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Wu R, Xie Y, Zhao L, Fu C, He W, Guo D, Xu W, Yi Y, Wang H. Effect mechanism of capsaicin and dihydrocapsaicin in chili on the oxidative stability of myoglobin in duck meat. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2024. [PMID: 38568724 DOI: 10.1002/jsfa.13508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 01/24/2024] [Accepted: 03/25/2024] [Indexed: 04/17/2024]
Abstract
BACKGROUND Myoglobin (Mb) in duck meat is commonly over-oxidized when heated at high temperatures, which may worsen the color of the meat. Enhancing the oxidative stability of Mb is essential for improving the color of duck meat. Capsaicin and dihydrocapsaicin (CA-DI) in chili exhibit antioxidant properties. This study investigated the effects of CA-DI on the structure and oxidative damage of Mb by fluorescence spectroscopy, differential scanning calorimetry analysis and particle size in duck meat during heat treatment. RESULTS When the ratio of CA-DI to Mb was 10:1 g kg-1 and heat-treated for 36 min, oxymyoglobin significantly increased, and metmyoglobin significantly decreased compared with the control group (P < 0.05). In parallel, the carbonyl content of Mb in the CA-DI group decreased by 43.40 ± 0.10%, the sulfhydryl content increased by 188 ± 0.21%, and the free radical scavenging activity of Mb was significantly enhanced (P < 0.05). Moreover, the addition of CA-DI resulted in a significant decrease in the particle size of the Mb surface (P < 0.05). When the ratio of CA-DI to Mb was 10:1 g kg-1, CA-DI enhanced the thermal stability and significantly increased the thermal denaturation temperature of Mb. The molecular docking results indicated that hydrophobic interactions and hydrogen bonds were involved in the binding of CA-DI to Mb. CONCLUSION CA-DI could combine with Mb and improve the oxidation stability of Mb in duck meat. This suggested that CA-DI could be a potential natural antioxidant that improves the color of meat products. © 2024 Society of Chemical Industry.
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Affiliation(s)
- Ruifang Wu
- College of Food Science and Engineering, Wuhan Polytechnic University, Wuhan, China
- Key Laboratory for Deep Processing of Major Grain and Oil, Ministry of Education, Wuhan, China
- Hubei Key Laboratory for Processing and Transformation of Agricultural Products, Wuhan, China
| | - Yuqing Xie
- College of Food Science and Engineering, Wuhan Polytechnic University, Wuhan, China
- Key Laboratory for Deep Processing of Major Grain and Oil, Ministry of Education, Wuhan, China
- Hubei Key Laboratory for Processing and Transformation of Agricultural Products, Wuhan, China
| | - Lingling Zhao
- College of Food Science and Engineering, Wuhan Polytechnic University, Wuhan, China
- Key Laboratory for Deep Processing of Major Grain and Oil, Ministry of Education, Wuhan, China
- Hubei Key Laboratory for Processing and Transformation of Agricultural Products, Wuhan, China
| | - Caiqi Fu
- College of Food Science and Engineering, Wuhan Polytechnic University, Wuhan, China
- Key Laboratory for Deep Processing of Major Grain and Oil, Ministry of Education, Wuhan, China
- Hubei Key Laboratory for Processing and Transformation of Agricultural Products, Wuhan, China
| | - Wenjie He
- College of Food Science and Engineering, Wuhan Polytechnic University, Wuhan, China
- Key Laboratory for Deep Processing of Major Grain and Oil, Ministry of Education, Wuhan, China
- Hubei Key Laboratory for Processing and Transformation of Agricultural Products, Wuhan, China
| | - Danjun Guo
- College of Food Science and Engineering, Wuhan Polytechnic University, Wuhan, China
- Key Laboratory for Deep Processing of Major Grain and Oil, Ministry of Education, Wuhan, China
- Hubei Key Laboratory for Processing and Transformation of Agricultural Products, Wuhan, China
| | - Wei Xu
- College of Food Science and Engineering, Wuhan Polytechnic University, Wuhan, China
- Key Laboratory for Deep Processing of Major Grain and Oil, Ministry of Education, Wuhan, China
- Hubei Key Laboratory for Processing and Transformation of Agricultural Products, Wuhan, China
| | - Yang Yi
- College of Food Science and Engineering, Wuhan Polytechnic University, Wuhan, China
- Key Laboratory for Deep Processing of Major Grain and Oil, Ministry of Education, Wuhan, China
- Hubei Key Laboratory for Processing and Transformation of Agricultural Products, Wuhan, China
| | - Hongxun Wang
- College of Food Science and Engineering, Wuhan Polytechnic University, Wuhan, China
- Key Laboratory for Deep Processing of Major Grain and Oil, Ministry of Education, Wuhan, China
- Hubei Key Laboratory for Processing and Transformation of Agricultural Products, Wuhan, China
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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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Sonkar KS, Pachauri M, Kumar A, Choudhary H, Jagannadham MV. Conformational stability of peroxidase from the latex of Artocarpus lakoocha: influence of pH, chaotropes, and temperature. FRONTIERS IN PLANT SCIENCE 2024; 15:1341454. [PMID: 38476686 PMCID: PMC10929713 DOI: 10.3389/fpls.2024.1341454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 02/02/2024] [Indexed: 03/14/2024]
Abstract
The latex of the medicinal plant Artocarpus lakoocha (A. lakoocha), which has been shown to have potential anti-inflammatory and wound-healing capabilities, contains a novel heme-peroxidase. This protein was subjected to activity assays, fluorescence spectroscopy, and far-UV circular dichroism to investigate its structure, dynamics, and stability. The results demonstrated the presence of three folding states: the native state (N) at neutral pH, intermediate states including molten globule (MG) at pH 2 and acid-unfolded (UA) at pH 1.5 or lower, and acid-refolded (A) at pH 0.5, along with alkaline denatured (UB) at pH 8-12 and the third denatured state (D) at GuHCl concentrations exceeding 5 M. Absorbance studies indicated the presence of loosely associated form of heme in the pH range of 1-2. The protein showed stability and structural integrity across a wide pH range (3-10), temperature (70°C), and high concentrations of GuHCl (5 M) and urea (8 M). This study is the first to report multiple 'partially folded intermediate states' of A. lakoocha peroxidase, with varying amounts of secondary structure, stability, and compactness. These results demonstrate the high stability of A. lakoocha peroxidase and its potential for biotechnological and industrial applications, making it a valuable model system for further studies on its structure-function relationship.
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Affiliation(s)
- Kirti Shila Sonkar
- Molecular Biology Unit, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | | | - Amit Kumar
- Department of Biochemistry, University of Delhi, New Delhi, India
| | - Himanshi Choudhary
- Molecular Pathology Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
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4
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Sonpasare K, Lalchandani DS, Chenkual L, Sathala PK, Khatoon R, Porwal PK. Effect of glycation-induced concentration-dependent change in albumin structure and alteration in its binding capacity. J Biomol Struct Dyn 2024:1-10. [PMID: 38381667 DOI: 10.1080/07391102.2024.2316783] [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: 11/20/2023] [Accepted: 02/03/2024] [Indexed: 02/23/2024]
Abstract
Reducing sugars causes confirmatory alterations in albumin structure by the nonenzymatic glycation of the amino group of serum albumin. In this study, glucose and its hazardous metabolic products like glyoxal and methylglyoxal were incubated with bovine serum albumin (BSA). The confirmational changes in BSA molecule's structure by glycating substances was investigated using a variety of spectroscopic methods, including deconvolutionFourier Transform Infra-red (FT-IR) spectroscopy, fluorescence spectroscopy, UV spectroscopy and circular dichroism (CD) spectroscopy. Dynamic fluorescence quenching was observed in the case of glucose, while static quenching was observed in the case of methyl glyoxal and glyoxal. Similarly, employing deconvolution FT-IR spectroscopy and CD spectroscopy for determination of change in secondary structures in terms signature of α-helix, β-turn, β-sheet and random coil modifications. Destabilization or unfolding of the albumin structure, due to the disruption of the hydrogen bonding pattern that stabilizes the albumin manifold, causes a 25-50% reduction in α-helix and a 2-fold increase in β-sheet and turns in glycated BSA. The competitive displacement interaction studies with warfarin were performed using the ultrafiltration technique and quantitative determination of free drug in ultrafiltrate using LC-MS/MS. The binding of carbamazepine (CBZ) or its active metabolite to proteins was unaffected by the glycation of BSA with glucose and methyl glyoxal. Nevertheless, with glyoxal-modified BSA, it changed the binding of selected analytes significantly. Based on in vitro observations and results, it could be anticipated that the serum CBZ concentration variation may be worsened in uncontrolled diabetes circumstances, with an overall variance of 30-40% possible.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Kailas Sonpasare
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research-Guwahati (NIPER-G), Guwahati, Assam, India
| | - Dimple S Lalchandani
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research-Guwahati (NIPER-G), Guwahati, Assam, India
| | - Laltanpuii Chenkual
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research-Guwahati (NIPER-G), Guwahati, Assam, India
| | - Pavan Kumar Sathala
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research-Guwahati (NIPER-G), Guwahati, Assam, India
| | - Raheema Khatoon
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research-Guwahati (NIPER-G), Guwahati, Assam, India
| | - Pawan Kumar Porwal
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research-Guwahati (NIPER-G), Guwahati, Assam, India
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5
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Raju B, Narendra G, Verma H, Kumar M, Sapra B, Kaur G, Jain SK, Sandeep Chary P, Mehra NK, Silakari O. Scaffold hopping for designing of potent and selective CYP1B1 inhibitors to overcome docetaxel resistance: synthesis and evaluation. J Biomol Struct Dyn 2024:1-19. [PMID: 38356135 DOI: 10.1080/07391102.2024.2310770] [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: 05/19/2023] [Accepted: 01/20/2024] [Indexed: 02/16/2024]
Abstract
Cytochrome P450 1B1, a tumor-specific overexpressed enzyme, significantly impairs the pharmacokinetics of several commonly used anticancer drugs including docetaxel, paclitaxel and cisplatin, leading to the problem of resistance to these drugs. Currently, there is no CYP1B1 inhibition-based adjuvant therapy available to treat this resistance problem. Hence, in the current study, exhaustive in-silico studies including scaffold hopping followed by molecular docking, three-dimensional quantitative structure-activity relationships (3D-QSAR), molecular dynamics and free energy perturbation studies were carried out to identify potent and selective CYP1B1 inhibitors. Initially, scaffold hopping analysis was performed against a well-reported potent and selective CYP1B1 inhibitor (i.e. compound 3n). A total of 200 scaffolds were identified along with their shape and field similarity scores. The top three scaffolds were further selected on the basis of these scores and their synthesis feasibility to design some potent and selective CYP1B1 inhibitors using the aforementioned in-silico techniques. Designed molecules were further synthesized to evaluate their CYP1B1 inhibitory activity and docetaxel resistance reversal potential against CYP1B1 overexpressed drug resistance MCF-7 cell line. In-vitro results indicated that compounds 2a, 2c and 2d manifested IC50 values for CYP1B1 ranging from 0.075, 0.092 to 0.088 μM with at least 10-fold selectivity. At low micromolar concentrations, compounds 1e, 1f, 2a and 2d exhibited promising cytotoxic effects in the docetaxel-resistant CYP1B1 overexpressed MCF-7 cell line. In particular, compound 2a is most effective in reversing the resistance with IC50 of 29.0 ± 3.6 μM. All of these discoveries could pave the way for the development of adjuvant therapy capable of overcoming CYP1B1-mediated resistance.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Baddipadige Raju
- Molecular Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, Punjab, India
| | - Gera Narendra
- Molecular Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, Punjab, India
| | - Himanshu Verma
- Molecular Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, Punjab, India
| | - Manoj Kumar
- Molecular Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, Punjab, India
| | - Bharti Sapra
- Molecular Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, Punjab, India
| | - Gurleen Kaur
- Center for Basic and Translational Research in Health Sciences, Guru Nanak Dev University, Amritsar, Punjab, India
| | - Subheet Kumar Jain
- Center for Basic and Translational Research in Health Sciences, Guru Nanak Dev University, Amritsar, Punjab, India
| | - Padakanti Sandeep Chary
- Pharmaceutical Nanotechnology Research Laboratory, Department of Pharmaceutical, National Institute of Pharmaceutical Science and Drug Research, Hyderabad, Telangana, India
| | - Neelesh Kumar Mehra
- Pharmaceutical Nanotechnology Research Laboratory, Department of Pharmaceutical, National Institute of Pharmaceutical Science and Drug Research, Hyderabad, Telangana, India
| | - Om Silakari
- Molecular Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, Punjab, India
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6
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Lakshmanan M, Yadav SA, Meti M, Kaveri S, Subban R, Celestina SK, Subramanyam R. Molecular interaction studies of P3CL on bovine serum albumin through biophysical approach. J Biomol Struct Dyn 2024:1-9. [PMID: 38321944 DOI: 10.1080/07391102.2024.2313153] [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: 08/14/2023] [Accepted: 01/25/2024] [Indexed: 02/08/2024]
Abstract
In the fields of pharmacology and life sciences, it is essential to study how prescribed drugs interact with carrier proteins in human serum albumin. The current study has evaluated the binding properties of rhodanine derivative; (z)-2-(4-(5-((3-(3-chlorophenyl)-1-phenyl-1H-pyrazol-4-oxo-2-thioxothiazolidin-3-yl)benzamido)acetic acid (P3CL) on bovine serum albumin (BSA) by biophysical approach. BSA is a homology model of Human serum albumin. Due to the cost-effectiveness of Human Serum Albumin (HSA) we have studied the binding properties of rhodanine derivative (P3CL) on BSA. The BSA-P3CL interactions were investigated by fluorescence spectroscopy and revealed the presence of a static quenching mechanism. P3CL possesses good binding affinity on BSA with binding constant KP3CL = 5.36330 × 1013 M-1 binding free energy. We have calculated the binding free energy, the number of binding sites, and the binding constants. The establishment of hydrogen bonds and the active participation of amino acids in drug binding were confirmed by molecular docking studies. As conventional processes for the investigation of pharmacological drugs, therapeutic combinations, and coordinated drug intake, the offered strategies are simple to comprehend, accurate, and rapid to put into practice. Our findings will support an additional investigation into ligand's pharmacological activity.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Malasree Lakshmanan
- Department of Biotechnology, Karpagam Academy of Higher Education, Coimbatore, Tamil Nadu, India
| | | | - Manjunath Meti
- Department of Plant Science, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | - Sundaram Kaveri
- Department of Chemistry, Karpagam Academy of Higher Education, Coimbatore, Tamil Nadu, India
| | - Ravi Subban
- Department of Chemistry, Karpagam Academy of Higher Education, Coimbatore, Tamil Nadu, India
| | - Stephen Kumar Celestina
- Department of Chemistry, Karpagam Academy of Higher Education, Coimbatore, Tamil Nadu, India
| | - Rajagopal Subramanyam
- Department of Plant Science, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
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7
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Yuan D, Du J, Xin M, Bai G, Zhang C, Liu G. Influence of myoglobin on the antibacterial activity of carvacrol and the binding mechanism between the two compounds. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2024; 104:1063-1073. [PMID: 37743570 DOI: 10.1002/jsfa.13005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 06/30/2023] [Accepted: 09/25/2023] [Indexed: 09/26/2023]
Abstract
BACKGROUND Myoglobin (MB), a pigmentation protein, can adversely affect the antibacterial activity of carvacrol (CAR) and weaken its bacteriostasis effect. This study aimed to clarify the influence of MB on the antibacterial activity of CAR and ascertain the mechanism involved in the observed influence, especially the interaction between the two compounds. RESULTS Microbiological analysis indicated that the presence of MB significantly suppressed the antibacterial activity of CAR against Listeria monocytogenes. Ultraviolet-visible spectrometry and fluorescence spectroscopic analysis confirmed the interaction between CAR and MB. The stoichiometric number was determined as ~0.7 via double logarithmic Stern-Volmer equation analysis, while thermodynamic analysis showed that the conjugation of the two compounds occurred as an exothermal reaction (ΔH° = -32.3 ± 11.4 kJ mol-1 and ΔS° = -75 J mol-1 K-1 ). Circular dichroism, Fourier transform infrared spectroscopy and nuclear magnetic resonance spectroscopy showed hydrogen bonding in the carvacrol-myoglobin complex (CAR-MB). Molecular docking analysis confirmed that amino acid residues, including GLY80 and HIS82, were most likely to form hydrogen bonds with CAR, while hydrogen bonds represented the main driving force for CAR-MB formation. CONCLUSION CAR antibacterial activity was significantly inhibited by the presence of MB in the environment due to the notable reduction in the effective concentration of CAR caused by CAR-MB formation. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Dongdong Yuan
- Key Laboratory of Geriatric Nutrition and Health (Beijing Technology and Business University), Ministry of Education, School of Food and Health, Beijing Technology and Business University, Beijing, China
- Beijing Engineering and Technology Research Center of Food Additives, School of Food and Health, Beijing Technology and Business University, Beijing, China
| | - Jing Du
- Key Laboratory of Geriatric Nutrition and Health (Beijing Technology and Business University), Ministry of Education, School of Food and Health, Beijing Technology and Business University, Beijing, China
- Beijing Engineering and Technology Research Center of Food Additives, School of Food and Health, Beijing Technology and Business University, Beijing, China
| | - Mengna Xin
- Beijing Engineering and Technology Research Center of Food Additives, School of Food and Health, Beijing Technology and Business University, Beijing, China
- China Food Flavor and Nutrition Health Innovation Center, School of Food and Health, Beijing Technology and Business University, Beijing, China
| | - Guohui Bai
- Beijing Engineering and Technology Research Center of Food Additives, School of Food and Health, Beijing Technology and Business University, Beijing, China
- China Food Flavor and Nutrition Health Innovation Center, School of Food and Health, Beijing Technology and Business University, Beijing, China
| | - Chan Zhang
- Beijing Engineering and Technology Research Center of Food Additives, School of Food and Health, Beijing Technology and Business University, Beijing, China
- China Food Flavor and Nutrition Health Innovation Center, School of Food and Health, Beijing Technology and Business University, Beijing, China
| | - Guorong Liu
- Key Laboratory of Geriatric Nutrition and Health (Beijing Technology and Business University), Ministry of Education, School of Food and Health, Beijing Technology and Business University, Beijing, China
- Beijing Engineering and Technology Research Center of Food Additives, School of Food and Health, Beijing Technology and Business University, Beijing, China
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8
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Zhang Z, Li T, Zhang Y, Shao J, Ye C, Wang H, Zhu B, Zhang Y. Effect of polysaccharides on conformational changes and functional properties of protein-polyphenol binary complexes: A comparative study. Int J Biol Macromol 2023; 253:126890. [PMID: 37716302 DOI: 10.1016/j.ijbiomac.2023.126890] [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: 07/19/2023] [Revised: 09/05/2023] [Accepted: 09/11/2023] [Indexed: 09/18/2023]
Abstract
This study aimed to investigate the effect of different polysaccharides on the binding behavior and functional properties of soybean protein isolate (SPI)-quercetin (Que) complex. The binding behavior was assessed using multi-spectral technique with the Stern-Volmer equation, which confirmed the presence of static fluorescence quenching in Que and SPI. The addition of sodium alginate (SA) resulted in a reduction of the binding affinity between SPI and Que, while dextran (DX) exhibited some promoting effect. A slight blue shift was observed in amide I and amide II bands, indicating the presence of hydrophobic and electrostatic interactions. Circular dichroism spectra revealed the ordered structures transformed into a more disordered state when polysaccharides were added, leading to an increase in random coils (SA: 18.5 %, DX: 15.4 %). Docking and dynamic simulations demonstrated that SA displayed greater stability within the hydrophobic compartments of SPI than DX, increased rigidity and stability of the SPI structure in SPI-Que-SA complexes. Electrostatic forces played a significant role between SPI and SA, while van der Waals forces were the main driving forces in SPI-DX complexes. Overall, the introduction of SA led to a looser and stable structure of SPI-Que complexes, resulting in an improvement of their emulsifying, foaming, and antioxidant properties.
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Affiliation(s)
- Zifan Zhang
- College of Public Health and Health Sciences, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Taoran Li
- College of Public Health and Health Sciences, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Yubo Zhang
- College of Public Health and Health Sciences, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Juanjuan Shao
- Department of Science and Technology, Hebei Agricultural University, Hebei 061100, China
| | - Chengxiang Ye
- College of Public Health and Health Sciences, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Hongwu Wang
- College of Public Health and Health Sciences, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Beibei Zhu
- College of Chinese Medicine Pharmaceutical Engineering, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China..
| | - Yating Zhang
- College of Public Health and Health Sciences, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China.
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Paul M, Banerjee A, Maiti S, Mitra D, DasMohapatra PK, Thatoi H. Evaluation of substrate specificity and catalytic promiscuity of Bacillus albus cellulase: an insight into in silico proteomic study aiming at enhanced production of renewable energy. J Biomol Struct Dyn 2023:1-23. [PMID: 38126200 DOI: 10.1080/07391102.2023.2295971] [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: 05/09/2023] [Accepted: 12/11/2023] [Indexed: 12/23/2023]
Abstract
Cellulases are enzymes that aid in the hydrolysis of cellulosic fibers and have a wide range of industrial uses. In the present in silico study, sequence alignment between cellulases from different Bacillus species revealed that most of the residues are conserved in those aligned enzymes. Three dimensional structures of cellulase enzymes from 23 different Bacillus species have been predicted and based on the alignment between the modeled structures, those enzymes have been categorized into 7 different groups according to the homology in their conformational folds. There are two structural contents in Gr-I cellulase namely β1-α2 and β3-α5 loops which varies greatly according to their static position. Molecular docking study between the B. albus cellulase and its various cellulosic substrates including xylanoglucan oligosaccharides revealed that residues viz. Phe154, Tyr258, Tyr282, Tyr285, and Tyr376 of B. albus cellulase are significantly involved in formation stacking interaction during enzyme-substrate binding. Residue interaction network and binding energy analysis for the B. albus cellulase with different cellulosic substrates depicted the strong affinity of XylGlc3 substrate with the receptor enzyme. Molecular interaction and molecular dynamics simulation studies exhibited structural stability of enzyme-substrate complexes which are greatly influenced by the presence of catalytic promiscuity in their substrate binding sites. Screening of B. albus in carboxymethylcellulose (CMC) and xylan supplemented agar media revealed the capability of the bacterium in degrading both cellulose and xylan. Overall, the study demonstrated B. albus cellulase as an effective biocatalyst candidate with the potential role of catalytic promiscuity for possible applications in biofuel industries.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Manish Paul
- Department of Biotechnology, Maharaja Sriram Chandra Bhanja Deo University, Baripada, India
- Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Amrita Banerjee
- Oriental Institute of Science and Technology, Midnapore, India
| | - Smarajit Maiti
- Oriental Institute of Science and Technology, Midnapore, India
| | - Debanjan Mitra
- Department of Microbiology, Raiganj University, Raiganj, India
| | - Pradeep K DasMohapatra
- Department of Microbiology, Raiganj University, Raiganj, India
- PAKB Environment Conservation Centre, Raiganj University, Raiganj, India
| | - Hrudayanath Thatoi
- Department of Biotechnology, Maharaja Sriram Chandra Bhanja Deo University, Baripada, India
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10
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Bai G, Pan Y, Zhang Y, Li Y, Wang J, Wang Y, Teng W, Jin G, Geng F, Cao J. Research advances of molecular docking and molecular dynamic simulation in recognizing interaction between muscle proteins and exogenous additives. Food Chem 2023; 429:136836. [PMID: 37453331 DOI: 10.1016/j.foodchem.2023.136836] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 05/21/2023] [Accepted: 07/05/2023] [Indexed: 07/18/2023]
Abstract
During storage and processing, muscle proteins, e.g. myosin and myoglobin, will inevitably undergo degeneration, which is thus accompanied by quality deterioration of muscle foods. Some exogenous additives have been widely used to interact with muscle proteins to stabilize the quality of muscle foods. Molecular docking and molecular dynamics simulation (MDS) are regarded as promising tools for recognizing dynamic molecular information at atomic level. Molecular docking and MDS can explore chemical bonds, specific binding sites, spatial structure changes, and binding energy between additives and muscle proteins. Development and workflow of molecular docking and MDS are systematically summarized in this review. Roles of molecular simulations are, for the first time, comprehensively discussed in recognizing the interaction details between muscle proteins and exogenous additives aimed for stabilizing color, texture, flavor, and other properties of muscle foods. Finally, research directions of molecular docking and MDS for improving the qualities of muscle foods are discussed.
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Affiliation(s)
- Genpeng Bai
- Key Laboratory of Geriatric Nutrition and Health (Beijing Technology and Business University), Ministry of Education, 100048 Beijing, China; Beijing Engineering and Technology Research Center of Food Additives, School of Food and Health, Beijing Technology and Business University, 100048 Beijing, China
| | - Yiling Pan
- Key Laboratory of Geriatric Nutrition and Health (Beijing Technology and Business University), Ministry of Education, 100048 Beijing, China; Beijing Engineering and Technology Research Center of Food Additives, School of Food and Health, Beijing Technology and Business University, 100048 Beijing, China
| | - Yuemei Zhang
- Key Laboratory of Geriatric Nutrition and Health (Beijing Technology and Business University), Ministry of Education, 100048 Beijing, China; Beijing Engineering and Technology Research Center of Food Additives, School of Food and Health, Beijing Technology and Business University, 100048 Beijing, China.
| | - Yang Li
- Key Laboratory of Geriatric Nutrition and Health (Beijing Technology and Business University), Ministry of Education, 100048 Beijing, China; Beijing Engineering and Technology Research Center of Food Additives, School of Food and Health, Beijing Technology and Business University, 100048 Beijing, China
| | - Jinpeng Wang
- Key Laboratory of Geriatric Nutrition and Health (Beijing Technology and Business University), Ministry of Education, 100048 Beijing, China; Beijing Engineering and Technology Research Center of Food Additives, School of Food and Health, Beijing Technology and Business University, 100048 Beijing, China
| | - Ying Wang
- Key Laboratory of Geriatric Nutrition and Health (Beijing Technology and Business University), Ministry of Education, 100048 Beijing, China; Beijing Engineering and Technology Research Center of Food Additives, School of Food and Health, Beijing Technology and Business University, 100048 Beijing, China
| | - Wendi Teng
- Key Laboratory of Geriatric Nutrition and Health (Beijing Technology and Business University), Ministry of Education, 100048 Beijing, China; Beijing Engineering and Technology Research Center of Food Additives, School of Food and Health, Beijing Technology and Business University, 100048 Beijing, China
| | - Guofeng Jin
- Key Laboratory of Geriatric Nutrition and Health (Beijing Technology and Business University), Ministry of Education, 100048 Beijing, China; Beijing Engineering and Technology Research Center of Food Additives, School of Food and Health, Beijing Technology and Business University, 100048 Beijing, China
| | - Fang Geng
- Meat Processing Key Laboratory of Sichuan Province, School of Food and Biological Engineering, Chengdu University, 610106 Chengdu, China
| | - Jinxuan Cao
- Key Laboratory of Geriatric Nutrition and Health (Beijing Technology and Business University), Ministry of Education, 100048 Beijing, China; Beijing Engineering and Technology Research Center of Food Additives, School of Food and Health, Beijing Technology and Business University, 100048 Beijing, China.
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11
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Sharma S, Takkella D, Vishwakarma J, Gavvala K. Spectroscopy and dynamics of beta-lactoglobulin complexed with rifampicin. J Biomol Struct Dyn 2023:1-14. [PMID: 37904335 DOI: 10.1080/07391102.2023.2275191] [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: 05/10/2023] [Accepted: 10/20/2023] [Indexed: 11/01/2023]
Abstract
In this paper, we report the binding interaction of milk protein, beta-lactoglobulin (BLG), with an antibiotic against tuberculosis, rifampicin (RIF). BLG intrinsic fluorescence from tryptophan (Trp) amino acids was monitored to understand protein-drug interactions. Binding parameters and stoichiometry were estimated with the help of fluorescence spectral changes. Synchronous fluorescence spectroscopy was employed to exclusively monitor the Trp and Tyrosine (Tyr) environment in the presence of RIF. With the help of steady state fluorescence at different temperatures supported by time-resolved fluorescence, we confirmed that the protein forms a static complex with RIF. Thermodynamic parameters, ΔH and ΔS values, showed the involvement of hydrophobic forces between the RIF and BLG. Competitive displacement assay with ANS confirmed the BLG calyx as the binding site for RIF. Energy transfer mechanism from Trp to RIF was attributed to the fluorescence changes in protein upon complexation. The Förster resonance energy transfer (FRET) was used to find distance, energy transfer efficiency and rate of energy transfer between donor (BLG) and acceptor (RIF). Fourier-transform infrared (FTIR) spectroscopy was utilized for estimating changes in the secondary structure of BLG induced by RIF. Molecular docking was used to visualise the binding location of RIF on BLG. Molecular dynamics (MD) simulation studies showed a consistent binding interactions between BLG and RIF during the 100 ns simulation period and this well supported the increased beta sheet content in FTIR. Overall our results establish the potential of intrinsic fluorescence of BLG in combination with biophysical tools to rationalize drug-protein interactions.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sudhanshu Sharma
- Department of Chemistry, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, India
| | - Dineshbabu Takkella
- Department of Chemistry, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, India
| | - Jyoti Vishwakarma
- Department of Chemistry, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, India
| | - Krishna Gavvala
- Department of Chemistry, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, India
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12
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Sun N, Wang J, Shi H, Li X, Guo S, Wang Y, Hu S, Liu R, Gao C. Compound effect and mechanism of oxidative damage induced by nanoplastics and benzo [a] pyrene. JOURNAL OF HAZARDOUS MATERIALS 2023; 460:132513. [PMID: 37708649 DOI: 10.1016/j.jhazmat.2023.132513] [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: 06/29/2023] [Revised: 09/03/2023] [Accepted: 09/07/2023] [Indexed: 09/16/2023]
Abstract
Nanoplastics and polycyclic aromatic hydrocarbons (PAHs) are ubiquitous in soil environments. In order to objectively evaluate the toxic interaction between polystyrene nanoplastics (PS NPs) and benzo [a] pyrene (BaP), oxidative damage at the level of earthworm cells and biomacromolecules was investigated by experiments combined with molecular dynamics simulation. Studies on cells reveal that PS NPs and BaP had synergistic toxicity when it came to causing oxidative stress. Cellular reactive oxygen species (ROS) levels under combined pollutant exposure were 24% and 19% higher, respectively than when PS NPs and BaP were exposed alone (compared to the blank group). In addition, BaP and PS NPs inhibited the ability of CAT to decompose H2O2 by affecting the structure of the proximal amino acid Tyr 357 in the active center of CAT, which exacerbated oxidative stress to a certain extent. Therefore, the synergistic toxic effect of BaP and PS NPs is due to the mutual complement of the two to the induction of protein structural looseness, and the strengthening of the stability of the conjugate (CAT-BaP-PS) under the weak interaction. This work provides a new perspective and approach on how to talk about the toxicity of combined pollutants.
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Affiliation(s)
- Ning Sun
- School of Environmental Science and Engineering, Shandong University, China-America CRC for Environment & Health, Shandong Province, 72# Jimo Binhai Road, Qingdao, Shandong 266237, PR China
| | - Jinhu Wang
- College of Chemistry, Chemical Engineering and Material Science, Zaozhuang University, Zaozhuang, Shandong Province 277160, PR China
| | - Huijian Shi
- School of Environmental Science and Engineering, Shandong University, China-America CRC for Environment & Health, Shandong Province, 72# Jimo Binhai Road, Qingdao, Shandong 266237, PR China
| | - Xiangxiang Li
- School of Environmental Science and Engineering, Shandong University, China-America CRC for Environment & Health, Shandong Province, 72# Jimo Binhai Road, Qingdao, Shandong 266237, PR China
| | - Shuqi Guo
- School of Environmental Science and Engineering, Shandong University, China-America CRC for Environment & Health, Shandong Province, 72# Jimo Binhai Road, Qingdao, Shandong 266237, PR China
| | - Yaoyue Wang
- School of Environmental Science and Engineering, Shandong University, China-America CRC for Environment & Health, Shandong Province, 72# Jimo Binhai Road, Qingdao, Shandong 266237, PR China
| | - Shaoyang Hu
- School of Environmental Science and Engineering, Shandong University, China-America CRC for Environment & Health, Shandong Province, 72# Jimo Binhai Road, Qingdao, Shandong 266237, PR China
| | - Rutao Liu
- School of Environmental Science and Engineering, Shandong University, China-America CRC for Environment & Health, Shandong Province, 72# Jimo Binhai Road, Qingdao, Shandong 266237, PR China.
| | - Canzhu Gao
- School of Environmental Science and Engineering, Shandong University, China-America CRC for Environment & Health, Shandong Province, 72# Jimo Binhai Road, Qingdao, Shandong 266237, PR China.
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13
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Gao Y, Wang H, Li X, Niu X. Molecular mechanism of green tea polyphenol epicatechin gallate attenuating Staphylococcus aureus pathogenicity by targeting Ser/Thr phosphatase Stp1. Food Funct 2023; 14:4792-4806. [PMID: 37128867 DOI: 10.1039/d3fo00170a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
In this study, through virtual screening and in vitro bioactivity assays, we discovered that (-)-epicatechin gallate (ECG), a polyphenol compound extracted from green tea, demonstrated marked anti-Ser/Thr phosphatase (Stp1) activity towards Staphylococcus aureus (S. aureus) with an IC50 value of 8.35 μM. By targeting S. aureus Stp1, ECG prevented the up-regulation of virulence gene and the formation of antibody membrane and protected the mice from S. aureus infection. Through MD simulation, the allosteric inhibitory mechanism of ECG on Stp1 was determined. The Stp1-ECG complex model underwent a significant change in conformation; its flap subdomain changed from opening to closing, whereas Stp1 activity was lost when bound to ECG. In addition, the MD simulation results of Stp1 and several tea polyphenol compounds showed that gallate groups and fewer adjacent phenolic hydroxyl groups contributed to the binding of Stp1 and inhibitors. As an inhibitor targeting S. aureus Stp1, ECG reduced the pathogenicity of S. aureus without inhibiting S. aureus, which largely reduced the possibility of drug resistance. Our findings demonstrated a novel molecular mechanism of green tea as the usual drink against S. aureus infection and elucidated the future design of allosteric inhibitors targeting Stp1.
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Affiliation(s)
- Yawen Gao
- College of Food Science and Engineering, Jilin University, Changchun 130062, P.R. China.
| | - Hongsu Wang
- College of Food Science and Engineering, Jilin University, Changchun 130062, P.R. China.
| | - Xuening Li
- College of Food Science and Engineering, Jilin University, Changchun 130062, P.R. China.
| | - Xiaodi Niu
- College of Food Science and Engineering, Jilin University, Changchun 130062, P.R. China.
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14
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Eslami-Farsani R, Farhadian S, Shareghi B, Momeni L. molecular interaction of ethylene glycol to hurt Myoglobin: Insights from spectroscopic and molecular modeling studies. J Mol Liq 2023. [DOI: 10.1016/j.molliq.2023.121399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
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15
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Interaction of Thioflavin T (ThT) and 8-anilino-1-naphthalene sulfonic acid (ANS) with macromolecular crowding agents and their monomers: Biophysical analysis using in vitro and computational approaches. J Mol Liq 2023. [DOI: 10.1016/j.molliq.2023.121270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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16
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Hu X, Zeng Z, Zhang J, Wu D, Li H, Geng F. Molecular dynamics simulation of the interaction of food proteins with small molecules. Food Chem 2022; 405:134824. [DOI: 10.1016/j.foodchem.2022.134824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 10/21/2022] [Accepted: 10/30/2022] [Indexed: 11/06/2022]
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17
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Farajzadeh-Dehkordi N, Zahraei Z, Farhadian S, Gholamian-Dehkordi N. The interactions between Reactive Black 5 and human serum albumin: combined spectroscopic and molecular dynamics simulation approaches. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:70114-70124. [PMID: 35583763 DOI: 10.1007/s11356-022-20736-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 05/05/2022] [Indexed: 06/15/2023]
Abstract
Azo dyes are made in significant amounts annually and released into the environment after being employed in the industry. There are some reports about the toxic effects of these dyes on several organisms. Thus, the textile dye Reactive Black 5 (RB5) has been examined for its cytotoxic effects on the human serum albumin (HSA) structure. Molecular interaction between RB5 and HSA indicated the combination of docking methods, molecular dynamic simulation, and multi-spectroscopic approaches. HSA's intrinsic fluorescence was well quenched with enhancing RB5 level, confirming complex formation. Molecular dynamics (MD) simulation was done to study the cytotoxic effects of RB5 and HSA conformation. Molecular modeling revealed that the RB5-HSA complex was stabilized by hydrogen bonds and van der Waals interactions. The results of molecular docking revealed that the binding energy of RB5 to HSA was - 27.94 kJ/mol. The change in secondary structure causes the annihilation of hydrogen bonding networks and the reduction of biological activity. This research can indicate a suitable molecular modeling interaction of RB5 and HAS and broaden our knowledge for azo dye toxicity under natural conditions.
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Affiliation(s)
- Nazanin Farajzadeh-Dehkordi
- Department of Cell and Molecular Biology, Faculty of Chemistry, University of Kashan, Kashan, 8731751167, Iran
| | - Zohreh Zahraei
- Department of Cell and Molecular Biology, Faculty of Chemistry, University of Kashan, Kashan, 8731751167, Iran.
| | - Sadegh Farhadian
- Department of Biology, Faculty of Science, Shahrekord University, P. O. Box 115, Shahrekord, Iran
- Member of Chahar Mahal & Bakhtiari Science and Technology Park, SaNa Zist Pardaz Co, Shahrekord, Iran
| | - Neda Gholamian-Dehkordi
- Department of Molecular Medicine, School of Advanced Technologies, Shahrekord University of Medical Sciences, Shahrekord, Iran
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18
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Liu H, Li Q, Jiang S, Zhang M, Zhao D, Shan K, Li C. Exploring the underlying mechanisms on NaCl-induced reduction in digestibility of myoglobin. Food Chem 2022; 380:132183. [DOI: 10.1016/j.foodchem.2022.132183] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 01/11/2022] [Accepted: 01/14/2022] [Indexed: 11/30/2022]
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Eslami-Farsani R, Farhadian S, Shareghi B. Exploring the structural basis of conformational alterations of myoglobin in the presence of spermine through computational modeling, molecular dynamics simulations, and spectroscopy methods. J Biomol Struct Dyn 2022; 40:3581-3594. [PMID: 33308044 DOI: 10.1080/07391102.2020.1848633] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Spermine as polyamines can have interaction with the myoglobin (Mb). The intent of this pondering to evaluate the impact of spermine on Mb properties, for example, the structure and thermal stability. For this analysis, the following approaches are employed. Thermodynamics, molecular dynamics (MD), and docking and the use of other spectroscopic procedures. The results of fluorescence spectroscopy and docking showed that binding spermine to Mb was spontaneous. Spermine quenched the fluorescence of Mb through the static quenching process. The thermal stability of Mb was incremented when the concentration of spermine increased. The CD spectra showed Mb's secondary structure shift with a rise in β-sheet and a decrease in α-helicity Mb's in spermine presence. Molecular docking and MD simulation outcomes demonstrate that electrostatic forces show a critical function in stabilizing of this complex, which is in conforming to spectroscopic results.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Sadegh Farhadian
- Department of Biology, Shahrekord University, Shahrekord, Iran.,Central Laboratory, Shahrekord University, Shahrekord, Iran
| | - Behzad Shareghi
- Department of Biology, Shahrekord University, Shahrekord, Iran.,Central Laboratory, Shahrekord University, Shahrekord, Iran
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20
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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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21
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Mavani A, Ovung A, Luikham S, Suresh Kumar G, Das A, Ray D, Aswal VK, Bhattacharyya J. Biophysical and molecular modeling evidences for the binding of sulfa molecules with hemoglobin. J Biomol Struct Dyn 2022; 41:3779-3790. [PMID: 35380096 DOI: 10.1080/07391102.2022.2057358] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The molecular mechanism of the heme protein, hemoglobin (Hb) interaction with sulfa molecule, sulfadiazine (SDZ) has been investigated through spectroscopic, neutron scattering and molecular modeling techniques. Absorption and emission spectroscopic studies showed that SDZ molecules were bound to Hb protein, non-cooperatively. The binding affinityof SDZ-Hb complex at standard experimental condition was evaluated to be around (4.2 ± 0.07) ×104, M-1with 1:1 stoichiometry. Drug induced structural perturbation of the 3 D protein moiety was confirmed through circular dichroism (CD), synchronous fluorescence and small angle neutron scattering methods. From the temperature dependent spectrofluorometric studies, the negative standard molar Gibbs energy change suggested the spontaneity of the reaction. The negative enthalpy and positive entropy change(s) indicated towards the involvement of both electrostatic and hydrophobic forces during the association process. Salt dependent fluorescence study revealed major contributions from non-poly-electrolytic forces. Molecular modeling studies determined the probable binding sites, types of interaction involved and the conformational alteration of the compactness of the Hb structure upon interaction with SDZ molecule. Overall, the study provides detailed insights into the binding mechanism of SDZ antibiotics to Hb protein.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- A. Mavani
- Department of Chemistry, National Institute of Technology Nagaland, Dimapur, Nagaland, India
| | - Aben Ovung
- Department of Chemistry, National Institute of Technology Nagaland, Dimapur, Nagaland, India
| | - Soching Luikham
- Department of Chemistry, National Institute of Technology Nagaland, Dimapur, Nagaland, India
| | - Gopinatha Suresh Kumar
- Biophysical Chemistry Laboratory, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Abhi Das
- Biophysical Chemistry Laboratory, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Debes Ray
- Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Vinod K. Aswal
- Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Jhimli Bhattacharyya
- Department of Chemistry, National Institute of Technology Nagaland, Dimapur, Nagaland, India
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22
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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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