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Rupreo V, Tissopi R, Baruah K, Roy AS, Bhattacharyya J. Multispectroscopic and Theoretical Investigation on the Binding Interaction of a Neurodegenerative Drug, Lobeline with Human Serum Albumin: Perturbation in Protein Conformation and Hydrophobic-Hydrophilic Surface. Mol Pharm 2024; 21:4169-4182. [PMID: 39037173 DOI: 10.1021/acs.molpharmaceut.4c00651] [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] [Indexed: 07/23/2024]
Abstract
Lobeline (LOB), a naturally occurring alkaloid, has a broad spectrum of pharmacological activities and therapeutic potential, including applications in central nervous system disorders, drug misuse, multidrug resistance, smoking cessation, depression, and epilepsy. LOB represents a promising compound for developing treatments in various medical fields. However, despite extensive pharmacological profiling, the biophysical interaction between the LOB and proteins remains largely unexplored. In the current article, a range of complementary photophysical and cheminformatics methodologies were applied to study the interaction mechanism between LOB and the carrier protein HSA. Steady-state fluorescence and fluorescence lifetime experiments confirmed the static-quenching mechanisms in the HSA-LOB system. "K" (binding constant) of the HSA-LOB system was determined to be 105 M-1, with a single preferable binding site in HSA. The forces governing the HSA-LOB stable complex were analyzed by thermodynamic parameters and electrostatic contribution. The research also investigated how various metal ions affect complex binding. Site-specific binding studies depict Site I as probable binding in HSA by LOB. We conducted synchronous fluorescence, 3D fluorescence, and circular dichroism studies to explore the structural alteration occurring in the microenvironment of amino acids. To understand the robustness of the HSA-LOB complex, we used theoretical approaches, including molecular docking and MD simulations, and analyzed the principal component analysis and free energy landscape. These comprehensive studies of the structural features of biomolecules in ligand binding are of paramount importance for designing targeted drugs and delivery systems.
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Affiliation(s)
- Vibeizonuo Rupreo
- Department of Chemistry, National Institute of Technology Nagaland, Chumukedima, Nagaland 797103, India
| | - Rengka Tissopi
- Department of Chemistry, National Institute of Technology Nagaland, Chumukedima, Nagaland 797103, India
| | - Kakali Baruah
- Department of Chemical & Biological Sciences, National Institute of Technology Meghalaya, Shillong 793003, India
| | - Atanu Singha Roy
- Department of Chemical & Biological Sciences, National Institute of Technology Meghalaya, Shillong 793003, India
| | - Jhimli Bhattacharyya
- Department of Chemistry, National Institute of Technology Nagaland, Chumukedima, Nagaland 797103, India
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2
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Wang J, Shen Y, Zhuang Y, Wang J, Zhang Y. Multimodal Affinity-Modulated Efficient Separation of Lysozyme with a Hierarchical MXene@MOF Hybrid Framework. Anal Chem 2024; 96:12102-12111. [PMID: 39001808 DOI: 10.1021/acs.analchem.4c02183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/15/2024]
Abstract
The development of abiotic protein affinity adsorbents remains challenging for the accurate acquisition and analysis of specific protein species. Inspired by bacterial cell walls, a hierarchical hybrid framework is fabricated through the oriented growth of an Fe-based metal organic framework (MOF) on V2C MXene for the efficient separation of lysozyme (Lys). After directed evolution of adsorptive materials, the MXene@MOF composite rich in hydroxyl groups (termed as MX@MOF-DH) is found exerting exceptional affinity for Lys. Benefiting from hydrogen-bonding, coordination, and electrostatic interaction-mediated multimodal and multivalent affinity, MX@MOF-DH reveals rapid adsorption rate (5 min), superb enrichment factor (83.1), and favorable binding capacity (609.7 mg g-1), which outperforms other latest adsorbents. Moreover, femtomolar sensitivity is achieved even in the presence of high-abundant interfering proteins, as confirmed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometer analysis. This work not only provides an efficient approach for selective enrichment of lysozyme but also paves an avenue to construct the protein affinity reagents for specific biological medicine and analysis applications.
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Affiliation(s)
- Jin Wang
- College of Chemistry and Pharmacy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yudan Shen
- College of Chemistry and Pharmacy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yuting Zhuang
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jinyi Wang
- College of Chemistry and Pharmacy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yue Zhang
- College of Chemistry and Pharmacy, Northwest A&F University, Yangling, Shaanxi 712100, China
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3
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Li M, Kong J, Chen Y, Li Y, Xuan H, Liu M, Zhang Q, Liu J. Comparative interaction study of soy protein isolate and three flavonoids (Chrysin, Apigenin and Luteolin) and their potential as natural preservatives. Food Chem 2023; 414:135738. [PMID: 36841103 DOI: 10.1016/j.foodchem.2023.135738] [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: 11/18/2022] [Revised: 02/15/2023] [Accepted: 02/16/2023] [Indexed: 02/22/2023]
Abstract
In this work, the potential of soy protein isolate (SPI)-luteolin (Lut)/apigenin (Ap)/chrysin (Chr) complexes as natural preservatives for food and cosmetics was evaluated by comparing their interactional and functional properties with structure-activity relationship. The results of spectrometry and molecular docking indicated that the B-ring hydroxylation of flavonoids affected their binding constants with SPI, which were determined as Lut (1.45 × 106 L/mol) > Ap (2.04 × 105 L/mol) > Chr (3.81 × 104 L/mol) at 298.15 K. It demonstrated that the hydrogen bonding force played an important role in binding flavonoids to SPI. Moreover, the anti-oxidation ability, antimicrobial effect, and foaming properties were positively correlated with increase in number of hydroxyl groups on the B-ring, but the amount and type of the preservative should be adjusted aimed at the nutrition components. This study provides a theoretical basis for the use of flavonoids and SPI-flavonoid complexes as natural preservatives for food and cosmetics.
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Affiliation(s)
- Mingyuan Li
- School of Chemistry and Chemical Engineering, Liaocheng University, Liaocheng, Shandong 252059, PR China
| | - Jing Kong
- School of Chemistry and Chemical Engineering, Liaocheng University, Liaocheng, Shandong 252059, PR China
| | - Yanrong Chen
- School of Chemistry and Chemical Engineering, Liaocheng University, Liaocheng, Shandong 252059, PR China
| | - Yutong Li
- School of Chemistry and Chemical Engineering, Liaocheng University, Liaocheng, Shandong 252059, PR China
| | - Hongzhuan Xuan
- School of Life Science, Liaocheng University, Liaocheng, Shandong 252059, PR China
| | - Min Liu
- School of Chemistry and Chemical Engineering, Liaocheng University, Liaocheng, Shandong 252059, PR China
| | - Qian Zhang
- School of Chemistry and Chemical Engineering, Liaocheng University, Liaocheng, Shandong 252059, PR China.
| | - Jie Liu
- School of Chemistry and Chemical Engineering, Liaocheng University, Liaocheng, Shandong 252059, PR China.
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4
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Parveen S, Ali MS, Al-Lohedan HA, Hoti N, Tabassum S. Molecular interaction of lysozyme with therapeutic drug azithromycin: Effect of sodium dodecyl sulfate on binding profile. Int J Biol Macromol 2023; 242:124844. [PMID: 37210056 DOI: 10.1016/j.ijbiomac.2023.124844] [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: 01/11/2023] [Revised: 05/08/2023] [Accepted: 05/09/2023] [Indexed: 05/22/2023]
Abstract
This paper describes an inclusive biophysical study elucidating the interaction of therapeutic drug azithromycin (Azith) with hen egg white lysozyme (HEWL). Spectroscopic and computational tools have been employed to study the interaction of Azith with HEWL at pH 7.4. The fluorescence quenching constant values (Ksv) exhibited a decrease with the increase in temperature which revealed the occurrence of static quenching mechanism between Azith and HEWL. The thermodynamic data demonstrated that hydrophobic interactions were predominantly involved in the Azith-HEWL interaction. The negative value of standard Gibbs free energy (ΔG°) stated that the Azith-HEWL complex formed via spontaneous molecular interactions. The effect of sodium dodecyl sulfate (SDS) surfactant monomers on the binding propensity of Azith with HEWL was insignificant at lower concentrations however the binding significantly decreased at increased concentrations of the former. Far-UV CD data revealed alteration in the secondary structure of HEWL in the presence of Azith and the overall HEWL conformation changed. Molecular docking results revealed that the binding of Azith with HEWL takes place through hydrophobic interactions and hydrogen bonds.
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Affiliation(s)
- Sabiha Parveen
- Department of Chemistry, Aligarh Muslim University, Aligarh 202002, India
| | - Mohd Sajid Ali
- Department of Chemistry, College of Sciences, King Saud University, Riyadh 11451, the Kingdom of Saudi Arabia
| | - Hamad A Al-Lohedan
- Department of Chemistry, College of Sciences, King Saud University, Riyadh 11451, the Kingdom of Saudi Arabia
| | | | - Sartaj Tabassum
- Department of Chemistry, Aligarh Muslim University, Aligarh 202002, India.
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5
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Rial R, González-Durruthy M, Liu Z, Ruso JM. Conformational binding mechanism of lysozyme induced by interactions with penicillin antibiotic drugs. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119081] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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6
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Mahmoodi Y, Mehrnejad F, Khanmohammadi S, Shahriari M, Rahimi F, Vakili MR, Lavasanifar A. Molecular insights into the crystalline nanocellulose and human lysozyme interactions: An experimental and theoretical research. Int J Biol Macromol 2022; 213:83-95. [PMID: 35598725 DOI: 10.1016/j.ijbiomac.2022.05.113] [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: 01/29/2022] [Revised: 05/16/2022] [Accepted: 05/16/2022] [Indexed: 11/18/2022]
Abstract
In the present research, we performed a combination of detailed computational and spectroscopic methods to determine the effect of crystalline nanocellulose (CNC) on the structure and dynamics of human lysozyme (hLyz). Fluorescence spectroscopy revealed static quenching as the major mechanism in forming a stable CNC-hLyz complex, and the binding was energetically favorable. The obtained values of the thermodynamic parameters (∆G, ∆H, and ∆S) proposed that the complex formation between the enzyme and cellulose nanocrystals is driven by electrostatic interactions, which were also confirmed by molecular dynamics (MD) simulation. Additionally, the MD simulation analysis displays that the enzyme's structural elements and tertiary structure were primarily maintained, and only loops regions were affected in the presence of cellulose nanocrystals. At the same time, circular dichroism (CD) outcomes highlighted that higher cellulose nanocrystals concentration caused a reduction in the secondary structure of hLyz. Our observations proved that low cellulose nanocrystals concentrations have no considerable effect on the human lysozyme structure. The current research results provide a valuable opportunity to elucidate the molecular interactions between protein and nanocelluloses, guiding further investigations of CNC-based material for biomedical, pharmaceutical, and food industry applications.
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Affiliation(s)
- Yasaman Mahmoodi
- Department of Life Sciences Engineering, Faculty of New Sciences and Technologies, University of Tehran, 14395-1561 Tehran, Iran
| | - Faramarz Mehrnejad
- Department of Life Sciences Engineering, Faculty of New Sciences and Technologies, University of Tehran, 14395-1561 Tehran, Iran.
| | - Somayeh Khanmohammadi
- Department of Life Sciences Engineering, Faculty of New Sciences and Technologies, University of Tehran, 14395-1561 Tehran, Iran
| | - Masoud Shahriari
- Department of Life Sciences Engineering, Faculty of New Sciences and Technologies, University of Tehran, 14395-1561 Tehran, Iran
| | - Fereshteh Rahimi
- Department of Life Sciences Engineering, Faculty of New Sciences and Technologies, University of Tehran, 14395-1561 Tehran, Iran
| | - Mohammad Reza Vakili
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton AB T6G 2E1, Canada
| | - Afsaneh Lavasanifar
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton AB T6G 2E1, Canada
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7
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Li B, Hao C, Liu H, Yang H, Zhong K, Zhang M, Sun R. Interaction of graphene oxide with lysozyme:Insights from conformational structure and surface charge investigations. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 264:120207. [PMID: 34419829 DOI: 10.1016/j.saa.2021.120207] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 06/26/2021] [Accepted: 07/16/2021] [Indexed: 06/13/2023]
Abstract
Lysozyme (Lyz) is an important antibacterial protein that exists widely in nature. In recent years, the application of graphene oxide (GO) in the field of biotechnology electronics, optics, chemistry and energy storage has been extensively studied. However, due to the unique properties of GO, the mechanism of its interaction with biomacromolecule proteins is very complex. To further explore the interaction between GO and proteins we explore the influence of different pH and heat treatment conditions on the interaction between GO and Lyz, the GO (0-20 μg/mL) was added at a fixed Lyz concentration (0.143 mg/mL) under different pHs. The structure and surface charge changes of Lyz were measured by spectroscopic analysis and zeta potential. The results showed that the interaction between GO and Lyz depends on temperature and pH, significant changes have taken place in its tertiary and secondary structures. By analyzing the UV absorption spectrum, it was found that lysozyme and GO formed a stable complex, and the conformation of the enzyme was changed. In acidic pH conditions (i.e., pH < pI), a high density of Lyz were found to adsorb on the GO surface, whereas an increase in pH resulted in a progressive decrease in the density of the adsorbed Lyz. This pH-dependent adsorption is ascribed to the electrostatic interactions between the negatively charged GO surface and the tunable ionization of the Lyz molecules. The secondary structure of Lyz adsorbed on GO was also found to be highly dependent on the pH. In this paper, we investigated the exact mechanism of pH-influenced GO binding to lysozyme, which has important guidance significance for the potential toxicity of GO biology and its applications in biomedical fields such as structure-based drug design.
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Affiliation(s)
- Binbin Li
- School of Physics and Information Technology, Shaanxi Normal University, Xi'an 710062, China
| | - Changchun Hao
- School of Physics and Information Technology, Shaanxi Normal University, Xi'an 710062, China.
| | - Hengyu Liu
- School of Physics and Information Technology, Shaanxi Normal University, Xi'an 710062, China
| | - Haiyan Yang
- School of Physics and Information Technology, Shaanxi Normal University, Xi'an 710062, China
| | - Kunfeng Zhong
- School of Physics and Information Technology, Shaanxi Normal University, Xi'an 710062, China
| | - Mingduo Zhang
- School of Physics and Information Technology, Shaanxi Normal University, Xi'an 710062, China.
| | - Runguang Sun
- School of Physics and Information Technology, Shaanxi Normal University, Xi'an 710062, China
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8
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Molecular interaction of Sunset Yellow with whey protein: Multi-spectroscopic techniques and computational study. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2021.117838] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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9
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Parveen S, Ali MS, Al-Lohedan HA, Tabassum S. Interaction of Carrier Protein with Potential Metallic Drug Candidate N-Glycoside 'GATPT': Validation by Multi-Spectroscopic and Molecular Docking Approaches. Molecules 2021; 26:6641. [PMID: 34771048 PMCID: PMC8587009 DOI: 10.3390/molecules26216641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 10/25/2021] [Accepted: 10/27/2021] [Indexed: 12/02/2022] Open
Abstract
Lysozyme is often used as a model protein to study interaction with drug molecules and to understand biological processes which help in illuminating the therapeutic effectiveness of the drug. In the present work, in vitro interaction studies of 1-{(2-hydroxyethyl)amino}-2-amino-1,2-dideoxy-d-glucose triphenyl tin (IV) (GATPT) complex with lysozyme were carried out by employing various biophysical methods such as absorption, fluorescence, and circular dichroism (CD) spectroscopies. The experimental results revealed efficient binding affinity of GATPT with lysozyme with intrinsic binding (Kb) and binding constant (K) values in the order of 105 M-1. The number of binding sites and thermodynamic parameters ΔG, ΔH, and ΔS at four different temperatures were also calculated and the interaction of GATPT with lysozyme was found to be enthalpy and entropy driven. The CD spectra revealed alterations in the population of α-helical content within the secondary structure of lysozyme in presence of GATPT complex. The morphological analysis of the complex with lysozyme and lysozyme-DNA condensates was carried out by employing confocal and SEM studies. Furthermore, the molecular docking studies confirmed the interaction of GATPT within the larger hydrophobic pocket of the lysozyme via several non-covalent interactions.
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Affiliation(s)
- Sabiha Parveen
- Department of Chemistry, Aligarh Muslim University, Aligarh 202002, India;
| | - Mohd. Sajid Ali
- Department of Chemistry, College of Sciences, King Saud University, Riyadh 11451, Saudi Arabia; (M.S.A.); (H.A.A.-L.)
| | - Hamad A. Al-Lohedan
- Department of Chemistry, College of Sciences, King Saud University, Riyadh 11451, Saudi Arabia; (M.S.A.); (H.A.A.-L.)
| | - Sartaj Tabassum
- Department of Chemistry, Aligarh Muslim University, Aligarh 202002, India;
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10
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Nassab CN, Arooj M, Shehadi IA, Parambath JBM, Kanan SM, Mohamed AA. Lysozyme and Human Serum Albumin Proteins as Potential Nitric Oxide Cardiovascular Drug Carriers: Theoretical and Experimental Investigation. J Phys Chem B 2021; 125:7750-7762. [PMID: 34232651 DOI: 10.1021/acs.jpcb.1c04614] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nitric oxide-containing drugs present a critical remedy for cardiovascular diseases. Nitroglycerin (NG, O-NO) and S-nitrosoglutathione (SNG, S-NO) are the most common nitric oxide drugs for cardiovascular diseases. Insights regarding the binding affinity of NO drugs with lysozyme and human serum albumin (HSA) proteins and their dissociation mechanism will provide inquisitive information regarding the potential of the proteins as drug carriers. For the first time, the binding interactions and affinities are investigated using molecular docking, conventional molecular dynamics, steered molecular dynamics, and umbrella sampling to explore the ability of both proteins to act as nitric oxide drug carriers. The molecular dynamics simulation results showed higher stability of lysozyme-drug complexes compared to HSA. For lysozyme, cardiovascular drugs were bound in the protein cavity mainly by the electrostatic and hydrogen bond interactions with residues ASP53, GLN58, ILE59, ARG62, TRP64, ASP102, and TRP109. For HSA, key binding residues were ARG410, TYR411, LYS414, ARG485, GLU450, ARG486, and SER489. The free energy profiles produced from umbrella sampling also suggest that lysozyme-drug complexes had better binding affinity than HSA-drug. Binding characteristics of nitric oxide-containing drugs NG and SNG to lysozyme and HSA proteins were studied using fluorescence and UV-vis absorption spectroscopy. The relative change in the fluorescence intensity as a function of drug concentrations was analyzed using Stern-Volmer calculations. This was also confirmed by the change in the UV-vis spectra. Fluorescence quenching results of both proteins with the drugs, based on the binding constant values, demonstrated significantly weak binding affinity to NG and strong binding affinity to SNG. Both computational and experimental studies provided important data for understanding protein-drug interactions and will aid in developing potential drug carrier systems in cardiovascular diseases.
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Affiliation(s)
- Chahlaa N Nassab
- Department of Chemistry, College of Sciences, University of Sharjah, Sharjah 27272, UAE
| | - Mahreen Arooj
- Department of Chemistry, College of Sciences, University of Sharjah, Sharjah 27272, UAE
| | - Ihsan A Shehadi
- Department of Chemistry, College of Sciences, University of Sharjah, Sharjah 27272, UAE
| | - Javad B M Parambath
- Department of Chemistry, College of Sciences, University of Sharjah, Sharjah 27272, UAE
| | - Sofian M Kanan
- Department of Biology, Chemistry and Environmental Sciences, American University of Sharjah, Sharjah 26666, UAE
| | - Ahmed A Mohamed
- Department of Chemistry, College of Sciences, University of Sharjah, Sharjah 27272, UAE
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11
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Singh N, Chandra R. Probing the binding interaction of ortho-vanillin derived chalcone with lysozyme: A biophysical studies aided by in silico calculations. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2020.114490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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12
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Swain BC, Subadini S, Rout J, Sakshi, Mishra PP, Sahoo H, Tripathy U. Biophysical study on complex formation between β-Lactoglobulin and vitamin B12. Food Chem 2020; 312:126064. [DOI: 10.1016/j.foodchem.2019.126064] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 12/03/2019] [Accepted: 12/14/2019] [Indexed: 01/27/2023]
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13
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Ali MS, Al-Lohedan HA. Spectroscopic and Molecular Docking Investigation on the Noncovalent Interaction of Lysozyme with Saffron Constituent "Safranal". ACS OMEGA 2020; 5:9131-9141. [PMID: 32363265 PMCID: PMC7191604 DOI: 10.1021/acsomega.9b04291] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Accepted: 03/26/2020] [Indexed: 05/05/2023]
Abstract
Owing to the various beneficial properties of the popular spice saffron, the interaction of safranal, a secondary metabolite of the former, with hen egg white lysozyme was investigated. The formation of a complex was evidenced by UV-visible spectroscopy. Fluorescence quenching experiments were also performed to understand the binding mechanism and to evaluate the forces involved in binding. The strong absorption of safranal in the range of excitation and emission wavelengths of lysozyme fluorescence required the correction of the inner filter effect for fluorescence spectra to obtain the apparent extent of binding. There was a considerable difference between the observed spectra and corrected spectra, and a similar observation was found in the case of synchronous fluorescence spectra. From the analysis of quenching data, it was found that the mechanism involved in quenching was static with 1:1 binding between them. The interaction was found to be driven, mainly, by hydrophobic forces and hydrogen bonding. Safranal had negligible impact on the secondary structure of lysozyme. The interaction was also studied by molecular docking, and the results were in good agreement with the results obtained experimentally. The binding site of safranal was in the big hydrophobic cavity of lysozyme. The amino acids involved in the interaction were Asp52, Ile58, Gln57, Asn59, Trp62, Trp63, Trp108, Ile98, Asp101, and Ala107.
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14
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Bonarek P, Loch JI, Tworzydło M, Cooper DR, Milto K, Wróbel P, Kurpiewska K, Lewiński K. Structure-based design approach to rational site-directed mutagenesis of β-lactoglobulin. J Struct Biol 2020; 210:107493. [PMID: 32169624 DOI: 10.1016/j.jsb.2020.107493] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 03/06/2020] [Accepted: 03/09/2020] [Indexed: 12/30/2022]
Abstract
Recombinant proteins play an important role in medicine and have diverse applications in industrial biotechnology. Lactoglobulin has shown great potential for use in targeted drug delivery and body fluid detoxification because of its ability to bind a variety of molecules. In order to modify the biophysical properties of β-lactoglobulin, a series of single-site mutations were designed using a structure-based approach. A 3-dimensional structure alignment of homologous molecules led to the design of nine β-lactoglobulin variants with mutations introduced in the binding pocket region. Seven stable and correctly folded variants (L39Y, I56F, L58F, V92F, V92Y, F105L, M107L) were thoroughly characterized by fluorescence, circular dichroism, isothermal titration calorimetry, size-exclusion chromatography, and X-ray structural investigations. The effects of the amino acid substitutions were observed as slight rearrangements of the binding pocket geometry, but they also significantly influenced the global properties of the protein. Most of the mutations increased the thermal/chemical stability without altering the dimerization constant or pH-dependent conformational behavior. The crystal structures reveal that the I56F and F105L mutations reduced the depth of the binding pocket, which is advantageous since it can reduce the affinity to endogenous fatty acids. The F105L mutant created a unique binding mode for a fatty acid, supporting the idea that lactoglobulin can be altered to bind unique molecules. Selected variants possessing a unique combination of their individual properties can be used for further, more advanced mutagenesis, and the presented results support further research using β-lactoglobulin as a therapeutic delivery agent or a blood detoxifying molecule.
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Affiliation(s)
- Piotr Bonarek
- Jagiellonian University, Faculty of Biochemistry, Biophysics and Biotechnology, Gronostajowa 7, 30-387 Kraków, Poland
| | - Joanna I Loch
- Jagiellonian University, Faculty of Chemistry, Gronostajowa 2, 30-387 Kraków, Poland
| | - Magdalena Tworzydło
- Jagiellonian University, Faculty of Biochemistry, Biophysics and Biotechnology, Gronostajowa 7, 30-387 Kraków, Poland
| | - David R Cooper
- University of Virginia, Department of Molecular Physiology and Biological Physics, 1340 Jefferson Park Avenue, Charlottesville, VA 22908, USA
| | - Katažyna Milto
- Jagiellonian University, Faculty of Biochemistry, Biophysics and Biotechnology, Gronostajowa 7, 30-387 Kraków, Poland
| | - Paulina Wróbel
- Jagiellonian University, Faculty of Chemistry, Gronostajowa 2, 30-387 Kraków, Poland
| | - Katarzyna Kurpiewska
- Jagiellonian University, Faculty of Chemistry, Gronostajowa 2, 30-387 Kraków, Poland
| | - Krzysztof Lewiński
- Jagiellonian University, Faculty of Chemistry, Gronostajowa 2, 30-387 Kraków, Poland.
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15
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A spectroscopic and computational intervention of interaction of lysozyme with 6-mercaptopurine. Anal Bioanal Chem 2020; 412:2565-2577. [DOI: 10.1007/s00216-020-02483-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 01/09/2020] [Accepted: 02/03/2020] [Indexed: 12/26/2022]
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16
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Patel BK, Sepay N, Mahapatra A. Structural alteration of myoglobin with two homologous cationic surfactants and effect of β-cyclodextrin: multifaceted insight and molecular docking study. NEW J CHEM 2020. [DOI: 10.1039/d0nj01113d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Structural alteration and regeneration of myoglobin.
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Affiliation(s)
| | - Nayim Sepay
- Department of Chemistry
- Jadavpur University
- Kolkata 700 032
- India
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17
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Sood D, Kumar N, Singh A, Tomar V, Dass SK, Chandra R. Deciphering the Binding Mechanism of Noscapine with Lysozyme: Biophysical and Chemoinformatic Approaches. ACS OMEGA 2019; 4:16233-16241. [PMID: 31592173 PMCID: PMC6777127 DOI: 10.1021/acsomega.9b02578] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Accepted: 09/04/2019] [Indexed: 05/26/2023]
Abstract
Lysozyme is a well-characterized protein in terms of its structure, dynamics, and functions. It has thus emerged as a potential target to understand protein-drug interactions. The aim of our study is to gain a biophysical outlook on the interaction of lysozyme (Lyz), a well-known model protein, with Noscapine, a potent tubulin-binding anticancer drug. Noscapine (Nos) is effective against a wide range of cancer and shows low toxicity and few side effects. We report the underlying mechanism of complex formation between Nos and Lyz using spectroscopic and advanced computational avenues. The spectroscopic techniques, that is, absorption and steady-state and time-resolved fluorescence, proved that Lyz-Nos forms a complex, and the quenching mechanism was of the static type. The binding constant was in the order of 103 indicative of moderate binding, while the stoichiometry of the protein-drug complex was 1:1 at 298 K. The secondary structural analysis using CD and UV thermal denaturation further confirmed the conformational changes in the protein upon binding with Nos. Molecular dynamics simulation studies confirmed the stable binding with minimum deviations in RMSD. The above conclusions are significant to the development of the pharmacokinetics and pharmacodynamic properties of Nos, and its successful interaction with a versatile protein like Lyz will help in overcoming its previous limitations.
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Affiliation(s)
- Damini Sood
- Department of Chemistry, University of
Delhi, Delhi 110007, India
| | - Neeraj Kumar
- Department of Chemistry, University of
Delhi, Delhi 110007, India
| | - Anju Singh
- Department of Chemistry, University of
Delhi, Delhi 110007, India
| | - Vartika Tomar
- Department of Chemistry, University of
Delhi, Delhi 110007, India
| | - Sujata K. Dass
- BLK
Super Speciality Hospital, Pusa Road, New Delhi 110005, India
| | - Ramesh Chandra
- Department of Chemistry, University of
Delhi, Delhi 110007, India
- Dr
.B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi 110007, India
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Patel BK, Sepay N, Mahapatra A. Curious Results in the Prospective Binding Interactions of the Food Additive Tartrazine with β-Lactoglobulin. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:11579-11589. [PMID: 31385703 DOI: 10.1021/acs.langmuir.9b01242] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The detailed characterizations of the binding interactions between food additive tartrazine (TZ) and β-lactoglobulin (β-LG) have been investigated through spectroscopic techniques combined with a molecular modeling study. A series of analyses, such as hyperchromic change in the UV-visible spectra, temperature-dependent quenching constant, time-resolved fluorescence, and Rayleigh scattering measurements, show that quenching of β-LG proceeds by a static quenching mechanism. TZ specifically binds with β-LG in a stoichiometry ratio of 1:1, and the observed binding constants (104, K) are 7.64, 9.13, 9.72, and 10.79 at 293, 298, 303, and 308 K, respectively. However, the curious results of binding constants (K) with temperature, encountered in the static quenching, have been well explained on the basis of Le Chatelier's principle. Thermodynamic data and pH-dependent studies along with the surface hydrophobicity binding displacement assay reveal that the durable mode of binding is chiefly entropy-driven, revealing noteworthy interactions of such ionic molecules with the hydrophobic part of β-LG. The modulation of protein conformation has been investigated through steady-state absorption spectroscopy, synchronous emission spectroscopy, circular dichroism, and dynamic light scattering studies. TZ acts as a potential inhibitor in fibrillogenesis. Furthermore, the molecular docking study offers accurate insights about the binding of TZ with β-LG, in consistence with the experimental results. This study would be helpful in pharmaceutical, food, and industrial engineering chemistry research.
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Affiliation(s)
- Biman Kumar Patel
- Department of Chemistry , Jadavpur University , Kolkata 700 032 , India
| | - Nayim Sepay
- Department of Chemistry , Jadavpur University , Kolkata 700 032 , India
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19
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Maity A, Pal U, Chakraborty B, Sengupta C, Sau A, Chakraborty S, Basu S. Preferential photochemical interaction of Ru (III) doped carbon nano dots with bovine serum albumin over human serum albumin. Int J Biol Macromol 2019; 137:483-494. [DOI: 10.1016/j.ijbiomac.2019.06.126] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Revised: 06/16/2019] [Accepted: 06/17/2019] [Indexed: 12/11/2022]
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20
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Saha S, Chowdhury J. Binding Interaction of Juglone with Lysozyme: Spectroscopic Studies Aided by In Silico Calculations. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2019; 193:89-99. [DOI: 10.1016/j.jphotobiol.2019.02.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 02/05/2019] [Accepted: 02/20/2019] [Indexed: 12/15/2022]
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21
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Świątek S, Komorek P, Turner G, Jachimska B. β-Lactoglobulin as a potential carrier for bioactive molecules. Bioelectrochemistry 2018; 126:137-145. [PMID: 30590224 DOI: 10.1016/j.bioelechem.2018.12.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 12/17/2018] [Accepted: 12/18/2018] [Indexed: 12/18/2022]
Abstract
In this study, the interaction and binding behavior of anesthetic tetracaine (TET) with bovine β-lactoglobulin (LGB) isoform A and a mixture of isoforms A and B were investigated under varying environmental conditions (pH, ionic strength, concentration, LGB-TET complex molar ratio). A wide range of analytical techniques (dynamic light scattering (DLS), electrophoretic mobility, UV-Vis spectroscopy, circular dichroism (CD), quartz crystal microbalance (QCM-D) were used to analyze the physicochemical properties of the complexes in bulk solution and on the surface of gold. The experiments revealed that TET, which is amphiphilic, could bind with LGB not only in the β-barrel but also onto the surface. The zeta potential of the LGB becomes more positively charged upon interaction with TET due to electrostatic interaction of the amino group present in the TET structure. Changes in the zeta potential values are mostly visible above pH 6 for all tested systems. CD spectra show that interaction with the ligand does not change the secondary structure of the protein. The physicochemical properties of LGB-TET complex were examined in an adsorbed state on a gold surface using the QCM-D method. Additionally, molecular docking was used to evaluate the most likely binding site for TET with LGB.
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Affiliation(s)
- S Świątek
- Polish Academy of Sciences, Jerzy Haber Institute of Catalysis and Surface Chemistry, Niezapominajek 8, Cracow 30-239, Poland
| | - P Komorek
- Polish Academy of Sciences, Jerzy Haber Institute of Catalysis and Surface Chemistry, Niezapominajek 8, Cracow 30-239, Poland
| | - G Turner
- Department of Chemical and Process Engineering, University of Strathclyde, James Weir Building, 75 Montrose Street, Glasgow, UK
| | - B Jachimska
- Polish Academy of Sciences, Jerzy Haber Institute of Catalysis and Surface Chemistry, Niezapominajek 8, Cracow 30-239, Poland.
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