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Zhang Y, Deng Y, Yang X, Xue H, Lang Y. The Relationship Between Protein S-Nitrosylation and Human Diseases: A Review. Neurochem Res 2020; 45:2815-2827. [PMID: 32984933 DOI: 10.1007/s11064-020-03136-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/18/2020] [Accepted: 09/19/2020] [Indexed: 01/12/2023]
Abstract
S-nitrosylation (SNO) is a covalent post-translational oxidative modification. The reaction is the nitroso group (-NO) to a reactive cysteine thiol within a protein to form the SNO. In recent years, a variety of proteins in human body have been found to undergo thiol nitrosylation under specific conditions. Protein SNO, which is closely related to cardiovascular disease, Parkinson's syndrome, Alzheimer's disease and tumors, plays an important role in regulatory mechanism of protein function in both physiological and pathological pathways, such as in cellular homeostasis and metabolism. This review discusses possible molecular mechanisms protein SNO modification, such as the role of NO in vivo and the formation mechanism of SNO, with particular emphasis on mechanisms utilized by SNO to cause certain diseases of human. Importantly, the effect of SNO on diseases is multifaceted and multi-channel, and its critical value in vivo is not well defined. Intracellular redox environment is also a key factor affecting its level. Therefore, we should pay more attention to the equilibrium relationship between SNO and denitrosylation pathway in the future researches. These findings provide theoretical support for the improvement or treatment of diseases from the point of view of SNO.
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Affiliation(s)
- Yadi Zhang
- Key Laboratory of Public Health Safety of Hebei Province, College of Public Health, Hebei University, No. 180 Wusidong Road, Baoding, 071002, People's Republic of China.,Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of Ministry of Education, Institute of Life Science and Green Development, Hebei University, Baoding, 071002, People's Republic of China
| | - Yuzhen Deng
- Key Laboratory of Public Health Safety of Hebei Province, College of Public Health, Hebei University, No. 180 Wusidong Road, Baoding, 071002, People's Republic of China.,Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of Ministry of Education, Institute of Life Science and Green Development, Hebei University, Baoding, 071002, People's Republic of China
| | - Xiaoxi Yang
- Key Laboratory of Public Health Safety of Hebei Province, College of Public Health, Hebei University, No. 180 Wusidong Road, Baoding, 071002, People's Republic of China.,Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of Ministry of Education, Institute of Life Science and Green Development, Hebei University, Baoding, 071002, People's Republic of China
| | - Hongmei Xue
- Key Laboratory of Public Health Safety of Hebei Province, College of Public Health, Hebei University, No. 180 Wusidong Road, Baoding, 071002, People's Republic of China.,Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of Ministry of Education, Institute of Life Science and Green Development, Hebei University, Baoding, 071002, People's Republic of China
| | - Yumiao Lang
- Key Laboratory of Public Health Safety of Hebei Province, College of Public Health, Hebei University, No. 180 Wusidong Road, Baoding, 071002, People's Republic of China. .,Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of Ministry of Education, Institute of Life Science and Green Development, Hebei University, Baoding, 071002, People's Republic of China.
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Zhou C, Liang J, Cheng S, Shi T, Houk KN, Wei DQ, Zhao YL. Ab initio molecular metadynamics simulation for S-nitrosylation by nitric oxide: S-nitroxide as the key intermediate. MOLECULAR SIMULATION 2017. [DOI: 10.1080/08927022.2017.1319059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Chao Zhou
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, MOE-LSB & MOE-LSC, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Juan Liang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, MOE-LSB & MOE-LSC, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Shangli Cheng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, MOE-LSB & MOE-LSC, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Ting Shi
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, MOE-LSB & MOE-LSC, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - K. N. Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA
| | - Dong-Qing Wei
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, MOE-LSB & MOE-LSC, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Yi-Lei Zhao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, MOE-LSB & MOE-LSC, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, P.R. China
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3
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Fedorova IV, Krestyaninov MA, Safonova LP. Ab initio molecular dynamics study of H-bonding and proton transfer in the phosphoric acid-N,N-Dimethylformamide system. J Chem Phys 2016; 145:124507. [PMID: 27782676 DOI: 10.1063/1.4963401] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Car-Parrinello molecular dynamics simulations of phosphoric acid (H3PO4)-N,N-dimethylformamide (DMF) mixtures over the whole composition range have been carried out. It has been found that the neutral molecules are the dominant species in this system. The concentration dependences of the average number of H-bonds per proton acceptor atom in P=O and C=O groups as well as per proton donor atom in DMFH+ ions towards phosphate species have been discussed. The H-bonding between components in all investigated mixtures of H3PO4 and DMF is possible. A significant fraction of the protonated DMF forms appears at phosphoric acid mole fraction higher than 0.37, indicating a high probability of proton transfer from phosphate species to oxygen atoms in C=O groups. The intermolecular proton transfer between phosphate species themselves is mainly observed when xH3PO4 > 0.19. Satisfactory agreement with available experimental data for structural characteristics of the investigated system was obtained.
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Affiliation(s)
- Irina V Fedorova
- G. A. Krestov Institute of Solution Chemistry of Russian Academy of Sciences, 1 Akademicheskaya Street, Ivanovo 153045, Russia
| | - Michael A Krestyaninov
- G. A. Krestov Institute of Solution Chemistry of Russian Academy of Sciences, 1 Akademicheskaya Street, Ivanovo 153045, Russia
| | - Lyubov P Safonova
- G. A. Krestov Institute of Solution Chemistry of Russian Academy of Sciences, 1 Akademicheskaya Street, Ivanovo 153045, Russia
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Meyer B, Genoni A, Boudier A, Leroy P, Ruiz-Lopez MF. Structure and Stability Studies of Pharmacologically Relevant S-Nitrosothiols: A Theoretical Approach. J Phys Chem A 2016; 120:4191-200. [PMID: 27249061 DOI: 10.1021/acs.jpca.6b02230] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Nowadays, S-nitrosothiols (RSNOs) represent a promising class of nitric oxide (NO) donors that could be successfully used as drugs to compensate the decrease of NO production that usually arises in conjunction with cardiovascular diseases. Nevertheless, notwithstanding their pharmacological interest, the structure-stability relationship in RSNOs is still unclear, and this issue, together with the mechanism of NO donation in the physiological medium, deserves further investigation. As a first step forward in this direction, in this paper, the overall stability and structural preference of two pharmacologically relevant S-nitrosothiol molecules were studied in detail by means of computational strategies. In particular, performing calculations in implicit solvent (water) on the S-nitroso-N-acetylpenicillamine and the S-nitroso-N-acetylcysteine and analyzing the noncovalent interactions networks of their most stable conformers, we observed that the structure and the stability of these molecules can be directly related to the formation of stabilizing hydrogen-bond and chalcogen-chalcogen intramolecular interactions. The obtained results represent the starting point for further investigations to be conducted also on larger RSNOs to shed further light on the role played by intra- and intermolecular interactions and by solvation effects in stabilizing this class of molecules. The obtained insights will be hopefully helpful to design new RSNO-based drugs characterized by an enhanced pharmacological potency.
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Affiliation(s)
- Benjamin Meyer
- CNRS, Laboratoire SRSMC, UMR 7565 , Vandoeuvre-lès-Nancy F-54506, France.,Université de Lorraine, Laboratoire SRSMC, UMR 7565 , Vandoeuvre-lès-Nancy F-54506, France
| | - Alessandro Genoni
- CNRS, Laboratoire SRSMC, UMR 7565 , Vandoeuvre-lès-Nancy F-54506, France.,Université de Lorraine, Laboratoire SRSMC, UMR 7565 , Vandoeuvre-lès-Nancy F-54506, France
| | - Ariane Boudier
- Université de Lorraine, Laboratoire CITHÉFOR, EA 3452 , Nancy F-54001, France
| | - Pierre Leroy
- Université de Lorraine, Laboratoire CITHÉFOR, EA 3452 , Nancy F-54001, France
| | - Manuel F Ruiz-Lopez
- CNRS, Laboratoire SRSMC, UMR 7565 , Vandoeuvre-lès-Nancy F-54506, France.,Université de Lorraine, Laboratoire SRSMC, UMR 7565 , Vandoeuvre-lès-Nancy F-54506, France
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Pahari S, Roy S. Proton transport mechanism of imidazole, triazole and phosphoric acid mixtures from ab initio molecular dynamics simulations. Phys Chem Chem Phys 2015; 17:30551-9. [PMID: 26523706 DOI: 10.1039/c5cp05735c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
We performed first principles molecular dynamics simulations to elucidate the mechanism and role of 1,2,3-triazole in proton transport while it is mixed with phosphoric acid (PA) and a phosphoric acid imidazole mixture. PA doped imidazole based polymer acts as an efficient polyelectrolyte membrane for fuel cells. The conductivity of this membrane increases when triazole is added to the system. For the first time we performed ab initio molecular dynamics simulations of complex mixtures of PA, imidazole and triazole. We have quantitatively estimated the structural diffusion and vehicular motion of protons. We found that upon the addition of triazole in PA and the PA imidazole mixture, the structural diffusion of protons increases significantly. The mechanism of proton transport is different when triazole is added to the mixture. We have also identified two different paths for structural diffusion (constructive and non-constructive) that contribute to long and short range proton transport.
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Affiliation(s)
| | - Sudip Roy
- National Chemical Laboratory, Pune, India.
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Cheng S, Shi T, Wang XL, Liang J, Wu H, Xie L, Li Y, Zhao YL. Features of S-nitrosylation based on statistical analysis and molecular dynamics simulation: cysteine acidity, surrounding basicity, steric hindrance and local flexibility. MOLECULAR BIOSYSTEMS 2015; 10:2597-606. [PMID: 25030274 DOI: 10.1039/c4mb00322e] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
S-Nitrosylation is involved in protein functional regulation and cellular signal transduction. Although intensive efforts have been made, the molecular mechanisms of S-nitrosylation have not yet been fully understood. In this work, we carried out a survey on 213 protein structures with S-nitrosylated cysteine sites and molecular dynamic simulations of hemoglobin as a case study. It was observed that the S-nitrosylated cysteines showed a lower pKa, a higher population of basic residues, a lower population of big-volume residues in the neighborhood, and relatively higher flexibility. The case study of hemoglobin showed that, compared to that in the T-state, Cysβ93 in the R-state hemoglobin possessed the above structural features, in agreement with the previous report that the R-state was more reactive in S-nitrosylation. Moreover, basic residues moved closer to the Cysβ93 in the dep-R-state hemoglobin, while big-volume residues approached the Cysβ93 in the dep-T-state. Using the four characteristics, i.e. cysteine acidity, surrounding basicity, steric hindrance, and local flexibility, a 3-dimensional model of S-nitrosylation was constructed to explain 61.9% of the S-nitrosylated and 58.1% of the non-S-nitrosylated cysteines. Our study suggests that cysteine deprotonation is a prerequisite for protein S-nitrosylation, and these characteristics might be useful in identifying specificity of protein S-nitrosylation.
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Affiliation(s)
- Shangli Cheng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
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