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Li C, Song Z, Huang M, Zheng Y, Nong C, Jiang T, Li Z, Liu H, Yi Z. The molecular mechanisms of TRβ receptor interaction with polychlorinated biphenyls: A multispectral and computational exploration. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 326:125216. [PMID: 39340948 DOI: 10.1016/j.saa.2024.125216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2024] [Revised: 09/14/2024] [Accepted: 09/23/2024] [Indexed: 09/30/2024]
Abstract
The thyroid hormone (TH) system is susceptible to the toxic effects of polychlorinated biphenyls (PCBs). Pollutants may disrupt the TH system by binding to serum TH transport proteins or interacting with thyroid hormone receptors (TRs) in target cells. However, the molecular mechanism of interaction with the Thyroid Hormone Receptor Beta (TRβ) is not fully understood. This study employed fluorescence, UV-visible absorption, three-dimensional fluorescence, and Fourier-transform infrared spectroscopy, along with molecular docking and molecular dynamics simulations, to investigate the interaction between TRβ and PCBs. Moreover, molecular docking and fluorescence resonance energy transfer (FRET) findings suggest that TRβ and PCBs underwent resonance energy transfer consistent with Förster's theory. The root mean square deviation (RMSD) and docking outcomes indicate that the TRβ-PCB29 complex exhibited optimal structural stability. Thus, the study concludes that integrating spectroscopic data with molecular docking is essential for a comprehensive analysis. Further analysis of intermolecular interactions using quantum chemistry and reduced density gradient analysis (RDG) analysis revealed that van der Waals forces are the primary drivers of PCBs to TRβ.
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Affiliation(s)
- Cancan Li
- College of Chemistry and Bioengineering, Guilin University of Technology, Guilin 541004, China
| | - Zeyu Song
- College of Chemistry and Bioengineering, Guilin University of Technology, Guilin 541004, China
| | - Manting Huang
- College of Chemistry and Bioengineering, Guilin University of Technology, Guilin 541004, China
| | - Yanhong Zheng
- College of Chemistry and Bioengineering, Guilin University of Technology, Guilin 541004, China
| | - Chunke Nong
- College of Chemistry and Bioengineering, Guilin University of Technology, Guilin 541004, China
| | - Tinghao Jiang
- College of Chemistry and Bioengineering, Guilin University of Technology, Guilin 541004, China
| | - Zhanji Li
- College of Chemistry and Bioengineering, Guilin University of Technology, Guilin 541004, China
| | - Hongyan Liu
- College of Chemistry and Bioengineering, Guilin University of Technology, Guilin 541004, China.
| | - Zhongsheng Yi
- College of Chemistry and Bioengineering, Guilin University of Technology, Guilin 541004, China.
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Mohammadi MA, Shareghi B, Farhadian S, Uversky VN. Investigating the effect of pH on the interaction of cypermethrin with human serum albumin: Insights from spectroscopic and molecular dynamics simulation studies. Int J Biol Macromol 2024; 257:128459. [PMID: 38035951 DOI: 10.1016/j.ijbiomac.2023.128459] [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: 10/09/2023] [Revised: 11/17/2023] [Accepted: 11/25/2023] [Indexed: 12/02/2023]
Abstract
To efficiently combat the negative consequences of the utilization of pesticides and hazardous substances with biomolecules, it is crucial to comprehend the features of the corresponding compounds. In this study, interactions between cypermethrin (CYP) and HSA at neutral and acidic pH were investigated using a set of spectroscopic and computational tools, such as UV/VIS's absorption spectroscopy, fluorescence, Fourier-transform infrared (FTIR) spectroscopy, molecular docking, and molecular dynamics. Furthermore, the effect of CYP on the HSA thermal stability was investigated. The increase in the CYP concentration at acidic and neutral pH resulted in static HSA fluorescence quenching. In the interaction between HSA and CYP at both pH, increasing the temperature led to a decrease in the Stern-Volmer quenching constant and the binding constant. We also revealed that with increasing CYP concentration, the melting temperature of HSA increases at both pH values.
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Affiliation(s)
- Mohammad Ali Mohammadi
- Department of Biology, Faculty of Science, Shahr-e Kord University, Shahr-e Kord, P. O. Box.115, Iran
| | - Behzad Shareghi
- Department of Biology, Faculty of Science, Shahr-e Kord University, Shahr-e Kord, P. O. Box.115, Iran.
| | - Sadegh Farhadian
- Department of Biology, Faculty of Science, Shahr-e Kord University, Shahr-e Kord, P. O. Box.115, Iran
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
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Habibi A, Farhadian S, Shareghi B, Hashemi-Shahraki F. Structural change study of pepsin in the presence of spermidine trihydrochloride: Insights from spectroscopic to molecular dynamics methods. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 291:122264. [PMID: 36652806 DOI: 10.1016/j.saa.2022.122264] [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: 10/15/2022] [Revised: 12/12/2022] [Accepted: 12/17/2022] [Indexed: 06/17/2023]
Abstract
Spermidine is an aliphatic polyamine that directs a set of biological processes. This work aimed to use UV-Vis spectroscopy, fluorescence spectroscopy, thermal stability, kinetic methods, docking, and molecular dynamic simulations to examine the influence of spermidine trihydrochloride (SP) on the structure and function of pepsin. The results of the fluorescence emission spectra indicated that spermidine could quench pepsin's intrinsic emission in a static quenching process, resulting in the formation of the pepsin-spermidine complex. The results discovered that spermidine had a strong affinity to the pepsin structure because of its high binding constant. The obtained results from spectroscopy and molecular dynamic approaches showed the binding interaction between spermidine and pepsin, induced micro-environmental modifications around tryptophan residues that caused a change in the tertiary and secondary structure of the enzyme. FTIR analysis showed hypochromic effects in the spectra of amide I and II and redistribution of the helical structure. Moreover, the molecular dynamic (MD) and docking studies confirmed the experimental data. Both experimental and molecular dynamics simulation results clarified that electrostatic bond interactions were dominant forces.
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Affiliation(s)
- Atefeh Habibi
- Department of Biology, Faculty of Science, Shahrekord University, Shahrekord, P.O. Box 115, Iran; Central Laboratory, Shahrekord University, Shahrekord, Iran
| | - Sadegh Farhadian
- Department of Biology, Faculty of Science, Shahrekord University, Shahrekord, P.O. Box 115, Iran; Central Laboratory, Shahrekord University, Shahrekord, Iran.
| | - Behzad Shareghi
- Department of Biology, Faculty of Science, Shahrekord University, Shahrekord, P.O. Box 115, Iran; Central Laboratory, Shahrekord University, Shahrekord, Iran.
| | - Fatemeh Hashemi-Shahraki
- Department of Biology, Faculty of Science, Shahrekord University, Shahrekord, P.O. Box 115, Iran; Central Laboratory, Shahrekord University, Shahrekord, Iran
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Liu K, Zhang Y, Zhang W, Liu L, Yu Z. A Study on the Interactions of Proteinase K with Myricetin and Myricitrin by Multi-Spectroscopy and Molecular Modeling. Int J Mol Sci 2023; 24:ijms24065317. [PMID: 36982397 PMCID: PMC10048853 DOI: 10.3390/ijms24065317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 02/28/2023] [Accepted: 03/08/2023] [Indexed: 03/16/2023] Open
Abstract
Myricetin (MYR) and myricitrin (MYT) are well recognized for their nutraceutical value, such as antioxidant, hypoglycemic, and hypotensive effects. In this work, fluorescence spectroscopy and molecular modeling were adopted to investigate the conformational and stability changes of proteinase K (PK) in the presence of MYR and MYT. The experimental results showed that both MYR and MYT could quench fluorescence emission via a static quenching mechanism. Further investigation demonstrated that both hydrogen bonding and van der Waals forces play significant roles in the binding of complexes, which is consistent with the conclusions of molecular modeling. Synchronous fluorescence spectroscopy, Förster resonance energy transfer, and site-tagged competition experiments were performed to prove that the binding of MYR or MYT to PK could alter its micro-environment and conformation. Molecular docking results revealed that either MYR or MYT spontaneously interacted with PK at a single binding site via hydrogen bonding and hydrophobic interactions, which is consistent with the results of spectroscopic measurements. A 30 ns molecular dynamics simulation was conducted for both PK-MYR and PK-MYT complexes. The calculation results showed that no large structural distortions or interaction changes occurred during the entire simulation time span. The average RMSD changes of PK in PK-MYR and PK-MYT were 2.06 and 2.15 Å, respectively, indicating excellent stability of both complexes. The molecular simulation results suggested that both MYR and MYT could interact with PK spontaneously, which is in agreement with spectroscopic results. This agreement between experimental and theoretical results indicates that the method herein could be feasible and worthwhile for protein–ligand complex studies.
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Affiliation(s)
- Kefan Liu
- College of Chemistry and Chemical Engineering, Shenyang Normal University, Shenyang 110034, China
| | - Yubo Zhang
- College of Chemistry and Chemical Engineering, Shenyang Normal University, Shenyang 110034, China
| | - Wei Zhang
- College of Chemistry and Chemical Engineering, Shenyang Normal University, Shenyang 110034, China
| | - Liyan Liu
- College of Chemistry and Chemical Engineering, Shenyang Normal University, Shenyang 110034, China
| | - Zhan Yu
- College of Chemistry and Chemical Engineering, Shenyang Normal University, Shenyang 110034, China
- Provincial Key Laboratory for Separation and Analysis of Complex Systems in Liaoning Universities, Shenyang Normal University, Shenyang 110034, China
- Correspondence:
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Insight into the binding of alpha-linolenic acid (ALA) on Human Serum Albumin using spectroscopic and molecular dynamics (MD) studies. Process Biochem 2022. [DOI: 10.1016/j.procbio.2022.09.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Eslami-Farsani R, Farhadian S, Shareghi B. Exploring the structural basis of conformational alterations of myoglobin in the presence of spermine through computational modeling, molecular dynamics simulations, and spectroscopy methods. J Biomol Struct Dyn 2022; 40:3581-3594. [PMID: 33308044 DOI: 10.1080/07391102.2020.1848633] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Spermine as polyamines can have interaction with the myoglobin (Mb). The intent of this pondering to evaluate the impact of spermine on Mb properties, for example, the structure and thermal stability. For this analysis, the following approaches are employed. Thermodynamics, molecular dynamics (MD), and docking and the use of other spectroscopic procedures. The results of fluorescence spectroscopy and docking showed that binding spermine to Mb was spontaneous. Spermine quenched the fluorescence of Mb through the static quenching process. The thermal stability of Mb was incremented when the concentration of spermine increased. The CD spectra showed Mb's secondary structure shift with a rise in β-sheet and a decrease in α-helicity Mb's in spermine presence. Molecular docking and MD simulation outcomes demonstrate that electrostatic forces show a critical function in stabilizing of this complex, which is in conforming to spectroscopic results.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Sadegh Farhadian
- Department of Biology, Shahrekord University, Shahrekord, Iran.,Central Laboratory, Shahrekord University, Shahrekord, Iran
| | - Behzad Shareghi
- Department of Biology, Shahrekord University, Shahrekord, Iran.,Central Laboratory, Shahrekord University, Shahrekord, Iran
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de Souza FG, de Araújo FF, Orlando EA, Rodrigues FM, Chávez DWH, Pallone JAL, Neri-Numa IA, Sawaya ACHF, Pastore GM. Characterization of Buritirana ( Mauritiella armata) Fruits from the Brazilian Cerrado: Biometric and Physicochemical Attributes, Chemical Composition and Antioxidant and Antibacterial Potential. Foods 2022; 11:786. [PMID: 35327209 PMCID: PMC8949527 DOI: 10.3390/foods11060786] [Citation(s) in RCA: 6] [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: 01/23/2022] [Revised: 03/01/2022] [Accepted: 03/07/2022] [Indexed: 01/12/2023] Open
Abstract
The buritirana is a little-explored species of the Arecaceae family. The biometric and physicochemical characteristics, nutritional and chemical composition and antioxidant and antibacterial potential of the buritirana fruit fractions were evaluated here for the first time. The fruits presented an oblong shape. The pulp represented 16.58% of the whole-fruit weight (10.07 g). The moisture, ash and soluble fiber contents were similar for the whole fraction without seed (WS) and pulp. Although the total carbohydrate content was the same for seed and peel (23.24 g·100 g-1), the seed showed higher protein and insoluble fiber contents. Except for glucose (1256.63 mg·100 g-1), the seed showed the highest concentrations of mono-, di- and oligosaccharides. Mineral content ranged from 0.43 to 800 mg·100 g-1 in all fractions. The peel fraction showed the highest content of vitamin C. The physicochemical results indicate the pulp and WS fraction have potential for the production of fruit-derived food products. Protocatechuic and quinic acids and epicatechin/catechin were found in all fractions. The assay antioxidant capacity DPPH, phenolic content and total flavonoids were higher in the pulp; TEAC and ORACHF values were lower in the seed. Volatile organic compounds were not identified, and the fractions did not show antibacterial activity.
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Affiliation(s)
- Florisvaldo Gama de Souza
- Department of Food Science, Faculty of Food Engineering, University of Campinas, Campinas 13083-862, SP, Brazil; (F.F.d.A.); (E.A.O.); (J.A.L.P.); (I.A.N.-N.); (G.M.P.)
| | - Fábio Fernandes de Araújo
- Department of Food Science, Faculty of Food Engineering, University of Campinas, Campinas 13083-862, SP, Brazil; (F.F.d.A.); (E.A.O.); (J.A.L.P.); (I.A.N.-N.); (G.M.P.)
| | - Eduardo Adilson Orlando
- Department of Food Science, Faculty of Food Engineering, University of Campinas, Campinas 13083-862, SP, Brazil; (F.F.d.A.); (E.A.O.); (J.A.L.P.); (I.A.N.-N.); (G.M.P.)
| | - Fernando Morais Rodrigues
- Department of Food Science and Technology, Federal Institute of Education, Science and Technology of Tocantins, Paraíso of Tocantins 77600-000, TO, Brazil;
| | - Davy William Hidalgo Chávez
- Department of Food Science and Technology, Federal Rural University of Rio de Janeiro, Seropédica 23890-000, RJ, Brazil;
| | - Juliana Azevedo Lima Pallone
- Department of Food Science, Faculty of Food Engineering, University of Campinas, Campinas 13083-862, SP, Brazil; (F.F.d.A.); (E.A.O.); (J.A.L.P.); (I.A.N.-N.); (G.M.P.)
| | - Iramaia Angélica Neri-Numa
- Department of Food Science, Faculty of Food Engineering, University of Campinas, Campinas 13083-862, SP, Brazil; (F.F.d.A.); (E.A.O.); (J.A.L.P.); (I.A.N.-N.); (G.M.P.)
| | | | - Glaucia Maria Pastore
- Department of Food Science, Faculty of Food Engineering, University of Campinas, Campinas 13083-862, SP, Brazil; (F.F.d.A.); (E.A.O.); (J.A.L.P.); (I.A.N.-N.); (G.M.P.)
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A comparative study of structural and dynamical properties of bovine serum albumin in the presence of spermine. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.115853] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Farajzadeh-Dehkordi N, Farhadian S, Zahraei Z, Gholamian-Dehkordi N, Shareghi B. Interaction of reactive Red195 with human serum albumin: Determination of the binding mechanism and binding site by spectroscopic and molecular modeling methods. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2020.114835] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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The modifier action of NiO nanoparticles on the activity, structure, and stability of proteinase K. MONATSHEFTE FUR CHEMIE 2020. [DOI: 10.1007/s00706-020-02552-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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