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Cruz FT, Rosa DP, Vasconcelos AVB, de Oliveira JS, Bleicher L, Santos AMC. Purification and partial physical-chemical characterization of a new bovine trypsin proteoform (zeta-trypsin). Int J Biol Macromol 2024; 268:131860. [PMID: 38670206 DOI: 10.1016/j.ijbiomac.2024.131860] [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: 12/03/2023] [Revised: 04/01/2024] [Accepted: 04/23/2024] [Indexed: 04/28/2024]
Abstract
Recent advancements in enzyme research have unveiled a new proteoform of bovine trypsin, expanding our understanding of this well-characterized enzyme. While generally similar to other trypsins, this novel proteoform comprises three polypeptide chains, marking a significant difference in activity, kinetic properties, and conformational stability. Compared with the already known bovine trypsin proteoforms, the results showed a lower: activity, kcat and kcat.KM-1 and protein 'foldedness' ratio for the new proteoform. Molecular autolysis, a common feature in trypsin and chymotrypsin, has been explored through comparative physical chemistry properties with other proteoforms. This new proteoform of trypsin not only enriches the existing enzyme repertoire but also promises to shed light on the intricate physiological pathway for enzyme inactivation. Our results suggest that the new trypsin proteoform is one of the likely final pathways for enzyme inactivation in a physiological environment. This discovery opens up new avenues for further research into the functional implications of this new trypsin proteoform.
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Affiliation(s)
- Fabiano Torres Cruz
- Pos-Graduate Program of Biotechnology - Federal University of Espírito Santo, Vitória, ES, Brazil
| | - Dayanne Pinho Rosa
- Pos-Graduate Program of Biochemistry - Federal University of Espírito Santo, Vitória, ES, Brazil
| | | | - Jamil Silvano de Oliveira
- Department of Biochemistry and Immunology - Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Lucas Bleicher
- Department of Biochemistry and Immunology - Federal University of Minas Gerais, Belo Horizonte, MG, Brazil; Pos-Graduate at Biochemistry and Immunology - Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Alexandre Martins Costa Santos
- Pos-Graduate Program of Biotechnology - Federal University of Espírito Santo, Vitória, ES, Brazil; Pos-Graduate Program of Biochemistry - Federal University of Espírito Santo, Vitória, ES, Brazil.
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2
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Yadollahi E, Shareghi B, Farhadian S, Hashemi Shahraki F. Conformational dynamics of trypsin in the presence of caffeic acid: a spectroscopic and computational investigation. J Biomol Struct Dyn 2024; 42:3108-3117. [PMID: 37278377 DOI: 10.1080/07391102.2023.2212077] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 05/01/2023] [Indexed: 06/07/2023]
Abstract
Caffeic acid is one of the widely distributed phenolic compounds in nature and can be found in planet products. On the other hand, trypsin is a vital digestive enzyme in the intestine that plays an essential role in the immune response, blood coagulation, apoptosis and protein maturation like protein digestion. Several studies have revealed the inhibitory effects of the phenolic compound on the digestive enzyme. The present study reports functional and conformational alteration of trypsin after caffeic acid addition using multiple experimental and computational techniques for the first time. The intrinsic fluorescence of trypsin is quenched in the presence of caffeic acid via a static mechanism. The percent of secondary structures (α-helix and β-sheet) of trypsin alter after caffeic acid addition. In the kinetic study, a reduction in the trypsin function is obtained with a lower Vmax and Kcat upon interaction with caffeic acid. The thermal study reveals an unstable structure of trypsin upon complex formation with this phenolic compound. Also, the binding sites and conformational changes of trypsin are elucidated through molecular docking and molecular dynamic simulation.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Elham Yadollahi
- Department of Biology, Faculty of Science, Shahrekord University, Shahrekord, Iran
- Central Laboratory, Shahrekord University, Shahrekord, Iran
| | - Behzad Shareghi
- Department of Biology, Faculty of Science, Shahrekord University, Shahrekord, Iran
- Central Laboratory, Shahrekord University, Shahrekord, Iran
| | - Sadegh Farhadian
- Department of Biology, Faculty of Science, Shahrekord University, Shahrekord, Iran
- Central Laboratory, Shahrekord University, Shahrekord, Iran
| | - Fatemeh Hashemi Shahraki
- Department of Biology, Faculty of Science, Shahrekord University, Shahrekord, Iran
- Central Laboratory, Shahrekord University, Shahrekord, Iran
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3
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Fu M, Gao J, Mao K, Sun J, Ahmed Sadiq F, Sang Y. Interaction mechanism between surface layer protein and yeast mannan: Insights from multi-spectroscopic and molecular dynamics simulation analyses. Food Chem 2024; 433:137352. [PMID: 37678123 DOI: 10.1016/j.foodchem.2023.137352] [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: 03/17/2023] [Revised: 08/05/2023] [Accepted: 08/28/2023] [Indexed: 09/09/2023]
Abstract
Tibet kefir grain (TKG) formation is mainly dependent on the aggregation of lactobacillus and yeasts. The interaction of surface layer protein (SLP) and yeast mannan plays an important role in mediating the co-aggregation of Lactobacillus kefiri with Saccharomyces cerevisiae. The interaction mechanism of the two was researched through multispectral spectroscopy, morphology observation and silico approaches. Fluorescence spectra data revealed that mannan was bound to SLP through a spontaneous binding process. The particle size of the binding complex increased as the mannan concentration increased. Synchronous fluorescence spectroscopy and circular dichroism (CD) spectra showed the conformational and microenvironment alteration of SLP treated with mannan. Molecular docking results indicated that hydrophobic interactions played major roles in the formation of SLP-mannan complexes. These findings provide a deeper insight into the interactions of protein and polysaccharide, and this knowledge is valuable in the application of SLP and mannan in co-fermentation systems.
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Affiliation(s)
- Mengqi Fu
- Collage of Food Science and Technology, Hebei Agricultural University, Baoding, China
| | - Jie Gao
- Collage of Food Science and Technology, Hebei Agricultural University, Baoding, China.
| | - Kemin Mao
- Collage of Food Science and Technology, Hebei Agricultural University, Baoding, China
| | - Jilu Sun
- Collage of Food Science and Technology, Hebei Agricultural University, Baoding, China
| | | | - Yaxin Sang
- Collage of Food Science and Technology, Hebei Agricultural University, Baoding, China.
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4
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Mostafavi ES, Asoodeh A, Chamani J. New insights on the binding of butyl-paraben to trypsin: experimental and computational approaches. J Biomol Struct Dyn 2023; 41:10302-10314. [PMID: 36510660 DOI: 10.1080/07391102.2022.2154268] [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: 08/23/2022] [Accepted: 11/26/2022] [Indexed: 12/15/2022]
Abstract
Butyl-paraben (BP) is one of the most widely used preservatives in numerous foodstuffs, skin care products, and a variety of drugs, and trypsin is the main digestive enzyme, the research on the binding between the two is essential for human health. In the present paper, the effect of BP on trypsin has been explored using experimental and computational techniques to evaluate BP toxicity at the protein level. The obtained results from molecular docking and kinetic assay revealed BP was embedded in the hydrophobic cavity-S1 binding pocket of the enzyme to inhibit its activity by a competitive model. Intrinsic fluorescence of trypsin after interaction with BP revealed the static mode of quenching. FRET indicated that the distance of the enzyme to BP is 1.89 nm with high energy efficiency. Thermodynamic results proved that BP spontaneously bound to trypsin in an enthalpy-driven manner, the van der Waals interactions and H-bonds serving as the predominant forces in binding processes. CD spectroscopy and molecular dynamics (MD) simulation revealed that the trypsin structure transformed from the β-Sheet structure to the unordered Coil structure upon interacting with BP. Resonance light scattering (RLS), synchronous fluorescence, and three-dimensional (3 D) spectroscopies further supported the alteration in the conformation of trypsin. Differential scanning calorimetry (DSC) showed that trypsin was somewhat destabilized in the presence of BP. Accordingly, all of the experimental data were confirmed by MD simulation.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Elham Sadat Mostafavi
- Department of Chemistry, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Ahmad Asoodeh
- Department of Chemistry, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
- Cellular and Molecular Research Group, Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Jamshidkhan Chamani
- Department of Biology, Faculty of Science, Mashhad Branch, Islamic Azad University, Mashhad, Iran
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5
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Shen W, Dalby PA, Guo Z, Li W, Zhu C, Fan D. Residue Effect-Guided Design: Engineering of S. Solfataricus β-Glycosidase to Enhance Its Thermostability and Bioproduction of Ginsenoside Compound K. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:16669-16680. [PMID: 37812684 DOI: 10.1021/acs.jafc.3c04575] [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: 10/11/2023]
Abstract
β-Glycosidase from Sulfolobus solfataricus (SS-BGL) is a highly effective biocatalyst for the synthesis of compound K (CK) from glycosylated protopanaxadiol ginsenosides. In order to improve the thermal stability of SS-BGL, molecular dynamics simulations were used to determine the residue-level binding energetics of ginsenoside Rd in the SS-BGL-Rd docked complex and to identify the top ten critical contributors. Target sites for mutations were determined using dynamic cross-correlation mapping of residues via the Ohm server to identify networks of distal residues that interact with the key binding residues. Target mutations were determined rationally based on site characteristics. Single mutants and then recombination of top hits led to the two most promising variants SS-BGL-Q96E/N97D/N302D and SS-BGL-Q96E/N97D/N128D/N302D with 2.5-fold and 3.3-fold increased half-lives at 95 °C, respectively. The enzyme activities relative to those of wild-type for ginsenoside conversion were 161 and 116%, respectively..
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Affiliation(s)
- Wenfeng Shen
- Engineering Research Center of Western Resource Innovation Medicine Green Manufacturing, Ministry of Education, School of Chemical Engineering, Northwest University, Xi'an 710069, China
- Shaanxi R&D Center of Biomaterials and Fermentation Engineering, School of Chemical Engineering, Northwest University, Xi'an 710069, China
- Biotech. & Biomed. Research Institute, Northwest University, Xi'an 710069, China
| | - Paul A Dalby
- Department of Biochemical Engineering, UCL, London WCIE 6BT, U.K
| | - Zheng Guo
- Department of Biological and Chemical Engineering, Faculty of Science and Technology, Aarhus University, Gustav Wied Vej 10, Aarhus 8000, Denmark
| | - Weina Li
- Engineering Research Center of Western Resource Innovation Medicine Green Manufacturing, Ministry of Education, School of Chemical Engineering, Northwest University, Xi'an 710069, China
- Shaanxi R&D Center of Biomaterials and Fermentation Engineering, School of Chemical Engineering, Northwest University, Xi'an 710069, China
- Biotech. & Biomed. Research Institute, Northwest University, Xi'an 710069, China
| | - Chenhui Zhu
- Engineering Research Center of Western Resource Innovation Medicine Green Manufacturing, Ministry of Education, School of Chemical Engineering, Northwest University, Xi'an 710069, China
- Shaanxi R&D Center of Biomaterials and Fermentation Engineering, School of Chemical Engineering, Northwest University, Xi'an 710069, China
- Biotech. & Biomed. Research Institute, Northwest University, Xi'an 710069, China
| | - Daidi Fan
- Engineering Research Center of Western Resource Innovation Medicine Green Manufacturing, Ministry of Education, School of Chemical Engineering, Northwest University, Xi'an 710069, China
- Shaanxi R&D Center of Biomaterials and Fermentation Engineering, School of Chemical Engineering, Northwest University, Xi'an 710069, China
- Biotech. & Biomed. Research Institute, Northwest University, Xi'an 710069, China
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Wang X, Zhao J, Ding S, Zhang H. Interaction of polystyrene nanoplastics with human fibrinogen. Int J Biol Macromol 2023; 238:124049. [PMID: 36931485 DOI: 10.1016/j.ijbiomac.2023.124049] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 03/01/2023] [Accepted: 03/12/2023] [Indexed: 03/17/2023]
Abstract
Nanoplastics are an emerging environmental contaminant that can penetrate biological barriers to enter the bloodstream and risk human health. In this context, nanoplastics are likely to interact with proteins in the blood to possibly affect protein structure and function and consequently induce biological effects. Here we report that polystyrene (PS), PS-NH2, and PS-COOH nanoplastics disrupt the structure of human fibrinogen (HF) in a dose-dependent manner, as revealed by UV-vis and fluorescence spectroscopy. All three nanoplastics interacted with HF in a similar way, with PS-NH2 having the greatest effect on HF structure. Furthermore, fibrinogen polymerization experiments demonstrated that nanoplastics have the potential to promote blood coagulation, with PS-NH2 again having a stronger effect. Collectively, these results provide insights into the interactions occurring between nanoplastics and HF, the likely transport and fate of nanoplastics in organisms, and their potential pathophysiological consequences.
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Affiliation(s)
- Xiuxiu Wang
- Shandong Provincial Key Laboratory of Animal Resistance Biology, Key Laboratory of Food Nutrition and Safety of Shandong Normal University, College of Life Sciences, Shandong Normal University, Jinan 250014, PR China
| | - Juan Zhao
- Shandong Provincial Key Laboratory of Animal Resistance Biology, Key Laboratory of Food Nutrition and Safety of Shandong Normal University, College of Life Sciences, Shandong Normal University, Jinan 250014, PR China
| | - Shengli Ding
- Shandong Provincial Key Laboratory of Animal Resistance Biology, Key Laboratory of Food Nutrition and Safety of Shandong Normal University, College of Life Sciences, Shandong Normal University, Jinan 250014, PR China
| | - Hongyan Zhang
- Shandong Provincial Key Laboratory of Animal Resistance Biology, Key Laboratory of Food Nutrition and Safety of Shandong Normal University, College of Life Sciences, Shandong Normal University, Jinan 250014, PR China.
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7
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Hashemi-Shahraki F, Shareghi B, Farhadian S. Investigation of the interaction behavior between quercetin and pepsin by spectroscopy and MD simulation methods. Int J Biol Macromol 2023; 227:1151-1161. [PMID: 36464189 DOI: 10.1016/j.ijbiomac.2022.11.296] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 10/23/2022] [Accepted: 11/29/2022] [Indexed: 12/04/2022]
Abstract
The ability of a therapeutic compound to bind to proteins is critical for characterizing its therapeutic impacts. We have selected quercetin (Qu), a most common flavonoid found in plants and vegetables among therapeutic molecules that are known to have anti-inflammatory, antioxidant, anti-genotoxic, and anti-cancer effects. The current study aimed to see how quercetin interacts with pepsin in an aqueous environment under physiological conditions. Absorbance and emission spectroscopy, circular dichroism (CD), and kinetic methods, as well as molecular dynamic (MD) simulation and docking, were applied to study the effects of Qu on the structure, dynamics, and kinetics of pepsin. Stern-Volmer (Ksv) constants were computed for the pepsin-quercetin complex at three temperatures, showing that Qu reduces enzyme emission spectra using a static quenching. With Qu binding, the Vmax and the kcat/Km values decreased. UV-vis absorption spectra, fluorescence emission spectroscopy, and CD result indicated that Qu binding to pepsin leads to microenvironmental changes around the enzyme, which can alter the enzyme's secondary structure. Therefore, quercetin caused alterations in the function and structure of pepsin. Thermodynamic parameters, MD binding, and docking simulation analysis showed that non-covalent reactions, including the hydrophobic forces, played a key role in the interaction of Qu with pepsin. The findings conclude of spectroscopic experiments were supported by molecular dynamics simulations and molecular docking results.
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Affiliation(s)
- Fatemeh Hashemi-Shahraki
- 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.
| | - Sadegh Farhadian
- Department of Biology, Faculty of Science, Shahrekord University, Shahrekord, P. O. Box.115, Iran; Central Laboratory, Shahrekord University, Shahrekord, Iran.
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8
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Enzyme Inhibition-Based Assay to Estimate the Contribution of Formulants to the Effect of Commercial Pesticide Formulations. Int J Mol Sci 2023; 24:ijms24032268. [PMID: 36768591 PMCID: PMC9916951 DOI: 10.3390/ijms24032268] [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: 12/11/2022] [Revised: 01/13/2023] [Accepted: 01/19/2023] [Indexed: 01/26/2023] Open
Abstract
Pesticides can affect the health of individual organisms and the function of the entire ecosystem. Therefore, thorough assessment of the risks associated with the use of pesticides is a high-priority task. An enzyme inhibition-based assay is used in this study as a convenient and quick tool to study the effects of pesticides at the molecular level. The contribution of formulants to toxicological properties of the pesticide formulations has been studied by analyzing effects of 7 active ingredients of pesticides (AIas) and 10 commercial formulations based on them (AIfs) on the function of a wide range of enzyme assay systems differing in complexity (single-, coupled, and three-enzyme assay systems). Results have been compared with the effects of AIas and AIfs on bioluminescence of the luminous bacterium Photobacterium phosphoreum. Mostly, AIfs produce a considerably stronger inhibitory effect on the activity of enzyme assay systems and bioluminescence of the luminous bacterium than AIas, which confirms the contribution of formulants to toxicological properties of the pesticide formulation. Results of the current study demonstrate that "inert" ingredients are not ecotoxicologically safe and can considerably augment the inhibitory effect of pesticide formulations; therefore, their use should be controlled more strictly. Circular dichroism and fluorescence spectra of the enzymes used for assays do not show any changes in the protein structure in the presence of commercial pesticide formulations during the assay procedure. This finding suggests that pesticides produce the inhibitory effect on enzymes through other mechanisms.
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9
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Yadollahi E, Shareghi B, Farhadian S. Binding parameters and molecular dynamics of Trypsin-Acid Yellow 17 complexation as a function of concentration. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 281:121589. [PMID: 35872431 DOI: 10.1016/j.saa.2022.121589] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 06/02/2022] [Accepted: 06/30/2022] [Indexed: 06/15/2023]
Abstract
Acid Yellow 17 is a kind of azo dye used in food, textile, and cosmetics. Several studies explain the toxicity of azo dye for our body, but one could not find further information about the effects of these dyes on human macromolecules. In the current study, the interaction of AY17 with trypsin is investigated using several techniques. The UV analysis displayed that the absorption of trypsin could be decreased in the presence of this color. The fluorescence investigation indicated that a static form of quenching happens, and a 50% decrease in the fluorescence intensity, also showed the Vander Waals and hydrogen bond are the main forces in the interaction of this color and trypsin. Furthermore, we can observe that the Tm point of trypsin decreases from 46.5 to 42. On the other hand, the CD results were indicated that the interaction of this color with trypsin could decrease the percent of turn, coil and α-helix in trypsin structure. The computational study was undertaken to obtain more information about the interaction between trypsin and AY17. The results were in agreement with the experimental investigation and indicated that the interaction between this color and trypsin leads to less compactness in the trypsin structure.
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Affiliation(s)
- Elham Yadollahi
- Department of Biology, Faculty of Science, Shahrekord University, P.O. Box 115, Shahrekord, Iran; Central Laboratory, Shahrekord University, Shahrekord, Iran
| | - Behzad Shareghi
- Department of Biology, Faculty of Science, Shahrekord University, P.O. Box 115, Shahrekord, Iran; Central Laboratory, Shahrekord University, Shahrekord, Iran.
| | - Sadegh Farhadian
- Department of Biology, Faculty of Science, Shahrekord University, P.O. Box 115, Shahrekord, Iran; Central Laboratory, Shahrekord University, Shahrekord, Iran.
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10
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Asemi-Esfahani Z, Shareghi B, Farhadian S, Momeni L. Food additive dye–lysozyme complexation: Determination of binding constants and binding sites by fluorescence spectroscopy and modeling methods. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119749] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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11
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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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12
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Fernández-Sainz J, Pacheco-Liñán PJ, Granadino-Roldán JM, Bravo I, Rubio-Martínez J, Albaladejo J, Garzón-Ruiz A. Shedding light on the binding mechanism of kinase inhibitors BI-2536, Volasetib and Ro-3280 with their pharmacological target PLK1. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2022; 232:112477. [PMID: 35644070 DOI: 10.1016/j.jphotobiol.2022.112477] [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: 03/19/2021] [Revised: 03/01/2022] [Accepted: 05/16/2022] [Indexed: 06/15/2023]
Abstract
In the present work, the interactions of the novel kinase inhibitors BI-2536, Volasetib (BI-6727) and Ro-3280 with the pharmacological target PLK1 have been studied by fluorescence spectroscopy and molecular dynamics calculations. High Stern-Volmer constants were found in fluorescence experiments suggesting the formation of stable protein-ligand complexes. In addition, it was observed that the binding constant between BI-2536 and PLK1 increases about 100-fold in presence of the phosphopeptide Cdc25C-p that docks to the polo box domain of the protein and releases the kinase domain. All the determined binding constants are higher for the kinase inhibitors than for their competitor for the active center (ATP) being BI-2536 and Volasertib the inhibitors that showed more affinity for PLK1. Calculated binding free energies confirmed the higher affinity of PLK1 for BI-2536 and Volasertib than for ATP. The higher affinity of the inhibitors to PLK1 compared to ATP was mainly attributed to stronger van der Waals interactions. Results may help with the challenge of designing and developing new kinase inhibitors more effective in clinical cancer therapy.
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Affiliation(s)
- Jesús Fernández-Sainz
- Departamento de Química Física, Facultad de Farmacia, Universidad de Castilla-La Mancha, Cronista Ballesteros Gómez, 1, 02071 Albacete, Spain
| | - Pedro J Pacheco-Liñán
- Departamento de Química Física, Facultad de Farmacia, Universidad de Castilla-La Mancha, Cronista Ballesteros Gómez, 1, 02071 Albacete, Spain
| | - José M Granadino-Roldán
- Departamento de Química Física y Analítica, Facultad de Ciencias Experimentales, Universidad de Jaén, Campus "Las Lagunillas" s/n, 23071 Jaén, Spain
| | - Iván Bravo
- Departamento de Química Física, Facultad de Farmacia, Universidad de Castilla-La Mancha, Cronista Ballesteros Gómez, 1, 02071 Albacete, Spain
| | - Jaime Rubio-Martínez
- Departament de Ciència dels Materials i Química Física, Universitat de Barcelona (UB), Institut de Recerca en Quimica Teorica i Computacional (IQTCUB), Martí i Franqués 1, 08028 Barcelona, Spain
| | - José Albaladejo
- Departamento de Química Física, Facultad de Ciencias Químicas, Universidad de Castilla-La Mancha, Avenida Camilo José Cela, 10, 13071 Ciudad Real, Spain
| | - Andrés Garzón-Ruiz
- Departamento de Química Física, Facultad de Farmacia, Universidad de Castilla-La Mancha, Cronista Ballesteros Gómez, 1, 02071 Albacete, Spain.
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Khashkhashi-Moghadam S, Ezazi-Toroghi S, Kamkar-Vatanparast M, Jouyaeian P, Mokaberi P, Yazdyani H, Amiri-Tehranizadeh Z, Reza Saberi M, Chamani J. Novel perspective into the interaction behavior study of the cyanidin with human serum albumin-holo transferrin complex: Spectroscopic, calorimetric and molecular modeling approaches. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119042] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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14
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Excellent performance separation of trypsin by novel ternary magnetic composite adsorbent based on betaine-urea- glycerol natural deep eutectic solvent modified MnFe 2O 4-MWCNTs. Talanta 2022; 248:123566. [PMID: 35653959 DOI: 10.1016/j.talanta.2022.123566] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 05/08/2022] [Accepted: 05/16/2022] [Indexed: 12/20/2022]
Abstract
The effective trypsin purification methods should be established since trypsin plays a crucial role in biosome. In this work, a novel ternary magnetic composite adsorbent (MnFe2O4-MWCNTs@B-U-G) with the features of strong specific selectivity, good adsorption effect, simple and efficient separation process, no secondary pollution brought in was prepared by integrating the superior physicochemical properties of ternary based natural deep eutectic solvent, multi-walled carbon nanotubes and MnFe2O4. The property, composition and microtopography structure of MnFe2O4-MWCNTs@B-U-G were characterized in detail. Combined with magnetic solid-phase extraction, MnFe2O4-MWCNTs@B-U-G was utilized to adsorb trypsin. Response surface methodology experiment was prepared under Box-Behnken design to optimize the adsorption conditions and the results showed that the practical maximum adsorption capacity for trypsin was 1020.1 mg g-1. Besides, the adsorption isotherms, adsorption kinetics, regeneration studies and method validation studies were investigated systematically to evaluate the established adsorption separation system. Mechanism exploration proved that electrostatic interaction, hydrogen bonding interaction and chelation interaction were the dominant forces for the high-performance adsorption of trypsin. The activity of trypsin after elution had been analyzed by UV-vis spectrophotometer and CD spectrometer with three methods, which illustrated that the enzyme activity, conformation and secondary structure of trypsin did not change significantly during the adsorption-desorption process. In addition, the proposed method was successful and practical applicability to isolation trypsin from crude bovine pancreas. As a result, due to the superiority of the MnFe2O4-MWCNTs@B-U-G, the proposed method not only exhibites high-performance adsorption of trypsin, but also provides a green and sustainable potential value in the adsorption of biomacromolecule.
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15
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Comparative study of the binding between chlorogenic acid and four proteins by isothermal titration calorimetry, spectroscopy and docking methods. Pharmacol Rep 2022; 74:523-538. [PMID: 35545727 DOI: 10.1007/s43440-022-00369-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 04/20/2022] [Accepted: 04/21/2022] [Indexed: 10/18/2022]
Abstract
As a polyphenolic compound, chlorogenic acid has antioxidant, anti-inflammatory, antiviral, anti-obesity and other effects. Based on the interactions between chlorogenic acid and the proteins (human serum albumin (HSA), pepsin (Pep), trypsin (Try), fat mass and obesity-associated protein (FTO)), results will provide clues for screening effective inhibitors. The interaction between chlorogenic acid and the four proteins (HSA, Pep, Try, FTO) was analyzed by the aid of fluorescence quenching, synchronous fluorescence, three-dimensional fluorescence, isothermal titration calorimetry, and molecular docking. It can be concluded that there is no obvious interaction between chlorogenic acid and FTO. The binding affinity between chlorogenic acid and three proteins is HSA > Try > Pep. The binding process is spontaneous, and the quenching type is static quenching. Hydrophobic interaction and hydrogen bonding is observed in the binding process. This study provides valuable information for understanding the interaction mechanism between chlorogenic acid and proteins, and provides clues for screening inhibitors.
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16
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Liu Y, Zhu J, Yu J, Chen X, Zhang S, Cai Y, Li L. Curcumin as a mild natural α‐glucosidase inhibitor: a study on its mechanism
in vitro. Int J Food Sci Technol 2022. [DOI: 10.1111/ijfs.15433] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Yujia Liu
- Key Laboratory of Healthy Food Development and Nutrition Regulation of China National Light Industry School of Chemical Engineering and Energy Technology Dongguan University of Technology Dongguan 523808 China
| | - Jie Zhu
- Key Laboratory of Healthy Food Development and Nutrition Regulation of China National Light Industry School of Chemical Engineering and Energy Technology Dongguan University of Technology Dongguan 523808 China
| | - Jiamei Yu
- Key Laboratory of Healthy Food Development and Nutrition Regulation of China National Light Industry School of Chemical Engineering and Energy Technology Dongguan University of Technology Dongguan 523808 China
| | - Xu Chen
- Key Laboratory of Healthy Food Development and Nutrition Regulation of China National Light Industry School of Chemical Engineering and Energy Technology Dongguan University of Technology Dongguan 523808 China
| | - Shuyan Zhang
- Key Laboratory of Healthy Food Development and Nutrition Regulation of China National Light Industry School of Chemical Engineering and Energy Technology Dongguan University of Technology Dongguan 523808 China
| | - Yanxue Cai
- Key Laboratory of Healthy Food Development and Nutrition Regulation of China National Light Industry School of Chemical Engineering and Energy Technology Dongguan University of Technology Dongguan 523808 China
| | - Lin Li
- Key Laboratory of Healthy Food Development and Nutrition Regulation of China National Light Industry School of Chemical Engineering and Energy Technology Dongguan University of Technology Dongguan 523808 China
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Ashrafi N, Shareghi B, Farhadian S, Hosseini-Koupaei M. A comparative study of the interaction of naringenin with lysozyme by multi-spectroscopic methods, activity comparisons, and molecular modeling procedures. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 271:120931. [PMID: 35085994 DOI: 10.1016/j.saa.2022.120931] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 12/31/2021] [Accepted: 01/17/2022] [Indexed: 06/14/2023]
Abstract
The present study applied steady-state fluorescence, UV-Vis spectrophotometry, molecular docking studies, and circular dichroism (CD) to investigate the interaction of naringenin with lysozyme in an aqueous medium. The UV-Vis measurement indicated the changes in lysozyme secondary and tertiary structure change as a function of the concentration of naringenin. Naringenin could be used to turn the static quenching mechanism into the intrinsic fluorescence of lysozyme. The negative amount of Gibbs free energy (ΔG°) suggested that the binding operation was spontaneous. Fluorescence studies also demonstrated the changes occurring in the Trp microenvironment upon the concatenation into lysozyme. Analysis of thermodynamic parameters also revealed that hydrophobic forces played a fundamental role in determining the complex stability; this was consistent with the previous modeling studies. Circular dichroism also suggested that the alpha-helicity of lysozyme was enhanced as ligand was bound. Naringenin inhibited lysozyme enzymatic activity, displaying its affinity with the lysozyme active site. Further, molecular docking studies demonstrated that naringenin could bind to both residues essential for catalytic activity in the proximity of Trp 62 and Trp 63.
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Affiliation(s)
- Narges Ashrafi
- Department of Biology, Faculty of Science, Shahrekord University, Shahrekord, Iran
| | - Behzad Shareghi
- Department of Biology, Faculty of Science, Shahrekord University, Shahrekord, Iran; Central Laboratory, Shahrekord University, Shahrekord, Iran.
| | - Sadegh Farhadian
- Department of Biology, Faculty of Science, Shahrekord University, Shahrekord, Iran; Central Laboratory, Shahrekord University, Shahrekord, Iran.
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18
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Multi spectroscopy and molecular modeling aspects related to drug interaction of aspirin with alpha chymotrypsin; structural change and protease activity. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.118698] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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19
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Mohammadi M, Shareghi B, Farhadian S, Momeni L, Saboury AA. The interaction of xylitol with carboxypeptidase A: The influence of xylitol on enzyme structure and activity. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.131877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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20
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Moradi S, Shareghi B, Saboury AA, Farhadian S. The influence of Cadaverine on the structure, stability, and activity of acid phosphatase. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.131372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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21
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Moradi S, Shareghi B, Saboury AA, Farhadian S. Molecular aspects of the interaction of acid phosphatase with TiO2 nanoparticles: Kinetic and multispectroscopic studies. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.131268] [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]
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22
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Investigation on the interaction behavior between safranal and pepsin by spectral and MD simulation studies. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.117903] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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23
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Hashemi-Shahraki F, Shareghi B, Farhadian S. Characterizing the binding affinity and molecular interplay between quinoline yellow and pepsin. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.117317] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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24
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Evaluation of interaction between citrus flavonoid, naringenin, and pepsin using spectroscopic analysis and docking simulation. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116763] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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25
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Evaluation of interactions between food colorant, tartrazine, and Apo-transferrin using spectroscopic analysis and docking simulation. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116715] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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26
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Hasan S, Naeem A. The modulation of structural stability of horseradish peroxidase as a consequence of macromolecular crowding. J Mol Recognit 2021; 34:e2902. [PMID: 34013591 DOI: 10.1002/jmr.2902] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 03/24/2021] [Accepted: 04/05/2021] [Indexed: 11/07/2022]
Abstract
Macromolecular crowding plays an inevitable role in all biological processes influencing association, conformation, and other characteristics of proteins. Present study is based on the effect of macromolecular crowding on structure of horseradish peroxidase (HRP) enzyme. Concentration-dependent conformational changes induced by crowding agents, dextran 70 and polyethylene glycol (PEG)-4000, were monitored employing a range of biophysical techniques. The intrinsic fluorescence spectra showed transition of protein from native to unfolded state. Marked increase in 8-Anilino-1-naphthalene-sulphonoic acid and Thioflavin T fluorescence indicated presence of non-native moieties with 80 mg/mL dextran. Enhanced absorbance in turbidity, Soret, and Congo red in corroboration with scattering intensity at 350nm results revealed incidence of HRP aggregates. A new peak around 218 nm in CD spectra pointed towards change in secondary structure towards β-sheets. Significant loss of enzyme activity upon structural disruption was seen. Comet assay demonstrated DNA damage and genotoxic nature of HRP aggregates, supporting spectroscopic, and fluorescence results. The normalized results were obtained with 120 mg/mL PEG-4000 close to that of native HRP implying no disruptive effect on structure. It can be hypothesized that macromolecular crowding is a vital element, which can have diverse effects. In this study, dextran 70 was observed to have pro-aggregatory effect while enhanced stability of native enzyme was witnessed with PEG. Hence, it can be stated that PEG has potentially better crowder as it helps retain the native enzyme structure. Routine addition of crowding agents is recommended if biological molecules are to be studied under more physiologically appropriate environments.
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Affiliation(s)
- Samra Hasan
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, India
| | - Aabgeena Naeem
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, India
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27
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Mohammadi M, Shareghi B, Farhadian S, Saboury AA. The effect of sorbitol on the structure and activity of carboxypeptidase A: Insights from a spectroscopic and computational approach. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.115710] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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28
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A new functionality study of vanillin as the inhibitor for α-glucosidase and its inhibition kinetic mechanism. Food Chem 2021; 353:129448. [PMID: 33711702 DOI: 10.1016/j.foodchem.2021.129448] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 02/20/2021] [Accepted: 02/21/2021] [Indexed: 12/20/2022]
Abstract
Vanillin is a natural phenolic compound mainly used as flavors in food industry. In this work, a new functionality of vanillin as the α-glucosidase inhibitor was studied based on the inhibition kinetic mechanism. The inhibitory effect (IC50) of vanillin against α-glucosidase was 28.34 ± 0.89 mg/mL, which belongs to mixed inhibition mechanism and its process was spontaneous. Vanillin could bind to α-glucosidase by hydrophobic interactions and hydrogen bonds with -8.42 kcal/mol intermolecular energy to form the steric hindrance. The average binding distances was calculated as 2.20 nm according to energy transfer theory. In addition, the protein secondary structure and denaturation temperature (decreasing about 10 °C) were changed significantly after vanillin binding to α-glucosidase, resulting in an inhibitory effect. The findings of this research provide insights for the development of vanillin as potential inhibitor for α-glucosidase in special dietary foods.
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29
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Li Y, Liu X, Zhou H, Li B, Mazurenko IK. Inhibitory Mechanism of Engeletin Against α-Glucosidase. Nat Prod Commun 2021. [DOI: 10.1177/1934578x20986723] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The inhibitory mechanism of engeletin against α-glucosidase was investigated for the first time by fluorescence spectroscopy and molecular docking. The results showed that engeletin could inhibit α-glucosidase in a noncompetitive inhibition mode with a half-maximal inhibitory concentration value of 48.5 ± 6.0 µg/mL (0.11 ± 0.014 mmol/L). It was found that engeletin could cause static fluorescence quenching of α-glucosidase by forming a complex with α-glucosidase. The thermodynamic parameters indicated that the combination of engeletin and α-glucosidase was driven by hydrophobic force. The molecular docking results confirmed that some amino acid residues of α-glucosidase (Trp391, Arg428, Glu429, Gly566, Trp710, Glu771) could interact with engeletin by hydrogen bonding.
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Affiliation(s)
- Yunbo Li
- School of Food Science, Henan Institute of Science and Technology, Xinxiang, P. R. China
- Department of Food Technology, Sumy National Agrarian University, Sumy, Ukraine
| | - Xiaoling Liu
- School of Food Science, Henan Institute of Science and Technology, Xinxiang, P. R. China
| | - Haoyu Zhou
- School of Food Science, Henan Institute of Science and Technology, Xinxiang, P. R. China
| | - Bo Li
- School of Food Science, Henan Institute of Science and Technology, Xinxiang, P. R. China
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30
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Konar M, Sahoo H. Exploring the chemistry behind protein-glycosaminoglycan conjugate: A steady-state and kinetic spectroscopy based approach. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 242:118726. [PMID: 32745937 DOI: 10.1016/j.saa.2020.118726] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 07/03/2020] [Accepted: 07/04/2020] [Indexed: 06/11/2023]
Abstract
The impact of glycosaminoglycan (chondroitin sulphate, CS) on bone morphogenetic protein - 2 (BMP - 2) structure, stability (thermal and chemical), association kinetics and conformation was monitored by multiple spectroscopic techniques (UV-Visible, fluorescence and circular dichroism). The absorbance in peptide region and fluorescence intensity of BMP - 2 was quenched in presence of CS; thus, confirming the formation of a ground-state complex. As there was an increase in Stern-Volmer constant observed as a function of temperature, idea of dynamic quenching was established. However, the negligible changes in lifetime indicated static quenching; thus, making the process a combination of static-dynamic quenching. Basically, the protein - glycan interaction was driven by entropy of the system and mediated by hydrophobic interactions. Secondary structure (CD spectroscopy) of native protein was significantly affected (intensity became more negative) in presence of CS, thus, introducing more compactness in the protein. CS infused thermal and chemical stability into BMP - 2 via alteration in its conformation. The rate of association was inversely proportional to concentration of quencher (CS), which confirmed the correlation between large size (~ 5 times the size of protein) and structural complexity of CS with fewer binding sites present in BMP - 2. The rate of association in presence of urea, suggested a decrease in association rate as a function of urea concentration for 15 μM CS. Experimental evidences suggested an interaction between protein and glycan mediated by hydrophobic interactions, which deciphers structural, thermal and chemical stability into protein.
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Affiliation(s)
- Monidipa Konar
- Biophysical Chemistry Lab, Department of Chemistry, National Institute of Technology Rourkela, Rourkela 769008, Odisha, India
| | - Harekrushna Sahoo
- Biophysical Chemistry Lab, Department of Chemistry, National Institute of Technology Rourkela, Rourkela 769008, Odisha, India.
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31
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The interaction of Naphthol Yellow S (NYS) with pepsin: Insights from spectroscopic to molecular dynamics studies. Int J Biol Macromol 2020; 165:1842-1851. [DOI: 10.1016/j.ijbiomac.2020.10.093] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 10/06/2020] [Accepted: 10/08/2020] [Indexed: 12/15/2022]
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32
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Insight into the binding of glycerol with myoglobin: Spectroscopic and MD simulation approach. Int J Biol Macromol 2020; 159:433-443. [PMID: 32360459 DOI: 10.1016/j.ijbiomac.2020.04.065] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 04/05/2020] [Accepted: 04/08/2020] [Indexed: 12/18/2022]
Abstract
Stability of proteins plays a significant role not only in their biological function but also in medical science and protein engineering. Since proteins are only stable in special conditions, maintaining their stability and function in biological and biotechnological applications may pose serious challenges. Osmolytes provide a general method of shielding proteins from the unfolding and aggregation caused by extreme stress on the environment. In such studies, the researchers used spectroscopic and simulation approaches to study the alterations of the myoglobin structure and stability in glycerol presence. Experimental results showed a stability improvement of the complex myoglobin-glycerol. After the addition of glycerol resulting in the initiation of hydrogen bonds and higher levels of hydrophobicity, the increase of the Tm was observed. The static mode quenching observed in this study. Van der Waals forces and hydrogen bindings had a decisive and significant role concerning the stability of protein which was consistent with the modeling results. Molecular dynamics simulation showed that the glycerol presence could enhance myoglobin stability. The consistency between the theoretical studies and experimental findings demonstrates that the method proposed in this study could provide a useful method for protein-ligand complex investigations.
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33
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Hasan S, Isar M, Naeem A. Macromolecular crowding stabilises native structure of α-chymotrypsinogen-A against hexafluoropropanol-induced aggregates. Int J Biol Macromol 2020; 164:3780-3788. [PMID: 32835802 DOI: 10.1016/j.ijbiomac.2020.08.149] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 08/06/2020] [Accepted: 08/19/2020] [Indexed: 12/20/2022]
Abstract
Cell interior is extremely congested with tightly packed biological macromolecules that exerts macromolecular crowding effect, influencing biophysical properties of proteins. To have a deeper insight into it we studied consequences of crowding on aggregation susceptibility and structural stability of α-chymotrypsinogen-A, pro-enzyme of serine protease family, upon addition of co-solvent reported to exert stress on polypeptides crafting favourable conditions for aggregation. Hexafluoropropan-2-ol (HFIP), a fluorinated alcohol caused structural disruption at 5% v/v unveiled by reduced intrinsic intensity and blue shifted ANS spectra. Significantly enhanced, red-shifted ThT and Congo red spectra sustained conformational changes concomitant with aggregation. FTIR and CD results confirmed transition of native structure to non-native extended, cross-linked beta-sheets. Transmission electron micrographs visibly exhibited incidence of amorphous aggregates. Macromolecular crowding, typically mimicked by concentrated solutions of dextran 70, was noticeably witnessed to defend conformational stability under denaturing condition. The native structure was retained maximally in presence of 100 mg/ml followed by 200 and 300 mg/ml dextran indicating concentration dependent deceleration of aggregate formation. It can be established that explicit consideration of crowding effects using relevant range of inert crowding agents must be a requisite for presumptions on intracellular conformational behaviour of proteins deduced from in vitro experiments.
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Affiliation(s)
- Samra Hasan
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, 202002, U.P., India
| | - Mohd Isar
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, 202002, U.P., India
| | - Aabgeena Naeem
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, 202002, U.P., India.
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34
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Moradi S, Shareghi B, Saboury AA, Farhadian S. Investigation on the interaction of acid phosphatase with putrescine using docking, simulations methods and multispectroscopic techniques. Int J Biol Macromol 2020; 150:90-101. [DOI: 10.1016/j.ijbiomac.2020.02.057] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 02/04/2020] [Accepted: 02/06/2020] [Indexed: 02/06/2023]
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35
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Jafari A, Shareghi B, Hosseini-Koupaei M, Farhadian S. Characterization of osmolyte-enzyme interactions using different spectroscopy and molecular dynamic techniques: Binding of sucrose to proteinase K. Int J Biol Macromol 2020; 151:1250-1258. [DOI: 10.1016/j.ijbiomac.2019.10.171] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Revised: 10/01/2019] [Accepted: 10/22/2019] [Indexed: 12/20/2022]
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36
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Liu M, Liu T, Shi Y, Zhao Y, Yan H, Sun B, Wang Q, Wang Z, Han J. Comparative study on the interaction of oxyresveratrol and piceatannol with trypsin and lysozyme: binding ability, activity and stability. Food Funct 2020; 10:8182-8194. [PMID: 31696185 DOI: 10.1039/c9fo01888c] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Natural polyphenols showing a variety of beneficial effects will interact with multiple proteases after administration. The interactions of oxyresveratrol and piceatannol with trypsin and lysozyme were investigated using fluorescence spectroscopy, UV-vis absorption spectroscopy, circular dichroism spectroscopy, differential scanning calorimetry and molecular docking. Fluorescence quenching results and UV-vis absorption difference spectra revealed that the quenching process was a static mode initiated by ground-state complex formation. The different binding ability of oxyresveratrol and piceatannol with trypsin and lysozyme was discussed based on their different molecular structures. Moreover, the major driving force for the binding process was elucidated as hydrogen bonding and van der Waals forces by the negative enthalpy and entropy changes. Synchronous fluorescence, three-dimensional fluorescence and circular dichroism spectral analysis suggested that the binding of oxyresveratrol and piceatannol to trypsin and lysozyme induced some microenvironmental and conformational changes of the two enzymes. The thermal stability of the enzymes in the presence of polyphenols was studied based on the change in melting temperature by differential scanning calorimetry. The above experimental results were validated by the protein-ligand docking studies which showed the location of the two ligands in the enzymes and the surrounding amino acid residues. Furthermore, enzyme activity assays indicated that the enzymatic activity of trypsin and lysozyme was inhibited by oxyresveratrol and piceatannol. The effect of trypsin and lysozyme on the antioxidant activity and stability of oxyresveratrol and piceatannol was also investigated. In conclusion, the comparative study on the interaction of oxyresveratrol and piceatannol with trypsin and lysozyme showed that the positions of hydroxyl groups of the polyphenols had an important influence on their interaction with enzymes and their antioxidant activity and stability as well as the enzyme activities. The obtained results are expected to provide a theoretical basis for the application of polyphenols in functional foods and pharmaceuticals.
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Affiliation(s)
- Min Liu
- Institute of BioPharmceutical Research, Liaocheng University, Liaocheng 252059, China.
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37
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Sadeghi-kaji S, Shareghi B, Saboury AA, Farhadian S. Investigating the interaction of porcine pancreatic elastase and propanol: A spectroscopy and molecular simulation study. Int J Biol Macromol 2020; 146:687-691. [DOI: 10.1016/j.ijbiomac.2019.12.119] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 12/13/2019] [Accepted: 12/14/2019] [Indexed: 10/25/2022]
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38
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Study of alkaline phosphatase interaction with putrescine using multi-spectroscopic and docking methods. Colloids Surf B Biointerfaces 2020; 185:110509. [DOI: 10.1016/j.colsurfb.2019.110509] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 09/13/2019] [Accepted: 09/14/2019] [Indexed: 12/19/2022]
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39
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Farhadian S, Shareghi B, Tirgir F, Reiisi S, Dehkordi NG, Momeni L, Heidari E. Design, synthesis, and anti-gastric cancer activity of novel 2,5-diketopiperazine. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.111585] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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40
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Sadeghi-kaji S, Shareghi B, Saboury AA, Farhadian S. Investigation on the structure and function of porcine pancreatic elastase (PPE) under the influence of putrescine: A spectroscopy and molecular simulation study. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.111115] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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41
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Structural characterization of α‑chymotrypsin after binding to curcumin: Spectroscopic and computational analysis of their binding mechanism. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.111111] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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42
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Konar M, Sahoo H. Phosphate and sulphate-mediated structure and stability of bone morphogenetic protein - 2 (BMP - 2): A spectroscopy enabled investigation. Int J Biol Macromol 2019; 135:1123-1133. [DOI: 10.1016/j.ijbiomac.2019.06.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 06/01/2019] [Accepted: 06/03/2019] [Indexed: 01/20/2023]
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43
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Sadeghi-kaji S, Shareghi B, Saboury AA, Farhadian S, Hemmati R. A molecular investigation into the interaction of SiO2 nanoparticles with elastase by multispectroscopic techniques and kinetic studies. Int J Biol Macromol 2019; 134:216-222. [DOI: 10.1016/j.ijbiomac.2019.05.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 04/28/2019] [Accepted: 05/02/2019] [Indexed: 12/18/2022]
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44
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Gao S, Cao Z, Niu Q, Zong W, Liu R. Probing the toxicity of long-chain fluorinated surfactants: Interaction mechanism between perfluorodecanoic acid and lysozyme. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.04.134] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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45
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Asgharzadeh S, Shareghi B, Farhadian S. Experimental and theoretical investigations on the interaction of l-methionine molecules with α-chymotrypsin in the aqueous solution using various methods. Int J Biol Macromol 2019; 131:548-556. [PMID: 30876904 DOI: 10.1016/j.ijbiomac.2019.03.080] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 03/11/2019] [Accepted: 03/11/2019] [Indexed: 11/17/2022]
Abstract
l-Methionine (l-Met) is one of the necessary amino acids that play unparalleled roles, influencing both the protein structure and metabolism. Understanding the interactions between proteins and small molecules can be realized by various perspectives, and this is significant for the progression of basic sciences and drug development. In this study, the variations in the stability, function, and structure of α-Chymotrypsin (α-Chy) in the presence of l-Met were investigated using spectroscopic and computational approaches. The results of the UV-vis absorption demonstrated that α-Chy had a maximum peak at 280 nm due to the Trp residue. Hyperchromism shift was seen in the presence of l-Met. Ground state system was formed in the presence of l-Met, as confirmed by the fluorescence studies. Fluorescence variations also revealed static quenching. The CD spectra also represented the alteration of the enzyme with an increase in the α-helix and a decrease in the β-sheet. The activity of α-Chy was incremented in the presence of l-Met. Therefore, l-Met served as an activator. Molecular docking results also indicated a negative amount for the Gibbs free energy of the binding of l-Met to the enzyme. α-Chy became more stable in the presence of l-Met, based on the molecular dynamics simulation.
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Affiliation(s)
- Sanaz Asgharzadeh
- Department of Biology, Faculty of Science, Shahrekord University, Shahrekord, P. O. Box.115, Iran
| | - Behzad Shareghi
- Department of Biology, Faculty of Science, Shahrekord University, Shahrekord, P. O. Box.115, Iran.
| | - Sadegh Farhadian
- Department of Biology, Faculty of Science, Shahrekord University, Shahrekord, P. O. Box.115, Iran; Central Laboratory, Shahrekord University, Shahrekord, Iran.
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Spectroscopic and molecular docking studies on the interaction between spermidine and pancreatic elastase. Int J Biol Macromol 2019; 131:473-483. [DOI: 10.1016/j.ijbiomac.2019.03.084] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Revised: 02/26/2019] [Accepted: 03/13/2019] [Indexed: 01/30/2023]
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47
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Evaluation of maltose binding to proteinase K: Insights from spectroscopic and computational approach. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.01.170] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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48
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Allahdad Z, Varidi M, Zadmard R, Saboury AA, Haertlé T. Binding of β-carotene to whey proteins: Multi-spectroscopic techniques and docking studies. Food Chem 2019; 277:96-106. [DOI: 10.1016/j.foodchem.2018.10.057] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 10/10/2018] [Accepted: 10/10/2018] [Indexed: 01/22/2023]
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49
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Wang Y, Li M, Xu X, Tang W, Xiong L, Sun Q. Formation of Protein Corona on Nanoparticles with Digestive Enzymes in Simulated Gastrointestinal Fluids. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:2296-2306. [PMID: 30721043 DOI: 10.1021/acs.jafc.8b05702] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The protein corona (PC), which defines the biological identity of nanoparticles in the blood, is well-known, but no comprehensive and systematic study has been conducted yet on the formation of PCs in the gastrointestinal environment. Thus, this study aimed to explore the interaction between model polystyrene nanoparticles (PS-NPs) of 50-100 nm and three digestive enzymes, namely, pepsin, α-amylase, and trypsin. Results showed that the thicknesses of the PCs formed by α-amylase and trypsin were 25-100 and 50-100 nm, respectively. The zeta-potential values of PS-NPs after incubation significantly increased. The fluorescence quenching and ultraviolet-visible-absorption spectra suggested that interactions between the nanoparticles and the enzymes occurred. Synchronous fluorescence spectra showed that the PS-NPs could induce microenvironmental changes in digestive enzymes. The thermodynamic parameters suggested that the interaction was mainly driven by hydrogen bonds and van der Waals forces.
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Affiliation(s)
- Yihui Wang
- College of Food Science and Engineering , Qingdao Agricultural University , Qingdao , Shandong Province 266109 , China
| | - Man Li
- College of Food Science and Engineering , Qingdao Agricultural University , Qingdao , Shandong Province 266109 , China
| | - Xingfeng Xu
- College of Food Science and Engineering , Qingdao Agricultural University , Qingdao , Shandong Province 266109 , China
| | - Wenting Tang
- College of Food Science and Engineering , Qingdao Agricultural University , Qingdao , Shandong Province 266109 , China
| | - Liu Xiong
- College of Food Science and Engineering , Qingdao Agricultural University , Qingdao , Shandong Province 266109 , China
| | - Qingjie Sun
- College of Food Science and Engineering , Qingdao Agricultural University , Qingdao , Shandong Province 266109 , China
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Sadeghi-Kaji S, Shareghi B, Saboury AA, Farhadian S. Spermine as a porcine pancreatic elastase activator: spectroscopic and molecular simulation studies. J Biomol Struct Dyn 2019; 38:78-88. [DOI: 10.1080/07391102.2019.1568306] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
| | - Behzad Shareghi
- Department of Biology, Shahrekord University, Shahrekord, Iran
| | - Ali Akbar Saboury
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
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