1
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Huang J, De Veirman L, Van Breusegem F. Cysteine thiol sulfinic acid in plant stress signaling. PLANT, CELL & ENVIRONMENT 2024; 47:2766-2779. [PMID: 38251793 DOI: 10.1111/pce.14827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 12/25/2023] [Accepted: 01/09/2024] [Indexed: 01/23/2024]
Abstract
Cysteine thiols are susceptible to various oxidative posttranslational modifications (PTMs) due to their high chemical reactivity. Thiol-based PTMs play a crucial role in regulating protein functions and are key contributors to cellular redox signaling. Although reversible thiol-based PTMs, such as disulfide bond formation, S-nitrosylation, and S-glutathionylation, have been extensively studied for their roles in redox regulation, thiol sulfinic acid (-SO2H) modification is often perceived as irreversible and of marginal significance in redox signaling. Here, we revisit this narrow perspective and shed light on the redox regulatory roles of -SO2H in plant stress signaling. We provide an overview of protein sulfinylation in plants, delving into the roles of hydrogen peroxide-mediated and plant cysteine oxidase-catalyzed formation of -SO2H, highlighting the involvement of -SO2H in specific regulatory signaling pathways. Additionally, we compile the existing knowledge of the -SO2H reducing enzyme, sulfiredoxin, offering insights into its molecular mechanisms and biological relevance. We further summarize current proteomic techniques for detecting -SO2H and furnish a list of experimentally validated cysteine -SO2H sites across various species, discussing their functional consequences. This review aims to spark new insights and discussions that lead to further investigations into the functional significance of protein -SO2H-based redox signaling in plants.
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Affiliation(s)
- Jingjing Huang
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Lindsy De Veirman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Frank Van Breusegem
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, VIB, Ghent, Belgium
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2
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Oldemeyer S, La Greca M, Langner P, Lê Công KL, Schlesinger R, Heberle J. Nanosecond Transient IR Spectroscopy of Halorhodopsin in Living Cells. J Am Chem Soc 2024; 146:19118-19127. [PMID: 38950551 PMCID: PMC11258790 DOI: 10.1021/jacs.4c03891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 06/23/2024] [Accepted: 06/25/2024] [Indexed: 07/03/2024]
Abstract
The ability to track minute changes of a single amino acid residue in a cellular environment is causing a paradigm shift in the attempt to fully understand the responses of biomolecules that are highly sensitive to their environment. Detecting early protein dynamics in living cells is crucial to understanding their mechanisms, such as those of photosynthetic proteins. Here, we elucidate the light response of the microbial chloride pump NmHR from the marine bacterium Nonlabens marinus, located in the membrane of living Escherichia coli cells, using nanosecond time-resolved UV/vis and IR absorption spectroscopy over the time range from nanoseconds to seconds. Transient structural changes of the retinal cofactor and the surrounding apoprotein are recorded using light-induced time-resolved UV/vis and IR difference spectroscopy. Of particular note, we have resolved the kinetics of the transient deprotonation of a single cysteine residue during the photocycle of NmHR out of the manifold of molecular vibrations of the cells. These findings are of high general relevance, given the successful development of optogenetic tools from photoreceptors to interfere with enzymatic and neuronal pathways in living organisms using light pulses as a noninvasive trigger.
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Affiliation(s)
- Sabine Oldemeyer
- Experimental
Molecular Biophysics, Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Mariafrancesca La Greca
- Genetic
Biophysics, Department of Physics, Freie
Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Pit Langner
- Experimental
Molecular Biophysics, Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Karoline-Luisa Lê Công
- Experimental
Molecular Biophysics, Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Ramona Schlesinger
- Genetic
Biophysics, Department of Physics, Freie
Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Joachim Heberle
- Experimental
Molecular Biophysics, Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
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3
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Saponaro A, Krumbach JH, Chaves-Sanjuan A, Sharifzadeh AS, Porro A, Castelli R, Hamacher K, Bolognesi M, DiFrancesco D, Clarke OB, Thiel G, Moroni A. Structural determinants of ivabradine block of the open pore of HCN4. Proc Natl Acad Sci U S A 2024; 121:e2402259121. [PMID: 38917012 PMCID: PMC11228525 DOI: 10.1073/pnas.2402259121] [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: 02/07/2024] [Accepted: 05/26/2024] [Indexed: 06/27/2024] Open
Abstract
HCN1-4 channels are the molecular determinants of the If/Ih current that crucially regulates cardiac and neuronal cell excitability. HCN dysfunctions lead to sinoatrial block (HCN4), epilepsy (HCN1), and chronic pain (HCN2), widespread medical conditions awaiting subtype-specific treatments. Here, we address the problem by solving the cryo-EM structure of HCN4 in complex with ivabradine, to date the only HCN-specific drug on the market. Our data show ivabradine bound inside the open pore at 3 Å resolution. The structure unambiguously proves that Y507 and I511 on S6 are the molecular determinants of ivabradine binding to the inner cavity, while F510, pointing outside the pore, indirectly contributes to the block by controlling Y507. Cysteine 479, unique to the HCN selectivity filter (SF), accelerates the kinetics of block. Molecular dynamics simulations further reveal that ivabradine blocks the permeating ion inside the SF by electrostatic repulsion, a mechanism previously proposed for quaternary ammonium ions.
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Affiliation(s)
- Andrea Saponaro
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Milan 20133, Italy
| | - Jan H Krumbach
- Department of Physics, Technische Universität Darmstadt, Darmstadt 64289, Germany
- Department of Biology and Centre for Synthetic Biology, Technische Universität Darmstadt, Darmstadt 64287, Germany
| | | | | | - Alessandro Porro
- Department of Biosciences, University of Milan, Milan 20133, Italy
| | - Roberta Castelli
- Department of Biosciences, University of Milan, Milan 20133, Italy
| | - Kay Hamacher
- Department of Physics, Technische Universität Darmstadt, Darmstadt 64289, Germany
- Department of Biology and Centre for Synthetic Biology, Technische Universität Darmstadt, Darmstadt 64287, Germany
| | | | - Dario DiFrancesco
- Department of Biosciences, University of Milan, Milan 20133, Italy
- Institute of Biophysics-Milan, Consiglio Nazionale delle Ricerche, Milan 20133, Italy
| | - Oliver B Clarke
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032
- Department of Anesthesiology, Columbia University Irving Medical Center, New York, NY 10032
- Irving Institute for Clinical and Translational Research, Columbia University, New York, NY 10032
| | - Gerhard Thiel
- Department of Biology and Centre for Synthetic Biology, Technische Universität Darmstadt, Darmstadt 64287, Germany
- Department of Biosciences, University of Milan, Milan 20133, Italy
| | - Anna Moroni
- Department of Biosciences, University of Milan, Milan 20133, Italy
- Institute of Biophysics-Milan, Consiglio Nazionale delle Ricerche, Milan 20133, Italy
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4
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Cannon AE, Horn PJ. The Molecular Frequency, Conservation and Role of Reactive Cysteines in Plant Lipid Metabolism. PLANT & CELL PHYSIOLOGY 2024; 65:826-844. [PMID: 38113384 DOI: 10.1093/pcp/pcad163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 11/21/2023] [Accepted: 12/18/2023] [Indexed: 12/21/2023]
Abstract
Cysteines (Cys) are chemically reactive amino acids containing sulfur that play diverse roles in plant biology. Recent proteomics investigations in Arabidopsis thaliana have revealed the presence of thiol post-translational modifications (PTMs) in several Cys residues. These PTMs are presumed to impact protein structure and function, yet mechanistic data regarding the specific Cys susceptible to modification and their biochemical relevance remain limited. To help address these limitations, we have conducted a wide-ranging analysis by integrating published datasets encompassing PTM proteomics (comparing S-sulfenylation, persulfidation, S-nitrosylation and S-acylation), genomics and protein structures, with a specific focus on proteins involved in plant lipid metabolism. The prevalence and distribution of modified Cys residues across all analyzed proteins is diverse and multifaceted. Nevertheless, by combining an evaluation of sequence conservation across 100+ plant genomes with AlphaFold-generated protein structures and physicochemical predictions, we have unveiled structural propensities associated with Cys modifications. Furthermore, we have identified discernible patterns in lipid biochemical pathways enriched with Cys PTMs, notably involving beta-oxidation, jasmonic acid biosynthesis, fatty acid biosynthesis and wax biosynthesis. These collective findings provide valuable insights for future investigations targeting the mechanistic foundations of Cys modifications and the regulation of modified proteins in lipid metabolism and other metabolic pathways.
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Affiliation(s)
- Ashley E Cannon
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, 1155 Union Circle, Denton, TX 76203, USA
| | - Patrick J Horn
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, 1155 Union Circle, Denton, TX 76203, USA
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5
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Povea-Cabello S, Brischigliaro M, Fernández-Vizarra E. Emerging mechanisms in the redox regulation of mitochondrial cytochrome c oxidase assembly and function. Biochem Soc Trans 2024; 52:873-885. [PMID: 38526156 DOI: 10.1042/bst20231183] [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: 01/30/2024] [Revised: 03/12/2024] [Accepted: 03/14/2024] [Indexed: 03/26/2024]
Abstract
In eukaryotic cells, mitochondria perform cellular respiration through a series of redox reactions ultimately reducing molecular oxygen to water. The system responsible for this process is the respiratory chain or electron transport system (ETS) composed of complexes I-IV. Due to its function, the ETS is the main source of reactive oxygen species (ROS), generating them on both sides of the mitochondrial inner membrane, i.e. the intermembrane space (IMS) and the matrix. A correct balance between ROS generation and scavenging is important for keeping the cellular redox homeostasis and other important aspects of cellular physiology. However, ROS generated in the mitochondria are important signaling molecules regulating mitochondrial biogenesis and function. The IMS contains a large number of redox sensing proteins, containing specific Cys-rich domains, that are involved in ETS complex biogenesis. The large majority of these proteins function as cytochrome c oxidase (COX) assembly factors, mainly for the handling of copper ions necessary for the formation of the redox reactive catalytic centers. A particular case of ROS-regulated COX assembly factor is COA8, whose intramitochondrial levels are increased by oxidative stress, promoting COX assembly and/or protecting the enzyme from oxidative damage. In this review, we will discuss the current knowledge concerning the role played by ROS in regulating mitochondrial activity and biogenesis, focusing on the COX enzyme and with a special emphasis on the functional role exerted by the redox sensitive Cys residues contained in the COX assembly factors.
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Affiliation(s)
- Suleva Povea-Cabello
- Department of Biomedical Sciences, University of Padova, 35131 Padova, Italy
- Veneto Institute of Molecular Medicine, 35129 Padova, Italy
| | - Michele Brischigliaro
- Department of Biomedical Sciences, University of Padova, 35131 Padova, Italy
- Veneto Institute of Molecular Medicine, 35129 Padova, Italy
| | - Erika Fernández-Vizarra
- Department of Biomedical Sciences, University of Padova, 35131 Padova, Italy
- Veneto Institute of Molecular Medicine, 35129 Padova, Italy
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6
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Liu R, Clayton J, Shen M, Bhatnagar S, Shen J. Machine Learning Models to Interrogate Proteome-Wide Covalent Ligandabilities Directed at Cysteines. JACS AU 2024; 4:1374-1384. [PMID: 38665640 PMCID: PMC11040703 DOI: 10.1021/jacsau.3c00749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 02/22/2024] [Accepted: 02/23/2024] [Indexed: 04/28/2024]
Abstract
Machine learning (ML) identification of covalently ligandable sites may accelerate targeted covalent inhibitor design and help expand the druggable proteome space. Here, we report the rigorous development and validation of the tree-based models and convolutional neural networks (CNNs) trained on a newly curated database (LigCys3D) of over 1000 liganded cysteines in nearly 800 proteins represented by over 10,000 three-dimensional structures in the protein data bank. The unseen tests yielded 94 and 93% area under the receiver operating characteristic curves for the tree models and CNNs, respectively. Based on the AlphaFold2 predicted structures, the ML models recapitulated the newly liganded cysteines in the PDB with over 90% recall values. To assist the community of covalent drug discoveries, we report the predicted ligandable cysteines in 392 human kinases and their locations in the sequence-aligned kinase structure, including the PH and SH2 domains. Furthermore, we disseminate a searchable online database LigCys3D (https://ligcys.computchem.org/) and a web prediction server DeepCys (https://deepcys.computchem.org/), both of which will be continuously updated and improved by including newly published experimental data. The present work represents an important step toward the ML-led integration of big genome data and structure models to annotate the human proteome space for the next-generation covalent drug discoveries.
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Affiliation(s)
- Ruibin Liu
- Department
of Pharmaceutical Sciences, University of
Maryland School of Pharmacy, Baltimore, Maryland 21201, United States
| | - Joseph Clayton
- Department
of Pharmaceutical Sciences, University of
Maryland School of Pharmacy, Baltimore, Maryland 21201, United States
- Division
of Applied Regulatory Science, Office of Clinical Pharmacology, Center
for Drug Evaluation and Research, U.S. Food
and Drug Administration, Silver
Spring, Maryland 20993, United States
| | - Mingzhe Shen
- Department
of Pharmaceutical Sciences, University of
Maryland School of Pharmacy, Baltimore, Maryland 21201, United States
| | - Shubham Bhatnagar
- Department
of Computer Science, University of Maryland
at College Park, College
Park, Maryland 20742, United States
| | - Jana Shen
- Department
of Pharmaceutical Sciences, University of
Maryland School of Pharmacy, Baltimore, Maryland 21201, United States
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7
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Khorashad JS, Rizzo S, Tonks A. Reactive oxygen species and its role in pathogenesis and resistance to therapy in acute myeloid leukemia. CANCER DRUG RESISTANCE (ALHAMBRA, CALIF.) 2024; 7:5. [PMID: 38434766 PMCID: PMC10905166 DOI: 10.20517/cdr.2023.125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 01/24/2024] [Accepted: 02/19/2024] [Indexed: 03/05/2024]
Abstract
Relapse following a short clinical response to therapy is the major challenge for the management of acute myeloid leukemia (AML) patients. Leukemic stem cells (LSC), as the source of relapse, have been investigated for their metabolic preferences and their alterations at the time of relapse. As LSC rely on oxidative phosphorylation (OXPHOS) for energy requirement, reactive oxygen species (ROS), as by-products of OXPHOS, have been investigated for their role in the effectiveness of the standard AML therapy. Increased levels of non-mitochondrial ROS, generated by nicotinamide adenine dinucleotide phosphate oxidase, in a subgroup of AML patients add to the complexity of studying ROS. Although there are various studies presenting the contribution of ROS to AML pathogenesis, resistance, and its inhibition or activation as a target, a model that can clearly explain its role in AML has not been conceptualized. This is due to the heterogeneity of AML, the dynamics of ROS production, which is influenced by factors such as the type of treatment, cell differentiation state, mitochondrial activity, and also the heterogeneous generation of non-mitochondrial ROS and limited available data on their interaction with the microenvironment. This review summarizes these challenges and the recent progress in this field.
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Affiliation(s)
- Jamshid Sorouri Khorashad
- Department of Immunology and inflammation, Imperial College London, London, W12 0NN, UK
- Department of Molecular Pathology, Institute of Cancer Research, Sutton, SM2 5PT, UK
- Department of Haematology, Division of Cancer & Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, UK
| | - Sian Rizzo
- Department of Haematology, Division of Cancer & Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, UK
| | - Alex Tonks
- Department of Haematology, Division of Cancer & Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, UK
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8
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Jiang Z, Tang Y, Lu J, Xu C, Niu Y, Zhang G, Yang Y, Cheng X, Tong L, Chen Z, Tang B. Identification of sulfhydryl-containing proteins and further evaluation of the selenium-tagged redox homeostasis-regulating proteins. Redox Biol 2024; 69:102969. [PMID: 38064764 PMCID: PMC10755098 DOI: 10.1016/j.redox.2023.102969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 11/16/2023] [Accepted: 11/16/2023] [Indexed: 01/01/2024] Open
Abstract
Chemoproteomic profiling of sulfhydryl-containing proteins has consistently been an attractive research hotspot. However, there remains a dearth of probes that are specifically designed for sulfhydryl-containing proteins, possessing sufficient reactivity, specificity, distinctive isotopic signature, as well as efficient labeling and evaluation capabilities for proteins implicated in the regulation of redox homeostasis. Here, the specific selenium-containing probes (Se-probes) in this work displayed high specificity and reactivity toward cysteine thiols on small molecules, peptides and purified proteins and showed very good competitive effect of proteins labeling in gel-ABPP. We identified more than 6000 candidate proteins. In TOP-ABPP, we investigated the peptide labeled by Se-probes, which revealed a distinct isotopic envelope pattern of selenium in both the primary and secondary mass spectra. This unique pattern can provide compelling evidence for identifying redox regulatory proteins and other target peptides. Furthermore, our examiation of post-translational modification (PTMs) of the cysteine site residues showed that oxidation PTMs was predominantly observed. We anticipate that Se-probes will enable broader and deeper proteome-wide profiling of sulfhydryl-containing proteins, provide an ideal tool for focusing on proteins that regulate redox homeostasis and advance the development of innovative selenium-based pharmaceuticals.
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Affiliation(s)
- Zhongyao Jiang
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Minis-try of Education, Institute of Molecular and Nano Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Shandong Normal University, Jinan, 250014, PR China
| | - Yue Tang
- Department of Emergency Medicine, Shandong Provincial Clinical Research Center for Emergency and Critical Care Medicine, Qilu Hospital of Shandong University, Jinan, PR China.
| | - Jun Lu
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Minis-try of Education, Institute of Molecular and Nano Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Shandong Normal University, Jinan, 250014, PR China
| | - Chang Xu
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Minis-try of Education, Institute of Molecular and Nano Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Shandong Normal University, Jinan, 250014, PR China
| | - Yaxin Niu
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Minis-try of Education, Institute of Molecular and Nano Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Shandong Normal University, Jinan, 250014, PR China
| | - Guanglu Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Minis-try of Education, Institute of Molecular and Nano Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Shandong Normal University, Jinan, 250014, PR China
| | - Yanmei Yang
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Minis-try of Education, Institute of Molecular and Nano Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Shandong Normal University, Jinan, 250014, PR China
| | - Xiufen Cheng
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Minis-try of Education, Institute of Molecular and Nano Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Shandong Normal University, Jinan, 250014, PR China
| | - Lili Tong
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Minis-try of Education, Institute of Molecular and Nano Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Shandong Normal University, Jinan, 250014, PR China
| | - Zhenzhen Chen
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Minis-try of Education, Institute of Molecular and Nano Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Shandong Normal University, Jinan, 250014, PR China.
| | - Bo Tang
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Minis-try of Education, Institute of Molecular and Nano Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Shandong Normal University, Jinan, 250014, PR China; Laoshan Laboratory, Qingdao, 266200, PR China.
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9
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Jeffries L, Mis EK, McWalter K, Donkervoort S, Brodsky NN, Carpier JM, Ji W, Ionita C, Roy B, Morrow JS, Darbinyan A, Iyer K, Aul RB, Banka S, Chao KR, Cobbold L, Cohen S, Custodio HM, Drummond-Borg M, Elmslie F, Finanger E, Hainline BE, Helbig I, Hewson S, Hu Y, Jackson A, Josifova D, Konstantino M, Leach ME, Mak B, McCormick D, McGee E, Nelson S, Nguyen J, Nugent K, Ortega L, Goodkin HP, Roeder E, Roy S, Sapp K, Saade D, Sisodiya SM, Stals K, Towner S, Wilson W, Khokha MK, Bönnemann CG, Lucas CL, Lakhani SA. Biallelic CRELD1 variants cause a multisystem syndrome, including neurodevelopmental phenotypes, cardiac dysrhythmias, and frequent infections. Genet Med 2024; 26:101023. [PMID: 37947183 PMCID: PMC10932913 DOI: 10.1016/j.gim.2023.101023] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 10/23/2023] [Accepted: 10/25/2023] [Indexed: 11/12/2023] Open
Abstract
PURPOSE We sought to delineate a multisystem disorder caused by recessive cysteine-rich with epidermal growth factor-like domains 1 (CRELD1) gene variants. METHODS The impact of CRELD1 variants was characterized through an international collaboration utilizing next-generation DNA sequencing, gene knockdown, and protein overexpression in Xenopus tropicalis, and in vitro analysis of patient immune cells. RESULTS Biallelic variants in CRELD1 were found in 18 participants from 14 families. Affected individuals displayed an array of phenotypes involving developmental delay, early-onset epilepsy, and hypotonia, with about half demonstrating cardiac arrhythmias and some experiencing recurrent infections. Most harbored a frameshift in trans with a missense allele, with 1 recurrent variant, p.(Cys192Tyr), identified in 10 families. X tropicalis tadpoles with creld1 knockdown displayed developmental defects along with increased susceptibility to induced seizures compared with controls. Additionally, human CRELD1 harboring missense variants from affected individuals had reduced protein function, indicated by a diminished ability to induce craniofacial defects when overexpressed in X tropicalis. Finally, baseline analyses of peripheral blood mononuclear cells showed similar proportions of immune cell subtypes in patients compared with healthy donors. CONCLUSION This patient cohort, combined with experimental data, provide evidence of a multisystem clinical syndrome mediated by recessive variants in CRELD1.
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Affiliation(s)
- Lauren Jeffries
- Yale University School of Medicine, Department of Pediatrics, New Haven, CT; Yale Pediatric Genomics Discovery Program, New Haven, CT
| | - Emily K Mis
- Yale University School of Medicine, Department of Pediatrics, New Haven, CT; Yale Pediatric Genomics Discovery Program, New Haven, CT
| | | | - Sandra Donkervoort
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD
| | - Nina N Brodsky
- Yale University School of Medicine, Department of Pediatrics, New Haven, CT; Yale Pediatric Genomics Discovery Program, New Haven, CT; Yale University School of Medicine, Department of Immunobiology, New Haven, CT
| | - Jean-Marie Carpier
- Yale University School of Medicine, Department of Immunobiology, New Haven, CT
| | - Weizhen Ji
- Yale University School of Medicine, Department of Pediatrics, New Haven, CT; Yale Pediatric Genomics Discovery Program, New Haven, CT
| | - Cristian Ionita
- Yale University School of Medicine, Department of Pediatrics, New Haven, CT
| | - Bhaskar Roy
- Yale University School of Medicine, Department of Neurology, New Haven, CT
| | - Jon S Morrow
- Yale University School of Medicine, Department of Pathology, New Haven, CT
| | - Armine Darbinyan
- Yale University School of Medicine, Department of Pathology, New Haven, CT
| | - Krishna Iyer
- Yale University School of Medicine, Department of Pathology, New Haven, CT
| | - Ritu B Aul
- Hospital for Sick Children, Division of Clinical and Metabolic Genetics, Toronto, Ontario, Canada
| | - Siddharth Banka
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, United Kingdom; Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Katherine R Chao
- Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Laura Cobbold
- South West Thames Regional Genetics Service, St George's, University of London, London, United Kingdom
| | - Stacey Cohen
- Children's Hospital of Philadelphia, Division of Neurology, Philadelphia, PA; The Epilepsy NeuroGenetics Initiative (ENGIN), Children's Hospital of Philadelphia, Philadelphia, PA; University of Pennsylvania Perelman School of Medicine, Department of Neurology, Philadelphia, PA
| | - Helena M Custodio
- Department of Clinical and Experimental Epilepsy, University College London Queen Square Institute of Neurology, London, WC1N 3BG, United Kingdom; Chalfont Centre for Epilepsy, Buckinghamshire, United Kingdom
| | | | - Frances Elmslie
- South West Thames Regional Genetics Service, St George's, University of London, London, United Kingdom
| | | | - Bryan E Hainline
- Indiana University School of Medicine, Indiana University Health Physicians, Indianapolis, IN
| | - Ingo Helbig
- Children's Hospital of Philadelphia, Division of Neurology, Philadelphia, PA; University of Pennsylvania Perelman School of Medicine, Department of Neurology, Philadelphia, PA
| | - Stacy Hewson
- Hospital for Sick Children, Division of Clinical and Metabolic Genetics, Toronto, Ontario, Canada
| | - Ying Hu
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD
| | - Adam Jackson
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, United Kingdom; Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Dragana Josifova
- Guys and St Thomas NHS Trust, Clinical Genetics, London, United Kingdom
| | | | | | - Bryan Mak
- University of California Los Angeles, David Geffen School of Medicine, Department of Human Genetics, Los Angeles, CA; Current affiliation: Genome Medical, South San Francisco, CA
| | - David McCormick
- King's College Hospital, Paediatric Neurosciences, London, United Kingdom
| | - Elisabeth McGee
- University of California Los Angeles, David Geffen School of Medicine, Department of Human Genetics, Los Angeles, CA; University of California Los Angeles, Clinical Genomics Center, Los Angeles, CA; University of California Los Angeles, Center for Duchenne Muscular Dystrophy, Los Angeles, CA
| | - Stanley Nelson
- University of California Los Angeles, David Geffen School of Medicine, Department of Human Genetics, Los Angeles, CA; University of California Los Angeles, Clinical Genomics Center, Los Angeles, CA; University of California Los Angeles, Center for Duchenne Muscular Dystrophy, Los Angeles, CA
| | - Joanne Nguyen
- Cook Children's Medical Center, Division of Genetics, Fort Worth, TX
| | - Kimberly Nugent
- Baylor College of Medicine, Department of Pediatrics, Houston, TX; Baylor College of Medicine, Department of Molecular and Human Genetics, Houston, TX; Current affiliation: Cooper Surgical, Trumbull, CT
| | - Lucy Ortega
- Cook Children's Medical Center, Division of Genetics, Fort Worth, TX
| | | | - Elizabeth Roeder
- Baylor College of Medicine, Department of Pediatrics, Houston, TX; Baylor College of Medicine, Department of Molecular and Human Genetics, Houston, TX
| | - Sani Roy
- Cook Children's Medical Center, Division of Endocrinology and Diabetes, Fort Worth, TX
| | - Katie Sapp
- Indiana University School of Medicine, Indiana University Health Physicians, Indianapolis, IN
| | - Dimah Saade
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD; Current affiliation: University of Iowa Carver College of Medicine, Iowa City, IA
| | - Sanjay M Sisodiya
- Department of Clinical and Experimental Epilepsy, University College London Queen Square Institute of Neurology, London, WC1N 3BG, United Kingdom; Chalfont Centre for Epilepsy, Buckinghamshire, United Kingdom
| | - Karen Stals
- Royal Devon & Exeter NHS Foundation Trust, Exeter Genomics Laboratory, Exeter, United Kingdom
| | - Shelley Towner
- University of Virginia School of Medicine, Charlottesville, VA
| | - William Wilson
- University of Virginia School of Medicine, Charlottesville, VA
| | - Mustafa K Khokha
- Yale University School of Medicine, Department of Pediatrics, New Haven, CT; Yale Pediatric Genomics Discovery Program, New Haven, CT; Yale University School of Medicine, Department of Genetics, New Haven, CT
| | - Carsten G Bönnemann
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD
| | - Carrie L Lucas
- Yale Pediatric Genomics Discovery Program, New Haven, CT; Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD
| | - Saquib A Lakhani
- Yale University School of Medicine, Department of Pediatrics, New Haven, CT; Yale Pediatric Genomics Discovery Program, New Haven, CT.
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10
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Graf A, Bassukas AEL, Xiao Y, Barbosa ICR, Mergner J, Grill P, Michalke B, Kuster B, Schwechheimer C. D6PK plasma membrane polarity requires a repeated CXX(X)P motif and PDK1-dependent phosphorylation. NATURE PLANTS 2024; 10:300-314. [PMID: 38278951 PMCID: PMC10881395 DOI: 10.1038/s41477-023-01615-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 12/15/2023] [Indexed: 01/28/2024]
Abstract
D6 PROTEIN KINASE (D6PK) is a polarly localized plasma-membrane-associated kinase from Arabidopsis thaliana that activates polarly distributed PIN-FORMED auxin transporters. D6PK moves rapidly to and from the plasma membrane, independent of its PIN-FORMED targets. The middle D6PK domain, an insertion between kinase subdomains VII and VIII, is required and sufficient for association and polarity of the D6PK plasma membrane. How D6PK polarity is established and maintained remains to be shown. Here we show that cysteines from repeated middle domain CXX(X)P motifs are S-acylated and required for D6PK membrane association. While D6PK S-acylation is not detectably regulated during intracellular transport, phosphorylation of adjacent serine residues, in part in dependence on the upstream 3-PHOSPHOINOSITIDE-DEPENDENT PROTEIN KINASE, promotes D6PK transport, controls D6PK residence time at the plasma membrane and prevents its lateral diffusion. We thus identify new mechanisms for the regulation of D6PK plasma membrane interaction and polarity.
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Affiliation(s)
- Alina Graf
- Plant Systems Biology, School of Life Sciences, Technical University of Munich, Freising, Germany
| | | | - Yao Xiao
- Plant Systems Biology, School of Life Sciences, Technical University of Munich, Freising, Germany
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Inês C R Barbosa
- Plant Systems Biology, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Julia Mergner
- Proteomics and Bioanalytics, School of Life Sciences, Technical University of Munich, Freising, Germany
- Bavarian Center for Biomolecular Mass Spectrometry at Klinikum rechts der Isar, Center for Translational Cancer Research, Munich, Germany
| | - Peter Grill
- Helmholtz Zentrum München, German Research Center for Environmental Health, Analytical BioGeoChemistry, Neuherberg, Germany
| | - Bernhard Michalke
- Helmholtz Zentrum München, German Research Center for Environmental Health, Analytical BioGeoChemistry, Neuherberg, Germany
| | - Bernhard Kuster
- Proteomics and Bioanalytics, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Claus Schwechheimer
- Plant Systems Biology, School of Life Sciences, Technical University of Munich, Freising, Germany.
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11
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Yao F, Yuan K, Zhou W, Tang W, Tang T, Yang X, Liu H, Li F, Xu Q, Peng C. Unlocking growth potential in Halomonas bluephagenesis for enhanced PHA production with sulfate ions. J Ind Microbiol Biotechnol 2024; 51:kuae013. [PMID: 38632039 DOI: 10.1093/jimb/kuae013] [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: 01/30/2024] [Accepted: 04/16/2024] [Indexed: 04/19/2024]
Abstract
The mutant strain Halomonas bluephagenesis (TDH4A1B5P) was found to produce PHA under low-salt, non-sterile conditions, but the yield was low. To improve the yield, different nitrogen sources were tested. It was discovered that urea was the most effective nitrogen source for promoting growth during the stable stage, while ammonium sulfate was used during the logarithmic stage. The growth time of H. bluephagenesis (TDH4A1B5P) and its PHA content were significantly prolonged by the presence of sulfate ions. After 64 hr in a 5-L bioreactor supplemented with sulfate ions, the dry cell weight (DCW) of H. bluephagenesis weighed 132 g/L and had a PHA content of 82%. To promote the growth and PHA accumulation of H. bluephagenesis (TDH4A1B5P), a feeding regimen supplemented with nitrogen sources and sulfate ions with ammonium sodium sulfate was established in this study. The DCW was 124 g/L, and the PHA content accounted for 82.3% (w/w) of the DCW, resulting in a PHA yield of 101 g/L in a 30-L bioreactor using the optimized culture strategy. In conclusion, stimulating H. bluephagenesis (TDH4A1B5P) to produce PHA is a feasible and suitable strategy for all H. bluephagenesis.
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Affiliation(s)
- Fuwei Yao
- School of food science and pharmaceutical engineering, Nanjing Normal University (NNU), Nanjing, 210023, China
- Biotechnology Center, COFCO Nutrition and Health Research Institute Co., Ltd., Beijing, 102209, China
| | - Kai Yuan
- Biotechnology Center, COFCO Nutrition and Health Research Institute Co., Ltd., Beijing, 102209, China
- COFCO Bio-Chemical Energy (Yushu) Co., Ltd., COFCO Biotechnology Co., Ltd., Changchun, 130400, China
| | - Weiqiang Zhou
- Biotechnology Center, COFCO Nutrition and Health Research Institute Co., Ltd., Beijing, 102209, China
- COFCO Bio-Chemical Energy (Yushu) Co., Ltd., COFCO Biotechnology Co., Ltd., Changchun, 130400, China
| | - Weitao Tang
- Biotechnology Center, COFCO Nutrition and Health Research Institute Co., Ltd., Beijing, 102209, China
- COFCO Bio-Chemical Energy (Yushu) Co., Ltd., COFCO Biotechnology Co., Ltd., Changchun, 130400, China
| | - Tang Tang
- Biotechnology Center, COFCO Nutrition and Health Research Institute Co., Ltd., Beijing, 102209, China
- COFCO Bio-Chemical Energy (Yushu) Co., Ltd., COFCO Biotechnology Co., Ltd., Changchun, 130400, China
| | - Xiaofan Yang
- Biotechnology Center, COFCO Nutrition and Health Research Institute Co., Ltd., Beijing, 102209, China
- COFCO Bio-Chemical Energy (Yushu) Co., Ltd., COFCO Biotechnology Co., Ltd., Changchun, 130400, China
| | - Haijun Liu
- Biotechnology Center, COFCO Nutrition and Health Research Institute Co., Ltd., Beijing, 102209, China
- COFCO Bio-Chemical Energy (Yushu) Co., Ltd., COFCO Biotechnology Co., Ltd., Changchun, 130400, China
| | - Fangliang Li
- Biotechnology Center, COFCO Nutrition and Health Research Institute Co., Ltd., Beijing, 102209, China
- COFCO Bio-Chemical Energy (Yushu) Co., Ltd., COFCO Biotechnology Co., Ltd., Changchun, 130400, China
| | - Qing Xu
- School of food science and pharmaceutical engineering, Nanjing Normal University (NNU), Nanjing, 210023, China
| | - Chao Peng
- Biotechnology Center, COFCO Nutrition and Health Research Institute Co., Ltd., Beijing, 102209, China
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12
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Yang M, Silverstein RL. Targeting Cysteine Oxidation in Thrombotic Disorders. Antioxidants (Basel) 2024; 13:83. [PMID: 38247507 PMCID: PMC10812781 DOI: 10.3390/antiox13010083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 12/29/2023] [Accepted: 01/05/2024] [Indexed: 01/23/2024] Open
Abstract
Oxidative stress increases the risk for clinically significant thrombotic events, yet the mechanisms by which oxidants become prothrombotic are unclear. In this review, we provide an overview of cysteine reactivity and oxidation. We then highlight recent findings on cysteine oxidation events in oxidative stress-related thrombosis. Special emphasis is on the signaling pathway induced by a platelet membrane protein, CD36, in dyslipidemia, and by protein disulfide isomerase (PDI), a member of the thiol oxidoreductase family of proteins. Antioxidative and chemical biology approaches to target cysteine are discussed. Lastly, the knowledge gaps in the field are highlighted as they relate to understanding how oxidative cysteine modification might be targeted to limit thrombosis.
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Affiliation(s)
- Moua Yang
- Division of Hemostasis and Thrombosis, Beth Israel Deaconess Medical Center, Harvard Medical School, 3 Blackfan Circle, CLS-924, Boston, MA 02115, USA
| | - Roy L. Silverstein
- Department of Medicine, Medical College of Wisconsin, Hub 8745, 8701 W Watertown Plank Rd., Milwaukee, WI 53226, USA
- Versiti Blood Research Institute, Milwaukee, WI 53226, USA
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13
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Liu R, Clayton J, Shen M, Bhatnagar S, Shen J. Machine Learning Models to Interrogate Proteomewide Covalent Ligandabilities Directed at Cysteines. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.08.17.553742. [PMID: 37662346 PMCID: PMC10473668 DOI: 10.1101/2023.08.17.553742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Machine learning (ML) identification of covalently ligandable sites may accelerate targeted covalent inhibitor design and help expand the druggable proteome space. Here we report the rigorous development and validation of the tree-based models and convolutional neural networks (CNNs) trained on a newly curated database (LigCys3D) of over 1,000 liganded cysteines in nearly 800 proteins represented by over 10,000 three-dimensional structures in the protein data bank. The unseen tests yielded 94% and 93% AUCs (area under the receiver operating characteristic curve) for the tree models and CNNs, respectively. Based on the AlphaFold2 predicted structures, the ML models recapitulated the newly liganded cysteines in the PDB with over 90% recall values. To assist the community of covalent drug discoveries, we report the predicted ligandable cysteines in 392 human kinases and their locations in the sequence-aligned kinase structure including the PH and SH2 domains. Furthermore, we disseminate a searchable online database LigCys3D (https://ligcys.computchem.org/) and a web prediction server DeepCys (https://deepcys.computchem.org/), both of which will be continuously updated and improved by including newly published experimental data. The present work represents a first step towards the ML-led integration of big genome data and structure models to annotate the human proteome space for the next-generation covalent drug discoveries.
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Affiliation(s)
- Ruibin Liu
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD 21201, USA
| | - Joseph Clayton
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD 21201, USA
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Mingzhe Shen
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD 21201, USA
| | - Shubham Bhatnagar
- Department of Computer Science, University of Maryland at College Park, College Park, MD 20742, USA
| | - Jana Shen
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD 21201, USA
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14
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Evic V, Soic R, Mocibob M, Kekez M, Houser J, Wimmerová M, Matković-Čalogović D, Gruic-Sovulj I, Kekez I, Rokov-Plavec J. Evolutionarily conserved cysteines in plant cytosolic seryl-tRNA synthetase are important for its resistance to oxidation. FEBS Lett 2023; 597:2975-2992. [PMID: 37804069 DOI: 10.1002/1873-3468.14748] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 09/08/2023] [Accepted: 09/22/2023] [Indexed: 10/08/2023]
Abstract
We have previously identified a unique disulfide bond in the crystal structure of Arabidopsis cytosolic seryl-tRNA synthetase involving cysteines evolutionarily conserved in all green plants. Here, we discovered that both cysteines are important for protein stability, but with opposite effects, and that their microenvironment may promote disulfide bond formation in oxidizing conditions. The crystal structure of the C244S mutant exhibited higher rigidity and an extensive network of noncovalent interactions correlating with its higher thermal stability. The activity of the wild-type showed resistance to oxidation with H2 O2 , while the activities of cysteine-to-serine mutants were impaired, indicating that the disulfide link may enable the protein to function under oxidative stress conditions which can be beneficial for an efficient plant stress response.
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Affiliation(s)
- Valentina Evic
- Division of Biochemistry, Department of Chemistry, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Ruzica Soic
- Division of General and Inorganic Chemistry, Department of Chemistry, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Marko Mocibob
- Division of Biochemistry, Department of Chemistry, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Mario Kekez
- Division of Biochemistry, Department of Chemistry, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Josef Houser
- Central European Institute of Technology (CEITEC), Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Michaela Wimmerová
- Central European Institute of Technology (CEITEC), Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Dubravka Matković-Čalogović
- Division of General and Inorganic Chemistry, Department of Chemistry, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Ita Gruic-Sovulj
- Division of Biochemistry, Department of Chemistry, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Ivana Kekez
- Division of General and Inorganic Chemistry, Department of Chemistry, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Jasmina Rokov-Plavec
- Division of Biochemistry, Department of Chemistry, Faculty of Science, University of Zagreb, Zagreb, Croatia
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15
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Vaissier Welborn V. Understanding Cysteine Reactivity in Protein Environments with Electric Fields. J Phys Chem B 2023; 127:9936-9942. [PMID: 37962274 DOI: 10.1021/acs.jpcb.3c05749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
The role cysteine residues play in proteins is mediated by their protonation state, whereby the thiolate form of the side chain is highly reactive while the thiol form is more inert. However, the pKa of cysteine residues is hard to predict as it can differ widely from its reference value in solution, an effect that is accentuated by local effects in the heterogeneous protein environment. Here, we present a new approach to the prediction of cysteine reactivity based on electric field calculations at the thiol/thiolate group. We validated our approach by predicting the protonation state of cysteine residues in different protein environments (in the active site, at the protein surface, and buried within the protein interior), including Cys-25 in papaya protease omega, which was proven problematic for the more traditional constant pH molecular dynamics (MD) technique. We predict pKa shifts consistent with experimental observations, and the decomposition of the electric fields into contributions from molecular fragments provides a direct handle to rationalize local pH and pKa effects in proteins without introducing parameters other than those of the force field used for MD simulations.
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Affiliation(s)
- Valerie Vaissier Welborn
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24060, United States
- Macromolecules Innovation Institute (MII),Virginia Tech, Blacksburg, Virginia 24060, United States
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16
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Hocking B, Armstrong A, Mann DJ. Covalent fragment libraries in drug discovery-Design, synthesis, and screening methods. PROGRESS IN MEDICINAL CHEMISTRY 2023; 62:105-146. [PMID: 37981350 DOI: 10.1016/bs.pmch.2023.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2023]
Abstract
As the development of drugs with a covalent mode of action is becoming increasingly popular, well-validated covalent fragment-based drug discovery (FBDD) methods have been comparatively slow to keep up with the demand. In this chapter the principles of covalent fragment reactivity, library design, synthesis, and screening methods are explored in depth, focussing on literature examples with direct applications to practical covalent fragment library design and screening. Further, questions about the future of the field are explored and potential useful advances are proposed.
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Affiliation(s)
- Brad Hocking
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Alan Armstrong
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, London, United Kingdom
| | - David J Mann
- Department of Life Sciences, Imperial College London, London, United Kingdom.
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17
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Okoye CN, Koren SA, Wojtovich AP. Mitochondrial complex I ROS production and redox signaling in hypoxia. Redox Biol 2023; 67:102926. [PMID: 37871533 PMCID: PMC10598411 DOI: 10.1016/j.redox.2023.102926] [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: 08/31/2023] [Revised: 09/29/2023] [Accepted: 10/06/2023] [Indexed: 10/25/2023] Open
Abstract
Mitochondria are a main source of cellular energy. Oxidative phosphorylation (OXPHOS) is the major process of aerobic respiration. Enzyme complexes of the electron transport chain (ETC) pump protons to generate a protonmotive force (Δp) that drives OXPHOS. Complex I is an electron entry point into the ETC. Complex I oxidizes nicotinamide adenine dinucleotide (NADH) and transfers electrons to ubiquinone in a reaction coupled with proton pumping. Complex I also produces reactive oxygen species (ROS) under various conditions. The enzymatic activities of complex I can be regulated by metabolic conditions and serves as a regulatory node of the ETC. Complex I ROS plays diverse roles in cell metabolism ranging from physiologic to pathologic conditions. Progress in our understanding indicates that ROS release from complex I serves important signaling functions. Increasing evidence suggests that complex I ROS is important in signaling a mismatch in energy production and demand. In this article, we review the role of ROS from complex I in sensing acute hypoxia.
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Affiliation(s)
- Chidozie N Okoye
- Department of Anesthesiology and Perioperative Medicine, University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Shon A Koren
- Department of Neurobiology, Harvard Medical School, Boston, MA, 02115, USA
| | - Andrew P Wojtovich
- Department of Anesthesiology and Perioperative Medicine, University of Rochester Medical Center, Rochester, NY, 14642, USA; Department of Pharmacology and Physiology, University of Rochester Medical Center, Rochester, NY, 14642, USA.
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18
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Ding X, Yang B, Liu Z, Shen M, Fan Z, Wang X, Yu W. A novel intramolecular charge transfer-based near-infrared fluorescent probe with large Stokes shift for highly sensitive detection of cysteine in vivo. Anal Chim Acta 2023; 1280:341873. [PMID: 37858558 DOI: 10.1016/j.aca.2023.341873] [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: 07/25/2023] [Revised: 09/22/2023] [Accepted: 10/03/2023] [Indexed: 10/21/2023]
Abstract
Cysteine (Cys) distribute widely in organisms as the crucial components of proteins, and play important roles in pathophysiological processes of human body. Low level of Cys might induce hepatic injury, edema and growth retardation, while superfluous level of Cys is found to be closely relevant to Alzheimer's and Parkinson's diseases. In this work, a novel near-infrared (NIR) fluorescent probe PFQ-C was developed for highly selective detection of Cys in living cells and mice by utilizing the cyclization removal reaction between acrylate group and Cys. The superior sensitivity (limit of detection, 0.036 μM), NIR emission (655 nm), large Stokes shift (135 nm) and low cytotoxicity of the probe highlight its broad potential for future clinical applications. The response mechanism of the probe towards Cys was clarified by spectroscopy, chromatography and theoretical calculation. In addition, results of fluorescence imaging of cells and mice revealed the good performance of the probe for monitoring the distributions and variations of Cys activity in vivo, which is very useful for the researches on diseases associated with Cys.
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Affiliation(s)
- Xiangdong Ding
- Department of Plastic and Reconstructive Microsurgery, China-Japan Union Hospital, Jilin University, Xiantai Street 126, Changchun, 130033, PR China
| | - Bin Yang
- College of Chemistry, Jilin University, Qianjin Street 2699, Changchun, 130012, PR China; State Key Laboratory of Supramolecular Structure and Materials, Jilin University, Qianjin Street 2699, Changchun, 130012, PR China
| | - Zhongling Liu
- China-Japan Union Hospital, Jilin University, Xiantai Street 126, Changchun, 130033, PR China
| | - Meidi Shen
- School of Nursing, Peking University, Xueyuan Street 38, Beijing, 100191, PR China
| | - Zheyuan Fan
- Department of Plastic and Reconstructive Microsurgery, China-Japan Union Hospital, Jilin University, Xiantai Street 126, Changchun, 130033, PR China
| | - Xinghua Wang
- College of Chemistry, Jilin University, Qianjin Street 2699, Changchun, 130012, PR China.
| | - Wei Yu
- Department of Plastic and Reconstructive Microsurgery, China-Japan Union Hospital, Jilin University, Xiantai Street 126, Changchun, 130033, PR China.
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19
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Beutel J, Tannig P, Di Vincenzo R, Schumacher T, Überla K, Eichler J. Bind&Bite: covalently stabilized heterodimeric coiled-coil peptides for the site-selective, cysteine-free chemical modification of proteins. RSC Chem Biol 2023; 4:794-803. [PMID: 37799587 PMCID: PMC10549240 DOI: 10.1039/d3cb00122a] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 07/16/2023] [Indexed: 10/07/2023] Open
Abstract
Ensuring site-selectivity in covalent chemical modification of proteins is one of the major challenges in chemical biology and related biomedical disciplines. Most current strategies either utilize the selectivity of proteases, or are based on reactions involving the thiol groups of cysteine residues. We have modified a pair of heterodimeric coiled-coil peptides to enable the selective covalent stabilization of the dimer without using enzymes or cysteine moieties. Fusion of one peptide to the protein of interest, in combination with linking the desired chemical modification to the complementary peptide, facilitates stable, regio-selective attachment of the chemical moiety to the protein, through the formation of the covalently stabilized coiled-coil. This ligation method, which is based on the formation of isoeptide and squaramide bonds, respectively, between the coiled-coil peptides, was successfully used to selectively modify the HIV-1 envelope glycoprotein. Covalent stabilization of the coiled-coil also facilitated truncation of the peptides by one heptad sequence. Furthermore, selective addressing of individual positions of the peptides enabled the generation of mutually selective coiled-coils. The established method, termed Bind&Bite, can be expected to be beneficial for a range of biotechnological and biomedical applications, in which chemical moieties need to be stably attached to proteins in a site-selective fashion.
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Affiliation(s)
- Jannis Beutel
- Department of Chemistry and Pharmacy, University of Erlangen-Nürnberg (FAU) Erlangen Germany
- Institut Virion-Serion GmbH Würzburg Germany
| | - Pierre Tannig
- Institute of Clinical and Molecular Virology, University of Erlangen-Nürnberg (FAU) Erlangen Germany
| | - Riccardo Di Vincenzo
- Institute of Clinical and Molecular Virology, University of Erlangen-Nürnberg (FAU) Erlangen Germany
| | | | - Klaus Überla
- Institute of Clinical and Molecular Virology, University of Erlangen-Nürnberg (FAU) Erlangen Germany
| | - Jutta Eichler
- Department of Chemistry and Pharmacy, University of Erlangen-Nürnberg (FAU) Erlangen Germany
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20
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Levings DC, Pathak SS, Yang YM, Slattery M. Limited expression of Nrf2 in neurons across the central nervous system. Redox Biol 2023; 65:102830. [PMID: 37544245 PMCID: PMC10428127 DOI: 10.1016/j.redox.2023.102830] [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: 03/24/2023] [Revised: 07/24/2023] [Accepted: 07/25/2023] [Indexed: 08/08/2023] Open
Abstract
Nrf2, encoded by the gene Nfe2l2, is a broadly expressed transcription factor that regulates gene expression in response to reactive oxygen species (ROS) and oxidative stress. It is commonly referred to as a ubiquitous pathway, but this generalization overlooks work indicating that Nrf2 is essentially unexpressed in some neuronal populations. To explore whether this pattern extends throughout the central nervous system (CNS), we quantified Nfe2l2 expression and chromatin accessibility at the Nfe2l2 locus across multiple single cell datasets. In both the mouse and human CNS, Nfe2l2 was repressed in almost all mature neurons, but highly expressed in non-neuronal support cells, and this pattern was robust across multiple human CNS diseases. A subset of key Nrf2 target genes, like Slc7a11, also remained low in neurons. Thus, these data suggest that while most cells express Nfe2l2, with activity determined by ROS levels, neurons actively avoid Nrf2 activity by keeping Nfe2l2 expression low.
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Affiliation(s)
- Daniel C Levings
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth, MN, 55812, USA
| | - Salil Saurav Pathak
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth, MN, 55812, USA
| | - Yi-Mei Yang
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth, MN, 55812, USA; Department of Neuroscience, University of Minnesota Medical School, Minneapolis, MN, 55455, USA
| | - Matthew Slattery
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth, MN, 55812, USA.
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21
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Lacher SE, Skon-Hegg C, Ruis BL, Krznarich J, Slattery M. An antioxidant response element regulates the HIF1α axis in breast cancer cells. Free Radic Biol Med 2023; 204:243-251. [PMID: 37179033 PMCID: PMC10321210 DOI: 10.1016/j.freeradbiomed.2023.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 04/28/2023] [Accepted: 05/02/2023] [Indexed: 05/15/2023]
Abstract
The redox sensitive transcription factor NRF2 is a central regulator of the transcriptional response to reactive oxygen species (ROS). NRF2 is widely recognized for its ROS-responsive upregulation of antioxidant genes that are essential for mitigating the damaging effects of oxidative stress. However, multiple genome-wide approaches have suggested that NRF2's regulatory reach extends well beyond the canonical antioxidant genes, with the potential to regulate many noncanonical target genes. Recent work from our lab and others suggests HIF1A, which encodes the hypoxia-responsive transcription factor HIF1α, is one such noncanonical NRF2 target. These studies found that NRF2 activity is associated with high HIF1A expression in multiple cellular contexts, HIF1A expression is partially dependent on NRF2, and there is a putative NRF2 binding site (antioxidant response element, or ARE) approximately 30 kilobases upstream of HIF1A. These findings all support a model in which HIF1A is a direct target of NRF2, but did not confirm the functional importance of the upstream ARE in HIF1A expression. Here we use CRISPR/Cas9 genome editing to mutate this ARE in its genomic context and test the impact on HIF1A expression. We find that mutation of this ARE in a breast cancer cell line (MDA-MB-231) eliminates NRF2 binding and decreases HIF1A expression at the transcript and protein levels, and disrupts HIF1α target genes as well as phenotypes driven by these HIF1α targets. Taken together, these results indicate that this NRF2 targeted ARE plays an important role in the expression of HIF1A and activity of the HIF1α axis in MDA-MB-231 cells.
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Affiliation(s)
- Sarah E Lacher
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth, MN, 55812, USA.
| | - Cara Skon-Hegg
- Whiteside Institute for Clinical Research, St. Luke's Hospital, University of Minnesota Medical School, Duluth, MN, 55812, USA
| | - Brian L Ruis
- Masonic Cancer Center, University of Minnesota Medical School, Minneapolis, MN, 55455, USA
| | - Jennifer Krznarich
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth, MN, 55812, USA
| | - Matthew Slattery
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth, MN, 55812, USA.
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22
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Geddes JW, Bondada V, Croall DE, Rodgers DW, Gal J. Impaired activity and membrane association of most calpain-5 mutants causal for neovascular inflammatory vitreoretinopathy. Biochim Biophys Acta Mol Basis Dis 2023; 1869:166747. [PMID: 37207905 PMCID: PMC10332796 DOI: 10.1016/j.bbadis.2023.166747] [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: 07/22/2022] [Revised: 03/29/2023] [Accepted: 05/02/2023] [Indexed: 05/21/2023]
Abstract
Neovascular inflammatory vitreoretinopathy (NIV) is a rare eye disease that ultimately leads to complete blindness and is caused by mutations in the gene encoding calpain-5 (CAPN5), with six pathogenic mutations identified. In transfected SH-SY5Y cells, five of the mutations resulted in decreased membrane association, diminished S-acylation, and reduced calcium-induced autoproteolysis of CAPN5. CAPN5 proteolysis of the autoimmune regulator AIRE was impacted by several NIV mutations. R243, L244, K250 and the adjacent V249 are on β-strands in the protease core 2 domain. Conformational changes induced by Ca2+binding result in these β-strands forming a β-sheet and a hydrophobic pocket which docks W286 side chain away from the catalytic cleft, enabling calpain activation based on comparison with the Ca2+-bound CAPN1 protease core. The pathologic variants R243L, L244P, K250N, and R289W are predicted to disrupt the β-strands, β-sheet, and hydrophobic pocket, impairing calpain activation. The mechanism by which these variants impair membrane association is unclear. G376S impacts a conserved residue in the CBSW domain and is predicted to disrupt a loop containing acidic residues which may contribute to membrane binding. G267S did not impair membrane association and resulted in a slight but significant increase in autoproteolytic and proteolytic activity. However, G267S is also identified in individuals without NIV. Combined with the autosomal dominant pattern of NIV inheritance and evidence that CAPN5 may dimerize, the results are consistent with a dominant negative mechanism for the five pathogenic variants which resulted in impaired CAPN5 activity and membrane association and a gain-of-function for the G267S variant.
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Affiliation(s)
- James W Geddes
- Spinal Cord and Brain Injury Research Center (SCoBIRC), University of Kentucky, Lexington, KY 40536, USA; Department of Neuroscience, University of Kentucky, Lexington, KY 40536, USA.
| | - Vimala Bondada
- Spinal Cord and Brain Injury Research Center (SCoBIRC), University of Kentucky, Lexington, KY 40536, USA
| | - Dorothy E Croall
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME 04469, USA.
| | - David W Rodgers
- Department of Molecular and Cellular Biochemistry and Center for Structural Biology, University of Kentucky, Lexington, KY 40536, USA.
| | - Jozsef Gal
- Spinal Cord and Brain Injury Research Center (SCoBIRC), University of Kentucky, Lexington, KY 40536, USA; Department of Neuroscience, University of Kentucky, Lexington, KY 40536, USA.
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23
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Kushwaha B, Mthembu SN, Sharma A, Albericio F, de la Torre BG. Serinol-Based Versatile Disulfide-Reducing Reagent. Molecules 2023; 28:5489. [PMID: 37513361 PMCID: PMC10384529 DOI: 10.3390/molecules28145489] [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: 06/19/2023] [Revised: 07/15/2023] [Accepted: 07/17/2023] [Indexed: 07/30/2023] Open
Abstract
Here, we report the synthesis of disulfide-reducing agents 2-(dibenzylamino) propane-1,3-dithiol (DPDT) and 2-(dibenzylamino)-2-methylpropane-1,3-dithiol (DMPDT) from serinol and methyl serinol, respectively. DPDT was found to show greater stability than DMPDT. Hence, the effectiveness of DPDT as a reducing agent was evaluated in both liquid and solid phases. The reducing capacity of this agent was comparable to that of DTT.
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Affiliation(s)
- Babita Kushwaha
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa
| | - Sinenhlanhla N Mthembu
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa
- Peptide Science Laboratory, School of Chemistry and Physics, University of KwaZulu-Natal, Durban 4000, South Africa
| | - Anamika Sharma
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa
- Peptide Science Laboratory, School of Chemistry and Physics, University of KwaZulu-Natal, Durban 4000, South Africa
- Department of Natural Products and Medicinal Chemistry, CSIR-Indian Institute of Chemical Technology, Hyderabad 500007, India
| | - Fernando Albericio
- Peptide Science Laboratory, School of Chemistry and Physics, University of KwaZulu-Natal, Durban 4000, South Africa
- CIBER-BBN, Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Department of Organic Chemistry, University of Barcelona, 08028 Barcelona, Spain
| | - Beatriz G de la Torre
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa
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24
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Holendova B, Plecita-Hlavata L. Cysteine residues in signal transduction and its relevance in pancreatic beta cells. Front Endocrinol (Lausanne) 2023; 14:1221520. [PMID: 37455926 PMCID: PMC10339824 DOI: 10.3389/fendo.2023.1221520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 06/13/2023] [Indexed: 07/18/2023] Open
Abstract
Cysteine is one of the least abundant but most conserved amino acid residues in proteins, playing a role in their structure, metal binding, catalysis, and redox chemistry. Thiols present in cysteines can be modified by post-translational modifications like sulfenylation, acylation, or glutathionylation, regulating protein activity and function and serving as signals. Their modification depends on their position in the structure, surrounding amino acids, solvent accessibility, pH, etc. The most studied modifications are the redox modifications by reactive oxygen, nitrogen, and sulfur species, leading to reversible changes that serve as cell signals or irreversible changes indicating oxidative stress and cell damage. Selected antioxidants undergoing reversible oxidative modifications like peroxiredoxin-thioredoxin system are involved in a redox-relay signaling that can propagate to target proteins. Cysteine thiols can also be modified by acyl moieties' addition (derived from lipid metabolism), resulting in protein functional modification or changes in protein anchoring in the membrane. In this review, we update the current knowledge on cysteine modifications and their consequences in pancreatic β-cells. Because β-cells exhibit well-balanced redox homeostasis, the redox modifications of cysteines here serve primarily for signaling purposes. Similarly, lipid metabolism provides regulatory intermediates that have been shown to be necessary in addition to redox modifications for proper β-cell function and, in particular, for efficient insulin secretion. On the contrary, the excess of reactive oxygen, nitrogen, and sulfur species and the imbalance of lipids under pathological conditions cause irreversible changes and contribute to oxidative stress leading to cell failure and the development of type 2 diabetes.
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Affiliation(s)
| | - Lydie Plecita-Hlavata
- Laboratory of Pancreatic Islet Research, Institute of Physiology, Czech Academy of Sciences, Prague, Czechia
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25
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Zhang S, Ke C, Jiang M, Li Y, Huang W, Dang Z, Guo C. S(-II) reactivates Cd 2+-stressed Shewanella oneidensis via promoting low-molecular-weight thiols synthesis and activating antioxidant defense. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 327:121516. [PMID: 36972810 DOI: 10.1016/j.envpol.2023.121516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 03/15/2023] [Accepted: 03/24/2023] [Indexed: 06/18/2023]
Abstract
Efficient remedies for living organisms including bacteria to counteract cadmium (Cd2+) toxicity are still highly needed. Plant toxicity studies have showed that exogenous S(-II) (including hydrogen sulfide and its ionic forms, i.e., H2S, HS-, and S2-) application can effectively alleviate adverse effects of Cd stress, but whether S(-II) could mitigate bacterial Cd toxicity remains unclear. In this study, S(-II) was applied exogenously to Cd-stressed Shewanella oneidensis MR-1 and the results showed that S(-II) can significantly reactivate impaired physiological processes including growth arrest and enzymatic ferric (Fe(III) reduction inhibition. The efficacy of S(-II) treatment is negatively correlated with the concentration and time length of Cd exposure. Energy-dispersive X-ray (EDX) analysis suggested the presence of cadmium sulfide inside cells treated with S(-II). Both compared proteomic analysis and RT-qPCR showed that enzymes associated with sulfate transport, sulfur assimilation, methionine, and glutathione biosynthesis were up-regulated in both mRNA and protein levels after the treatment, indicating S(-II) may induce the biosynthesis of functional low-molecular-weight (LMW) thiols to counteract Cd toxicity. Meanwhile, the antioxidant enzymes were positively modulated by S(-II) and thus the activity of intracellular reactive oxygen species was attenuated. The study demonstrated that exogenous S(-II) can effectively alleviate Cd stress for S. oneidensis likely through inducing intracellular trapping mechanisms and modulating cellular redox status. It suggested that S(-II) may be a highly effective remedy for bacteria such as S. oneidensis under Cd-polluted environments.
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Affiliation(s)
- Siyu Zhang
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, China; The Key Laboratory of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, Guangzhou, 510006, China
| | - Changdong Ke
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, China; The Key Laboratory of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, Guangzhou, 510006, China
| | - Mengge Jiang
- Guangzhou Metro Group Co., Ltd., Guangzhou, 510335, China
| | - Yuancheng Li
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, China; The Key Laboratory of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, Guangzhou, 510006, China
| | - Weilin Huang
- Department of Environmental Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - Zhi Dang
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, China; The Key Laboratory of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, Guangzhou, 510006, China
| | - Chuling Guo
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, China; The Key Laboratory of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, Guangzhou, 510006, China.
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26
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Neves RPD, Chagoyen M, Martinez-Lorente A, Iñiguez C, Calatrava A, Calabuig J, Iborra FJ. Each Cellular Compartment Has a Characteristic Protein Reactive Cysteine Ratio Determining Its Sensitivity to Oxidation. Antioxidants (Basel) 2023; 12:1274. [PMID: 37372004 DOI: 10.3390/antiox12061274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 06/05/2023] [Accepted: 06/07/2023] [Indexed: 06/29/2023] Open
Abstract
Signaling and detoxification of Reactive Oxygen Species (ROS) are important patho-physiologcal processes. Despite this, we lack comprehensive information on individual cells and cellular structures and functions affected by ROS, which is essential to build quantitative models of the effects of ROS. The thiol groups from cysteines (Cys) in proteins play a major role in redox defense, signaling, and protein function. In this study, we show that the proteins in each subcellular compartment contain a characteristic Cys amount. Using a fluorescent assay for -SH in thiolate form and amino groups in proteins, we show that the thiolate content correlates with ROS sensitivity and signaling properties of each compartment. The highest absolute thiolate concentration was found in the nucleolus, followed by the nucleoplasm and cytoplasm whereas protein thiolate groups per protein showed an inverse pattern. In the nucleoplasm, protein reactive thiols concentrated in SC35 speckles, SMN, and the IBODY that accumulated oxidized RNA. Our findings have important functional consequences, and explain differential sensitivity to ROS.
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Affiliation(s)
- Ricardo Pires das Neves
- Center for Neuroscience and Cell Biology, CIBB-Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, 3004-517 Coimbra, Portugal
- IIIUC-Institute of Interdisciplinary Research, University of Coimbra, 3030-789 Coimbra, Portugal
| | - Mónica Chagoyen
- Centro Nacional de Biotecnología, CSIC, Darwin 3, 28049 Madrid, Spain
| | - Antonio Martinez-Lorente
- Unidad de Investigación, Innovación y Docencia Médica, Hospital Universitario Vinalopó, 03293 Elx, Spain
- Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO), 46020 Valencia, Spain
- Department of Biotecnology, University of Alicante, 03690 Alicante, Spain
| | - Carlos Iñiguez
- Department of Biotecnology, University of Alicante, 03690 Alicante, Spain
| | - Ana Calatrava
- Department of Pathology, Fundación Instituto Valenciano de Oncología, 46009 Valencia, Spain
| | | | - Francisco J Iborra
- Instituto de Biomedicina de Valencia, CSIC, Jaime Roig 11, 46010 Valencia, Spain
- Centro de Investigación Príncipe Felipe (CIPF), Primo Yufera 3, 46012 Valencia, Spain
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27
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Lamolle G, Simón D, Iriarte A, Musto H. Main Factors Shaping Amino Acid Usage Across Evolution. J Mol Evol 2023:10.1007/s00239-023-10120-5. [PMID: 37264211 DOI: 10.1007/s00239-023-10120-5] [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: 03/22/2023] [Accepted: 05/17/2023] [Indexed: 06/03/2023]
Abstract
The standard genetic code determines that in most species, including viruses, there are 20 amino acids that are coded by 61 codons, while the other three codons are stop triplets. Considering the whole proteome each species features its own amino acid frequencies, given the slow rate of change, closely related species display similar GC content and amino acids usage. In contrast, distantly related species display different amino acid frequencies. Furthermore, within certain multicellular species, as mammals, intragenomic differences in the usage of amino acids are evident. In this communication, we shall summarize some of the most prominent and well-established factors that determine the differences found in the amino acid usage, both across evolution and intragenomically.
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Affiliation(s)
- Guillermo Lamolle
- Laboratorio de Genómica Evolutiva, Facultad de Ciencias, Universidad de La República, Montevideo, Uruguay
| | - Diego Simón
- Laboratorio de Genómica Evolutiva, Facultad de Ciencias, Universidad de La República, Montevideo, Uruguay
- Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de La República, Montevideo, Uruguay
- Laboratorio de Evolución Experimental de Virus, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Andrés Iriarte
- Laboratorio de Genómica Evolutiva, Facultad de Ciencias, Universidad de La República, Montevideo, Uruguay
- Laboratorio de Biología Computacional, Departamento de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, Universidad de La República, Montevideo, Uruguay
| | - Héctor Musto
- Laboratorio de Genómica Evolutiva, Facultad de Ciencias, Universidad de La República, Montevideo, Uruguay.
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28
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Levings DC, Pathak SS, Yang YM, Slattery M. Limited Expression of Nrf2 in Neurons Across the Central Nervous System. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.09.540014. [PMID: 37214946 PMCID: PMC10197674 DOI: 10.1101/2023.05.09.540014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Nrf2 is a broadly expressed transcription factor that regulates gene expression in response to reactive oxygen species (ROS) and oxidative stress. It is commonly referred to as a ubiquitous pathway, but this generalization overlooks work indicating that Nrf2 is essentially unexpressed in some neuronal populations. To explore whether this pattern extends throughout the central nervous system (CNS), we quantified Nrf2 expression and chromatin accessibility at the Nrf2 locus across multiple single cell datasets. In both the mouse and human CNS, Nrf2 was repressed in almost all mature neurons, but highly expressed in non-neuronal support cells, and this pattern was robust across multiple human CNS diseases. A subset of key Nrf2 target genes, like Slc7a11 , also remained low in neurons. Thus, these data suggest that while most cells express Nrf2, with activity determined by ROS levels, neurons actively avoid Nrf2 activity by keeping Nrf2 expression low.
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Affiliation(s)
- Daniel C. Levings
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth, MN 55812, USA
| | - Salil Saurav Pathak
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth, MN 55812, USA
| | - Yi-Mei Yang
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth, MN 55812, USA
- Department of Neuroscience, University of Minnesota Medical School, Minneapolis, MN, 55455, USA
| | - Matthew Slattery
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth, MN 55812, USA
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29
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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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30
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Timr S, Melchionna S, Derreumaux P, Sterpone F. Optimized OPEP Force Field for Simulation of Crowded Protein Solutions. J Phys Chem B 2023; 127:3616-3623. [PMID: 37071827 PMCID: PMC10150358 DOI: 10.1021/acs.jpcb.3c00253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2023]
Abstract
Macromolecular crowding has profound effects on the mobility of proteins, with strong implications on the rates of intracellular processes. To describe the dynamics of crowded environments, detailed molecular models are needed, capturing the structures and interactions arising in the crowded system. In this work, we present OPEPv7, which is a coarse-grained force field at amino-acid resolution, suited for rigid-body simulations of the structure and dynamics of crowded solutions formed by globular proteins. Using the OPEP protein model as a starting point, we have refined the intermolecular interactions to match the experimentally observed dynamical slowdown caused by crowding. The resulting force field successfully reproduces the diffusion slowdown in homogeneous and heterogeneous protein solutions at different crowding conditions. Coupled with the lattice Boltzmann technique, it allows the study of dynamical phenomena in protein assemblies and opens the way for the in silico rheology of protein solutions.
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Affiliation(s)
- Stepan Timr
- Laboratoire de Biochimie Théorique (UPR 9080), CNRS, Université de Paris, 13 rue Pierre et Marie Curie, Paris, 75005, France
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, PSL Research University, 13 rue Pierre et Marie Curie, Paris, 75005, France
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, Prague 8, 18223, Czech Republic
| | - Simone Melchionna
- IAC-CNR, Via dei Taurini 19, 00185, Rome, Italy
- Lexma Technology 1337 Massachusetts Avenue, Arlington, Massachusetts 02476, United States
| | - Philippe Derreumaux
- Laboratoire de Biochimie Théorique (UPR 9080), CNRS, Université de Paris, 13 rue Pierre et Marie Curie, Paris, 75005, France
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, PSL Research University, 13 rue Pierre et Marie Curie, Paris, 75005, France
- Institut Universitaire de France, 75005 Paris, France
| | - Fabio Sterpone
- Laboratoire de Biochimie Théorique (UPR 9080), CNRS, Université de Paris, 13 rue Pierre et Marie Curie, Paris, 75005, France
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, PSL Research University, 13 rue Pierre et Marie Curie, Paris, 75005, France
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31
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Eben SS, Imlay JA. Excess copper catalyzes protein disulfide bond formation in the bacterial periplasm but not in the cytoplasm. Mol Microbiol 2023; 119:423-438. [PMID: 36756756 PMCID: PMC10155707 DOI: 10.1111/mmi.15032] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 01/20/2023] [Accepted: 01/25/2023] [Indexed: 02/10/2023]
Abstract
Copper avidly binds thiols and is redox active, and it follows that one element of copper toxicity may be the generation of undesirable disulfide bonds in proteins. In the present study, copper oxidized the model thiol N-acetylcysteine in vitro. Alkaline phosphatase (AP) requires disulfide bonds for activity, and copper activated reduced AP both in vitro and when it was expressed in the periplasm of mutants lacking their native disulfide-generating system. However, AP was not activated when it was expressed in the cytoplasm of copper-overloaded cells. Similarly, this copper stress failed to activate OxyR, a transcription factor that responds to the creation of a disulfide bond. The elimination of cellular disulfide-reducing systems did not change these results. Nevertheless, in these cells, the cytoplasmic copper concentration was high enough to impair growth and completely inactivate enzymes with solvent-exposed [4Fe-4S] clusters. Experiments with N-acetylcysteine determined that the efficiency of thiol oxidation is limited by the sluggish pace at which oxygen regenerates copper(II) through oxidation of the thiyl radical-Cu(I) complex. We conclude that this slow step makes copper too inefficient a catalyst to create disulfide stress in the thiol-rich cytoplasm, but it can still impact the few thiol-containing proteins in the periplasm. It also ensures that copper accumulates intracellularly in the Cu(I) valence.
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Affiliation(s)
- Stefanie S. Eben
- Department of Microbiology, University of Illinois, Urbana, IL 61801
| | - James A. Imlay
- Department of Microbiology, University of Illinois, Urbana, IL 61801
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Xia Q, Casas-Martinez JC, Zarzuela E, Muñoz J, Miranda-Vizuete A, Goljanek-Whysall K, McDonagh B. Peroxiredoxin 2 is required for the redox mediated adaptation to exercise. Redox Biol 2023; 60:102631. [PMID: 36791646 PMCID: PMC9950660 DOI: 10.1016/j.redox.2023.102631] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/23/2023] [Accepted: 02/07/2023] [Indexed: 02/11/2023] Open
Abstract
Exercise generates a site-specific increase in Reactive Oxygen Species (ROS) within muscle that promotes changes in gene transcription and mitochondrial biogenesis, required for the beneficial adaptive response. We demonstrate that Peroxiredoxin 2 (Prdx2), an abundant cytoplasmic 2-Cys peroxiredoxin, is required for the adaptive hormesis response to physiological levels of H2O2 in myoblasts and following exercise in C. elegans. A short bolus addition of H2O2 increases mitochondrial capacity and improves myogenesis of cultured myoblasts, this beneficial adaptive response was suppressed in myoblasts with decreased expression of cytoplasmic Prdxs. Moreover, a swimming exercise protocol in C. elegans increased mitochondrial content, fitness, survival and longevity in wild type (N2) worms. In contrast, prdx-2 mutant worms had decreased fitness, disrupted mitochondria, reduced survival and lifespan following exercise. Global proteomics following exercise identified distinct changes in the proteome of N2 and prdx-2 mutants. Furthermore, a redox proteomic approach to quantify reversible oxidation of specific Cysteine residues revealed a more reduced redox state in the non-exercised prdx-2 mutant strain that become oxidized following exercise. In contrast, specific Cys residues from regulatory proteins become more reduced in the N2 strain following exercise, establishing the key regulatory role of PRDX-2 in a redox signalling cascade following endogenous ROS generation. Our results demonstrate that conserved cytoplasmic 2-Cys Peroxiredoxins are required for the beneficial adaptive response to a physiological redox stress.
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Affiliation(s)
- Qin Xia
- Discipline of Physiology, School of Medicine, University of Galway, Ireland; Apoptosis Research Centre, University of Galway, Ireland
| | - Jose C Casas-Martinez
- Discipline of Physiology, School of Medicine, University of Galway, Ireland; Apoptosis Research Centre, University of Galway, Ireland
| | - Eduardo Zarzuela
- Proteomics Unit, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Javier Muñoz
- Proteomics Unit, Spanish National Cancer Research Centre (CNIO), Madrid, Spain; Cell Signalling and Clinical Proteomics Group, Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
| | - Antonio Miranda-Vizuete
- Instituto de Biomedicina de Sevilla, IBiS/Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Spain
| | - Katarzyna Goljanek-Whysall
- Discipline of Physiology, School of Medicine, University of Galway, Ireland; Apoptosis Research Centre, University of Galway, Ireland; Institute of Lifecourse and Medical Sciences, University of Liverpool, UK
| | - Brian McDonagh
- Discipline of Physiology, School of Medicine, University of Galway, Ireland; Apoptosis Research Centre, University of Galway, Ireland.
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33
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Lee SB, Yu J, Kim H, Kim KW, Jeong JW, Kim YL, Park SJ, Koo TS, Lee C, Hong KB, Choi S. Novel Strategy To Inhibit Transthyretin Amyloidosis via the Synergetic Effect of Chemoselective Acylation and Noncovalent Inhibitor Release. J Med Chem 2023; 66:2893-2903. [PMID: 36749109 DOI: 10.1021/acs.jmedchem.2c01926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Strategies for developing targeted covalent inhibitors (TCIs), which have the advantages of a prolonged duration of action and selectivity toward a drug target, have attracted great interest in drug discovery. Herein, we report chemoselective covalent inhibitors that specifically target lysine ε-amine groups that conjugate with an endogenous protein to prevent disease-causing protein misfolding and aggregation. These TCIs are unique because the benzoyl group is preferentially conjugated to Lys15 at the top of the T4 binding site within transthyretin (TTR) while simultaneously releasing a potent noncovalent TTR kinetic stabilizer. The potency of these covalent inhibitors is superior to tafamidis, the only FDA-approved drug for the treatment of hereditary TTR amyloidosis. In addition to investigations into the covalent modification of TTR via reverse-phase high-performance liquid chromatography, direct methods are performed to confirm and visualize the presumed covalent interaction via mass spectrometry and X-ray crystallography.
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Affiliation(s)
- Seok Beom Lee
- Graduate School of New Drug Discovery and Development, Chungnam National University, Daejon 34134, Republic of Korea
| | - Jaeni Yu
- Graduate School of New Drug Discovery and Development, Chungnam National University, Daejon 34134, Republic of Korea
| | - Hyunwoo Kim
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Kun Woo Kim
- Graduate School of New Drug Discovery and Development, Chungnam National University, Daejon 34134, Republic of Korea
| | - Jong Woo Jeong
- Graduate School of New Drug Discovery and Development, Chungnam National University, Daejon 34134, Republic of Korea
| | - Yun Lan Kim
- Graduate School of New Drug Discovery and Development, Chungnam National University, Daejon 34134, Republic of Korea
| | - Sung Jean Park
- College of Pharmacy and Gachon Institute of Pharmaceutical Sciences, Gachon University, Incheon 21936, Republic of Korea
| | - Tae-Sung Koo
- Graduate School of New Drug Discovery and Development, Chungnam National University, Daejon 34134, Republic of Korea
| | - Changwook Lee
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Ki Bum Hong
- New Drug Development Center (NDDC), Daegu-Gyeongbuk Medical Innovation Foundation (DGMIF), Daegu 41061, Republic of Korea
| | - Sungwook Choi
- Graduate School of New Drug Discovery and Development, Chungnam National University, Daejon 34134, Republic of Korea
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Zhou Y, Dai J, Qi J, Wu J, Huang Y, Shen B, Zhi X, Fu Y. Construction of a red emission fluorescent probe for selectively detection of cysteine in living cells. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 286:121946. [PMID: 36242837 DOI: 10.1016/j.saa.2022.121946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 09/08/2022] [Accepted: 10/01/2022] [Indexed: 06/16/2023]
Abstract
Cysteine (Cys) is a vital amino acid in the body, and its abnormal expression level is associated with many diseases. In this study, a novel fluorescent probe ACHB was synthesized, showing high selectivity, anti-interference ability and achieving accurate detection of cysteine. Different from most previous off-on probes, ACHB showed an on-off fluorescence response to Cys. Acrylic ester was used as a recognizer while green fluorescence protein (GFP) chromophore derivative 4-hydroxybenzylidene-imidazolinone (HBI) was used as the fluorophore. The addition of Cys leads to the hydrolysis of the red-emitting probe (613 nm), releasing a precursor with a lower fluorescent signal and showing an on-off spectral signal, which was ideal for obtaining sensitive detection with high specificity. Furthermore, the probe was successfully applied for simultaneous determination of cysteine (Cys) in living cells and biological sample (mouse serum). In conclusion, probe ACHB is a promising tool to display the intracellular cysteine concentration level, providing a good visualization method for clinical diagnosis and scientific basic research.
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Affiliation(s)
- Yufeng Zhou
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, Jiangsu 210023, China
| | - Jianan Dai
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, Jiangsu 210023, China
| | - Jinzhi Qi
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, Jiangsu 210023, China
| | - Jichun Wu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, Jiangsu 210023, China
| | - Yubo Huang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, Jiangsu 210023, China
| | - Baoxing Shen
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, Jiangsu 210023, China.
| | - Xu Zhi
- State Key Laboratory of Coordination Chemistry, Collaborative Innovation Center of Advanced Microstructures, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China.
| | - Yongqian Fu
- School of Life Science, Taizhou University, Taizhou, Zhejiang 318000, China.
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35
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Sharina I, Martin E. Cellular Factors That Shape the Activity or Function of Nitric Oxide-Stimulated Soluble Guanylyl Cyclase. Cells 2023; 12:471. [PMID: 36766813 PMCID: PMC9914232 DOI: 10.3390/cells12030471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 01/29/2023] [Accepted: 01/31/2023] [Indexed: 02/04/2023] Open
Abstract
NO-stimulated guanylyl cyclase (SGC) is a hemoprotein that plays key roles in various physiological functions. SGC is a typical enzyme-linked receptor that combines the functions of a sensor for NO gas and cGMP generator. SGC possesses exclusive selectivity for NO and exhibits a very fast binding of NO, which allows it to function as a sensitive NO receptor. This review describes the effect of various cellular factors, such as additional NO, cell thiols, cell-derived small molecules and proteins on the function of SGC as cellular NO receptor. Due to its vital physiological function SGC is an important drug target. An increasing number of synthetic compounds that affect SGC activity via different mechanisms are discovered and brought to clinical trials and clinics. Cellular factors modifying the activity of SGC constitute an opportunity for improving the effectiveness of existing SGC-directed drugs and/or the creation of new therapeutic strategies.
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Affiliation(s)
| | - Emil Martin
- Department of Internal Medicine, Cardiology Division, The University of Texas—McGovern Medical School, 1941 East Road, Houston, TX 77054, USA
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36
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Bhanot V, Panwar J. Unveiling the potential of Lichtheimia ramosa AJP11 for myco-transformation of polystyrene sulfonate and its driving molecular mechanism. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 325:116579. [PMID: 36302301 DOI: 10.1016/j.jenvman.2022.116579] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 10/16/2022] [Accepted: 10/17/2022] [Indexed: 06/16/2023]
Abstract
Plastic pollution is a major environmental concern due to its deleterious effects on various ecosystems. The limitations and shortcomings of waste management strategies has led to the over-accumulation of plastic waste, mainly comprised of single-use plastics, such as polystyrene (PS). Considering the advantages of biotransformation over the other plastic disposal methods, it has become a major focus of the modern research. Biotransformation of plastics involves its microbial hydrolysis into short chain oligomers and monomers that are eventually assimilated as carbon source by the microbes leading to the release of CO2. As fungi are known to possess multifarious and highly regulated enzyme system capable of utilizing diverse nutrient sources, the present study explored the potential of Lichtheimia ramosa AJP11 towards myco-transformation of polystyrene sulfonate (PSS), a structural analogue of polystyrene (PS). During the 30-day incubation period of L. ramosa AJP11 in minimal salt medium (MSM)+1% PSS, the fungus showed 41.6% increment in its fresh weight biomass, indicating the utilization of PSS as sole carbon source. Further analysis revealed the generation of various reaction intermediates such as alkanes and fatty acids, crucial for the continuum of fungal metabolic pathways. Moreover, detection of PS oligomers such as cyclohexane and 2,4-DTBP confirmed the myco-transformation of PSS. The extracellular fungal protein profile showed considerable overexpression of a 14.4 kDa protein, characterized to be a hydrophobic surface binding (Hsb) protein, which is hypothesized to adsorb onto the PSS to facilitate its transformation. Further, in silico analysis of Hsb protein indicated it to be an amphiphilic α-helical protein with ability to bind styrene sulfonate unit via both hydrogen and hydrophobic interactions, with a binding energy of -5.02 kcal mol-1. These findings open new avenues for over expression of Hsb under controlled reactor conditions to accelerate the PS waste disposal.
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Affiliation(s)
- Vishalakshi Bhanot
- Department of Biological Sciences, Birla Institute of Technology and Sciences, Pilani, 333031, Rajasthan, India
| | - Jitendra Panwar
- Department of Biological Sciences, Birla Institute of Technology and Sciences, Pilani, 333031, Rajasthan, India.
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Willems P, Huang J, Messens J, Van Breusegem F. Functionally annotating cysteine disulfides and metal binding sites in the plant kingdom using AlphaFold2 predicted structures. Free Radic Biol Med 2023; 194:220-229. [PMID: 36493985 DOI: 10.1016/j.freeradbiomed.2022.12.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/14/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022]
Abstract
Deep learning algorithms such as AlphaFold2 predict three-dimensional protein structure with high confidence. The recent release of more than 200 million structural models provides an unprecedented resource for functional protein annotation. Here, we used AlphaFold2 predicted structures of fifteen plant proteomes to functionally and evolutionary analyze cysteine residues in the plant kingdom. In addition to identification of metal ligands coordinated by cysteine residues, we systematically analyzed cysteine disulfides present in these structural predictions. Our analysis demonstrates most of these predicted disulfides are trustworthy due their high agreement (∼96%) with those present in X-ray and NMR protein structures, their characteristic disulfide stereochemistry, the biased subcellular distribution of their proteins and a higher degree of oxidation of their respective cysteines as measured by proteomics. Adopting an evolutionary perspective, zinc binding sites are increasingly present at the expense of iron-sulfur clusters in plants. Interestingly, disulfide formation is increased in secreted proteins of land plants, likely promoting sequence evolution to adapt to changing environments encountered by plants. In summary, Alphafold2 predicted structural models are a rich source of information for studying the role of cysteines residues in proteins of interest and for protein redox biology in general.
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Affiliation(s)
- Patrick Willems
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium; VIB Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, 9052, Ghent, Belgium; Center for Medical Biotechnology, VIB, 9052, Ghent, Belgium.
| | - Jingjing Huang
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium; VIB Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
| | - Joris Messens
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, B-1050, Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, B-1050, Brussels, Belgium; Brussels Center for Redox Biology, Vrije Universiteit Brussel, B-1050, Brussels, Belgium
| | - Frank Van Breusegem
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium; VIB Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
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38
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Protein targeting by the itaconate family in immunity and inflammation. Biochem J 2022; 479:2499-2510. [PMID: 36546613 DOI: 10.1042/bcj20220364] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/06/2022] [Accepted: 12/07/2022] [Indexed: 12/24/2022]
Abstract
Immune cells are metabolically plastic and respond to inflammatory stimuli with large shifts in metabolism. Itaconate is one of the most up-regulated metabolites in macrophages in response to the gram negative bacterial product LPS. As such, itaconate has recently been the subject of intense research interest. The artificial derivatives, including 4-Octyl Itaconate (4-OI) and Dimethyl Itaconate (DI) and naturally produced isomers, mesaconate and citraconate, have been tested in relation to itaconate biology with similarities and differences in the biochemistry and immunomodulatory properties of this family of compounds emerging. Both itaconate and 4-OI have been shown to modify cysteines on a range of target proteins, with the modification being linked to a functional change. Targets include KEAP1 (the NRF2 inhibitor), GAPDH, NLRP3, JAK1, and the lysosomal regulator, TFEB. 4-OI and DI are more electrophilic, and are therefore stronger NRF2 activators, and inhibit the production of Type I IFNs, while itaconate inhibits SDH and the dioxygenase, TET2. Additionally, both itaconate and derivates have been shown to be protective across a wide range of mouse models of inflammatory and infectious diseases, through both distinct and overlapping mechanisms. As such, continued research involving the comparison of itaconate and related molecules holds exciting prospects for the study of cysteine modification and pathways for immunomodulation and the potential for new anti-inflammatory therapeutics.
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39
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Bedendi G, De Moura Torquato LD, Webb S, Cadoux C, Kulkarni A, Sahin S, Maroni P, Milton RD, Grattieri M. Enzymatic and Microbial Electrochemistry: Approaches and Methods. ACS MEASUREMENT SCIENCE AU 2022; 2:517-541. [PMID: 36573075 PMCID: PMC9783092 DOI: 10.1021/acsmeasuresciau.2c00042] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 08/12/2022] [Accepted: 08/15/2022] [Indexed: 06/17/2023]
Abstract
The coupling of enzymes and/or intact bacteria with electrodes has been vastly investigated due to the wide range of existing applications. These span from biomedical and biosensing to energy production purposes and bioelectrosynthesis, whether for theoretical research or pure applied industrial processes. Both enzymes and bacteria offer a potential biotechnological alternative to noble/rare metal-dependent catalytic processes. However, when developing these biohybrid electrochemical systems, it is of the utmost importance to investigate how the approaches utilized to couple biocatalysts and electrodes influence the resulting bioelectrocatalytic response. Accordingly, this tutorial review starts by recalling some basic principles and applications of bioelectrochemistry, presenting the electrode and/or biocatalyst modifications that facilitate the interaction between the biotic and abiotic components of bioelectrochemical systems. Focus is then directed toward the methods used to evaluate the effectiveness of enzyme/bacteria-electrode interaction and the insights that they provide. The basic concepts of electrochemical methods widely employed in enzymatic and microbial electrochemistry, such as amperometry and voltammetry, are initially presented to later focus on various complementary methods such as spectroelectrochemistry, fluorescence spectroscopy and microscopy, and surface analytical/characterization techniques such as quartz crystal microbalance and atomic force microscopy. The tutorial review is thus aimed at students and graduate students approaching the field of enzymatic and microbial electrochemistry, while also providing a critical and up-to-date reference for senior researchers working in the field.
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Affiliation(s)
- Giada Bedendi
- Department
of Inorganic and Analytical Chemistry, Faculty of Sciences, University of Geneva, Quai Ernest-Ansermet 30, 1211 Geneva 4, Switzerland
| | | | - Sophie Webb
- Department
of Inorganic and Analytical Chemistry, Faculty of Sciences, University of Geneva, Quai Ernest-Ansermet 30, 1211 Geneva 4, Switzerland
- National
Centre of Competence in Research (NCCR) Catalysis, University of Geneva, Quai Ernest-Ansermet 30, 1211 Geneva 4, Switzerland
| | - Cécile Cadoux
- Department
of Inorganic and Analytical Chemistry, Faculty of Sciences, University of Geneva, Quai Ernest-Ansermet 30, 1211 Geneva 4, Switzerland
- National
Centre of Competence in Research (NCCR) Catalysis, University of Geneva, Quai Ernest-Ansermet 30, 1211 Geneva 4, Switzerland
| | - Amogh Kulkarni
- Department
of Inorganic and Analytical Chemistry, Faculty of Sciences, University of Geneva, Quai Ernest-Ansermet 30, 1211 Geneva 4, Switzerland
| | - Selmihan Sahin
- Department
of Inorganic and Analytical Chemistry, Faculty of Sciences, University of Geneva, Quai Ernest-Ansermet 30, 1211 Geneva 4, Switzerland
| | - Plinio Maroni
- Department
of Inorganic and Analytical Chemistry, Faculty of Sciences, University of Geneva, Quai Ernest-Ansermet 30, 1211 Geneva 4, Switzerland
| | - Ross D. Milton
- Department
of Inorganic and Analytical Chemistry, Faculty of Sciences, University of Geneva, Quai Ernest-Ansermet 30, 1211 Geneva 4, Switzerland
- National
Centre of Competence in Research (NCCR) Catalysis, University of Geneva, Quai Ernest-Ansermet 30, 1211 Geneva 4, Switzerland
| | - Matteo Grattieri
- Dipartimento
di Chimica, Università degli Studi
di Bari “Aldo Moro”, via E. Orabona 4, Bari 70125, Italy
- IPCF-CNR
Istituto per i Processi Chimico Fisici, Consiglio Nazionale delle Ricerche, via E. Orabona 4, Bari 70125, Italy
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40
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Cox D, Ormsby AR, Reid GE, Hatters DM. Protein painting reveals pervasive remodeling of conserved proteostasis machinery in response to pharmacological stimuli. NPJ Syst Biol Appl 2022; 8:46. [DOI: 10.1038/s41540-022-00256-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 10/25/2022] [Indexed: 11/29/2022] Open
Abstract
AbstractThe correct spatio-temporal organization of the proteome is essential for cellular homeostasis. However, a detailed mechanistic understanding of this organization and how it is altered in response to external stimuli in the intact cellular environment is as-yet unrealized. ‘Protein painting methods provide a means to address this gap in knowledge by monitoring the conformational status of proteins within cells at the proteome-wide scale. Here, we demonstrate the ability of a protein painting method employing tetraphenylethene maleimide (TPE-MI) to reveal proteome network remodeling in whole cells in response to a cohort of commonly used pharmacological stimuli of varying specificity. We report specific, albeit heterogeneous, responses to individual stimuli that coalesce on a conserved set of core cellular machineries. This work expands our understanding of proteome conformational remodeling in response to cellular stimuli, and provides a blueprint for assessing how these conformational changes may contribute to disorders characterized by proteostasis imbalance.
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41
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Plasma Amino Acids in Horses Suffering from Pituitary Pars Intermedia Dysfunction. Animals (Basel) 2022; 12:ani12233315. [PMID: 36496836 PMCID: PMC9737035 DOI: 10.3390/ani12233315] [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: 10/02/2022] [Revised: 11/24/2022] [Accepted: 11/25/2022] [Indexed: 11/30/2022] Open
Abstract
Pituitary pars intermedia dysfunction is one of the most common diseases of aged horses and ponies. In Parkinson's disease, which is, similar to PPID, a disease that involves oxidative damage to dopaminergic pathways but with different clinical signs, alterations to the serum amino acid profile have been reported. To examine changes in the plasma amino acid profile in horses with PPID, EDTA plasma of horses that were presented for various reasons that required laboratory examinations of blood anticoagulated with EDTA was collected. With this plasma, the basal ACTH concentration as well as the amino acid profile was determined. Horses were considered PPID patients if the ACTH concentration was ≥ 100 pg/mL, i.e., they would be considered affected at any time. Horses were defined as non-PPID (nPPID) patients if the ACTH concentration was below 30 pg/mL. Horses receiving pergolide with ACTH ≤ 30 pg/mL were allocated to the group PPIDrr (PPID, ACTH in reference range) and horses receiving pergolide with ACTH ≥ 100 pg/mL to the group PPIDarr (PPID, ACTH above reference range). In total, 93 horses were examined, including 88 horses at the clinic and 5 horses at a private practice. Of these, 53 horses fulfilled the inclusion criteria (ACTH ≤ 30 pg/mL or ACTH ≥ 100 pg/mL). A total of 25 horses were diagnosed as nPPID, 20 as PPID, 5 as PPIDrr, and 3 as PPIDarr. Arginine was significantly higher in PPIDrr than in PPID and nPPID, asparagine was significantly higher in PPID, PPIDrr, and PPIDarr than in nPPID, citrulline was significantly higher in PPIDrr than in nPPID and PPID, cysteine was significantly lower in PPIDrr than in PPID, nPPID, and PPIDarr, and glutamine was significantly higher in PPID and PPIDarr than in nPPID. Especially, asparagine, citrulline, and glutamine may be potential diagnostic markers and may offer interesting approaches for research regarding amino supplementation in PPID.
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42
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Mthembu SN, Chakraborty A, Schönleber R, Albericio F, de la Torre BG. Solid-Phase Synthesis of C-Terminus Cysteine Peptide Acids. Org Process Res Dev 2022. [DOI: 10.1021/acs.oprd.2c00321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Sinenhlanhla N. Mthembu
- Peptide Science Laboratory, School of Chemistry and Physics, University of KwaZulu-Natal, Westville, Durban 4000, South Africa
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa
| | - Amit Chakraborty
- Peptide Science Laboratory, School of Chemistry and Physics, University of KwaZulu-Natal, Westville, Durban 4000, South Africa
| | | | - Fernando Albericio
- Peptide Science Laboratory, School of Chemistry and Physics, University of KwaZulu-Natal, Westville, Durban 4000, South Africa
- CIBER-BBN, Networking Centre on Bioengineering, Biomaterials and Nanomedicine, and Department of Organic Chemistry, University of Barcelona, Barcelona 08028, Spain
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), 08034 Barcelona, Spain
| | - Beatriz G. de la Torre
- Peptide Science Laboratory, School of Chemistry and Physics, University of KwaZulu-Natal, Westville, Durban 4000, South Africa
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa
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43
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Yin K, Tong M, Sun F, Wu R. Quantitative Structural Proteomics Unveils the Conformational Changes of Proteins under the Endoplasmic Reticulum Stress. Anal Chem 2022; 94:13250-13260. [PMID: 36108266 PMCID: PMC9789690 DOI: 10.1021/acs.analchem.2c03076] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Protein structures are decisive for their activities and interactions with other molecules. Global analysis of protein structures and conformational changes cannot be achieved by commonly used abundance-based proteomics. Here, we integrated cysteine covalent labeling, selective enrichment, and quantitative proteomics to study protein structures and structural changes on a large scale. This method was applied to globally investigate protein structures in HEK293T cells and protein structural changes in the cells with the tunicamycin (Tm)-induced endoplasmic reticulum (ER) stress. We quantified several thousand cysteine residues, which contain unprecedented and valuable information of protein structures. Combining this method with pulsed stable isotope labeling by amino acids in cell culture, we further analyzed the folding state differences between pre-existing and newly synthesized proteins in cells under the Tm treatment. Besides newly synthesized proteins, unexpectedly, many pre-existing proteins were found to become unfolded upon ER stress, especially those related to gene transcription and protein translation. Furthermore, the current results reveal that N-glycosylation plays a more important role in the folding process of the tertiary and quaternary structures than the secondary structures for newly synthesized proteins. Considering the importance of cysteine in protein structures, this method can be extensively applied in the biological and biomedical research fields.
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Affiliation(s)
- Kejun Yin
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Ming Tong
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Fangxu Sun
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Ronghu Wu
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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44
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Garrido Ruiz D, Sandoval-Perez A, Rangarajan AV, Gunderson EL, Jacobson MP. Cysteine Oxidation in Proteins: Structure, Biophysics, and Simulation. Biochemistry 2022; 61:2165-2176. [PMID: 36161872 PMCID: PMC9583617 DOI: 10.1021/acs.biochem.2c00349] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Cysteine side chains
can exist in distinct oxidation
states depending
on the pH and redox potential of the environment, and cysteine oxidation
plays important yet complex regulatory roles. Compared with the effects
of post-translational modifications such as phosphorylation, the effects
of oxidation of cysteine to sulfenic, sulfinic, and sulfonic acid
on protein structure and function remain relatively poorly characterized.
We present an analysis of the role of cysteine reactivity as a regulatory
factor in proteins, emphasizing the interplay between electrostatics
and redox potential as key determinants of the resulting oxidation
state. A review of current computational approaches suggests underdeveloped
areas of research for studying cysteine reactivity through molecular
simulations.
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Affiliation(s)
- Diego Garrido Ruiz
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
| | - Angelica Sandoval-Perez
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
| | - Amith Vikram Rangarajan
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
| | - Emma L Gunderson
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
| | - Matthew P Jacobson
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
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45
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Gugkaeva ZT, Mardiyan ZZ, Smol'yakov AF, Poghosyan AS, Saghyan AS, Maleev VI, Larionov VA. Sequential Heck Cross-Coupling and Hydrothiolation Reactions Taking Place in the Ligand Sphere of a Chiral Dehydroalanine Ni(II) Complex: Asymmetric Route to β-Aryl Substituted Cysteines. Org Lett 2022; 24:6230-6235. [PMID: 35950978 DOI: 10.1021/acs.orglett.2c02591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A practically useful protocol for the asymmetric synthesis of artificial β-aryl-substituted cysteine derivatives was developed through sequential Pd(II)-catalyzed Heck cross-coupling with aryl iodides and hydrothiolation reaction with various alkyl thiols in the presence of triethylamine taking place in the ligand sphere of a robust and bench-stable chiral dehydroalanine Ni(II) complex. The subsequent acidic decomposition of the single diastereomeric Ni(II) complexes led to the target enantiopure cysteine derivatives.
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Affiliation(s)
- Zalina T Gugkaeva
- A. N. Nesmeyanov Institute of Organoelement Compounds of Russian Academy of Sciences, Vavilov Str. 28, 119991 Moscow, Russian Federation
| | - Zorayr Z Mardiyan
- SPC "Armbiotechnology" SNPO NAS RA, Gyurjyan Str. 14, 0056 Yerevan, Armenia
| | - Alexander F Smol'yakov
- A. N. Nesmeyanov Institute of Organoelement Compounds of Russian Academy of Sciences, Vavilov Str. 28, 119991 Moscow, Russian Federation.,Plekhanov Russian University of Economics, Stremyanny Per. 36, 117997 Moscow, Russian Federation
| | | | - Ashot S Saghyan
- SPC "Armbiotechnology" SNPO NAS RA, Gyurjyan Str. 14, 0056 Yerevan, Armenia
| | - Victor I Maleev
- A. N. Nesmeyanov Institute of Organoelement Compounds of Russian Academy of Sciences, Vavilov Str. 28, 119991 Moscow, Russian Federation
| | - Vladimir A Larionov
- A. N. Nesmeyanov Institute of Organoelement Compounds of Russian Academy of Sciences, Vavilov Str. 28, 119991 Moscow, Russian Federation.,Peoples' Friendship University of Russia (RUDN University), Miklukho-Maklaya Str. 6, 117198 Moscow, Russian Federation
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46
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Focus on Nitric Oxide Homeostasis: Direct and Indirect Enzymatic Regulation of Protein Denitrosation Reactions in Plants. Antioxidants (Basel) 2022; 11:antiox11071411. [PMID: 35883902 PMCID: PMC9311986 DOI: 10.3390/antiox11071411] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 07/14/2022] [Accepted: 07/19/2022] [Indexed: 11/17/2022] Open
Abstract
Protein cysteines (Cys) undergo a multitude of different reactive oxygen species (ROS), reactive sulfur species (RSS), and/or reactive nitrogen species (RNS)-derived modifications. S-nitrosation (also referred to as nitrosylation), the addition of a nitric oxide (NO) group to reactive Cys thiols, can alter protein stability and activity and can result in changes of protein subcellular localization. Although it is clear that this nitrosative posttranslational modification (PTM) regulates multiple signal transduction pathways in plants, the enzymatic systems that catalyze the reverse S-denitrosation reaction are poorly understood. This review provides an overview of the biochemistry and regulation of nitro-oxidative modifications of protein Cys residues with a focus on NO production and S-nitrosation. In addition, the importance and recent advances in defining enzymatic systems proposed to be involved in regulating S-denitrosation are addressed, specifically cytosolic thioredoxins (TRX) and the newly identified aldo-keto reductases (AKR).
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47
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SLITRK2 variants associated with neurodevelopmental disorders impair excitatory synaptic function and cognition in mice. Nat Commun 2022; 13:4112. [PMID: 35840571 PMCID: PMC9287327 DOI: 10.1038/s41467-022-31566-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 06/22/2022] [Indexed: 11/08/2022] Open
Abstract
SLITRK2 is a single-pass transmembrane protein expressed at postsynaptic neurons that regulates neurite outgrowth and excitatory synapse maintenance. In the present study, we report on rare variants (one nonsense and six missense variants) in SLITRK2 on the X chromosome identified by exome sequencing in individuals with neurodevelopmental disorders. Functional studies showed that some variants displayed impaired membrane transport and impaired excitatory synapse-promoting effects. Strikingly, these variations abolished the ability of SLITRK2 wild-type to reduce the levels of the receptor tyrosine kinase TrkB in neurons. Moreover, Slitrk2 conditional knockout mice exhibited impaired long-term memory and abnormal gait, recapitulating a subset of clinical features of patients with SLITRK2 variants. Furthermore, impaired excitatory synapse maintenance induced by hippocampal CA1-specific cKO of Slitrk2 caused abnormalities in spatial reference memory. Collectively, these data suggest that SLITRK2 is involved in X-linked neurodevelopmental disorders that are caused by perturbation of diverse facets of SLITRK2 function.
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48
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Gold nanomaterials and their potential use as cryo-electron tomography labels. J Struct Biol 2022; 214:107880. [PMID: 35809758 DOI: 10.1016/j.jsb.2022.107880] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 06/30/2022] [Accepted: 07/04/2022] [Indexed: 12/14/2022]
Abstract
Rapid advances in cryo-electron tomography (cryo-ET) are driving a revolution in cellular structural biology. However, unambiguous identification of specific biomolecules within cellular tomograms remains challenging. Overcoming this obstacle and reliably identifying targets in the crowded cellular environment is of major importance for the understanding of cellular function and is a pre-requisite for high-resolution structural analysis. The use of highly-specific, readily visualised and adjustable labels would help mitigate this issue, improving both data quality and sample throughput. While progress has been made in cryo-CLEM and in the development of cloneable high-density tags, technical issues persist and a robust 'cryo-GFP' remains elusive. Readily-synthesized gold nanomaterials conjugated to small 'affinity modules' may represent a solution. The synthesis of materials including gold nanoclusters (AuNCs) and gold nanoparticles (AuNPs) is increasingly well understood and is now within the capabilities of non-specialist laboratories. The remarkable chemical and photophysical properties of <3nm diameter nanomaterials and their emergence as tools with widespread biomedical application presents significant opportunities to the cryo-microscopy community. In this review, we will outline developments in the synthesis, functionalisation and labelling uses of both AuNPs and AuNCs in cryo-ET, while discussing their potential as multi-modal probes for cryo-CLEM.
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49
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Cao X, Lu H, Wei Y, Jin L, Zhang Q, Liu B. A simple "turn-on" fluorescent probe capable of recognition cysteine with rapid response and high sensing in living cells and zebrafish. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 275:121167. [PMID: 35316627 DOI: 10.1016/j.saa.2022.121167] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 03/05/2022] [Accepted: 03/13/2022] [Indexed: 06/14/2023]
Abstract
Cysteine (Cys), an essential biological amino acid, participates several crucial functions in various physiological and pathological processes. The sensitive and specific detection of Cys is of great significance for understanding its biological function to disease diagnosis. Herein, we designed and synthesized a simple fluorescence sensor 2-(benzothiophen-2-yl)-4-oxo-4H-chromen-3-yl acrylate (BTCA) composed of a flavonol skeleton as the fluorophore and acrylic ester group as the recognition receptor. Probe BTCA displayed high selectivity and extremely fast response toward Cys in phosphate buffer solution in the presence of other competitive species even Homocysteine (Hcy) and Glutathione (GSH) owing to a specific conjugate addition-cyclization reaction between the acrylate moiety and Cys. The photoluminescence mechanism of probe BTCA toward Cys was modulated by excited state intramolecular proton transfer (ESIPT) process. The sensing property for Cys was studied by UV-Visible, fluorescence spectrophotometric analyses and time-dependent density functional theory (TD-DFT) calculations, those results indicated that probe BTCA possessed excellent sensitivity, higher specificity, dramatically "naked-eye" fluorescence enhancement (30-fold), high anti-interference ability, especially immediate response speed (within 40 s). Additionally, the practicability of sensor BTCA in exogenous and endogenous Cys imaging in living cells and zebrafish was elucidated as well, suggesting that it has remarkedly diagnostic significance in physiological and pathological process.
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Affiliation(s)
- Xiaoyan Cao
- Key Laboratory of Catalysis in Shaanxi Province, Shaanxi University of Technology, Hanzhong 723000, PR China.
| | - Hongzhao Lu
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong 723000, PR China
| | - Yifan Wei
- Key Laboratory of Catalysis in Shaanxi Province, Shaanxi University of Technology, Hanzhong 723000, PR China
| | - Lingxia Jin
- Key Laboratory of Catalysis in Shaanxi Province, Shaanxi University of Technology, Hanzhong 723000, PR China
| | - Qiang Zhang
- Key Laboratory of Catalysis in Shaanxi Province, Shaanxi University of Technology, Hanzhong 723000, PR China
| | - Bo Liu
- Key Laboratory of Catalysis in Shaanxi Province, Shaanxi University of Technology, Hanzhong 723000, PR China
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50
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West JD. Experimental Approaches for Investigating Disulfide-Based Redox Relays in Cells. Chem Res Toxicol 2022; 35:1676-1689. [PMID: 35771680 DOI: 10.1021/acs.chemrestox.2c00123] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Reversible oxidation of cysteine residues within proteins occurs naturally during normal cellular homeostasis and can increase during oxidative stress. Cysteine oxidation often leads to the formation of disulfide bonds, which can impact protein folding, stability, and function. Work in both prokaryotic and eukaryotic models over the past five decades has revealed several multiprotein systems that use thiol-dependent oxidoreductases to mediate disulfide bond reduction, formation, and/or rearrangement. Here, I provide an overview of how these systems operate to carry out disulfide exchange reactions in different cellular compartments, with a focus on their roles in maintaining redox homeostasis, transducing redox signals, and facilitating protein folding. Additionally, I review thiol-independent and thiol-dependent approaches for interrogating what proteins partner together in such disulfide-based redox relays. While the thiol-independent approaches rely either on predictive measures or standard procedures for monitoring protein-protein interactions, the thiol-dependent approaches include direct disulfide trapping methods as well as thiol-dependent chemical cross-linking. These strategies may prove useful in the systematic characterization of known and newly discovered disulfide relay mechanisms and redox switches involved in oxidant defense, protein folding, and cell signaling.
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Affiliation(s)
- James D West
- Biochemistry & Molecular Biology Program, Departments of Biology and Chemistry, The College of Wooster, Wooster, Ohio 44691, United States
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