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Carugo O. Location of S-nitrosylated cysteines in protein three-dimensional structures. Proteins 2024; 92:464-473. [PMID: 37941304 DOI: 10.1002/prot.26629] [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: 05/05/2023] [Revised: 10/13/2023] [Accepted: 10/23/2023] [Indexed: 11/10/2023]
Abstract
Although S-nitrosylation of cysteines is a common protein posttranslational modification, little is known about its three-dimensional structural features. This paper describes a systematic survey of the data available in the Protein Data Bank. Several interesting observations could be made. (1) As a result of radiation damage, S-nitrosylated cysteines (Snc) are frequently reduced, at least partially. (2) S-nitrosylation may be a protection against irreversible thiol oxidation; because the NO group of Snc is relatively accessible to the solvent, it may act as a cork to protect the sulfur atoms of cysteines from oxidation by molecular oxygen to sulfenic, sulfinic, and sulfonic acid; moreover, Snc are frequently found at the start or end of helices and strands and this might shield secondary structural elements from unfolding.
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Affiliation(s)
- Oliviero Carugo
- Department of Chemistry, University of Pavia, Pavia, Italy
- Department of Structural and Computational Biology, Max Perutz Labs University of Vienna, Vienna, Austria
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2
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Xu C, Zhang R, Duan M, Zhou Y, Bao J, Lu H, Wang J, Hu M, Hu Z, Zhou F, Zhu W. A polygenic stacking classifier revealed the complicated platelet transcriptomic landscape of adult immune thrombocytopenia. MOLECULAR THERAPY - NUCLEIC ACIDS 2022; 28:477-487. [PMID: 35505964 PMCID: PMC9046129 DOI: 10.1016/j.omtn.2022.04.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 04/01/2022] [Indexed: 01/19/2023]
Abstract
Immune thrombocytopenia (ITP) is an autoimmune disease with the typical symptom of a low platelet count in blood. ITP demonstrated age and sex biases in both occurrences and prognosis, and adult ITP was mainly induced by the living environments. The current diagnosis guideline lacks the integration of molecular heterogenicity. This study recruited the largest cohort of platelet transcriptome samples. A comprehensive procedure of feature selection, feature engineering, and stacking classification was carried out to detect the ITP biomarkers using RNA sequencing (RNA-seq) transcriptomes. The 40 detected biomarkers were loaded to train the final ITP detection model, with an overall accuracy 0.974. The biomarkers suggested that ITP onset may be associated with various transcribed components, including protein-coding genes, long intergenic non-coding RNA (lincRNA) genes, and pseudogenes with apparent transcriptions. The delivered ITP detection model may also be utilized as a complementary ITP diagnosis tool. The code and the example dataset is freely available on http://www.healthinformaticslab.org/supp/resources.php
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Affiliation(s)
- Chengfeng Xu
- Department of Hematology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, 110 Ganhe Road, Hongkou District, Shanghai 200437, China
| | - Ruochi Zhang
- College of Computer Science and Technology, Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin 130012, China
| | - Meiyu Duan
- College of Computer Science and Technology, Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin 130012, China
| | - Yongming Zhou
- Department of Hematology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, 110 Ganhe Road, Hongkou District, Shanghai 200437, China
| | - Jizhang Bao
- Department of Hematology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, 110 Ganhe Road, Hongkou District, Shanghai 200437, China
| | - Hao Lu
- Department of Hematology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, 110 Ganhe Road, Hongkou District, Shanghai 200437, China
| | - Jie Wang
- Department of Hematology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, 110 Ganhe Road, Hongkou District, Shanghai 200437, China
| | - Minghui Hu
- Department of Hematology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, 110 Ganhe Road, Hongkou District, Shanghai 200437, China
| | - Zhaoyang Hu
- Fun-Med Pharmaceutical Technology (Shanghai) Co., Ltd., RM. A310, 115 Xinjunhuan Road, Minhang District, Shanghai 201100, China
- Corresponding author Zhaoyang Hu, PhD, Fengneng Pharmaceutical Technology (Shanghai) Co., Ltd., RM. A310, 115 Xinjunhuan Road, Minhang District, Shanghai 201100, China.
| | - Fengfeng Zhou
- College of Computer Science and Technology, Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin 130012, China
- Corresponding author Fengfeng Zhou, PhD, College of Computer Science and Technology, and Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin 130012, China.
| | - Wenwei Zhu
- Department of Hematology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, 110 Ganhe Road, Hongkou District, Shanghai 200437, China
- Corresponding author Wenwei Zhu, PhD, Department of Hematology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, 110 Ganhe Road, Hongkou District, Shanghai 200437, China.
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Zhang Z, Wang L. Using Chou's 5-steps rule to identify N 6-methyladenine sites by ensemble learning combined with multiple feature extraction methods. J Biomol Struct Dyn 2022; 40:796-806. [PMID: 32948102 DOI: 10.1080/07391102.2020.1821778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
N6-methyladenine (m6A), a type of modification mostly affecting the downstream biological functions and determining the levels of gene expression, is mediated by the methylation of adenine in nucleic acids. It is also a key factor for influencing biological processes and has attracted attention as a target for treating diseases. Here, an ensemble predictor named as TL-Methy, was developed to identify m6A sites across the genome. TL-Methy is a 2-level machine learning method developed by combining the support vector machine model and multiple features extraction methods, including nucleic acid composition, di-nucleotide composition, tri-nucleotide composition, position-specific trinucleotide propensity, Bi-profile Bayes, binary encoding, and accumulated nucleotide frequency. For Homo sapiens, TL-Methy method reached the accuracy of 91.68% on jackknife test and of 92.23% on 10-fold cross validation test; For Mus musculus, TL-Methy method achieved the accuracy of 93.66% on jackknife test and of 97.07% on 10-fold cross validation test; For Saccharomyces cerevisiae, TL-Methy method obtained the accuracy of 81.57% on jackknife test and of 82.54% on 10-fold cross validation test; For rice genome, TL-Methy method achieved the accuracy of 91.87% on jackknife test and of 93.04% on 10-fold cross validation test. The results via these two test approaches demonstrated the robustness and practicality of our TL-Methy model. The TL-Methy model may be as a potential method for m6A site identification.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Zhongwang Zhang
- College of Science, Dalian Maritime University, Dalian, P.R. China
| | - Lidong Wang
- College of Science, Dalian Maritime University, Dalian, P.R. China
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Zhao Q, Ma J, Wang Y, Xie F, Lv Z, Xu Y, Shi H, Han K. Mul-SNO: A novel prediction tool for S-nitrosylation sites based on deep learning methods. IEEE J Biomed Health Inform 2021; 26:2379-2387. [PMID: 34762593 DOI: 10.1109/jbhi.2021.3123503] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Protein s-nitrosylation (SNO is one of the most important post-translational modifications and is formed by the covalent modification of nitric oxide and cysteine residues. Extensive studies have shown that SNO plays a pivotal role in the plant immune response and treating various major human diseases. In recent years, SNO sites have become a hot research topic. Traditional biochemical methods for SNO site identification are time-consuming and costly. In this study, we developed an economical and efficient SNO site prediction tool named Mul-SNO. Mul-SNO ensembled current popular and powerful deep learning model bidirectional long short-term memory (BiLSTM and bidirectional encoder representations from Transformers (BERT . Compared with existing state-of-the-art methods, Mul-SNO obtained better ACC of 0.911 and 0.796 based on 10-fold cross-validation and independent data sets, respectively. The prediction server can be obtained for free at http://lab.malab.cn/~mjq/Mul-SNO/.
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Massa CM, Liu Z, Taylor S, Pettit AP, Stakheyeva MN, Korotkova E, Popova V, Atochina-Vasserman EN, Gow AJ. Biological Mechanisms of S-Nitrosothiol Formation and Degradation: How Is Specificity of S-Nitrosylation Achieved? Antioxidants (Basel) 2021; 10:antiox10071111. [PMID: 34356344 PMCID: PMC8301044 DOI: 10.3390/antiox10071111] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 06/03/2021] [Accepted: 06/08/2021] [Indexed: 01/21/2023] Open
Abstract
The modification of protein cysteine residues underlies some of the diverse biological functions of nitric oxide (NO) in physiology and disease. The formation of stable nitrosothiols occurs under biologically relevant conditions and time scales. However, the factors that determine the selective nature of this modification remain poorly understood, making it difficult to predict thiol targets and thus construct informatics networks. In this review, the biological chemistry of NO will be considered within the context of nitrosothiol formation and degradation whilst considering how specificity is achieved in this important post-translational modification. Since nitrosothiol formation requires a formal one-electron oxidation, a classification of reaction mechanisms is proposed regarding which species undergoes electron abstraction: NO, thiol or S-NO radical intermediate. Relevant kinetic, thermodynamic and mechanistic considerations will be examined and the impact of sources of NO and the chemical nature of potential reaction targets is also discussed.
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Affiliation(s)
- Christopher M. Massa
- Department of Pharmacology & Toxicology, Ernest Mario School of Pharmacy, Rutgers University, Piscataway, NJ 08848, USA; (C.M.M.); (Z.L.); (S.T.); (A.P.P.)
| | - Ziping Liu
- Department of Pharmacology & Toxicology, Ernest Mario School of Pharmacy, Rutgers University, Piscataway, NJ 08848, USA; (C.M.M.); (Z.L.); (S.T.); (A.P.P.)
| | - Sheryse Taylor
- Department of Pharmacology & Toxicology, Ernest Mario School of Pharmacy, Rutgers University, Piscataway, NJ 08848, USA; (C.M.M.); (Z.L.); (S.T.); (A.P.P.)
| | - Ashley P. Pettit
- Department of Pharmacology & Toxicology, Ernest Mario School of Pharmacy, Rutgers University, Piscataway, NJ 08848, USA; (C.M.M.); (Z.L.); (S.T.); (A.P.P.)
| | - Marena N. Stakheyeva
- RASA Center in Tomsk, Tomsk Polytechnic University, 634050 Tomsk, Russia; (M.N.S.); (E.N.A.-V.)
- Institute of Natural Resources, Tomsk Polytechnic University, Lenin Av. 30, 634050 Tomsk, Russia; (E.K.); (V.P.)
| | - Elena Korotkova
- Institute of Natural Resources, Tomsk Polytechnic University, Lenin Av. 30, 634050 Tomsk, Russia; (E.K.); (V.P.)
| | - Valentina Popova
- Institute of Natural Resources, Tomsk Polytechnic University, Lenin Av. 30, 634050 Tomsk, Russia; (E.K.); (V.P.)
| | - Elena N. Atochina-Vasserman
- RASA Center in Tomsk, Tomsk Polytechnic University, 634050 Tomsk, Russia; (M.N.S.); (E.N.A.-V.)
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Andrew J. Gow
- Department of Pharmacology & Toxicology, Ernest Mario School of Pharmacy, Rutgers University, Piscataway, NJ 08848, USA; (C.M.M.); (Z.L.); (S.T.); (A.P.P.)
- RASA Center in Tomsk, Tomsk Polytechnic University, 634050 Tomsk, Russia; (M.N.S.); (E.N.A.-V.)
- Correspondence: ; Tel.: +1-848-445-4612
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Recent Advances in Predicting Protein S-Nitrosylation Sites. BIOMED RESEARCH INTERNATIONAL 2021; 2021:5542224. [PMID: 33628788 PMCID: PMC7892234 DOI: 10.1155/2021/5542224] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 01/24/2021] [Accepted: 01/25/2021] [Indexed: 01/09/2023]
Abstract
Protein S-nitrosylation (SNO) is a process of covalent modification of nitric oxide (NO) and its derivatives and cysteine residues. SNO plays an essential role in reversible posttranslational modifications of proteins. The accurate prediction of SNO sites is crucial in revealing a certain biological mechanism of NO regulation and related drug development. Identification of the sites of SNO in proteins is currently a very hot topic. In this review, we briefly summarize recent advances in computationally identifying SNO sites. The challenges and future perspectives for identifying SNO sites are also discussed. We anticipate that this review will provide insights into research on SNO site prediction.
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Zhu Y, Jia C, Li F, Song J. Inspector: a lysine succinylation predictor based on edited nearest-neighbor undersampling and adaptive synthetic oversampling. Anal Biochem 2020; 593:113592. [DOI: 10.1016/j.ab.2020.113592] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Revised: 01/14/2020] [Accepted: 01/17/2020] [Indexed: 12/13/2022]
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Premont RT, Reynolds JD, Zhang R, Stamler JS. Role of Nitric Oxide Carried by Hemoglobin in Cardiovascular Physiology: Developments on a Three-Gas Respiratory Cycle. Circ Res 2019; 126:129-158. [PMID: 31590598 DOI: 10.1161/circresaha.119.315626] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
A continuous supply of oxygen is essential for the survival of multicellular organisms. The understanding of how this supply is regulated in the microvasculature has evolved from viewing erythrocytes (red blood cells [RBCs]) as passive carriers of oxygen to recognizing the complex interplay between Hb (hemoglobin) and oxygen, carbon dioxide, and nitric oxide-the three-gas respiratory cycle-that insures adequate oxygen and nutrient delivery to meet local metabolic demand. In this context, it is blood flow and not blood oxygen content that is the main driver of tissue oxygenation by RBCs. Herein, we review the lines of experimentation that led to this understanding of RBC function; from the foundational understanding of allosteric regulation of oxygen binding in Hb in the stereochemical model of Perutz, to blood flow autoregulation (hypoxic vasodilation governing oxygen delivery) observed by Guyton, to current understanding that centers on S-nitrosylation of Hb (ie, S-nitrosohemoglobin; SNO-Hb) as a purveyor of oxygen-dependent vasodilatory activity. Notably, hypoxic vasodilation is recapitulated by native S-nitrosothiol (SNO)-replete RBCs and by SNO-Hb itself, whereby SNO is released from Hb and RBCs during deoxygenation, in proportion to the degree of Hb deoxygenation, to regulate vessels directly. In addition, we discuss how dysregulation of this system through genetic mutation in Hb or through disease is a common factor in oxygenation pathologies resulting from microcirculatory impairment, including sickle cell disease, ischemic heart disease, and heart failure. We then conclude by identifying potential therapeutic interventions to correct deficits in RBC-mediated vasodilation to improve oxygen delivery-steps toward effective microvasculature-targeted therapies. To the extent that diseases of the heart, lungs, and blood are associated with impaired tissue oxygenation, the development of new therapies based on the three-gas respiratory system have the potential to improve the well-being of millions of patients.
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Affiliation(s)
- Richard T Premont
- From the Institute for Transformative Molecular Medicine (R.T.P., J.D.R., R.Z., J.S.S.), Case Western Reserve University School of Medicine, OH.,Harrington Discovery Institute (R.T.P., J.D.R., J.S.S.), University Hospitals Cleveland Medical Center, OH
| | - James D Reynolds
- From the Institute for Transformative Molecular Medicine (R.T.P., J.D.R., R.Z., J.S.S.), Case Western Reserve University School of Medicine, OH.,Department of Anesthesiology and Perioperative Medicine (J.D.R.), Case Western Reserve University School of Medicine, OH.,Harrington Discovery Institute (R.T.P., J.D.R., J.S.S.), University Hospitals Cleveland Medical Center, OH
| | - Rongli Zhang
- From the Institute for Transformative Molecular Medicine (R.T.P., J.D.R., R.Z., J.S.S.), Case Western Reserve University School of Medicine, OH.,Department of Medicine, Cardiovascular Research Institute (R.Z., J.S.S.), Case Western Reserve University School of Medicine, OH
| | - Jonathan S Stamler
- From the Institute for Transformative Molecular Medicine (R.T.P., J.D.R., R.Z., J.S.S.), Case Western Reserve University School of Medicine, OH.,Department of Medicine, Cardiovascular Research Institute (R.Z., J.S.S.), Case Western Reserve University School of Medicine, OH.,Harrington Discovery Institute (R.T.P., J.D.R., J.S.S.), University Hospitals Cleveland Medical Center, OH
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