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Zhang Q, Fan S, Tang M, Wang C, Li X, Jin Y, Yang Z. Computation-Guided Rational Design of Cysteine-Less Protein Variants in Engineered hCGL. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:9937-9946. [PMID: 38651303 DOI: 10.1021/acs.jafc.3c06821] [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: 04/25/2024]
Abstract
The engineered human cystathionine-γ-lyase (hCGL) resulting in enhanced activity toward both cysteine and cystine unveils a potential robust antitumor activity. However, the presence of cysteine residues has the potential to induce oligomerization or incorrect disulfide bonding, which may decrease the bioavailability of biopharmaceuticals. Through a meticulous design process targeting the cysteine residues within engineered hCGL, a set of potential beneficial mutants were obtained by virtual screening employing Rosetta and ABACUS. Experimental measurements have revealed that most of the mutants showed increased activity toward both substrates l-Cys and CSSC. Furthermore, mutants C109V and C229D demonstrated Tm value increases of 8.2 and 1.8 °C, respectively. After an 80 min incubation at 60 °C, mutant C229D still maintained high residual activity. Unexpectedly, mutant C109V, displaying activity approximately 2-fold higher than the activity of wild type (WT) for both substrates, showed disappointing instability in plasma, which suggests that computational design still requires further consideration. Analysis of their structure and molecular dynamics (MD) simulation revealed the impact of hydrophobic interaction, hydrogen bonds, and near-attack conformation (NAC) stability on activity and stability. This study acquired information about mutants that exhibit enhanced activity or thermal resistance and serve as valuable guidance for subsequent specific cysteine modifications.
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Affiliation(s)
- Qian Zhang
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Shuai Fan
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Mengjia Tang
- School of Pharmacy, North China University of Science and Technology, Tangshan 063210, Hebei, China
| | - Chenyu Wang
- School of Pharmacy, North China University of Science and Technology, Tangshan 063210, Hebei, China
| | - Xiaoxiao Li
- School of Pharmacy, North China University of Science and Technology, Tangshan 063210, Hebei, China
| | - Yuanyuan Jin
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Zhaoyong Yang
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
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Urrutia PJ, Bórquez DA. Expanded bioinformatic analysis of Oximouse dataset reveals key putative processes involved in brain aging and cognitive decline. Free Radic Biol Med 2023; 207:200-211. [PMID: 37473875 DOI: 10.1016/j.freeradbiomed.2023.07.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/11/2023] [Accepted: 07/17/2023] [Indexed: 07/22/2023]
Abstract
The theory that aging is driven by the damage produced by reactive oxygen species (ROS) derived from oxidative metabolism dominated geroscience studies during the second half of the 20th century. However, increasing evidence that ROS also plays a key role in the physiological regulation of numerous processes through the reversible oxidation of cysteine residues in proteins, has challenged this notion. Currently, the scope of redox signaling has reached proteomic dimensions through mass spectrometry techniques. Here, we perform a comprehensive bioinformatics analysis of cysteine oxidation changes during mouse brain aging, using the quantitative data provided in the Oximouse dataset. Interestingly, our unbiased analysis identified hundreds of putative cysteine redox switches covering several pathways previously associated with aging. These include the ubiquitin-proteasome pathway and one-carbon metabolism (folate cycle, methionine cycle, transsulfuration and polyamine pathways). Surprisingly, cysteine oxidation changes are enriched in synaptic proteins in a highly asymmetric distribution: while postsynaptic proteins tend to increase cysteine oxidation with age, the opposite occurs for presynaptic proteins. Additionally, cysteine oxidation changes during aging are associated with proteins involved in the regulation of the mitochondrial transition pore opening and synaptic calcium homeostasis. Our analysis reinforces the concept that brain aging is associated with selective changes in the oxidation state of key proteins, rather than an overall trend toward increased oxidation. Also, we provide a prioritized list of specific cysteine residues with putative impact in aging processes for future experimental validation.
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Affiliation(s)
- Pamela J Urrutia
- Institute for Nutrition & Food Technology (INTA), Universidad de Chile, El Líbano 5524, Santiago, 7830490, Chile; Geroscience Center for Brain Health and Metabolism, Santiago, 7800003, Chile
| | - Daniel A Bórquez
- Laboratory of Cell Signaling & Bioinformatics, Center for Biomedical Research, Faculty of Medicine, Universidad Diego Portales, Ejército Libertador 141, Santiago, 8370007, Chile.
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Arrigo E, Comità S, Pagliaro P, Penna C, Mancardi D. Clinical Applications for Gasotransmitters in the Cardiovascular System: Are We There Yet? Int J Mol Sci 2023; 24:12480. [PMID: 37569855 PMCID: PMC10419417 DOI: 10.3390/ijms241512480] [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: 06/30/2023] [Revised: 07/28/2023] [Accepted: 08/03/2023] [Indexed: 08/13/2023] Open
Abstract
Ischemia is the underlying mechanism in a wide variety of acute and persistent pathologies. As such, understanding the fine intracellular events occurring during (and after) the restriction of blood supply is pivotal to improving the outcomes in clinical settings. Among others, gaseous signaling molecules constitutively produced by mammalian cells (gasotransmitters) have been shown to be of potential interest for clinical treatment of ischemia/reperfusion injury. Nitric oxide (NO and its sibling, HNO), hydrogen sulfide (H2S), and carbon monoxide (CO) have long been proven to be cytoprotective in basic science experiments, and they are now awaiting confirmation with clinical trials. The aim of this work is to review the literature and the clinical trials database to address the state of development of potential therapeutic applications for NO, H2S, and CO and the clinical scenarios where they are more promising.
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Araki S, Takata T, Ono K, Sawa T, Kasamatsu S, Ihara H, Kumagai Y, Akaike T, Watanabe Y, Tsuchiya Y. Cystathionine γ-Lyase Self-Inactivates by Polysulfidation during Cystine Metabolism. Int J Mol Sci 2023; 24:9982. [PMID: 37373128 DOI: 10.3390/ijms24129982] [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: 05/11/2023] [Revised: 06/06/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023] Open
Abstract
Cystathionine γ-lyase (CSE) is an enzyme responsible for the biosynthesis of cysteine from cystathionine in the final step of the transsulfuration pathway. It also has β-lyase activity toward cystine, generating cysteine persulfide (Cys-SSH). The chemical reactivity of Cys-SSH is thought to be involved in the catalytic activity of particular proteins via protein polysulfidation, the formation of -S-(S)n-H on their reactive cysteine residues. The Cys136/171 residues of CSE have been proposed to be redox-sensitive residues. Herein, we investigated whether CSE polysulfidation occurs at Cys136/171 during cystine metabolism. Transfection of wild-type CSE into COS-7 cells resulted in increased intracellular Cys-SSH production, which was significantly increased when Cys136Val or Cys136/171Val CSE mutants were transfected, instead of the wild-type enzyme. A biotin-polyethylene glycol-conjugated maleimide capture assay revealed that CSE polysulfidation occurs at Cys136 during cystine metabolism. In vitro incubation of CSE with CSE-enzymatically synthesized Cys-SSH resulted in the inhibition of Cys-SSH production. In contrast, the mutant CSEs (Cys136Val and Cys136/171Val) proved resistant to inhibition. The Cys-SSH-producing CSE activity of Cys136/171Val CSE was higher than that of the wild-type enzyme. Meanwhile, the cysteine-producing CSE activity of this mutant was equivalent to that of the wild-type enzyme. It is assumed that Cys-SSH-producing CSE activity could be auto-inactivated via the polysulfidation of the enzyme during cystine metabolism. Thus, the polysulfidation of CSE at the Cys136 residue may be an integral feature of cystine metabolism, which functions to down-regulate Cys-SSH synthesis by the enzyme.
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Affiliation(s)
- Shoma Araki
- Department of Pharmacology, Showa Pharmaceutical University, Machida 194-8543, Japan
| | - Tsuyoshi Takata
- Department of Pharmacology, Showa Pharmaceutical University, Machida 194-8543, Japan
- South Bend Campus, Indiana University School of Medicine, South Bend, IN 46617, USA
| | - Katsuhiko Ono
- Department of Microbiology, Graduate School of Medical Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Tomohiro Sawa
- Department of Microbiology, Graduate School of Medical Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Shingo Kasamatsu
- Department of Biological Chemistry, Graduate School of Science, Osaka Metropolitan University, Sakai 599-8531, Japan
| | - Hideshi Ihara
- Department of Biological Chemistry, Graduate School of Science, Osaka Metropolitan University, Sakai 599-8531, Japan
| | - Yoshito Kumagai
- Graduate School of Pharmaceutical Sciences, Kyusyu University, Fukuoka 812-8582, Japan
| | - Takaaki Akaike
- Department of Environmental Medicine and Molecular Toxicology, Graduate School of Medicine, Tohoku University, Sendai 980-8575, Japan
| | - Yasuo Watanabe
- Department of Pharmacology, Showa Pharmaceutical University, Machida 194-8543, Japan
| | - Yukihiro Tsuchiya
- Department of Pharmacology, Showa Pharmaceutical University, Machida 194-8543, Japan
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Sun J, Wang W, Hu X, Zhang X, Zhu C, Hu J, Ma R. Local delivery of gaseous signaling molecules for orthopedic disease therapy. J Nanobiotechnology 2023; 21:58. [PMID: 36810201 PMCID: PMC9942085 DOI: 10.1186/s12951-023-01813-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 02/13/2023] [Indexed: 02/24/2023] Open
Abstract
Over the past decade, a proliferation of research has used nanoparticles to deliver gaseous signaling molecules for medical purposes. The discovery and revelation of the role of gaseous signaling molecules have been accompanied by nanoparticle therapies for their local delivery. While most of them have been applied in oncology, recent advances have demonstrated their considerable potential in diagnosing and treating orthopedic diseases. Three of the currently recognized gaseous signaling molecules, nitric oxide (NO), carbon monoxide (CO), and hydrogen sulfide (H2S), are highlighted in this review along with their distinctive biological functions and roles in orthopedic diseases. Moreover, this review summarizes the progress in therapeutic development over the past ten years with a deeper discussion of unresolved issues and potential clinical applications.
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Affiliation(s)
- Jiaxuan Sun
- grid.59053.3a0000000121679639Department of Orthopedics, The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001 Anhui China
| | - Wenzhi Wang
- grid.59053.3a0000000121679639Department of Orthopedics, The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001 Anhui China
| | - Xianli Hu
- grid.59053.3a0000000121679639Department of Orthopedics, The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001 Anhui China
| | - Xianzuo Zhang
- grid.59053.3a0000000121679639Department of Orthopedics, The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001 Anhui China
| | - Chen Zhu
- Department of Orthopedics, The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001, Anhui, China.
| | - Jinming Hu
- Department of Pharmacy, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, CAS Key Laboratory of Soft Matter Chemistry, Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, 230001, Anhui, China.
| | - Ruixiang Ma
- Department of Orthopedics, The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001, Anhui, China.
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Hubbard D, Tutrow K, Gaston B. S-Nitroso-l-cysteine and ventilatory drive: A pediatric perspective. Pediatr Pulmonol 2022; 57:2291-2297. [PMID: 35785452 PMCID: PMC9489637 DOI: 10.1002/ppul.26036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 05/09/2022] [Accepted: 05/29/2022] [Indexed: 01/01/2023]
Abstract
Though endogenous S-nitroso-l-cysteine (l-CSNO) signaling at the level of the carotid body increases minute ventilation (v̇E ), neither the background data nor the potential clinical relevance are well-understood by pulmonologists in general, or by pediatric pulmonologists in particular. Here, we first review how regulation of the synthesis, activation, transmembrane transport, target interaction, and degradation of l-CSNO can affect the ventilatory drive. In particular, we review l-CSNO formation by hemoglobin R to T conformational change and by nitric oxide (NO) synthases (NOS), and the downstream effects on v̇E through interaction with voltage-gated K+ (Kv) channel proteins and other targets in the peripheral and central nervous systems. We will review how these effects are independent of-and, in fact may be opposite to-those of NO. Next, we will review evidence that specific elements of this pathway may underlie disorders of respiratory control in childhood. Finally, we will review the potential clinical implications of this pathway in the development of respiratory stimulants, with a particular focus on potential pediatric applications.
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Affiliation(s)
- Dallin Hubbard
- Division of Pediatric PulmonologyIndiana University School of MedicineIndianapolisIndianaUSA
| | - Kaylee Tutrow
- Division of Pediatric PulmonologyIndiana University School of MedicineIndianapolisIndianaUSA
| | - Benjamin Gaston
- Division of Pediatric PulmonologyIndiana University School of MedicineIndianapolisIndianaUSA
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