce functionally-distinct proteoforms: Like how mixing primary colours creates new shades, cysteine residue- and chemotype-specified chemical combinations can produce functionally-distinct proteoforms called oxiforms: Like how mixing primary colours creates new shades, cysteine residue- and chemotype-specified chemical combinations can produce functionally-distinct proteoforms called oxiforms. Bioessays 2023:e2200248. [PMID: 37147790 DOI: 10.1002/bies.202200248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 04/21/2023] [Indexed: 05/07/2023]
Abstract
A single protein molecule with one or more cysteine residues can occupy a plurality of unique residue and oxidation-chemotype specified proteoforms that I term oxiforms. In binary reduced or oxidised terms, one molecule with three cysteines will adopt one of eight unique oxiforms. Residue-defined sulfur chemistry endows specific oxiforms with distinct functionally-relevant biophysical properties (e.g., steric effects). Their emergent complexity means a functionally-relevant effect may only manifest when multiple cysteines are oxidised. Like how mixing colours makes new shades, combining discrete redox chemistries-colours-can create a kaleidoscope of oxiform hues. The sheer diversity of oxiforms co-existing within the human body provides a biological basis for redox heterogeneity. Of evolutionary significance, oxiforms may enable individual cells to mount a broad spectrum of responses to the same stimulus. Their biological significance, however plausible, is speculative because protein-specific oxiforms remain essentially unexplored. Excitingly, pioneering new techniques can push the field into uncharted territory by quantifying oxiforms. The oxiform concept can advance our understanding of redox-regulation in health and disease.
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Affiliation(s)
- James N Cobley
- Cysteine Redox Technology Group, Life Science Innovation Centre, University of the Highlands and Islands, Inverness, Scotland, UK
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Papaleo E, Tiberti M, Arnaudi M, Pecorari C, Faienza F, Cantwell L, Degn K, Pacello F, Battistoni A, Lambrughi M, Filomeni G. TRAP1 S-nitrosylation as a model of population-shift mechanism to study the effects of nitric oxide on redox-sensitive oncoproteins. Cell Death Dis 2023; 14:284. [PMID: 37085483 PMCID: PMC10121659 DOI: 10.1038/s41419-023-05780-6] [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: 12/11/2022] [Revised: 03/13/2023] [Accepted: 03/27/2023] [Indexed: 04/23/2023]
Abstract
S-nitrosylation is a post-translational modification in which nitric oxide (NO) binds to the thiol group of cysteine, generating an S-nitrosothiol (SNO) adduct. S-nitrosylation has different physiological roles, and its alteration has also been linked to a growing list of pathologies, including cancer. SNO can affect the function and stability of different proteins, such as the mitochondrial chaperone TRAP1. Interestingly, the SNO site (C501) of TRAP1 is in the proximity of another cysteine (C527). This feature suggests that the S-nitrosylated C501 could engage in a disulfide bridge with C527 in TRAP1, resembling the well-known ability of S-nitrosylated cysteines to resolve in disulfide bridge with vicinal cysteines. We used enhanced sampling simulations and in-vitro biochemical assays to address the structural mechanisms induced by TRAP1 S-nitrosylation. We showed that the SNO site induces conformational changes in the proximal cysteine and favors conformations suitable for disulfide bridge formation. We explored 4172 known S-nitrosylated proteins using high-throughput structural analyses. Furthermore, we used a coarse-grained model for 44 protein targets to account for protein flexibility. This resulted in the identification of up to 1248 proximal cysteines, which could sense the redox state of the SNO site, opening new perspectives on the biological effects of redox switches. In addition, we devised two bioinformatic workflows ( https://github.com/ELELAB/SNO_investigation_pipelines ) to identify proximal or vicinal cysteines for a SNO site with accompanying structural annotations. Finally, we analyzed mutations in tumor suppressors or oncogenes in connection with the conformational switch induced by S-nitrosylation. We classified the variants as neutral, stabilizing, or destabilizing for the propensity to be S-nitrosylated and undergo the population-shift mechanism. The methods applied here provide a comprehensive toolkit for future high-throughput studies of new protein candidates, variant classification, and a rich data source for the research community in the NO field.
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Affiliation(s)
- Elena Papaleo
- Cancer Structural Biology, Danish Cancer Society Research Center, 2100, Copenhagen, Denmark.
- Cancer Systems Biology, Section for Bioinformatics, Department of Health and Technology, Technical University of Denmark, 2800, Lyngby, Denmark.
| | - Matteo Tiberti
- Cancer Structural Biology, Danish Cancer Society Research Center, 2100, Copenhagen, Denmark
| | - Matteo Arnaudi
- Cancer Structural Biology, Danish Cancer Society Research Center, 2100, Copenhagen, Denmark
- Cancer Systems Biology, Section for Bioinformatics, Department of Health and Technology, Technical University of Denmark, 2800, Lyngby, Denmark
| | - Chiara Pecorari
- Redox Biology, Danish Cancer Society Research Center, 2100, Copenhagen, Denmark
| | - Fiorella Faienza
- Department of Biology, University of Rome Tor Vergata, 00133, Rome, Italy
| | - Lisa Cantwell
- Cancer Structural Biology, Danish Cancer Society Research Center, 2100, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kristine Degn
- Cancer Systems Biology, Section for Bioinformatics, Department of Health and Technology, Technical University of Denmark, 2800, Lyngby, Denmark
| | - Francesca Pacello
- Department of Biology, University of Rome Tor Vergata, 00133, Rome, Italy
| | - Andrea Battistoni
- Department of Biology, University of Rome Tor Vergata, 00133, Rome, Italy
| | - Matteo Lambrughi
- Cancer Structural Biology, Danish Cancer Society Research Center, 2100, Copenhagen, Denmark
| | - Giuseppe Filomeni
- Redox Biology, Danish Cancer Society Research Center, 2100, Copenhagen, Denmark
- Department of Biology, University of Rome Tor Vergata, 00133, Rome, Italy
- Center for Healthy Aging, Copenhagen University, 2200, Copenhagen, Denmark
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8
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Montllor-Albalate C, Thompson AE, Kim H, Reddi AR. Measuring the Oxidation State and Enzymatic Activity of Glyceraldehyde Phosphate Dehydrogenase (GAPDH). Methods Mol Biol 2023; 2675:219-236. [PMID: 37258767 DOI: 10.1007/978-1-0716-3247-5_17] [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: 06/02/2023]
Abstract
Glyceraldehyde phosphate dehydrogenase (GAPDH) is a highly conserved, essential, and abundant enzyme that catalyzes a rate-determining step of glycolysis. GAPDH catalyzes the nicotinamide adenine dinucleotide (NAD+)- and inorganic phosphate-dependent oxidation and phosphorylation of glyceraldehyde phosphate (GAP) to form 1,3-bisphosphoglycerate (BPG). As part of its mechanism of action, GAPDH employs a redox-sensitive cysteine that serves as a nucleophile to form a covalent adduct with GAP in order to set-up subsequent oxidation and phosphorylation steps. As a result of the redox sensitivity of the active site cysteine residue, GAPDH is susceptible to oxidative inactivation by oxidants such as hydrogen peroxide (H2O2). Indeed, numerous studies have demonstrated that oxidative inactivation of GAPDH has important metabolic consequences for adaptation to life in air and oxidative stress since decreased GAPDH activity results in the rerouting of carbon flux away from glycolysis and toward the pentose phosphate pathway to produce the key cellular reductant and antioxidant, NADPH. Thus, the ability to probe GAPDH oxidation and activity provides an important snapshot of the intracellular redox environment and glycolytic flux. Herein, we describe methods to measure reduced and oxidized GAPDH using thiol alkylation assays as well as GAPDH enzymatic activity.
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Affiliation(s)
- Claudia Montllor-Albalate
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
- Parker Petit Institute for Bioengineering and Biosciences, Atlanta, GA, USA
| | - Anna E Thompson
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
- Parker Petit Institute for Bioengineering and Biosciences, Atlanta, GA, USA
| | - Hyojung Kim
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
- Parker Petit Institute for Bioengineering and Biosciences, Atlanta, GA, USA
| | - Amit R Reddi
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA.
- Parker Petit Institute for Bioengineering and Biosciences, Atlanta, GA, USA.
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Kukulage DSK, Matarage Don NNJ, Ahn YH. Emerging chemistry and biology in protein glutathionylation. Curr Opin Chem Biol 2022; 71:102221. [PMID: 36223700 PMCID: PMC9844265 DOI: 10.1016/j.cbpa.2022.102221] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 09/08/2022] [Accepted: 09/09/2022] [Indexed: 01/27/2023]
Abstract
Protein S-glutathionylation serves a regulatory role in proteins and modulates distinct biological processes implicated in health and diseases. Despite challenges in analyzing the dynamic and reversible nature of S-glutathionylation, recent chemical and biological methods have significantly advanced the field of S-glutathionylation, culminating in selective identification and detection, structural motif analysis, and functional studies of S-glutathionylation. This review will highlight emerging studies of protein glutathionylation, beginning by introducing biochemical tools that enable mass spectrometric identification and live-cell imaging of S-glutathionylation. Next, it will spotlight recent examples of S-glutathionylation regulating physiology and inflammation. Lastly, we will feature two emerging lines of glutathionylation research in cryptic cysteine glutathionylation and protein C-glutathionylation.
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Affiliation(s)
| | | | - Young-Hoon Ahn
- Department of Chemistry, Drexel University, Philadelphia, PA 19104, USA.
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10
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Tuncay A, Noble A, Guille M, Cobley JN. RedoxiFluor: A microplate technique to quantify target-specific protein thiol redox state in relative percentage and molar terms. Free Radic Biol Med 2022; 181:118-129. [PMID: 35131446 PMCID: PMC8904371 DOI: 10.1016/j.freeradbiomed.2022.01.023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 01/12/2022] [Accepted: 01/23/2022] [Indexed: 12/12/2022]
Abstract
Unravelling how reactive oxygen species regulate fundamental biological processes is hampered by the lack of an accessible microplate technique to quantify target-specific protein thiol redox state in percentages and moles. To meet this unmet need, we present RedoxiFluor. RedoxiFluor uses two spectrally distinct thiol-reactive fluorescent conjugated reporters, a capture antibody, detector antibody and a standard curve to quantify target-specific protein thiol redox state in relative percentage and molar terms. RedoxiFluor can operate in global mode to assess the redox state of the bulk thiol proteome and can simultaneously assess the redox state of multiple targets in array mode. Extensive proof-of-principle experiments robustly validate the assay principle and the value of each RedoxiFluor mode in diverse biological contexts. In particular, array mode RedoxiFluor shows that the response of redox-regulated phosphatases to lipopolysaccharide (LPS) differs in human monocytes. Specifically, LPS increased PP2A-, SHP1-, PTP1B-, and CD45-specific reversible thiol oxidation without changing the redox state of calcineurin, PTEN, and SHP2. The relative percentage and molar terms are interpretationally useful and define the most complete and extensive microplate redox analysis achieved to date. RedoxiFluor is a new antibody technology with the power to quantify relative target-specific protein thiol redox state in percentages and moles relative to the bulk thiol proteome and selected other targets in a widely accessible, simple and easily implementable microplate format.
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Affiliation(s)
- Ahmet Tuncay
- Redox Biology Group, UHI, Inverness, IV2 3JH, UK
| | - Anna Noble
- European Xenopus Resource Centre, University of Portsmouth, Portsmouth, PO1 2DY, UK
| | - Matthew Guille
- European Xenopus Resource Centre, University of Portsmouth, Portsmouth, PO1 2DY, UK
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Gurram S, Srivastava G, Badve V, Nandre V, Gundu S, Doshi P. Pyridine Borane as Alternative Reducing Agent to Sodium Cyanoborohydride for the PEGylation of L-asparaginase. Appl Biochem Biotechnol 2022; 194:827-847. [PMID: 34550501 DOI: 10.1007/s12010-021-03657-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 09/03/2021] [Indexed: 11/30/2022]
Abstract
PEGylation is a reductive alkylation of a protein N-terminal/α-amine of protein with mPEG chain by reducing agent. To obtain quantitative and site-specific PEGylation, sodium cyanoborohydride is commonly used as a reducing agent. The reduction process of sodium cyanoborohydride produces highly poisonous hydrogen cyanide, which may render the final product toxic. Herein, we have studied various reducing agents such as dimethylamine borane, triethylamine borane, trimethylamine borane, pyridine borane, morpholine borane, 2-picoline borane, and 5-ethyl-2-methyl-pyridine borane were tested as alternatives to sodium cyanoborohydride for the PEGylation of L-asparaginase. The characterization of reacted pegaspargase was carried out by SDS-PAGE, Western blotting, SEC-HPLC, RP-HPLC, SEC-MALS, CD, enzyme activity, and cell proliferation assays using with lymphoblast cells and MTS/PMS as substrate. Pyridine borane was determined to be the best acceptable reducing agent for PEGylation in terms of purity and activity. As a result, instead of sodium cyanoborohydride, pyridine borane can be employed.
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Affiliation(s)
- Santosh Gurram
- Division of Biochemistry, Department of Chemistry, Savitribai Phule Pune University, Formerly University of Pune), Ganeshkhind, Pune, 411007, Maharashtra, India
| | - Gopal Srivastava
- Division of Biochemistry, Department of Chemistry, Savitribai Phule Pune University, Formerly University of Pune), Ganeshkhind, Pune, 411007, Maharashtra, India
| | - Vishnupriya Badve
- Division of Biochemistry, Department of Chemistry, Savitribai Phule Pune University, Formerly University of Pune), Ganeshkhind, Pune, 411007, Maharashtra, India
| | - Vinod Nandre
- Division of Biochemistry, Department of Chemistry, Savitribai Phule Pune University, Formerly University of Pune), Ganeshkhind, Pune, 411007, Maharashtra, India
| | - Shridevi Gundu
- Division of Biochemistry, Department of Chemistry, Savitribai Phule Pune University, Formerly University of Pune), Ganeshkhind, Pune, 411007, Maharashtra, India
| | - Pooja Doshi
- Division of Biochemistry, Department of Chemistry, Savitribai Phule Pune University, Formerly University of Pune), Ganeshkhind, Pune, 411007, Maharashtra, India.
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Sod1 integrates oxygen availability to redox regulate NADPH production and the thiol redoxome. Proc Natl Acad Sci U S A 2022; 119:2023328119. [PMID: 34969852 PMCID: PMC8740578 DOI: 10.1073/pnas.2023328119] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/14/2021] [Indexed: 12/12/2022] Open
Abstract
Cu/Zn superoxide dismutase (Sod1) is a key antioxidant enzyme, and its importance is underscored by the fact that its ablation in cell and animal models results in oxidative stress; metabolic defects; and reductions in cell proliferation, viability, and lifespan. Curiously, Sod1 detoxifies superoxide radicals (O2•−) in a manner that produces an oxidant as byproduct, hydrogen peroxide (H2O2). While much is known about the necessity of scavenging O2•−, it is less clear what the physiological roles of Sod1-derived H2O2 are. We discovered that Sod1-derived H2O2 plays an important role in antioxidant defense by stimulating the production of NADPH, a vital cellular reductant required for reactive oxygen species scavenging enzymes, as well as redox regulating a large network of enzymes. Cu/Zn superoxide dismutase (Sod1) is a highly conserved and abundant antioxidant enzyme that detoxifies superoxide (O2•−) by catalyzing its conversion to dioxygen (O2) and hydrogen peroxide (H2O2). Using Saccharomyces cerevisiae and mammalian cells, we discovered that a major aspect of the antioxidant function of Sod1 is to integrate O2 availability to promote NADPH production. The mechanism involves Sod1-derived H2O2 oxidatively inactivating the glycolytic enzyme, GAPDH, which in turn reroutes carbohydrate flux to the oxidative phase of the pentose phosphate pathway (oxPPP) to generate NADPH. The aerobic oxidation of GAPDH is dependent on and rate-limited by Sod1. Thus, Sod1 senses O2 via O2•− to balance glycolytic and oxPPP flux, through control of GAPDH activity, for adaptation to life in air. Importantly, this mechanism for Sod1 antioxidant activity requires the bulk of cellular Sod1, unlike for its role in protection against O2•− toxicity, which only requires <1% of total Sod1. Using mass spectrometry, we identified proteome-wide targets of Sod1-dependent redox signaling, including numerous metabolic enzymes. Altogether, Sod1-derived H2O2 is important for antioxidant defense and a master regulator of metabolism and the thiol redoxome.
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Noble A, Guille M, Cobley JN. ALISA: A microplate assay to measure protein thiol redox state. Free Radic Biol Med 2021; 174:272-280. [PMID: 34418513 DOI: 10.1016/j.freeradbiomed.2021.08.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 08/11/2021] [Accepted: 08/17/2021] [Indexed: 12/12/2022]
Abstract
Measuring protein thiol redox state is central to understanding redox signalling in health and disease. The lack of a microplate assay to measure target specific protein thiol redox state rate-limits progress on accessibility grounds: redox proteomics is inaccessible to most. Developing a microplate assay is important for accelerating discovery by widening access to protein thiol redox biology. Beyond accessibility, enabling high throughput time- and cost-efficient microplate analysis is important. To meet the pressing need for a microplate assay to measure protein thiol redox state, we present the Antibody-Linked Oxi-State Assay (ALISA). ALISA uses a covalently bound capture antibody to bind a thiol-reactive fluorescent conjugated maleimide (F-MAL) decorated target. The capture antibody-target complex is labelled with an amine-reactive fluorescent N-hydroxysuccinimide ester (F-NHS) to report total protein. The covalent bonds that immobilise the capture antibody to the epoxy group functionalised microplate enable one to selectively elute the target. Target specific redox state is ratiometrically calculated as: F-MAL (i.e., reversible thiol oxidation)/F-NHS (i.e., total protein). After validating the assay principle (i.e., increased target specific reversible thiol oxidation increases the ratio), we used ALISA to determine whether fertilisation-a fundamental biological process-changes Akt, a serine/threonine protein kinase, specific reversible thiol oxidation. Fertilisation significantly decreases Akt specific reversible thiol oxidation in Xenopus laevis 2-cell zygotes compared to unfertilised eggs. ALISA is an accessible microplate assay to advance knowledge of protein thiol redox biology in health and disease.
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Affiliation(s)
- Anna Noble
- European Xenopus Resource Centre, Portsmouth University, Portsmouth, PO1 2DY, UK
| | - Matthew Guille
- European Xenopus Resource Centre, Portsmouth University, Portsmouth, PO1 2DY, UK
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14
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Zamorano Cuervo N, Fortin A, Caron E, Chartier S, Grandvaux N. Pinpointing cysteine oxidation sites by high-resolution proteomics reveals a mechanism of redox-dependent inhibition of human STING. Sci Signal 2021; 14:14/680/eaaw4673. [PMID: 33906974 DOI: 10.1126/scisignal.aaw4673] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Protein function is regulated by posttranslational modifications (PTMs), among which reversible oxidation of cysteine residues has emerged as a key regulatory mechanism of cellular responses. Given the redox regulation of virus-host interactions, the identification of oxidized cysteine sites in cells is essential to understand the underlying mechanisms involved. Here, we present a proteome-wide identification of reversibly oxidized cysteine sites in oxidant-treated cells using a maleimide-based bioswitch method coupled to mass spectrometry analysis. We identified 2720 unique oxidized cysteine sites within 1473 proteins with distinct abundances, locations, and functions. Oxidized cysteine sites were found in numerous signaling pathways, many relevant to virus-host interactions. We focused on the oxidation of STING, the central adaptor of the innate immune type I interferon pathway, which is stimulated in response to the detection of cytosolic DNA by cGAS. We demonstrated the reversible oxidation of Cys148 and Cys206 of STING in cells. Molecular analyses led us to establish a model in which Cys148 oxidation is constitutive, whereas Cys206 oxidation is inducible by oxidative stress or by the natural ligand of STING, 2'3'-cGAMP. Our data suggest that the oxidation of Cys206 prevented hyperactivation of STING by causing a conformational change associated with the formation of inactive polymers containing intermolecular disulfide bonds. This finding should aid the design of therapies targeting STING that are relevant to autoinflammatory disorders, immunotherapies, and vaccines.
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Affiliation(s)
- Natalia Zamorano Cuervo
- CRCHUM-Centre Hospitalier de l'Université de Montréal, 900 rue Saint Denis, Montréal, H2X 0A9 Québec, Canada
| | - Audray Fortin
- CRCHUM-Centre Hospitalier de l'Université de Montréal, 900 rue Saint Denis, Montréal, H2X 0A9 Québec, Canada
| | - Elise Caron
- CRCHUM-Centre Hospitalier de l'Université de Montréal, 900 rue Saint Denis, Montréal, H2X 0A9 Québec, Canada
| | - Stéfany Chartier
- CRCHUM-Centre Hospitalier de l'Université de Montréal, 900 rue Saint Denis, Montréal, H2X 0A9 Québec, Canada
| | - Nathalie Grandvaux
- CRCHUM-Centre Hospitalier de l'Université de Montréal, 900 rue Saint Denis, Montréal, H2X 0A9 Québec, Canada. .,Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Université de Montréal, Montréal, H3C 3J7 Québec, Canada
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15
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Zhang T, Gaffrey MJ, Li X, Qian WJ. Characterization of cellular oxidative stress response by stoichiometric redox proteomics. Am J Physiol Cell Physiol 2020; 320:C182-C194. [PMID: 33264075 DOI: 10.1152/ajpcell.00040.2020] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The thiol redox proteome refers to all proteins whose cysteine thiols are subjected to various redox-dependent posttranslational modifications (PTMs) including S-glutathionylation (SSG), S-nitrosylation (SNO), S-sulfenylation (SOH), and S-sulfhydration (SSH). These modifications can impact various aspects of protein function such as activity, binding, conformation, localization, and interactions with other molecules. To identify novel redox proteins in signaling and regulation, it is highly desirable to have robust redox proteomics methods that can provide global, site-specific, and stoichiometric quantification of redox PTMs. Mass spectrometry (MS)-based redox proteomics has emerged as the primary platform for broad characterization of thiol PTMs in cells and tissues. Herein, we review recent advances in MS-based redox proteomics approaches for quantitative profiling of redox PTMs at physiological or oxidative stress conditions and highlight some recent applications. Considering the relative maturity of available methods, emphasis will be on two types of modifications: 1) total oxidation (i.e., all reversible thiol modifications), the level of which represents the overall redox state, and 2) S-glutathionylation, a major form of reversible thiol oxidation. We also discuss the significance of stoichiometric measurements of thiol PTMs as well as future perspectives toward a better understanding of cellular redox regulatory networks in cells and tissues.
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Affiliation(s)
- Tong Zhang
- Integrative Omics, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington
| | - Matthew J Gaffrey
- Integrative Omics, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington
| | - Xiaolu Li
- Integrative Omics, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington.,Bioproducts Sciences and Engineering Laboratory, Department of Biological Systems Engineering, Washington State University, Richland, Washington
| | - Wei-Jun Qian
- Integrative Omics, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington
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16
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Ortiz-Gómez V, Rodríguez-Ramos VD, Maldonado-Hernández R, González-Feliciano JA, Nicolau E. Antimicrobial Polymer-Peptide Conjugates Based on Maximin H5 and PEG to Prevent Biofouling of E. coli and P. aeruginosa. ACS APPLIED MATERIALS & INTERFACES 2020; 12:46991-47001. [PMID: 32937073 PMCID: PMC8177746 DOI: 10.1021/acsami.0c13492] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Many pathogens, such as Pseudomonas aeruginosa and Escherichia coli bacteria can easily attach to surfaces and form stable biofilms. The formation of such biofilms in surfaces presents a problem in environmental, biomedical, and industrial processes, among many others. Aiming to provide a plausible solution to this issue, the anionic and hydrophobic peptide Maximin H5 C-terminally deaminated isoform (MH5C) has been modified with a cysteine in the C-terminal (MH5C-Cys) and coupled to polyethylene glycol (PEG) polymers of varying sizes (i.e., 2 kDa and 5 kDa) to serve as a surface protective coating. Briefly, the MH5C-Cys was bioconjugated to PEG and purified by size exclusion chromatography while the reaction was confirmed via SDS-PAGE and MALDI ToF. Moreover, the preventive antimicrobial activity of the MH5C-Cys-PEG conjugates was performed via the growth curves method, showing inhibition of bacterial growth after 24 h. The efficacy of these peptide-polymer conjugates was extensively characterized via scanning electron microscopy (SEM), minimum inhibition concentration (MIC), minimum biofilm inhibition concentration (MBIC), and minimum biofilm eradication concentration (MBEC) assays to evaluate their ability to eradicate and prevent the biofilms. Interestingly, this work demonstrated a critical PEG polymer weight of 5 kDa as ideal when coupled to the peptide to achieve inhibition and eradication of the biofilm formation in both bacteria strains. According to the MICs (40 μM) and MBICs (300 μM), we can conclude that this conjugate (MH5C-Cys-5 kDa) has an action that prevents/inhibits the formation of biofilms and the eradication of biofilms (MBEC 500 μM). In contrast, the MH5C-Cys peptide with PEG polymer of 2 kDa did not show inhibition or eradication of the biofilms.
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Affiliation(s)
- Valerie Ortiz-Gómez
- Department of Biology, University of Puerto Rico, Río Piedras Campus, 17 Avenido, Universidad Suite 1701, San Juan, Puerto Rico 00925-2537
- Molecular Sciences Research Center, University of Puerto Rico, 1390 Ponce De Leon Avenido, Suite 2, San Juan Puerto Rico 00931-3346
| | - Victor D Rodríguez-Ramos
- Department of Biology, University of Puerto Rico, Río Piedras Campus, 17 Avenido, Universidad Suite 1701, San Juan, Puerto Rico 00925-2537
- Molecular Sciences Research Center, University of Puerto Rico, 1390 Ponce De Leon Avenido, Suite 2, San Juan Puerto Rico 00931-3346
| | - Rafael Maldonado-Hernández
- Department of Biology, University of Puerto Rico, Río Piedras Campus, 17 Avenido, Universidad Suite 1701, San Juan, Puerto Rico 00925-2537
- Molecular Sciences Research Center, University of Puerto Rico, 1390 Ponce De Leon Avenido, Suite 2, San Juan Puerto Rico 00931-3346
| | - José A González-Feliciano
- Molecular Sciences Research Center, University of Puerto Rico, 1390 Ponce De Leon Avenido, Suite 2, San Juan Puerto Rico 00931-3346
| | - Eduardo Nicolau
- Department of Chemistry, University of Puerto Rico, Río Piedras Campus, 17 Avenido, Universidad Suite 1701, San Juan, Puerto Rico 00925-2537
- Molecular Sciences Research Center, University of Puerto Rico, 1390 Ponce De Leon Avenido, Suite 2, San Juan Puerto Rico 00931-3346
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17
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Cobley JN. Mechanisms of Mitochondrial ROS Production in Assisted Reproduction: The Known, the Unknown, and the Intriguing. Antioxidants (Basel) 2020; 9:E933. [PMID: 33003362 PMCID: PMC7599503 DOI: 10.3390/antiox9100933] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 09/20/2020] [Accepted: 09/21/2020] [Indexed: 02/06/2023] Open
Abstract
The consensus that assisted reproduction technologies (ART), like in vitro fertilization, to induce oxidative stress (i.e., the known) belies how oocyte/zygote mitochondria-a major presumptive oxidative stressor-produce reactive oxygen species (ROS) with ART being unknown. Unravelling how oocyte/zygote mitochondria produce ROS is important for disambiguating the molecular basis of ART-induced oxidative stress and, therefore, to rationally target it (e.g., using site-specific mitochondria-targeted antioxidants). I review the known mechanisms of ROS production in somatic mitochondria to critique how oocyte/zygote mitochondria may produce ROS (i.e., the unknown). Several plausible site- and mode-defined mitochondrial ROS production mechanisms in ART are proposed. For example, complex I catalyzed reverse electron transfer-mediated ROS production is conceivable when oocytes are initially extracted due to at least a 10% increase in molecular dioxygen exposure (i.e., the intriguing). To address the term oxidative stress being used without recourse to the underlying chemistry, I use the species-specific spectrum of biologically feasible reactions to define plausible oxidative stress mechanisms in ART. Intriguingly, mitochondrial ROS-derived redox signals could regulate embryonic development (i.e., their production could be beneficial). Their potential beneficial role raises the clinical challenge of attenuating oxidative damage while simultaneously preserving redox signaling. This discourse sets the stage to unravel how mitochondria produce ROS in ART, and their biological roles from oxidative damage to redox signaling.
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Affiliation(s)
- James N Cobley
- Redox Biology Group, Institute for Health Sciences, University of the Highlands and Islands, Old Perth Road, Inverness IV2 3JH, UK
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18
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Cobley JN, Husi H. Immunological Techniques to Assess Protein Thiol Redox State: Opportunities, Challenges and Solutions. Antioxidants (Basel) 2020; 9:E315. [PMID: 32326525 PMCID: PMC7222201 DOI: 10.3390/antiox9040315] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 04/10/2020] [Accepted: 04/13/2020] [Indexed: 02/06/2023] Open
Abstract
To understand oxidative stress, antioxidant defense, and redox signaling in health and disease it is essential to assess protein thiol redox state. Protein thiol redox state is seldom assessed immunologically because of the inability to distinguish reduced and reversibly oxidized thiols by Western blotting. An underappreciated opportunity exists to use Click PEGylation to realize the transformative power of simple, time and cost-efficient immunological techniques. Click PEGylation harnesses selective, bio-orthogonal Click chemistry to separate reduced and reversibly oxidized thiols by selectively ligating a low molecular weight polyethylene glycol moiety to the redox state of interest. The resultant ability to disambiguate reduced and reversibly oxidized species by Western blotting enables Click PEGylation to assess protein thiol redox state. In the present review, to enable investigators to effectively harness immunological techniques to assess protein thiol redox state we critique the chemistry, promise and challenges of Click PEGylation.
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Affiliation(s)
- James Nathan Cobley
- Centre for Health Sciences, University of the Highlands and Islands, Inverness IV2 3JH, UK;
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19
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Cobley J, Noble A, Bessell R, Guille M, Husi H. Reversible Thiol Oxidation Inhibits the Mitochondrial ATP Synthase in Xenopus Laevis Oocytes. Antioxidants (Basel) 2020; 9:antiox9030215. [PMID: 32150908 PMCID: PMC7139892 DOI: 10.3390/antiox9030215] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 03/01/2020] [Accepted: 03/02/2020] [Indexed: 12/15/2022] Open
Abstract
Oocytes are postulated to repress the proton pumps (e.g., complex IV) and ATP synthase to safeguard mitochondrial DNA homoplasmy by curtailing superoxide production. Whether the ATP synthase is inhibited is, however, unknown. Here we show that: oligomycin sensitive ATP synthase activity is significantly greater (~170 vs. 20 nmol/min-1/mg-1) in testes compared to oocytes in Xenopus laevis (X. laevis). Since ATP synthase activity is redox regulated, we explored a regulatory role for reversible thiol oxidation. If a protein thiol inhibits the ATP synthase, then constituent subunits must be reversibly oxidised. Catalyst-free trans-cyclooctene 6-methyltetrazine (TCO-Tz) immunocapture coupled to redox affinity blotting reveals several subunits in F1 (e.g., ATP-α-F1) and Fo (e.g., subunit c) are reversibly oxidised. Catalyst-free TCO-Tz Click PEGylation reveals significant (~60%) reversible ATP-α-F1 oxidation at two evolutionary conserved cysteine residues (C244 and C294) in oocytes. TCO-Tz Click PEGylation reveals ~20% of the total thiols in the ATP synthase are substantially oxidised. Chemically reversing thiol oxidation significantly increased oligomycin sensitive ATP synthase activity from ~12 to 100 nmol/min-1/mg-1 in oocytes. We conclude that reversible thiol oxidation inhibits the mitochondrial ATP synthase in X. laevis oocytes.
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Affiliation(s)
- James Cobley
- Centre for Health Sciences, University of the Highlands and Islands, Inverness IV2 3JH, UK; (R.B.); (H.H.)
- Correspondence:
| | - Anna Noble
- School of Biological Sciences, European Xenopus Resource Centre, University of Portsmouth, King Henry Building, Portsmouth PO1 2DY, UK; (A.N.); (M.G.)
| | - Rachel Bessell
- Centre for Health Sciences, University of the Highlands and Islands, Inverness IV2 3JH, UK; (R.B.); (H.H.)
| | - Matthew Guille
- School of Biological Sciences, European Xenopus Resource Centre, University of Portsmouth, King Henry Building, Portsmouth PO1 2DY, UK; (A.N.); (M.G.)
| | - Holger Husi
- Centre for Health Sciences, University of the Highlands and Islands, Inverness IV2 3JH, UK; (R.B.); (H.H.)
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20
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Belén LH, Rangel-Yagui CDO, Beltrán Lissabet JF, Effer B, Lee-Estevez M, Pessoa A, Castillo RL, Farías JG. From Synthesis to Characterization of Site-Selective PEGylated Proteins. Front Pharmacol 2019; 10:1450. [PMID: 31920645 PMCID: PMC6930235 DOI: 10.3389/fphar.2019.01450] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 11/12/2019] [Indexed: 02/06/2023] Open
Abstract
Covalent attachment of therapeutic proteins to polyethylene glycol (PEG) is widely used for the improvement of its pharmacokinetic and pharmacological properties, as well as the reduction in reactogenicity and related side effects. This technique named PEGylation has been successfully employed in several approved drugs to treat various diseases, even cancer. Some methods have been developed to obtain PEGylated proteins, both in multiple protein sites or in a selected amino acid residue. This review focuses mainly on traditional and novel examples of chemical and enzymatic methods for site-selective PEGylation, emphasizing in N-terminal PEGylation, that make it possible to obtain products with a high degree of homogeneity and preserve bioactivity. In addition, the main assay methods that can be applied for the characterization of PEGylated molecules in complex biological samples are also summarized in this paper.
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Affiliation(s)
- Lisandra Herrera Belén
- Department of Chemical Engineering, Faculty of Engineering and Science, Universidad de La Frontera, Temuco, Chile
| | - Carlota de Oliveira Rangel-Yagui
- Department of Biochemical and Pharmaceutical Technology, School of Pharmaceutical Sciences, University of Sao Paulo, Sao Paulo, Brazil
| | - Jorge F. Beltrán Lissabet
- Department of Chemical Engineering, Faculty of Engineering and Science, Universidad de La Frontera, Temuco, Chile
| | - Brian Effer
- Department of Chemical Engineering, Faculty of Engineering and Science, Universidad de La Frontera, Temuco, Chile
| | - Manuel Lee-Estevez
- Faculty of Health Sciences, Universidad Autónoma de Chile, Temuco, Chile
| | - Adalberto Pessoa
- Department of Biochemical and Pharmaceutical Technology, School of Pharmaceutical Sciences, University of Sao Paulo, Sao Paulo, Brazil
| | - Rodrigo L. Castillo
- Department of Internal Medicine East, Faculty of Medicine, University of Chile, Santiago de Chile, Chile
| | - Jorge G. Farías
- Department of Chemical Engineering, Faculty of Engineering and Science, Universidad de La Frontera, Temuco, Chile
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21
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Cobley JN, Noble A, Jimenez-Fernandez E, Valdivia Moya MT, Guille M, Husi H. Catalyst-free Click PEGylation reveals substantial mitochondrial ATP synthase sub-unit alpha oxidation before and after fertilisation. Redox Biol 2019; 26:101258. [PMID: 31234016 PMCID: PMC6597785 DOI: 10.1016/j.redox.2019.101258] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 06/10/2019] [Accepted: 06/15/2019] [Indexed: 12/21/2022] Open
Abstract
Using non-reducing Western blotting to assess protein thiol redox state is challenging because most reduced and oxidised forms migrate at the same molecular weight and are, therefore, indistinguishable. While copper catalysed Click chemistry can be used to ligate a polyethylene glycol (PEG) moiety termed Click PEGylation to mass shift the reduced or oxidised form as desired, the potential for copper catalysed auto-oxidation is problematic. Here we define a catalyst-free trans-cyclooctene-methyltetrazine (TCO-Tz) inverse electron demand Diels Alder chemistry approach that affords rapid (k ~2000 M-1 s-1), selective and bio-orthogonal Click PEGylation. We used TCO-Tz Click PEGylation to investigate how fertilisation impacts reversible mitochondrial ATP synthase F1-Fo sub-unit alpha (ATP-α-F1) oxidation-an established molecular correlate of impaired enzyme activity-in Xenopus laevis. TCO-Tz Click PEGylation studies reveal substantial (~65%) reversible ATP-α-F1 oxidation at evolutionary conserved cysteine residues (i.e., C244 and C294) before and after fertilisation. A single thiol is, however, preferentially oxidised likely due to greater solvent exposure during the catalytic cycle. Selective reduction experiments show that: S-glutathionylation accounts for ~50-60% of the reversible oxidation observed, making it the dominant oxidative modification type. Intermolecular disulphide bonds may also contribute due to their relative stability. Substantial reversible ATP-α-F1 oxidation before and after fertilisation is biologically meaningful because it implies low mitochondrial F1-Fo ATP synthase activity. Catalyst-free TCO-Tz Click PEGylation is a valuable new tool to interrogate protein thiol redox state in health and disease.
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Affiliation(s)
- James N Cobley
- Free Radical Research Group, University of the Highlands and Islands, Centre for Health Sciences, Inverness, IV2 3JH, UK.
| | - Anna Noble
- European Xenopus Resource Centre, University of Portsmouth, School of Biological Sciences, King Henry Building, Portsmouth, PO1 2DY, UK
| | - Eduardo Jimenez-Fernandez
- Free Radical Research Group, University of the Highlands and Islands, Centre for Health Sciences, Inverness, IV2 3JH, UK
| | - Manuel-Thomas Valdivia Moya
- Free Radical Research Group, University of the Highlands and Islands, Centre for Health Sciences, Inverness, IV2 3JH, UK
| | - Matthew Guille
- European Xenopus Resource Centre, University of Portsmouth, School of Biological Sciences, King Henry Building, Portsmouth, PO1 2DY, UK
| | - Holger Husi
- Free Radical Research Group, University of the Highlands and Islands, Centre for Health Sciences, Inverness, IV2 3JH, UK
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McNelles SA, Marando VM, Adronov A. Globular Polymer Grafts Require a Critical Size for Efficient Molecular Sieving of Enzyme Substrates. Angew Chem Int Ed Engl 2019; 58:8448-8453. [PMID: 30893493 DOI: 10.1002/anie.201902864] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Indexed: 12/17/2022]
Affiliation(s)
- Stuart A. McNelles
- Department of Chemistry and Chemical BiologyMcMaster University 1280 Main Street West Hamilton Ontario L8S 4M1 Canada
| | - Victoria M. Marando
- Department of Chemistry and Chemical BiologyMcMaster University 1280 Main Street West Hamilton Ontario L8S 4M1 Canada
| | - Alex Adronov
- Department of Chemistry and Chemical BiologyMcMaster University 1280 Main Street West Hamilton Ontario L8S 4M1 Canada
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23
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McNelles SA, Marando VM, Adronov A. Globular Polymer Grafts Require a Critical Size for Efficient Molecular Sieving of Enzyme Substrates. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201902864] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Stuart A. McNelles
- Department of Chemistry and Chemical BiologyMcMaster University 1280 Main Street West Hamilton Ontario L8S 4M1 Canada
| | - Victoria M. Marando
- Department of Chemistry and Chemical BiologyMcMaster University 1280 Main Street West Hamilton Ontario L8S 4M1 Canada
| | - Alex Adronov
- Department of Chemistry and Chemical BiologyMcMaster University 1280 Main Street West Hamilton Ontario L8S 4M1 Canada
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24
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Shapiguzov A, Vainonen JP, Hunter K, Tossavainen H, Tiwari A, Järvi S, Hellman M, Aarabi F, Alseekh S, Wybouw B, Van Der Kelen K, Nikkanen L, Krasensky-Wrzaczek J, Sipari N, Keinänen M, Tyystjärvi E, Rintamäki E, De Rybel B, Salojärvi J, Van Breusegem F, Fernie AR, Brosché M, Permi P, Aro EM, Wrzaczek M, Kangasjärvi J. Arabidopsis RCD1 coordinates chloroplast and mitochondrial functions through interaction with ANAC transcription factors. eLife 2019; 8:43284. [PMID: 30767893 PMCID: PMC6414205 DOI: 10.7554/elife.43284] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 02/14/2019] [Indexed: 01/17/2023] Open
Abstract
Reactive oxygen species (ROS)-dependent signaling pathways from chloroplasts and mitochondria merge at the nuclear protein RADICAL-INDUCED CELL DEATH1 (RCD1). RCD1 interacts in vivo and suppresses the activity of the transcription factors ANAC013 and ANAC017, which mediate a ROS-related retrograde signal originating from mitochondrial complex III. Inactivation of RCD1 leads to increased expression of mitochondrial dysfunction stimulon (MDS) genes regulated by ANAC013 and ANAC017. Accumulating MDS gene products, including alternative oxidases (AOXs), affect redox status of the chloroplasts, leading to changes in chloroplast ROS processing and increased protection of photosynthetic apparatus. ROS alter the abundance, thiol redox state and oligomerization of the RCD1 protein in vivo, providing feedback control on its function. RCD1-dependent regulation is linked to chloroplast signaling by 3'-phosphoadenosine 5'-phosphate (PAP). Thus, RCD1 integrates organellar signaling from chloroplasts and mitochondria to establish transcriptional control over the metabolic processes in both organelles. Most plant cells contain two types of compartments, the mitochondria and the chloroplasts, which work together to supply the chemical energy required by life processes. Genes located in another part of the cell, the nucleus, encode for the majority of the proteins found in these compartments. At any given time, the mitochondria and the chloroplasts send specific, ‘retrograde’ signals to the nucleus to turn on or off the genes they need. For example, mitochondria produce molecules known as reactive oxygen species (ROS) if they are having problems generating energy. These molecules activate several regulatory proteins that move into the nucleus and switch on MDS genes, a set of genes which helps to repair the mitochondria. Chloroplasts also produce ROS that can act as retrograde signals. It is still unclear how the nucleus integrates signals from both chloroplasts and mitochondria to ‘decide’ which genes to switch on, but a protein called RCD1 may play a role in this process. Indeed, previous studies have found that Arabidopsis plants that lack RCD1 have defects in both their mitochondria and chloroplasts. In these mutant plants, the MDS genes are constantly active and the chloroplasts have problems making ROS. To investigate this further, Shapiguzov, Vainonen et al. use biochemical and genetic approaches to study RCD1 in Arabidopsis. The experiments confirm that this protein allows a dialog to take place between the retrograde signals of both mitochondria and chloroplasts. On one hand, RCD1 binds to and inhibits the regulatory proteins that usually activate the MDS genes under the control of mitochondria. This explains why, in the absence of RCD1, the MDS genes are always active, which is ultimately disturbing how these compartments work. On the other hand, RCD1 is also found to be sensitive to the ROS that chloroplasts produce. This means that chloroplasts may be able to affect when mitochondria generate energy by regulating the protein. Finally, further experiments show that MDS genes can affect both mitochondria and chloroplasts: by influencing how these genes are regulated, RCD1 therefore acts on the two types of compartments. Overall, the work by Shapiguzov, Vainonen et al. describes a new way Arabidopsis coordinates its mitochondria and chloroplasts. Further studies will improve our understanding of how plants regulate these compartments in different environments to produce the energy they need. In practice, this may also help plant breeders create new varieties of crops that produce energy more efficiently and which better resist to stress.
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Affiliation(s)
- Alexey Shapiguzov
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Viikki Plant Science Center, University of Helsinki, Helsinki, Finland.,Institute of Plant Physiology, Russian Academy of Sciences, Moscow, Russia
| | - Julia P Vainonen
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Viikki Plant Science Center, University of Helsinki, Helsinki, Finland
| | - Kerri Hunter
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Viikki Plant Science Center, University of Helsinki, Helsinki, Finland
| | - Helena Tossavainen
- Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, Helsinki, Finland.,Department of Chemistry, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - Arjun Tiwari
- Department of Biochemistry / Molecular Plant Biology, University of Turku, Turku, Finland
| | - Sari Järvi
- Department of Biochemistry / Molecular Plant Biology, University of Turku, Turku, Finland
| | - Maarit Hellman
- Department of Chemistry, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - Fayezeh Aarabi
- Max-Planck Institute for Molecular Plant Physiology, Potsdam, Germany
| | - Saleh Alseekh
- Max-Planck Institute for Molecular Plant Physiology, Potsdam, Germany.,Center of Plant System Biology and Biotechnology, Plovdiv, Bulgaria
| | - Brecht Wybouw
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Katrien Van Der Kelen
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Lauri Nikkanen
- Department of Biochemistry / Molecular Plant Biology, University of Turku, Turku, Finland
| | - Julia Krasensky-Wrzaczek
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Viikki Plant Science Center, University of Helsinki, Helsinki, Finland
| | - Nina Sipari
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Viikki Metabolomics Unit, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Markku Keinänen
- Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Finland
| | - Esa Tyystjärvi
- Department of Biochemistry / Molecular Plant Biology, University of Turku, Turku, Finland
| | - Eevi Rintamäki
- Department of Biochemistry / Molecular Plant Biology, University of Turku, Turku, Finland
| | - Bert De Rybel
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Jarkko Salojärvi
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Viikki Plant Science Center, University of Helsinki, Helsinki, Finland
| | - Frank Van Breusegem
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Alisdair R Fernie
- Max-Planck Institute for Molecular Plant Physiology, Potsdam, Germany.,Center of Plant System Biology and Biotechnology, Plovdiv, Bulgaria
| | - Mikael Brosché
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Viikki Plant Science Center, University of Helsinki, Helsinki, Finland.,Institute of Technology, University of Tartu, Tartu, Estonia
| | - Perttu Permi
- Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, Helsinki, Finland.,Department of Chemistry, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland.,Department of Biological and Environmental Science, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - Eva-Mari Aro
- Department of Biochemistry / Molecular Plant Biology, University of Turku, Turku, Finland
| | - Michael Wrzaczek
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Viikki Plant Science Center, University of Helsinki, Helsinki, Finland
| | - Jaakko Kangasjärvi
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Viikki Plant Science Center, University of Helsinki, Helsinki, Finland
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25
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Signes A, Cerutti R, Dickson AS, Benincá C, Hinchy EC, Ghezzi D, Carrozzo R, Bertini E, Murphy MP, Nathan JA, Viscomi C, Fernandez-Vizarra E, Zeviani M. APOPT1/COA8 assists COX assembly and is oppositely regulated by UPS and ROS. EMBO Mol Med 2019; 11:e9582. [PMID: 30552096 PMCID: PMC6328941 DOI: 10.15252/emmm.201809582] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 11/20/2018] [Accepted: 11/21/2018] [Indexed: 02/02/2023] Open
Abstract
Loss-of-function mutations in APOPT1, a gene exclusively found in higher eukaryotes, cause a characteristic type of cavitating leukoencephalopathy associated with mitochondrial cytochrome c oxidase (COX) deficiency. Although the genetic association of APOPT1 pathogenic variants with isolated COX defects is now clear, the biochemical link between APOPT1 function and COX has remained elusive. We investigated the molecular role of APOPT1 using different approaches. First, we generated an Apopt1 knockout mouse model which shows impaired motor skills, e.g., decreased motor coordination and endurance, associated with reduced COX activity and levels in multiple tissues. In addition, by achieving stable expression of wild-type APOPT1 in control and patient-derived cultured cells we ruled out a role of this protein in apoptosis and established instead that this protein is necessary for proper COX assembly and function. On the other hand, APOPT1 steady-state levels were shown to be controlled by the ubiquitination-proteasome system (UPS). Conversely, in conditions of increased oxidative stress, APOPT1 is stabilized, increasing its mature intramitochondrial form and thereby protecting COX from oxidatively induced degradation.
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Affiliation(s)
- Alba Signes
- MRC-Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - Raffaele Cerutti
- MRC-Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - Anna S Dickson
- Department of Medicine, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Cristiane Benincá
- MRC-Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | | | - Daniele Ghezzi
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico "Carlo Besta", Milan, Italy
- Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
| | - Rosalba Carrozzo
- Unit of Neuromuscular and Neurodegenerative Disorders, Bambino Gesù Children's Research Hospital, IRCCS, Rome, Italy
| | - Enrico Bertini
- Unit of Neuromuscular and Neurodegenerative Disorders, Bambino Gesù Children's Research Hospital, IRCCS, Rome, Italy
| | - Michael P Murphy
- MRC-Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - James A Nathan
- Department of Medicine, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Carlo Viscomi
- MRC-Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | | | - Massimo Zeviani
- MRC-Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
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26
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Lee YJ, Chang GD. Quantitative display of the redox status of proteins with maleimide-polyethylene glycol tagging. Electrophoresis 2018; 40:491-498. [DOI: 10.1002/elps.201800335] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 11/20/2018] [Accepted: 11/27/2018] [Indexed: 12/11/2022]
Affiliation(s)
- Yu-Jung Lee
- Institute of Biochemical Sciences; College of Life Science; National Taiwan University; Taipei Taiwan
| | - Geen-Dong Chang
- Institute of Biochemical Sciences; College of Life Science; National Taiwan University; Taipei Taiwan
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27
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Hinchy EC, Gruszczyk AV, Willows R, Navaratnam N, Hall AR, Bates G, Bright TP, Krieg T, Carling D, Murphy MP. Mitochondria-derived ROS activate AMP-activated protein kinase (AMPK) indirectly. J Biol Chem 2018; 293:17208-17217. [PMID: 30232152 PMCID: PMC6222118 DOI: 10.1074/jbc.ra118.002579] [Citation(s) in RCA: 195] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 09/10/2018] [Indexed: 01/07/2023] Open
Abstract
Mitochondrial reactive oxygen species (ROS) production is a tightly regulated redox signal that transmits information from the organelle to the cell. Other mitochondrial signals, such as ATP, are sensed by enzymes, including the key metabolic sensor and regulator, AMP-activated protein kinase (AMPK). AMPK responds to the cellular ATP/AMP and ATP/ADP ratios by matching mitochondrial ATP production to demand. Previous reports proposed that AMPK activity also responds to ROS, by ROS acting on redox-sensitive cysteine residues (Cys-299/Cys-304) on the AMPK α subunit. This suggests an appealing model in which mitochondria fine-tune AMPK activity by both adenine nucleotide–dependent mechanisms and by redox signals. Here we assessed whether physiological levels of ROS directly alter AMPK activity. To this end we added exogenous hydrogen peroxide (H2O2) to cells and utilized the mitochondria-targeted redox cycler MitoParaquat to generate ROS within mitochondria without disrupting oxidative phosphorylation. Mitochondrial and cytosolic thiol oxidation was assessed by measuring peroxiredoxin dimerization and by redox-sensitive fluorescent proteins. Replacing the putative redox-active cysteine residues on AMPK α1 with alanines did not alter the response of AMPK to H2O2. In parallel with measurements of AMPK activity, we measured the cell ATP/ADP ratio. This allowed us to separate the effects on AMPK activity due to ROS production from those caused by changes in this ratio. We conclude that AMPK activity in response to redox changes is not due to direct action on AMPK itself, but is a secondary consequence of redox effects on other processes, such as mitochondrial ATP production.
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Affiliation(s)
- Elizabeth C Hinchy
- From the MRC Mitochondrial Biology Unit, University of Cambridge, Wellcome Trust/MRC Building, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY
| | - Anja V Gruszczyk
- From the MRC Mitochondrial Biology Unit, University of Cambridge, Wellcome Trust/MRC Building, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY.,the University Department of Surgery and Cambridge NIHR Biomedical Research Centre Addenbrooke's Hospital, Cambridge CB2 0QQ
| | - Robin Willows
- the MRC London Institute of Medical Sciences, Hammersmith Hospital, Imperial College, London, W12 0NN, and
| | - Naveenan Navaratnam
- the MRC London Institute of Medical Sciences, Hammersmith Hospital, Imperial College, London, W12 0NN, and
| | - Andrew R Hall
- From the MRC Mitochondrial Biology Unit, University of Cambridge, Wellcome Trust/MRC Building, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY
| | - Georgina Bates
- From the MRC Mitochondrial Biology Unit, University of Cambridge, Wellcome Trust/MRC Building, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY
| | - Thomas P Bright
- From the MRC Mitochondrial Biology Unit, University of Cambridge, Wellcome Trust/MRC Building, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY
| | - Thomas Krieg
- the Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge CB2 0QQ, United Kingdom
| | - David Carling
- the MRC London Institute of Medical Sciences, Hammersmith Hospital, Imperial College, London, W12 0NN, and
| | - Michael P Murphy
- From the MRC Mitochondrial Biology Unit, University of Cambridge, Wellcome Trust/MRC Building, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY,
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