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Shanmugaraj K, Campos CH, Mangalaraja RV, Nandhini K, Aepuru R, Torres CC, Singh DP, Kumar D, Ilanchelian M, Sharma A, Vo DVN. Gold nanoparticle-decorated earth-abundant clay nanotubes as catalyst for the degradation of phenothiazine dyes and reduction of 4-(4-nitrophenyl)morpholine. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:124447-124458. [PMID: 35294686 DOI: 10.1007/s11356-022-19523-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 02/25/2022] [Indexed: 06/14/2023]
Abstract
In the present work, halloysite nanotubes modified with gold nanoparticles (AuNPs-HNT) are successfully prepared by wet chemical method for the catalytic degradation of phenothiazine dyes (azure B (AZB) and toluidine blue O (TBO)) and also cleaner reduction of 4-(4-nitrophenyl)morpholine (4NM) in the sodium borohydride (NaBH4) media. The catalyst is formulated by modifying the HNT support with a 0.964% metal loading using the HNT supports modified with 3-aminopropyl-trimethoxysilane (APTMS) coupling agent to facilitate the anchoring sites to trap the AuNPs and to prevent their agglomeration/aggregation. The AuNPs-HNT catalyst is investigated for structural and morphological characterization to get insights about the formation of the catalyst for the effective catalytic reduction of dyes and 4NM. The microscopic studies demonstrate that AuNPs (2.75 nm) are decorated on the outer surface of HNT. The as-prepared AuNPs-HNT catalyst demonstrates AZB and TBO dye degradation efficiency up to 96% in 10 and 11 min, respectively, and catalytic reduction of 4NM to 4-morpholinoaniline (MAN) is achieved up to 97% in 11 min, in the presence of NaBH4 without the formation of any by-products. The pseudo-first-order rate constant (K1) value of the AuNPs-HNT catalyst for AZB, TBO, and 4NM were calculated to be 0.0078, 0.0055, and 0.0066 s-1, respectively. Moreover, the synthesized catalyst shows an excellent reusability with stable catalytic reduction for 7 successive cycles for both the dyes and 4NM. A plausible mechanism for the catalytic dye degradation and reduction of 4NM by AuNPs-HNT catalyst is proposed as well. The obtained results clearly indicate the potential of AuNPs-HNT as an efficient catalyst for the removal of dye contaminants from the aquatic environments and cleaner reduction of 4NM to MAN, insinuating future pharmaceutical applications.
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Affiliation(s)
- Krishnamoorthy Shanmugaraj
- Advanced Ceramics and Nanotechnology Laboratory, Department of Materials Engineering, Universidad de Concepción, Concepción, Chile.
| | - Cristian H Campos
- Departamento de Físico-Química, Facultad de Ciencias Químicas, Universidad de Concepción, Edmundo Larenas 129, Casilla 160-C, Concepción, Chile
| | - Ramalinga Viswanathan Mangalaraja
- Advanced Ceramics and Nanotechnology Laboratory, Department of Materials Engineering, Universidad de Concepción, Concepción, Chile
- Technological Development Unit (UDT), University of Concepcion, Coronel Industrial Park, Coronel, Chile
| | - Karuppasamy Nandhini
- Department of Chemistry, Bharathiar University, Coimbatore, Tamil Nadu, 641 046, India
| | - Radhamanohar Aepuru
- Departamento de Ingeniería Mecánica, Facultad de Ingeniería, Universidad Tecnológica Metropolitana, Santiago, Chile
| | - Cecilia C Torres
- Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andres Bello, Autopista Concepción-Talcahuano, 7100, Sede Concepción, Talcahuano, Chile
| | - Dinesh Pratap Singh
- Physics Department and Millennium Institute for Research in Optics (MIRO- ANID), Faculty of Science, University of Santiago of Chile (USACH), Av. Ecuador 3493, 9170124, Estación Central, Santiago, Chile
| | - Deepak Kumar
- School of Chemical Engineering and Physical Science, Lovely Professional University, Phagwara, Punjab, 144411, India
| | | | - Ajit Sharma
- School of Chemical Engineering and Physical Science, Lovely Professional University, Phagwara, Punjab, 144411, India
| | - Dai-Viet N Vo
- Institute of Environmental Sciences, Nguyen Tat Thanh University, Ho Chi Minh City, 755414, Vietnam
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Manivel P, Marimuthu P, Yu S, Chen X. Multispectroscopic and Computational Investigations on the Binding Mechanism of Dicaffeoylquinic Acids with Ovalbumin. J Chem Inf Model 2022; 62:6133-6147. [PMID: 36398926 DOI: 10.1021/acs.jcim.2c01011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Recently, studies on the interactions between ovalbumin (OVA) and polyphenols have received a great deal of interest. This study explored the conformational changes and the interaction mechanism of the binding between OVA and chlorogenic acid (CGA) isomers such as 3,4-dicaffeoylquinic acids (3,4-diCQA), 4,5-dicaffeoylquinic acids (4,5-diCQA), and 3,5-dicaffeoylquinic acids (3,5-diCQA) using multispectroscopic and in silico analyses. The emission spectra show that the diCQAs caused strong quenching of OVA fluorescence under different temperatures through a static quenching mechanism with hydrogen bond (H-bond) and van der Waals (vdW) interactions. The values of binding constants (OVA-3,4-diCQA = 6.123 × 105, OVA-3,5-diCQA = 2.485 × 105, OVA-4,5-diCQA = 4.698 × 105 dm3 mol-1 at 298 K) suggested that diCQAs had a strong binding affinity toward OVA, among which OVA-3,4-diCQA exhibits higher binding constant. The results of UV-vis absorption and synchronous fluorescence indicated that the binding of all three diCQAs to OVA induced conformational and micro-environmental changes in the protein. The findings of molecular modeling further validate the significant role of vdW force and H-bond interactions in ensuring the stable binding of OVA-diCQA complexes. Temperature-dependent molecular dynamics simulation studies allow estimation of the individual components that contribute to the total bound free energy value, which allows evaluation of the nature of the interactions involved. This research can provide information for future investigations on food proteins' physicochemical stability and CGA bioavailability in vitro or in vivo.
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Affiliation(s)
- Perumal Manivel
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Jingkou District, Zhenjiang, Jiangsu212013, P.R. China
| | - Parthiban Marimuthu
- Structural Bioinformatics Laboratory (SBL─Biochemistry) and Pharmaceutical Science Laboratory (PSL─Pharmacy), Faculty of Science and Engineering, Åbo Akademi University, TurkuFI-20520, Finland
| | - Sun Yu
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Jingkou District, Zhenjiang, Jiangsu212013, P.R. China
| | - Xiumin Chen
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Jingkou District, Zhenjiang, Jiangsu212013, P.R. China.,Institute of Food Physical Processing, Jiangsu University, 301 Xuefu Road, Jingkou District, Zhenjiang, Jiangsu212013, P.R. China.,International Joint Research Laboratory of Intelligent Agriculture and Agri-products Processing, Jiangsu University, Zhenjiang212013, China
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袁 临, 马 利, 刘 润, 齐 伟, 张 栌, 王 贵, 王 宇. [Computer simulation of molecular docking between methylene blue and some proteins of Porphyromonas gingivalis]. BEIJING DA XUE XUE BAO. YI XUE BAN = JOURNAL OF PEKING UNIVERSITY. HEALTH SCIENCES 2022; 54:23-30. [PMID: 35165464 PMCID: PMC8860636 DOI: 10.19723/j.issn.1671-167x.2022.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Indexed: 06/14/2023]
Abstract
OBJECTIVE To study the binding target of photosensitizer and bacteria in antimicrobial photodynamic therapy with computer-simulated target prediction and molecular docking research methods and to calculate the binding energy. METHODS The protein names of Porphyromonas gingivalis (Pg) were obtained and summarized in Uniprot database and RCSB PDB database; the structure diagrams of methy-lene blue were screened in SciFinder database, PubChem database, ChemSpider database, and Chemical Book, and ChemBioDraw software was used to draw and confirm the three-dimensional structure for target prediction and Cytoscape software was used to build a visual network diagram; a protein interaction network was searched and built between the methylene blue target and the common target of Pg in the String database; then we selected FimA, Mfa4, RgpB, and Kgp K1 proteins, used AutoDock software to calculate the docking energy of methylene blue and the above-mentioned proteins and performed molecular docking. RESULTS The target prediction results showed that there were 19 common targets between the 268 potential targets of methylene blue and 1 865 Pg proteins. The 19 targets were: groS, radA, rplA, dps, fabH, pyrG, thyA, panC, RHO, frdA, ileS, bioA, def, ddl, TPR, murA, lepB, cobT, and gyrB. The results of the molecular docking showed that methylene blue could bind to 9 sites of FimA protein, with a binding energy of -6.26 kcal/mol; with 4 sites of Mfa4 protein and hydrogen bond formation site GLU47, and the binding energy of -5.91 kcal/mol, the binding energy of LYS80, the hydrogen bond forming site of RgpB protein, was -5.14 kcal/mol, and the binding energy of 6 sites of Kgp K1 protein and the hydrogen bond forming site GLY1114 of -5.07 kcal/mol. CONCLUSION Computer simulation of target prediction and molecular docking technology can initially reveal the binding, degree of binding and binding sites of methylene blue and Pg proteins. This method provides a reference for future research on the screening of binding sites of photosensitizers to cells and bacteria.
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Affiliation(s)
- 临天 袁
- 北京大学口腔医学院·口腔医院综合科, 国家口腔疾病临床医学研究中心, 口腔数字化医疗技术和材料国家工程实验室, 口腔数字医学北京市重点实验室,北京 100081Department of General Medicine, Peking University School and Hospital of Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Laboratory for Digital and Material Technology of Stomatology & Beijing Key Laboratory of Digital Stomatology, Beijing 100081, China
- 北京大学口腔医学院·口腔医院口腔医学数字化研究中心,北京 100081Center for Digital Dentistry, Peking University School and Hospital of Stomatology, Beijing 100081, China
| | - 利沙 马
- 北京大学口腔医学院·口腔医院口腔医学数字化研究中心,北京 100081Center for Digital Dentistry, Peking University School and Hospital of Stomatology, Beijing 100081, China
| | - 润园 刘
- 大连医科大学口腔医学院牙体牙髓科,辽宁大连 116044Department of Endodontics, College of Stomatology, Dalian Medical University, Dalian 116044, Liaoning, China
| | - 伟 齐
- 北京大学口腔医学院·口腔医院综合科, 国家口腔疾病临床医学研究中心, 口腔数字化医疗技术和材料国家工程实验室, 口腔数字医学北京市重点实验室,北京 100081Department of General Medicine, Peking University School and Hospital of Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Laboratory for Digital and Material Technology of Stomatology & Beijing Key Laboratory of Digital Stomatology, Beijing 100081, China
- 北京大学口腔医学院·口腔医院口腔医学数字化研究中心,北京 100081Center for Digital Dentistry, Peking University School and Hospital of Stomatology, Beijing 100081, China
| | - 栌丹 张
- 北京大学口腔医学院·口腔医院口腔医学数字化研究中心,北京 100081Center for Digital Dentistry, Peking University School and Hospital of Stomatology, Beijing 100081, China
- 北京大学口腔医学院·口腔医院门诊部,北京 100081First Clinical Division, Peking University School and Hospital of Stomatology, Beijing 100081, China
| | - 贵燕 王
- 北京大学口腔医学院·口腔医院口腔医学数字化研究中心,北京 100081Center for Digital Dentistry, Peking University School and Hospital of Stomatology, Beijing 100081, China
- 北京大学口腔医学院·口腔医院儿童口腔科,北京 100081Department of Pediatric Dentistry, Peking University School and Hospital of Stomatology, Beijing 100081, China
| | - 宇光 王
- 北京大学口腔医学院·口腔医院口腔医学数字化研究中心,北京 100081Center for Digital Dentistry, Peking University School and Hospital of Stomatology, Beijing 100081, China
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Perumal M, Paulpandi M, Chen X. Ovalbumin coated Fe3O4 nanoparticles as a nanocarrier for chlorogenic acid to promote the anticancer efficacy on MDA-MB-231 cells. NEW J CHEM 2022. [DOI: 10.1039/d2nj00716a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Chlorogenic acid (5-CQA), a phenolic acid abundant in plants and herbs, has various beneficial effects on human health. However, 5-CQA undergoes biotransformation during gastrointestinal digestion, which affects its biological accessibility....
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Chernysheva MG, Kasperovich AV, Skrabkova HS, Snitko AV, Arutyunyan AM, Badun GA. Lysozyme-dalargin self-organization at the aqueous-air and liquid-liquid interfaces. Colloids Surf B Biointerfaces 2021; 202:111695. [PMID: 33740631 DOI: 10.1016/j.colsurfb.2021.111695] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 12/24/2020] [Accepted: 03/10/2021] [Indexed: 01/04/2023]
Abstract
An experimental study of protein-peptide binding was performed by means of radiochemical and spectroscopic methods. Lysozyme and dalargin were chosen due to their biological and physiological importance. By means of tensiometry and radiochemical assays, it was found that dalargin possesses rather high surface activity at the aqueous-air and aqueous-p-xylene interfaces to be substituted by protein. Dalargin forms a hydrophobic complex with lysozyme in which the secondary structure of lysozyme is preserved. When lysozyme forms a mixed adsorption layer with dalargin at the aqueous-air surface, the peptide prevents protein from concentrating in the subsurface monolayer. In the presence of p-xylene protein in the interface, reorganization occurs quickly, so there is no lag in the interfacial tension time dependence. The interfacial tension in this case is controlled by protein and/or protein-peptide complexes. An increase in the enzymatic activity of lysozyme in the presence of dalargin was confirmed by a docking model that suggests the formation of hydrogen bonds between dalargin and amino acid residues in the active site.
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Affiliation(s)
| | | | - Hanna S Skrabkova
- Dpt. Chemistry, Lomonosov Moscow State University, 119991, Moscow, Russia
| | - Alexey V Snitko
- Dpt. Chemistry, Lomonosov Moscow State University, 119991, Moscow, Russia
| | - Alexander M Arutyunyan
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992, Moscow, Russia
| | - Gennadii A Badun
- Dpt. Chemistry, Lomonosov Moscow State University, 119991, Moscow, Russia
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Saha S, Bhattacharjee S, Chowdhury J. Exploring the binding interactions of janus green blue with serum albumins from spectroscopic and calorimetric studies aided by in silico calculations. J Biomol Struct Dyn 2021; 40:5328-5344. [PMID: 33410370 DOI: 10.1080/07391102.2020.1870156] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Binding interactions of the phenazinium dye Janus green blue (JGB) with human and bovine serum albumins (BSA - and BSA) have been explored for the first time from multi-spectroscopic and calorimetric measurements aided by in silico calculations. The formation of ground state complexes between JGB and the respective serum albumins have been suggested from the UV-Vis and steady-state fluorescence spectroscopic studies. The nonlinear Stern Volmer (SV) plots at higher concentrations of JGB primarily indicate the formation of more than one ground state complexes in BSA -/BSA-JGB systems. Modified SV plots and isothermal titration calorimetry (ITC) studies however signify the possibilities of one type of binding complexes between HSA/BSA - JGB systems. Binding constants and the thermodynamic parameters associated with the HSA/BSA-JGB complexes have also been estimated from the ITC studies. Förster distances (R0) for HSA-JGB and BSA-JGB complexes are estimated from Förster resonance energy transfer (FRET) results. Variations in the micro-environment of the Tyr and Trp residues of the serum proteins in presence of JGB have been observed from the synchronous fluorescence measurements. The conformational changes in the protein structures induced by the dye JGB have been revealed from 3 D fluorescence and circular dichroism (CD) studies. The experimental observations are supported by in silico calculations. This in depth investigation on the interactions of serum albumins with JGB may provide the fundamental information toward exploring the therapeutic efficacy of JGB as a potent drug molecule. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Saumen Saha
- Department of Physics, Jadavpur University, Kolkata, India
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Takalloo Z, Masroor MJ, Mani-Varnosfaderani A, Maroufi B, H Sajedi R. Probing heat and oxidation induced conformational changes of molecular chaperone artemin by excitation-emission fluorescence spectroscopy. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2020; 211:112013. [PMID: 32919176 DOI: 10.1016/j.jphotobiol.2020.112013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 07/17/2020] [Accepted: 08/31/2020] [Indexed: 12/18/2022]
Abstract
Artemin is a potent molecular chaperone, which protects Artemia embryos undergoing encystment against extreme environmental stresses. In the present work, we have examined the structural changes of artemin from A. urmiana upon exposure to oxidant and heat, by using CD measurements as well as excitation-emission fluorescence spectroscopy as a powerful tool for monitoring the conformational transitions and molecular interactions in proteins. We have also provided here the first document on reporting the three dimensional fluorescence spectra of a protein using ANS. Totally, the fluorescence results indicated that the microenvironments of tyrosine and tryptophan residues and the hydrophobic pockets as well as the polypeptide backbone or secondary structure of the chaperone were influenced in responses to heat and H2O2 in different degrees. Moreover, the native state of artemin did not induce a considerable exposure of the internal non-polar groups to the solvent. Besides, the excitation-emission spectra of heated artemin by ANS revealed new emission peaks at 430-450 nm when it was excited at 330 nm, which suggests probable exposure of new binding sites for hydrophobic or electrostatic interactions of the protein with ANS. The protein also showed a greater conformational sensitivity to the temperature fluctuations compared to oxidation. Here, we presented some evidence in support of the relation between artemin and its stress dependent activation in vitro and in vivo. This study can expect that the EEM fluorescence spectroscopy could provide a promising tool to study conformational transitions of proteins.
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Affiliation(s)
- Zeinab Takalloo
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Mohammad Javad Masroor
- Department of Chemistry, Faculty of Basic Sciences, Tarbiat Modares University, Tehran, Iran
| | | | | | - Reza H Sajedi
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.
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Anand K, Rajamanikandan R, Selva Sharma A, Ilanchelian M, Khan FI, Tiloke C, Katari NK, Boomi P, Balakumar C, Saravanan M, Palanisamy S, Ramesh M, Lai D, Chuturgoon A. Human serum albumin interaction, in silico and anticancer evaluation of Pine-Gold nanoparticles. Process Biochem 2020. [DOI: 10.1016/j.procbio.2019.09.036] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Bhuiya S, Chowdhury S, Das S. Molecular insight into the binding aspects of benzo[c]phenanthridine alkaloid nitidine with bovine hemoglobin: A biophysical exploration. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2019; 223:117293. [PMID: 31260885 DOI: 10.1016/j.saa.2019.117293] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Revised: 06/04/2019] [Accepted: 06/18/2019] [Indexed: 06/09/2023]
Abstract
The association of a putative bioactive alkaloid nitidine (NIT) with blood protein bovine hemoglobin (BHb) was investigated by employing various biophysical and molecular docking techniques. NIT binding to BHb was first characterized by hypochromic effect on the Soret band absorption of BHb from spectrophotometric studies. Spectrofluorimetric titration and unchanged fluorescence lifetime of BHb confirmed ground state complexation followed by the static nature of the emission quenching mechanism of the protein induced by NIT. Substantial conformational changes in the protein structure were established from circular dichroism study. Conformational perturbation results a lowering in the α-helical organization of the tetrameric protein structure. Thermodynamics of the binding suggest that the binding is exothermic with a favourable small positive entropy change and negative enthalpy change making a sense of electrostatic interaction as the major acting force. Experimentally calculated free energy change for the NIT-BHb interaction was found to be -7.50 kcal mol-1 which is in well agreement to the theoretical docking energy value of -6.36 kcal mol-1. AutoDock based molecular docking suggests the internal cavity of BHb as the preferred binding position of NIT. Overall this manuscript depicts consequences on the molecular interaction of NIT with BHb from structural and energetic standpoints providing a profound insight into protein-ligand association.
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Affiliation(s)
- Sutanwi Bhuiya
- Biophysical Chemistry Laboratory, Physical Chemistry Section, Department of Chemistry, Jadavpur University, Raja S. C. Mullick Road, Jadavpur, Kolkata 700 032, India
| | - Susmita Chowdhury
- Biophysical Chemistry Laboratory, Physical Chemistry Section, Department of Chemistry, Jadavpur University, Raja S. C. Mullick Road, Jadavpur, Kolkata 700 032, India
| | - Suman Das
- Biophysical Chemistry Laboratory, Physical Chemistry Section, Department of Chemistry, Jadavpur University, Raja S. C. Mullick Road, Jadavpur, Kolkata 700 032, India.
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Elucidation of the association of potential chemotherapeutic alkaloid chelerythrine with bovine hemoglobin by experimental probing and molecular docking simulation. Int J Biol Macromol 2019; 138:57-69. [DOI: 10.1016/j.ijbiomac.2019.07.069] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 06/26/2019] [Accepted: 07/09/2019] [Indexed: 12/30/2022]
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11
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Nithya P, Rajamanikandan R, Simpson J, Ilanchelian M, Govindarajan S. Solvent assisted synthesis, structural characterization and biological evaluation of cobalt(II) and nickel(II) complexes of Schiff bases generated from benzyl carbazate and cyclic ketones. Polyhedron 2018. [DOI: 10.1016/j.poly.2018.02.008] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Kazemi F, Divsalar A, Saboury AA. Structural analysis of the interaction between free, glycated and fructated hemoglobin with propolis nanoparticles: A spectroscopic study. Int J Biol Macromol 2018; 109:1329-1337. [DOI: 10.1016/j.ijbiomac.2017.11.143] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2017] [Revised: 11/14/2017] [Accepted: 11/22/2017] [Indexed: 12/19/2022]
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13
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Das S, Karn A, Sarmah R, Rohman MA, Koley S, Ghosh P, Roy AS. Characterization of non-covalent binding of 6-hydroxyflavone and 5,7-dihydroxyflavone with bovine hemoglobin: Multi-spectroscopic and molecular docking analyses. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2018; 178:40-52. [DOI: 10.1016/j.jphotobiol.2017.10.021] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 10/19/2017] [Accepted: 10/24/2017] [Indexed: 11/25/2022]
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14
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Akram M, Anwar S, Bhat IA, Kabir-ud-Din. In vitro evaluation of the non-covalent interactions of hemoglobin with distinctively modified gemini surfactants: Effect of structural variation. Colloids Surf A Physicochem Eng Asp 2017. [DOI: 10.1016/j.colsurfa.2017.05.021] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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Ding F, Peng W, Peng YK. Biophysical exploration of protein-flavonol recognition: effects of molecular properties and conformational flexibility. Phys Chem Chem Phys 2017; 18:11959-71. [PMID: 27095486 DOI: 10.1039/c5cp07754k] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The current work explores the biomolecular recognition of a series of flavonols by a protein and then uncovers the influences of the structural features of flavonols and the protein's own characteristics, e.g. the dynamics and flexibility, on the bioavailability of flavonols by using the pivotal biomacromolecule hemoglobin as a model. The experimental results revealed that flavonol may lead to a notable decrease in the steady-state fluorescence intensity of the β-37 Trp residue, and in the meantime the R-T transition of the protein transpired. Such noncovalent recognition forms the ground-state adduct, with an association intensity of 3.991 × 10(4) M(-1) in the reaction process, which has already been authenticated by the detailed analysis of time-resolved fluorescence and UV/vis absorption spectra. Furthermore, flavonol can form hydrogen bonds and π-conjugation effects with several amino acid residues on the polypeptide chain, for example, Trp-37, Arg-40, Asp-99 and Asn-102, and this event would induce self-regulation of the compact, regular conformation of the protein to a certain extent, which explicitly corroborates the results of circular dichroism. According to the study of molecular docking and structure-activity relationships, we could see that the recognition capacities of the protein-flavonols are inversely interrelated with the C log P values of the flavonol molecules. Moreover, the properties of the substituents in the structural B-ring unit of flavonols, i.e. polarity, position and number, will also prominently affect the degree of affinity and bioavailability of the protein-flavonol complexes. The analytical results of molecular dynamics (MD) simulation testified that the discussions of the structure-activity relationships are entirely logical, and the conformations of the amino acid residues forming noncovalent interactions tend to be stable in the MD simulation, as further elucidated from the dynamics data. Plainly, molecular recognition of the protein-flavonols might noticeably cause relatively large changes in protein flexibility, and then manifest different recognition strengths and corresponding biological activities. This issue will be carefully validated by the interpretation of root-mean-square fluctuation.
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Affiliation(s)
- Fei Ding
- College of Agriculture and Plant Protection, Qingdao Agricultural University, Qingdao 266109, China. and Department of Chemistry, China Agricultural University, Beijing 100193, China and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Wei Peng
- College of Agriculture and Plant Protection, Qingdao Agricultural University, Qingdao 266109, China. and College of Food Science and Engineering, Qingdao Agricultural University, Qingdao 266109, China
| | - Yu-Kui Peng
- Center for Food Quality Supervision & Testing, Ministry of Agriculture, College of Food Science & Engineering, Northwest A&F University, Yangling 712100, China
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Khemakhem M, Sotiroudis G, Mitsou E, Avramiotis S, Sotiroudis TG, Bouzouita N, Papadimitriou V. Melanin and humic acid-like polymer complex from olive mill waste waters. Part II. Surfactant properties and encapsulation in W/O microemulsions. J Mol Liq 2016. [DOI: 10.1016/j.molliq.2016.07.065] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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17
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Chatterjee S, Kumar GS. Binding of fluorescent acridine dyes acridine orange and 9-aminoacridine to hemoglobin: Elucidation of their molecular recognition by spectroscopy, calorimetry and molecular modeling techniques. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2016; 159:169-78. [PMID: 27077554 DOI: 10.1016/j.jphotobiol.2016.03.045] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 03/29/2016] [Indexed: 11/27/2022]
Abstract
The molecular interaction between hemoglobin (HHb), the major human heme protein, and the acridine dyes acridine orange (AO) and 9-aminoacridine (9AA) was studied by various spectroscopic, calorimetric and molecular modeling techniques. The dyes formed stable ground state complex with HHb as revealed from spectroscopic data. Temperature dependent fluorescence data showed the strength of the dye-protein complexation to be inversely proportional to temperature and the fluorescence quenching was static in nature. The binding-induced conformational change in the protein was investigated using circular dichroism, synchronous fluorescence, 3D fluorescence and FTIR spectroscopy results. Circular dichroism data also quantified the α-helicity change in hemoglobin due to the binding of acridine dyes. Calorimetric studies revealed the binding to be endothermic in nature for both AO and 9AA, though the latter had higher affinity, and this was also observed from spectroscopic data. The binding of both dyes was entropy driven. pH dependent fluorescence studies revealed the existence of electrostatic interaction between the protein and dye molecules. Molecular modeling studies specified the binding site and the non-covalent interactions involved in the association. Overall, the results revealed that a small change in the acridine chromophore leads to remarkable alteration in the structural and thermodynamic aspects of binding to HHb.
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Affiliation(s)
- Sabyasachi Chatterjee
- Biophysical Chemistry Laboratory, Organic and Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700 032, India
| | - Gopinatha Suresh Kumar
- Biophysical Chemistry Laboratory, Organic and Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700 032, India.
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18
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Ding F, Xie Y, Peng W, Peng YK. Measuring the bioactivity and molecular conformation of typically globular proteins with phenothiazine-derived methylene blue in solid and in solution: A comparative study using photochemistry and computational chemistry. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2016; 158:69-80. [PMID: 26950891 DOI: 10.1016/j.jphotobiol.2016.02.029] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2015] [Revised: 02/13/2016] [Accepted: 02/15/2016] [Indexed: 11/29/2022]
Abstract
Methylene blue is a phenothiazine agent, that possesses a diversity of biomedical and biological therapeutic purpose, and it has also become the lead compound for the exploitation of other pharmaceuticals such as chlorpromazine and the tricyclic antidepressants. However, the U.S. Food and Drug Administration has acquired cases of detrimental effects of methylene blue toxicities such as hemolytic anemia, methemoglobinemia and phototoxicity. In this work, the molecular recognition of methylene blue by two globular proteins, hemoglobin and lysozyme was characterized by employing fluorescence, circular dichroism (CD) along with molecular modeling at the molecular scale. The recognition of methylene blue with proteins appears fluorescence quenching via static type, this phenomenon does cohere with time-resolved fluorescence lifetime decay that nonfluorescent protein-drug conjugate formation has a strength of 10(4)M(-1), and the primary noncovalent bonds, that is hydrogen bonds, π-conjugated effects and hydrophobic interactions were operated and remained adduct stable. Meantime, the results of far-UV CD and synchronous fluorescence suggest that the α-helix of hemoglobin/lysozyme decreases from 78.2%/34.7% (free) to 58.7%/23.8% (complex), this elucidation agrees well with the elaborate description of three-dimensional fluorescence showing the polypeptide chain of proteins partially destabilized upon conjugation with methylene blue. Furthermore, both extrinsic fluorescent indicator and molecular modeling clearly exhibit methylene blue is situated within the cavity constituted by α1, β2 and α2 subunits of hemoglobin, while it was located at the deep fissure on the lysozyme surface and Trp-62 and Trp-63 residues are nearby. With the aid of computational analyses and combining the wet experiments, it can evidently be found that the recognition ability of proteins for methylene blue is patterned upon the following sequence: lysozyme<hemoglobin<albumin. Basically, the distinction originates from different spatial structures of proteins and noncovalent interactions between proteins and methylene blue. In addition, biological relevance of the biorecognition of methylene blue with proteins was briefly discussed. We hope that this study could provide further standpoint so that one explore the biological activity of methylene blue and also phenothiazines.
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Affiliation(s)
- Fei Ding
- College of Agriculture and Plant Protection, Qingdao Agricultural University, Qingdao 266109, China; Department of Chemistry, China Agricultural University, Beijing 100193, China; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Yong Xie
- State Key Laboratory of the Discovery and Development of Novel Pesticide, Shenyang Research Institute of Chemical Industry Co. Ltd., Shenyang 110021, China
| | - Wei Peng
- College of Agriculture and Plant Protection, Qingdao Agricultural University, Qingdao 266109, China; College of Food Science and Engineering, Qingdao Agricultural University, Qingdao 266109, China.
| | - Yu-Kui Peng
- Center for Food Quality Supervision & Testing, Ministry of Agriculture, College of Food Science & Engineering, Northwest A&F University, Yangling 712100, China
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Peng W, Ding F, Peng YK. In vitro evaluation of the conjugations of neonicotinoids with transport protein: photochemistry, ligand docking and molecular dynamics studies. RSC Adv 2016. [DOI: 10.1039/c5ra14661e] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The flexibility of ligand structures and the property of substituents in neonicotinoids play a pivotal role in protein–neonicotinoid and this type of biorecognition may have a great impact on the potential toxicity of these widely used agrochemicals.
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Affiliation(s)
- Wei Peng
- College of Agriculture and Plant Protection
- Qingdao Agricultural University
- Qingdao 266109
- China
- College of Food Science and Engineering
| | - Fei Ding
- College of Agriculture and Plant Protection
- Qingdao Agricultural University
- Qingdao 266109
- China
- Department of Biological Engineering
| | - Yu-Kui Peng
- Center for Food Quality Supervision & Testing
- Ministry of Agriculture
- College of Food Science & Engineering
- Northwest A&F University
- Yangling 712100
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Wang R, Li Z, Yang L, Ren T, Zhang L, Wang R. Studies on the interaction between neutral red and bovine hemoglobin by fluorescence spectroscopy and molecular modeling. J Mol Liq 2015. [DOI: 10.1016/j.molliq.2015.07.066] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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21
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Das A, Suresh Kumar G. Binding of the alkaloid aristololactam-β-D-glucoside and daunomycin to human hemoglobin: spectroscopy and calorimetry studies. J Biomol Struct Dyn 2015; 34:800-13. [DOI: 10.1080/07391102.2015.1055304] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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