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Pineda-Alemán R, Cabarcas-Herrera C, Alviz-Amador A, Galindo-Murillo R, Pérez-Gonzalez H, Rodríguez-Cavallo E, Méndez-Cuadro D. Molecular dynamics of structural effects of reactive carbonyl species derivate of lipid peroxidation on bovine serum albumin. Biochim Biophys Acta Gen Subj 2024; 1868:130613. [PMID: 38593934 DOI: 10.1016/j.bbagen.2024.130613] [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: 07/03/2023] [Revised: 03/09/2024] [Accepted: 04/04/2024] [Indexed: 04/11/2024]
Abstract
BACKGROUND Serum albumin is the most abundant protein in the Mammalia blood plasma at where plays a decisive role in the transport wide variety of hydrophobic ligands. BSA undergoes oxidative modifications like the carbonylation by the reactive carbonyl species (RCSs) 4-hydroxy-2-nonenal (HNE), 4 hydroxy-2-hexenal (HHE), malondialdehyde (MDA) and 4-oxo-2-nonenal (ONE), among others. The structural and functional changes induced by protein carbonylation have been associated with the advancement of neurodegenerative, cardiovascular, metabolic and cancer diseases. METHODS To elucidate structural effects of protein carbonylation with RCSs on BSA, parameters for six new non-standard amino acids were designated and molecular dynamics simulations of its mono‑carbonylated-BSA systems were conducted in the AMBER force field. Trajectories were evaluated by RMSD, RMSF, PCA, RoG and SASA analysis. RESULTS An increase in the conformational instability for all proteins modified with local changes were observed, without significant changes on the BSA global three-dimensional folding. A more relaxed compaction level and major solvent accessible surface area for modified systems was found. Four regions of high molecular fluctuation were identified in all modified systems, being the subdomains IA and IIIB those with the most remarkable local conformational changes. Regarding essential modes of domain movements, it was evidenced that the most representatives were those related to IA subdomain, while IIIB subdomain presented discrete changes. CONCLUSIONS RCSs induces local structural changes on mono‑carbonylated BSA. Also, this study extends our knowledge on how carbonylation by RCSs induce structural effects on proteins.
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Affiliation(s)
- Rafael Pineda-Alemán
- Analytical Chemistry and Biomedicine Group, Medicine Faculty, University of Cartagena, Cartagena, Colombia
| | - Camila Cabarcas-Herrera
- Analytical Chemistry and Biomedicine Group, Exact and Natural Sciences Faculty, University of Cartagena, Cartagena, Colombia
| | - Antistio Alviz-Amador
- Analytical Chemistry and Biomedicine Group, Pharmaceutical Sciences Faculty, University of Cartagena, Cartagena, Colombia
| | | | - Humberto Pérez-Gonzalez
- Department of Mathematics, Exact and Natural Sciences Faculty, University of Cartagena, Cartagena, Colombia
| | - Erika Rodríguez-Cavallo
- Analytical Chemistry and Biomedicine Group, Pharmaceutical Sciences Faculty, University of Cartagena, Cartagena, Colombia
| | - Darío Méndez-Cuadro
- Analytical Chemistry and Biomedicine Group, Exact and Natural Sciences Faculty, University of Cartagena, Cartagena, Colombia.
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2
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Ghanta KP, Bandyopadhyay S. Counteraction Effects of Ammonium-Based Ionic Liquids on Urea-Induced Denaturation of α-Lactalbumin: A Comprehensive Molecular Simulation Study. J Phys Chem B 2023; 127:7251-7265. [PMID: 37574910 DOI: 10.1021/acs.jpcb.3c03223] [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: 08/15/2023]
Abstract
Ionic liquids (ILs) are known to stabilize protein conformations in aqueous medium. Importantly, ILs can also act as refolding additives in urea-driven denaturation of proteins. However, despite the importance of the problem, detailed microscopic understanding of the counteraction effects of ILs on urea-induced protein denaturation remains elusive. In this work, atomistic molecular dynamics (MD) simulations of the protein α-lactalbumin have been carried out in pure aqueous medium, in 8 M binary urea-water solution and in ternary urea-IL-water solutions containing ammonium-based ethyl ammonium acetate (EAA) as the IL at different concentrations (1-4 M). Attempts have been made to quantify detailed molecular-level understanding of the origin behind the counteraction effects of the IL on urea-induced partial unfolding of the protein. The calculations revealed significant conformational changes of the protein with multiple free energy minima due to its partial unfolding in binary urea-water solution. The counteraction effect of the IL was evident from the enhanced structural rigidity of the protein with propensity to transform into a single native free energy minimum state in ternary urea-IL-water solutions. Such an effect has been found to be associated with preferential direct binding of the IL components with the protein and simultaneous expulsion of urea from the interface, thereby providing additional stabilization of the protein in ternary solutions. Most importantly, modified rearrangement of the hydrogen bond network at the interface due to the formation of stronger protein-cation (PC) and protein-anion (PA) hydrogen bonds by breaking relatively weaker protein-urea (PU) and protein-water (PW) hydrogen bonds has been recognized as the microscopic origin behind the counteraction effects of EAA on urea-induced partial unfolding of the protein.
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Affiliation(s)
- Krishna Prasad Ghanta
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Sanjoy Bandyopadhyay
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
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3
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Tian Z, Ding T, Niu H, Wang T, Zhang Z, Gao J, Kong M, Ming L, Tian Z, Ma J, Luo W, Wang C. 2-Phenylquinoline-polyamine conjugate (QPC): Interaction with bovine serum albumin (BSA). SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 300:122875. [PMID: 37276638 DOI: 10.1016/j.saa.2023.122875] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 05/08/2023] [Accepted: 05/10/2023] [Indexed: 06/07/2023]
Abstract
A novel 2-phenylquinoline-polyamine conjugate (QPC) was synthesized and characterized, its interaction with bovine serum albumin (BSA) was evaluated using UV-Vis, fluorescence and circular dichroism (CD) spectroscopy. The results showed that QPC caused a whole train of spectral variation, including enhancement of UV-vis absorption and reduction of fluorescence (FL), indicating QPC-BSA complex formed. FL results showed that the type of FL quenching waslarge static quenching, which was also accompanied with a process of dynamic quenching. Binding constants, thermodynamic parameters and docking results showed that the interaction between QPC and BSA was basically a Van der Waals, hydrogen bond and hydrophobic interaction. Synchronous and 3D-FL analysis revealed that QPC resulted in unapparent conformational alteration of BSA. The docking study suggested QPC was situated at the binding sites II of BSA, and 2-phenylquinoline moiety contributed to the hydrophobic interaction. The results of molecular dynamics revealed QPC altered the conformation of BSA, which showed that the inconsistency between experimental data and theoretical calculation results may be due to the instability of the compound.
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Affiliation(s)
- Zhiyong Tian
- Institute for Innovative Drug Design and Evaluation, School of Pharmacy, Henan University, Kaifeng 475004, China
| | - Tengli Ding
- Institute for Innovative Drug Design and Evaluation, School of Pharmacy, Henan University, Kaifeng 475004, China
| | - Hanjing Niu
- Institute for Innovative Drug Design and Evaluation, School of Pharmacy, Henan University, Kaifeng 475004, China
| | - Ting Wang
- The Key Laboratory of Natural Medicine and Immuno-Engineering, Henan University, Kaifeng 475004, China
| | - Zhongze Zhang
- Institute for Innovative Drug Design and Evaluation, School of Pharmacy, Henan University, Kaifeng 475004, China
| | - Jinhua Gao
- Institute for Innovative Drug Design and Evaluation, School of Pharmacy, Henan University, Kaifeng 475004, China
| | - Ming Kong
- Institute for Innovative Drug Design and Evaluation, School of Pharmacy, Henan University, Kaifeng 475004, China
| | - Li Ming
- Institute for Innovative Drug Design and Evaluation, School of Pharmacy, Henan University, Kaifeng 475004, China
| | - Zhihui Tian
- The National Supercomputing Center in Zhengzhou, Zhengzhou University, Henan 450001, China
| | - Jing Ma
- Institute for Innovative Drug Design and Evaluation, School of Pharmacy, Henan University, Kaifeng 475004, China.
| | - Wen Luo
- The Key Laboratory of Natural Medicine and Immuno-Engineering, Henan University, Kaifeng 475004, China.
| | - Chaojie Wang
- The Key Laboratory of Natural Medicine and Immuno-Engineering, Henan University, Kaifeng 475004, China.
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4
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Millan S, Susrisweta B, Sahoo H. Probing the interaction between niobium pentoxide nanoparticles and serum albumin proteins by Spectroscopic approaches. J Biomol Struct Dyn 2023; 41:15435-15445. [PMID: 36931873 DOI: 10.1080/07391102.2023.2188944] [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: 07/05/2022] [Accepted: 03/01/2023] [Indexed: 03/19/2023]
Abstract
Nanoparticles (NPs) can directly or indirectly enter into the body because of their small size; then they tend to alter the conformation and function of proteins upon interaction with them. Thus, it is crucial to understand the impact of NPs in a biological medium. Recently, niobium pentoxide nanoparticles (Nb2O5 NPs) are finding increasing applications in the biological system, for example, bone tissue and dental material, matrix for biosensing of proteins, etc. In all such applications, the Nb2O5 NP interacts with proteins and other biomolecules. Hence, the study of such interactions is of considerable importance. Here in this work, we present the impact of Nb2O5 NP on the structure, stability and activity of blood proteins, bovine serum albumin (BSA) and human serum albumin (HSA) by means of various spectroscopic approaches. Steady-state fluorescence studies indicated that intrinsic fluorescence intensities of both serum albumin proteins got quenched upon their interaction with NP. The nature of the quenching was elucidated by time-resolved fluorescence and absorption measurements. Using circular dichroism (CD) and synchronous fluorescence spectroscopy (SFS), the structural perturbations of the protein molecules after interaction with NP were investigated. Moreover, the role of temperature on protein stability upon complexation with NP was also explored. In addition, the effect of NP on protein functionality was probed by esterase-like activity assays.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sabera Millan
- Department of Chemistry, National Institute of Technology (NIT) Rourkela, Sundergarh, Odisha, India
| | - Behera Susrisweta
- Department of Chemistry, National Institute of Technology (NIT) Rourkela, Sundergarh, Odisha, India
| | - Harekrushna Sahoo
- Department of Chemistry, National Institute of Technology (NIT) Rourkela, Sundergarh, Odisha, India
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5
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Wang J, Yang B, Yu X, Chen S, Li W, Hong X. The impact of Zn doping on CdTe quantum dots-protein corona formation and the subsequent toxicity at the molecular and cellular level. Chem Biol Interact 2023; 373:110370. [PMID: 36731594 DOI: 10.1016/j.cbi.2023.110370] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 11/21/2022] [Accepted: 01/26/2023] [Indexed: 01/31/2023]
Abstract
Understanding the formation of protein corona (PC) is of vital importance for exploring the toxicity of nanoparticles and promoting their safe applications. In this study, CdTe QDs doping with 0, 1%, 5% and 10% Zn were synthesized using one-pot hydrothermal methods. Afterwards, this study explored and compared the formation of pure and Zn doped-QDs PC as well as the subsequent molecular and cellular toxicity. Result found that Zn doping regulated the toxicity of Cd-QDs by controlling their ability to adsorb serum proteins. The adsorption to Cd-QDs induced the dispersion, unfolding, secondary structural changes and the activity loss of bovine serum albumin (BSA). Among the synthesized Cd-QDs, 10%Zn-QDs exhibited the highest fluorescence quantum yield and lowest molecular toxicity. The formations of pure QDs and 10%Zn-QDs with BSA corona are majorly driven by different forces with different patterns. The regulation of BSA on the cytotoxicity differences of pure QDs and 10%Zn-QDs was similar with fetal bovine serum, proving the significant contribution of BSA to the cytotoxicity of Cd-QDs PC. Compared with pure QDs PC, the higher cytotoxicity and oxidative stress level of 10%Zn-QDs PC were correlated with higher intracellular [Cd2+]. Both larger amount of BSA adsorption and higher level of intracellular reactive oxygen species could accelerate the dissolution rates of 10%Zn-QDs and thus result in higher intracellular [Cd2+].
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Affiliation(s)
- Jing Wang
- School of Environmental and Material Engineering, Yantai University, 30# Qingquan Road, Yantai, 264005, PR China.
| | - Bin Yang
- School of Environmental and Material Engineering, Yantai University, 30# Qingquan Road, Yantai, 264005, PR China
| | - Xinping Yu
- School of Environmental and Material Engineering, Yantai University, 30# Qingquan Road, Yantai, 264005, PR China
| | - Shuji Chen
- School of Environmental and Material Engineering, Yantai University, 30# Qingquan Road, Yantai, 264005, PR China
| | - Wenxin Li
- School of Environmental and Material Engineering, Yantai University, 30# Qingquan Road, Yantai, 264005, PR China
| | - Xu Hong
- School of Environmental and Material Engineering, Yantai University, 30# Qingquan Road, Yantai, 264005, PR China
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Li W, Chen S, Hong X, Fang M, Zong W, Li X, Wang J. The molecular interaction of three haloacetic acids with bovine serum albumin and the underlying mechanisms. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
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7
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Gogoi NG, Rahman A, Saikia J, Dutta P, Baruah A, Handique JG. Enhanced biological activity of Curcumin Cinnamates: an experimental and computational analysis. Med Chem Res 2022. [DOI: 10.1007/s00044-022-02977-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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8
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Singh D, Kaur L, Rahman AJ, Singh P, Kumar Tiwari A, Ojha H. Binding and mechanistic studies of 5-HT7 specific benzothiazolone derivatives with Bovine Serum Albumin: Spectroscopic and In silico studies. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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9
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An Overview on the Recent Advances in Alternative Solvents as Stabilizers of Proteins and Enzymes. CHEMENGINEERING 2022. [DOI: 10.3390/chemengineering6040051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Currently, the use of alternative solvents is increasing, namely ionic liquids (ILs) and deep eutectic solvents (DESs) in diverse fields of knowledge, such as biochemistry, chemistry, chemical engineering, biotechnology and biomedicine. Particularly, when compared to traditional solvents, these alternative solvents have great importance for biomolecules due to the enhanced solubility, structure stability and the biological activity of biomolecules, such as protein and enzymes. Thus, in this review article, the recent developments and efforts on the technological developments carried out with ILs and DESs for the stabilization and activation of proteins and enzymes are provided. The most studied IL- and DES-based formulations for proteins and enzymes are discussed and the molecular mechanisms and interactions related to the increased stability promoted by these alternative solvents are disclosed, while emphasizing their main advantages.
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10
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Halder S, Aggrawal R, Saha SK. Concentration-dependent β-cyclodextrin-promoted refolding of gold nanoparticles-conjugated bovine serum albumin complexed with gemini surfactants with different spacer groups. Colloids Surf A Physicochem Eng Asp 2022. [DOI: 10.1016/j.colsurfa.2022.128862] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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11
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Belal F, Mabrouk M, Hammad S, Barseem A, Ahmed H. Multi-Spectroscopic, thermodynamic and molecular docking studies to investigate the interaction of eplerenone with human serum albumin. LUMINESCENCE 2022; 37:1162-1173. [PMID: 35489089 DOI: 10.1002/bio.4270] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Revised: 04/20/2022] [Accepted: 04/26/2022] [Indexed: 11/07/2022]
Abstract
The binding of small molecular drugs with human serum albumin (HSA) has a crucial influence on their pharmacokinetics. The binding interaction between the antihypertensive Eplerenone (EPL)and HSA was investigated using multi-spectroscopic techniques for the first time. These techniques include UV-Vis spectroscopy, Fourier Transform Infrared (FT-IR), native fluorescence spectroscopy, synchronous fluorescence spectroscopy and molecular docking approach. The fluorescence spectroscopic study showed that EPL quenched HSA inherent fluorescence. The mechanism for quenching of HSA by EPL has been determined to be static in nature and confirmed by UV absorption and fluorescence spectroscopy. The modified Stern-Volmer equation was used to estimate the binding constant (Kb ) as well as the number of bindings (n). The results indicated that the binding occurs at a single site (Kb;2.238 x 103 L mol-1 at 298 K). The enthalpy and entropy changes (∆H and ∆S) were 58.061 and 0.258 K J mol-1 , respectively, illustrating that the principal intermolecular interactions stabilizing the EPL-HSA system are hydrophobic forces. Synchronous fluorescence spectroscopy revealed that EPL binding to HSA occurred around the tyrosine residue (Tyr) and this agreed with the molecular docking study. The FRET analysis confirmed the static quenching mechanism. The esterase enzyme activity of HSA was also evaluated showing its decrease in the presence of EPL. Furthermore, docking analysis and site-specific markers experiment revealed that EPL binds with HSA at subdomain IB (site III).
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Affiliation(s)
- Fathalla Belal
- Department of Pharmaceutical Analytical Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Mokhtar Mabrouk
- Department of pharmaceutical analytical Chemistry, Faculty of Pharmacy, Tanta University, Tanta, Egypt
| | - Sherin Hammad
- Department of pharmaceutical analytical Chemistry, Faculty of Pharmacy, Tanta University, Tanta, Egypt
| | - Aya Barseem
- Pharmaceutical Analysis Department, Faculty of Pharmacy, Menoufia University, Egypt
| | - Hytham Ahmed
- Pharmaceutical Analysis Department, Faculty of Pharmacy, Menoufia University, Egypt
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12
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Khedri M, Moraveji MK. Microfluidic Engineering of RGD
[1]
‐Terminated Nanocarriers Micellization and In‐Situ Docetaxel Encapsulation: An Atomistic Insight. ChemistrySelect 2022. [DOI: 10.1002/slct.202103597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Mohammad Khedri
- Department of Chemical Engineering Amirkabir University of Technology (Tehran Polytechnic) c No. 350, Hafez Ave, Valiasr Square 15916-34311 Tehran Iran
| | - Mostafa keshavarz Moraveji
- Department of Chemical Engineering Amirkabir University of Technology (Tehran Polytechnic) c No. 350, Hafez Ave, Valiasr Square 15916-34311 Tehran Iran
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14
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Kumari M, Kumari P, Kashyap HK. Structural adaptations in the bovine serum albumin protein in archetypal deep eutectic solvent reline and its aqueous mixtures. Phys Chem Chem Phys 2022; 24:5627-5637. [PMID: 35175257 DOI: 10.1039/d1cp05829k] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The global concern over the environmental impact and challenges associated with the use of conventional solvents in biotransformation processes have pushed the search for alternative solvents. Recently, deep eutectic solvents (DESs) have appeared as a promising replacement with better biocompatibility and have been postulated to hold great potential in protein engineering and crystallization processes. In this context, herein, we have investigated the effect of reline (a choline chloride : urea mixture in 1 : 2 proportion) DES in its pure and hydrated forms on the structural stability and conformation of the bovine serum albumin (BSA) protein using all-atom molecular dynamics simulations. We observe a substantial overall expansion of the BSA structure with a simultaneous increment in the solvent accessible surface area, signifying the influence of reline on the BSA tertiary structure. These induced structural perturbations are quite pronounced in reline-water mixtures. Concomitantly, a notable reline concentration-dependent disruption of the BSA secondary structure through the melting of α-helices, mainly driven by H-bonding interactions, is observed. In the presence of pure reline, significant rigidity in the protein backbone is also observed. Thus, despite the expansion, the BSA tertiary structure in pure reline is found to be most close to the native protein structure and remains in a partially folded state at all the studied reline concentrations. In pure reline, BSA-urea hydrogen bonding is more prevalent than BSA-[Ch]+. We also observe that in aqueous reline systems, the BSA-water hydrogen bonds are mostly compensated by BSA-urea hydrogen bonds. The aqueous re-equilibration of these partially denatured protein conformations showed a significant recovery of secondary and tertiary structures, where the recovery is most profound for the BSA conformation extracted from pure reline.
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Affiliation(s)
- Monika Kumari
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India.
| | - Pratibha Kumari
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India.
| | - Hemant K Kashyap
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India.
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15
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Qiao Y, Zhang Y, Qiao Z, He W, Chen Y, Song D, Wang G, Guo N, Shao L, Tian Z, Wang Q, Yan L, Qian H. Discovery of (S)–N-(3-isopropylphenyl)-2-(5-phenylthiazol-2-yl)pyrrolidine-1-carboxamide as potent and brain-penetrant TRPV1 antagonist. Eur J Med Chem 2022; 233:114191. [DOI: 10.1016/j.ejmech.2022.114191] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 01/20/2022] [Accepted: 02/06/2022] [Indexed: 11/30/2022]
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16
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Moradi S, Shareghi B, Saboury AA, Farhadian S. The influence of Cadaverine on the structure, stability, and activity of acid phosphatase. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.131372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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17
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Rahman AJ, Kaur L, Pathak M, Singh A, Verma P, Singhal R, Kumar V, Ojha H. Spectroscopic studies of binding interactions of 2-chloroethylphenyl sulphide with bovine serum albumin. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.117144] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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18
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Ghanta KP, Mondal S, Mondal S, Bandyopadhyay S. Contrasting Effects of Ionic Liquids of Varying Degree of Hydrophilicity on the Conformational and Interfacial Properties of a Globular Protein. J Phys Chem B 2021; 125:9441-9453. [PMID: 34433280 DOI: 10.1021/acs.jpcb.1c04167] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ionic liquids (ILs), depending on their cation-anion combinations, are known to influence the conformational properties and activities of proteins in a nonuniform manner. To obtain microscopic understanding of such influence, it is important to characterize protein-IL interactions and explore the modified solvation environment around the protein. In this work, molecular dynamics (MD) simulations of the globular protein α-lactalbumin have been carried out in aqueous IL solutions containing 1-butyl-3-methylimidazolium cations (BMIM+) in combination with a series of anions with varying degree of hydrophilicity, namely, hexafluorophosphate (PF6-), ethyl sulfate (ETS-), acetate (OAc-), chloride (Cl-), dicyanamide (DCA-), and nitrate (NO3-) . The calculations revealed that ILs with hydrophobic and hydrophilic anions have contrasting influence on conformational flexibility of the protein. It is further observed that the BMIM+ cations exhibit site-specific orientations at the interface depending on the hydrophilicity of the anion component. Most importantly, the results demonstrated enhanced propensity of hydrophilic ILs to replace relatively weaker protein-water hydrogen bonds by stronger protein-IL hydrogen bonds at the protein surface as compared to the hydrophobic ILs. Such breaking of protein-water hydrogen bonds at a greater extent leads to greater loss of water hydrating the protein in the presence of hydrophilic ILs, thereby reducing the protein's stability.
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Affiliation(s)
- Krishna Prasad Ghanta
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India
| | - Souvik Mondal
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India
| | - Sandip Mondal
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India
| | - Sanjoy Bandyopadhyay
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India
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Subadini S, Bera K, Hritz J, Sahoo H. Polyethylene glycol perturbs the unfolding of CRABP I: A correlation between experimental and theoretical approach. Colloids Surf B Biointerfaces 2021; 202:111696. [PMID: 33770701 DOI: 10.1016/j.colsurfb.2021.111696] [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: 01/19/2021] [Revised: 02/25/2021] [Accepted: 03/11/2021] [Indexed: 10/21/2022]
Abstract
The importance of macromolecules paves the way towards a detailed molecular level investigation as all most all cellular processes occurring at the interior of cells in the form of proteins, enzymes, and other biological molecules are significantly affected because of their crowding. Thus, exploring the role of crowding environment on the denaturation and renaturation kinetics of protein molecules is of great importance. Here, CRABP I (cellular retinoic acid binding protein I) is employed as a model protein along with different molecular weights of Polyethylene glycol (PEG) as molecular crowders. The experimental evaluations are done by accessing the protein secondary structure analysis using circular dichroism (CD) spectroscopy and unfolding kinetics using intrinsic fluorescence of CRABP I at 37 °C to mimic the in vivo crowding environment. The unfolding kinetics results indicated that both PEG 2000 and PEG 4000 act as stabilizers by retarding the unfolding kinetic rates. Both kinetic and stability outcomes presented the importance of crowding environment on stability and kinetics of CRABP I. The molecular dynamics (MD) studies revealed that thirteen PEG 2000 molecules assembled during the 500 ns simulation, which increases the stability and percentage of β-sheet. The experimental findings are well supported by the molecular dynamics simulation results.
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Affiliation(s)
- Suchismita Subadini
- Biophysical and Protein Chemistry Lab, Department of Chemistry, NIT Rourkela, Rourkela, 769008, India
| | - Krishnendu Bera
- CEITEC MU, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - Jozef Hritz
- CEITEC MU, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic; Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - Harekrushna Sahoo
- Biophysical and Protein Chemistry Lab, Department of Chemistry, NIT Rourkela, Rourkela, 769008, India; Center of Nanomaterials, NIT Rourkela, Rourkela, 769008, India.
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Patel AY, Jonnalagadda KS, Paradis N, Vaden TD, Wu C, Caputo GA. Effects of Ionic Liquids on Metalloproteins. Molecules 2021; 26:514. [PMID: 33478102 PMCID: PMC7835893 DOI: 10.3390/molecules26020514] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 01/04/2021] [Accepted: 01/08/2021] [Indexed: 01/28/2023] Open
Abstract
In the past decade, innovative protein therapies and bio-similar industries have grown rapidly. Additionally, ionic liquids (ILs) have been an area of great interest and rapid development in industrial processes over a similar timeline. Therefore, there is a pressing need to understand the structure and function of proteins in novel environments with ILs. Understanding the short-term and long-term stability of protein molecules in IL formulations will be key to using ILs for protein technologies. Similarly, ILs have been investigated as part of therapeutic delivery systems and implicated in numerous studies in which ILs impact the activity and/or stability of protein molecules. Notably, many of the proteins used in industrial applications are involved in redox chemistry, and thus often contain metal ions or metal-associated cofactors. In this review article, we focus on the current understanding of protein structure-function relationship in the presence of ILs, specifically focusing on the effect of ILs on metal containing proteins.
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Affiliation(s)
- Aashka Y. Patel
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, NJ 08028, USA; (A.Y.P.); (N.P.); (T.D.V.); (C.W.)
| | | | - Nicholas Paradis
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, NJ 08028, USA; (A.Y.P.); (N.P.); (T.D.V.); (C.W.)
| | - Timothy D. Vaden
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, NJ 08028, USA; (A.Y.P.); (N.P.); (T.D.V.); (C.W.)
| | - Chun Wu
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, NJ 08028, USA; (A.Y.P.); (N.P.); (T.D.V.); (C.W.)
- Department of Molecular and Cellular Biosciences, Rowan University, Glassboro, NJ 08028, USA
| | - Gregory A. Caputo
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, NJ 08028, USA; (A.Y.P.); (N.P.); (T.D.V.); (C.W.)
- Department of Molecular and Cellular Biosciences, Rowan University, Glassboro, NJ 08028, USA
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21
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Mishra NP, Satish L, Mohapatra S, Nayak S, Sahoo H. A spectroscopic insight into the interaction of chromene 1,2,4-oxadiazole-based compounds with bovine serum albumin. RESEARCH ON CHEMICAL INTERMEDIATES 2020. [DOI: 10.1007/s11164-020-04323-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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22
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Tian Z, Tian L, Zhao S, Shi M, Guo S, Wang C, Tian Z, He X. Study on the interaction of polyamine transport (PAT) and 4-Chloro-naphthalimide-homospermidine conjugate (4-ClNAHSPD) by molecular docking and dynamics. J Biomol Struct Dyn 2020; 40:290-296. [PMID: 32856528 DOI: 10.1080/07391102.2020.1813199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Polyamine transporter (PAT) is a protein that can deliver "drug-polyamine" conjugates to tumor cells. 4-Chloro-naphthalimide- homospermidine (4-ClNAHSPD) displayed good antitumor activity and excellent cell selectivity via PAT pathway. In this paper, 4-ClNAHSPD and spermidine (SPD) were docked against PAT. The results showed that 4-ClNAHSPD could bind to PAT through hydrogen bond, Van der Waals, salt bridge or attractive charge and hydrophobic interaction. The interaction of SPD and PAT, however, was hydrogen bond and Van der Waals interaction. Moreover, their binding sites were also different. The primary binding sites of 4-ClNAHSPD with PAT are the residues of VAL59, HIS222, ASP61, ASP179 and GLU64, while SPD interacts with PAT in the sites of ASP37, ASP244, APS275 and SER36. The docked ligand-protein complexes were simulated for 5000ps. In simulations, various binding sites further resulted in the diverse root-mean-square deviation (RMSD) and root-mean-square deviation fluctuation (RMSF) values. The RMSD and RMSF values of 4-ClNAHSPD-PAT indicated that 4-ClNAHSPD caused a weak conformational change of PAT in a different style from SPD. More importantly, the interaction force numbers of 4-ClNAHSPD-PAT were also changed after the simulation. These results supported that 4-ClNAHSPD harnesses PAT pathway for cellular entrance.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Zhiyong Tian
- Institute for Innovative Drug Design and Evaluation, School of Pharmacy, Henan University, Kaifeng, China
| | - Luyao Tian
- School of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, China
| | - Sihan Zhao
- Institute for Innovative Drug Design and Evaluation, School of Pharmacy, Henan University, Kaifeng, China
| | - Man Shi
- Institute for Innovative Drug Design and Evaluation, School of Pharmacy, Henan University, Kaifeng, China
| | - Shudi Guo
- Institute for Innovative Drug Design and Evaluation, School of Pharmacy, Henan University, Kaifeng, China
| | - Chaojie Wang
- Institute for Innovative Drug Design and Evaluation, School of Pharmacy, Henan University, Kaifeng, China
| | - Zhihui Tian
- The Super Computer Center of Henan, Zhengzhou University, Zhengzhou, China
| | - Xiaohui He
- The Super Computer Center of Henan, Zhengzhou University, Zhengzhou, China
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23
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Tian Z, Tian L, Shi M, Zhao S, Guo S, Luo W, Wang C, Tian Z. Investigation of the interaction of a polyamine-modified flavonoid with bovine serum albumin (BSA) by spectroscopic methods and molecular simulation. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2020; 209:111917. [PMID: 32679511 DOI: 10.1016/j.jphotobiol.2020.111917] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 05/20/2020] [Accepted: 05/22/2020] [Indexed: 02/07/2023]
Abstract
The interaction between BSA and compound 1 was studied by UV-vis, fluorescence and circular dichroism spectroscopy under physiological conditions (pH = 7.4). Molecular docking and molecular dynamics analyses were also performed. The results showed that compound 1 could bind to BSA. When compound 1 bound to BSA, there were a series of changes in the spectral properties of BSA, which were an enhancement effect of the UV-Vis spectrum of BSA, fluorescence quenching and a weak conformational change in the CD spectrum. The results of the fluorescence experiments at 298, 303 and 310 K showed that fluorescence quenching caused by the addition of compound 1 to BSA was generally static quenching accompanied by a dynamic quenching process, which was shown by the quenching constants of 2.010 × 104 L∙M-1, 1.850 × 104 L∙M-1, and 1.970 × 104 L∙M-1 at the three different temperatures, respectively. From the obtained binding constants and thermodynamic parameters, it was found that hydrophobic forces played an important role in the binding process of 1 to BSA. The results of synchronous fluorescence and three-dimensional fluorescence showed that compound 1 caused a weak conformational change in BSA. Docking results showed that compound 1 was located at binding site II of bovine serum albumin protease. In addition, the flavonoid moiety of compound 1 contributes to the hydrophobic binding of compound 1 to BSA. The results of molecular dynamics, including the root-mean-square deviation (RMSD) and RMS fluctuation (RMSF) values, showed that the binding of compound 1 to BSA did not cause a significant conformational change in BSA.
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Affiliation(s)
- Zhiyong Tian
- Institute for innovative drug design and evaluation, School of Pharmacy, Henan University, Kaifeng 475004, China
| | - Luyao Tian
- School of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, Henan 475001, China
| | - Man Shi
- Institute for innovative drug design and evaluation, School of Pharmacy, Henan University, Kaifeng 475004, China
| | - Sihan Zhao
- Institute for innovative drug design and evaluation, School of Pharmacy, Henan University, Kaifeng 475004, China
| | - Shudi Guo
- Institute for innovative drug design and evaluation, School of Pharmacy, Henan University, Kaifeng 475004, China
| | - Wen Luo
- The Key Laboratory of Natural Medicine and Immuno-Engineering, Henan University, Kaifeng 475004, China.
| | - Chaojie Wang
- The Key Laboratory of Natural Medicine and Immuno-Engineering, Henan University, Kaifeng 475004, China.
| | - Zhihui Tian
- Smart city institute of Zhengzhou University, Zhengzhou, Henan 450001, China.
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24
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Moradi S, Shareghi B, Saboury AA, Farhadian S. Investigation on the interaction of acid phosphatase with putrescine using docking, simulations methods and multispectroscopic techniques. Int J Biol Macromol 2020; 150:90-101. [DOI: 10.1016/j.ijbiomac.2020.02.057] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 02/04/2020] [Accepted: 02/06/2020] [Indexed: 02/06/2023]
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25
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Konar M, Sahoo H. Tyrosine mediated conformational change in bone morphogenetic protein – 2: Biophysical implications of protein – phytoestrogen interaction. Int J Biol Macromol 2020; 150:727-736. [DOI: 10.1016/j.ijbiomac.2020.02.113] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 02/10/2020] [Accepted: 02/11/2020] [Indexed: 01/18/2023]
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26
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Ghanta KP, Pal T, Mondal S, Bandyopadhyay S. Microscopic Understanding of the Effect of Ionic Liquid on Protein from Molecular Simulation Studies. J Phys Chem B 2020; 124:3909-3921. [PMID: 32302476 DOI: 10.1021/acs.jpcb.0c02001] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
We have performed molecular dynamics (MD) simulations of the protein α-lactalbumin in aqueous solution containing the ionic liquid (IL) 1-butyl-3-methyl imidazolium tetrafluoroborate ([BMIM][BF4]) as the cosolvent at different concentrations. Attempts have been made to obtain quantitative understanding of the effects of the IL on the conformational features of the protein as well as the distributions of the IL and water around it. The calculations revealed enhanced rigidity of the protein with reduced conformational fluctuations and increasingly correlated local motions in the presence of the IL. Nonuniform relative population of the BMIM+ and BF4- ions at the protein surface with respect to that in the bulk solution has been observed. It is demonstrated that exchange of water by the IL around the protein results in rearrangement of the hydrogen bond network at the interface with breaking of protein-water hydrogen bonds and formation of protein-IL hydrogen bonds. Importantly, it is found that the protein forms increased number of stronger salt bridges in the presence of IL. This shows that the formation of a greater number of such stronger salt bridges is the origin behind the enhanced rigidity of the protein in the presence of the IL.
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Affiliation(s)
- Krishna Prasad Ghanta
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India
| | - Tamisra Pal
- Centre for Computational and Data Sciences, Indian Institute of Technology, Kharagpur 721302, India
| | - Sandip Mondal
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India
| | - Sanjoy Bandyopadhyay
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India.,Centre for Computational and Data Sciences, Indian Institute of Technology, Kharagpur 721302, India
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27
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Islam MM, Barik S, Preeyanka N, Sarkar M. Interaction of Lysozyme with Monocationic and Dicationic Ionic Liquids: Toward Finding a Suitable Medium for Biomacromolecules. J Phys Chem B 2020; 124:961-973. [DOI: 10.1021/acs.jpcb.9b10270] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mullah Muhaiminul Islam
- School of Chemical Sciences, National Institute of Science Education and Research, Bhubaneswar, HBNI, Bhimpur-Padanpur,
Jatni, Khurda, Bhubaneswar 752050, Odisha, India
| | - Sahadev Barik
- School of Chemical Sciences, National Institute of Science Education and Research, Bhubaneswar, HBNI, Bhimpur-Padanpur,
Jatni, Khurda, Bhubaneswar 752050, Odisha, India
| | - Naupada Preeyanka
- School of Chemical Sciences, National Institute of Science Education and Research, Bhubaneswar, HBNI, Bhimpur-Padanpur,
Jatni, Khurda, Bhubaneswar 752050, Odisha, India
| | - Moloy Sarkar
- School of Chemical Sciences, National Institute of Science Education and Research, Bhubaneswar, HBNI, Bhimpur-Padanpur,
Jatni, Khurda, Bhubaneswar 752050, Odisha, India
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28
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Bhakuni K, Yadav N, Venkatesu P. A novel amalgamation of deep eutectic solvents and crowders as biocompatible solvent media for enhanced structural and thermal stability of bovine serum albumin. Phys Chem Chem Phys 2020; 22:24410-24422. [DOI: 10.1039/d0cp04397d] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
This study unravels the effect of a novel solvent medium designed by amalgamation of macromolecular crowders and deep eutectic solvents (DESs) on bovine serum albumin (BSA).
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Affiliation(s)
- Kavya Bhakuni
- Department of Chemistry
- University of Delhi
- Delhi
- India
| | - Niketa Yadav
- Department of Chemistry
- University of Delhi
- Delhi
- India
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29
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Impact of bone extracellular matrix mineral based nanoparticles on structure and stability of purified bone morphogenetic protein 2 (BMP-2). JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2019; 198:111563. [DOI: 10.1016/j.jphotobiol.2019.111563] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 07/09/2019] [Accepted: 07/19/2019] [Indexed: 01/29/2023]
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30
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Baral A, Satish L, Das DP, Sahoo H, Ghosh MK. Molecular interactions of MnO 2@RGO (manganese dioxide-reduced graphene oxide) nanocomposites with bovine serum albumin. J Biomol Struct Dyn 2019; 38:2038-2046. [PMID: 31282288 DOI: 10.1080/07391102.2019.1640131] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Graphene based materials have attracted global attention due to their excellent properties. GO-metal oxide nanocomposites have been conjugated with biomolecules for the development of novel materials and potentially used as biomarkers. Herein, a detailed study on the interaction of Bovine serum albumin (BSA) with MnO2@RGO (manganese dioxide-reduced graphene oxide) nanocomposites (NC) has been carried out. MnO2@RGO nanocomposites were prepared through a template/surfactant free hydrothermal route at 180 °C for 12 h by varying the graphene oxide (GO) concentration. Different biophysical experiments have been carried out to evaluate molecular interactions between BSA and NCs. Intrinsic fluorescence has been used to quantify the quenching efficiency of NCs and the binding association of BSA-NC complexes. NCs effectively quenched the intrinsic fluorescence of BSA via static and dynamic mechanism. Further, the results indicate that the molecular interactions of NC with BSA are dependent on the GO percentage in NC. Circular dichroism results demonstrate nominal changes in the secondary structure of BSA in presence of NCs. Also, the esterase-like activity of BSA was marginally affected after adsorption upon NCs. In addition, the FESEM micrographs reveal that the protein-NC complexes consist of nanorod and sheet-like morphologies are forming aggregates of different sizes. We hope that this study will provide a basis for the design of novel graphene based and other related nanomaterials for several biological applications.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ayonbala Baral
- Hydro & Electrometallurgy Department, CSIR- Institute of Minerals and Materials Technology, Bhubaneswar, Odisha, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Lakkoji Satish
- Department of Chemistry, National Institute of Technology Rourkela, Rourkela, Odisha, India
| | - Dipti Prakasini Das
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India.,Colloids & Material Chemistry Department, CSIR- Institute of Minerals and Materials Technology, Bhubaneswar, Odisha, India
| | - Harekrushna Sahoo
- Department of Chemistry, National Institute of Technology Rourkela, Rourkela, Odisha, India
| | - Malay Kumar Ghosh
- Hydro & Electrometallurgy Department, CSIR- Institute of Minerals and Materials Technology, Bhubaneswar, Odisha, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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31
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Asgharzadeh S, Shareghi B, Farhadian S. Experimental and theoretical investigations on the interaction of l-methionine molecules with α-chymotrypsin in the aqueous solution using various methods. Int J Biol Macromol 2019; 131:548-556. [PMID: 30876904 DOI: 10.1016/j.ijbiomac.2019.03.080] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 03/11/2019] [Accepted: 03/11/2019] [Indexed: 11/17/2022]
Abstract
l-Methionine (l-Met) is one of the necessary amino acids that play unparalleled roles, influencing both the protein structure and metabolism. Understanding the interactions between proteins and small molecules can be realized by various perspectives, and this is significant for the progression of basic sciences and drug development. In this study, the variations in the stability, function, and structure of α-Chymotrypsin (α-Chy) in the presence of l-Met were investigated using spectroscopic and computational approaches. The results of the UV-vis absorption demonstrated that α-Chy had a maximum peak at 280 nm due to the Trp residue. Hyperchromism shift was seen in the presence of l-Met. Ground state system was formed in the presence of l-Met, as confirmed by the fluorescence studies. Fluorescence variations also revealed static quenching. The CD spectra also represented the alteration of the enzyme with an increase in the α-helix and a decrease in the β-sheet. The activity of α-Chy was incremented in the presence of l-Met. Therefore, l-Met served as an activator. Molecular docking results also indicated a negative amount for the Gibbs free energy of the binding of l-Met to the enzyme. α-Chy became more stable in the presence of l-Met, based on the molecular dynamics simulation.
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Affiliation(s)
- Sanaz Asgharzadeh
- Department of Biology, Faculty of Science, Shahrekord University, Shahrekord, P. O. Box.115, Iran
| | - Behzad Shareghi
- Department of Biology, Faculty of Science, Shahrekord University, Shahrekord, P. O. Box.115, Iran.
| | - Sadegh Farhadian
- Department of Biology, Faculty of Science, Shahrekord University, Shahrekord, P. O. Box.115, Iran; Central Laboratory, Shahrekord University, Shahrekord, Iran.
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32
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Jena BB, Satish L, Mahanta CS, Swain BR, Sahoo H, Dash BP, Satapathy R. Interaction of carborane-appended trimer with bovine serum albumin: A spectroscopic investigation. Inorganica Chim Acta 2019. [DOI: 10.1016/j.ica.2019.03.035] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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33
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Sustained activity and stability of lysozyme in aqueous ionic liquid solutions containing carboxymethylcellulose and polyethylene glycol. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.01.052] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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34
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Li N, Zhang Y, Huang B, Li H. Ultrasonic dispersion temperature- and pH-tuned spectral and electrochemical properties of bovine serum albumin on carbon nanotubes and its conformational transition. Electrochim Acta 2019. [DOI: 10.1016/j.electacta.2018.11.089] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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35
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Islam MM, Barik S, Sarkar M. Probing the Interactions of 1-Alkyl-3-methylimidazolium Tetrafluoroborate (Alkyl = Octyl, Hexyl, Butyl, and Ethyl) Ionic Liquids with Bovine Serum Albumin: An Alkyl Chain Length-Dependent Study. J Phys Chem B 2019; 123:1512-1526. [DOI: 10.1021/acs.jpcb.8b10795] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mullah Muhaiminul Islam
- School of Chemical Sciences, National Institute of Science Education and Research, Bhubaneswar, HBNI, Bhimpur-Padanpur,
Jatni, Khurda 752050, Odisha, India
| | - Sahadev Barik
- School of Chemical Sciences, National Institute of Science Education and Research, Bhubaneswar, HBNI, Bhimpur-Padanpur,
Jatni, Khurda 752050, Odisha, India
| | - Moloy Sarkar
- School of Chemical Sciences, National Institute of Science Education and Research, Bhubaneswar, HBNI, Bhimpur-Padanpur,
Jatni, Khurda 752050, Odisha, India
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36
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Alviz-Amador A, Galindo-Murillo R, Pineda-Alemán R, Pérez-González H, Rodríguez-Cavallo E, Vivas-Reyes R, Méndez-Cuadro D. 4-HNE carbonylation induces local conformational changes on bovine serum albumin and thioredoxin. A molecular dynamics study. J Mol Graph Model 2019; 86:298-307. [DOI: 10.1016/j.jmgm.2018.11.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Revised: 10/22/2018] [Accepted: 11/01/2018] [Indexed: 01/09/2023]
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37
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Precupas A, Leonties AR, Neacsu A, Sandu R, Popa VT. Gallic acid influence on bovine serum albumin thermal stability. NEW J CHEM 2019. [DOI: 10.1039/c9nj00115h] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
A thermoanalytical approach reveals the dual action of GA on BSA thermal stability.
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Affiliation(s)
- Aurica Precupas
- “Ilie Murgulescu” Institute of Physical Chemistry of the Romanian Academy
- 060021 – Bucharest
- Romania
| | - Anca Ruxandra Leonties
- “Ilie Murgulescu” Institute of Physical Chemistry of the Romanian Academy
- 060021 – Bucharest
- Romania
| | - Andreea Neacsu
- “Ilie Murgulescu” Institute of Physical Chemistry of the Romanian Academy
- 060021 – Bucharest
- Romania
| | - Romica Sandu
- “Ilie Murgulescu” Institute of Physical Chemistry of the Romanian Academy
- 060021 – Bucharest
- Romania
| | - Vlad Tudor Popa
- “Ilie Murgulescu” Institute of Physical Chemistry of the Romanian Academy
- 060021 – Bucharest
- Romania
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38
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Millan S, Satish L, Bera K, Sahoo H. Binding and inhibitory effect of the food colorants Sunset Yellow and Ponceau 4R on amyloid fibrillation of lysozyme. NEW J CHEM 2019. [DOI: 10.1039/c8nj05827j] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Amyloid fibrillogenesis of proteins is known to be the root cause of a large number of diseases like Parkinson's, Alzheimer's, and Huntington's disease, spongiform encephalopathy, amyloid polyneuropathy, type-II diabetes, etc.
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Affiliation(s)
- Sabera Millan
- Department of Chemistry
- National Institute of Technology (NIT)
- Rourkela-769008, Sundergarh
- India
| | - Lakkoji Satish
- Department of Chemistry
- National Institute of Technology (NIT)
- Rourkela-769008, Sundergarh
- India
| | - Krishnendu Bera
- CEITEC MU
- Masaryk University
- Kamenice 753/5
- 625 00 Brno
- Czech Republic
| | - Harekrushna Sahoo
- Department of Chemistry
- National Institute of Technology (NIT)
- Rourkela-769008, Sundergarh
- India
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39
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Mamashli F, Badraghi J, Delavari B, Lanjanian H, Sabbaghian M, Hosseini M, Saboury AA. Improvement of versatile peroxidase activity and stability by a cholinium-based ionic liquid. J Mol Liq 2018. [DOI: 10.1016/j.molliq.2018.09.128] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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40
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Patel R, Maurya N, Parray MUD, Farooq N, Siddique A, Verma KL, Dohare N. Esterase activity and conformational changes of bovine serum albumin toward interaction with mephedrone: Spectroscopic and computational studies. J Mol Recognit 2018; 31:e2734. [DOI: 10.1002/jmr.2734] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 03/26/2018] [Accepted: 05/08/2018] [Indexed: 12/20/2022]
Affiliation(s)
- Rajan Patel
- Biophysical Chemistry Laboratory, Centre for Interdisciplinary Research in Basic Sciences; Jamia Millia Islamia (A Central University); New Delhi India
| | - Neha Maurya
- Biophysical Chemistry Laboratory, Centre for Interdisciplinary Research in Basic Sciences; Jamia Millia Islamia (A Central University); New Delhi India
| | - Mehraj ud din Parray
- Biophysical Chemistry Laboratory, Centre for Interdisciplinary Research in Basic Sciences; Jamia Millia Islamia (A Central University); New Delhi India
| | - Nida Farooq
- Biophysical Chemistry Laboratory, Centre for Interdisciplinary Research in Basic Sciences; Jamia Millia Islamia (A Central University); New Delhi India
| | - Abrar Siddique
- Biophysical Chemistry Laboratory, Centre for Interdisciplinary Research in Basic Sciences; Jamia Millia Islamia (A Central University); New Delhi India
| | - Kanak Lata Verma
- Department of Chemistry, Regional Forensic Science Laboratory; Government of NCT of Delhi; New Delhi India
| | - Neeraj Dohare
- Biophysical Chemistry Laboratory, Centre for Interdisciplinary Research in Basic Sciences; Jamia Millia Islamia (A Central University); New Delhi India
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