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Sharma A, Mondal S, Ahuja T, Karmakar T, Siddhanta S. Ion-Mediated Protein Stabilization on Nanoscopic Surfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:1227-1237. [PMID: 36622301 DOI: 10.1021/acs.langmuir.2c03010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
The emergence of nanoparticles in biomedical applications has made their interactions with proteins inevitable. Nanoparticles conjugated with proteins and peptide-based constructs form an integral part of nanotherapeutics and have recently shown promise in treating a myriad of diseases. The proper functioning of proteins is critical to achieve their biological functions. However, interface issues result in the denaturation of proteins, and the loss of orientation and steric hindrance can adversely affect the function of the conjugate. Furthermore, surface-induced denaturation also triggers protein aggregation, resulting in amyloid-like species. Understanding the mechanistic underpinnings of protein-nanoparticle interactions and controlling their interfacial characteristics are critical and challenging due to the complex nature of the conjugates. In this milieu, we demonstrate that ionic liquids can be suitable candidates for stabilizing protein-nanoparticle interactions by virtue of their excellent protein-preserving properties. We also probe the previously unexplored mechanism of ion-mediated stabilization of the protein molecules on the nanoparticle surface. The protein-nanoparticle conjugates consist of lysozyme and choline-based ionic liquids characterized by optical and electron microscopy techniques combined with surface-sensitive plasmon-enhanced Raman spectroscopy. Furthermore, atomistic molecular dynamics simulations of the conjugates delineate interfacial interactions of the protein molecules and the modulation by the ions, particularly the conformational changes and the dynamic correlation when the protein and specific ionic liquid molecules are adsorbed on the nanoparticle surface. The combined experimental and computational studies showed the synergistic behavior of the ions of the ionic liquids, specifically the orientation and coverage of the anions aided by the cations to control the surface interactions and hence the overall protein stability. These studies pave the way for using ionic liquids, particularly their biocompatible counterparts in nanoparticle-based complexes, as stabilizing agents for biomedical applications.
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Affiliation(s)
- Arti Sharma
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, Delhi110016, India
| | - Soumya Mondal
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, Delhi110016, India
| | - Tripti Ahuja
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, Delhi110016, India
| | - Tarak Karmakar
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, Delhi110016, India
| | - Soumik Siddhanta
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, Delhi110016, India
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Chen G, Khan IM, He W, Li Y, Jin P, Campanella OH, Zhang H, Huo Y, Chen Y, Yang H, Miao M. Rebuilding the lid region from conformational and dynamic features to engineering applications of lipase in foods: Current status and future prospects. Compr Rev Food Sci Food Saf 2022; 21:2688-2714. [PMID: 35470946 DOI: 10.1111/1541-4337.12965] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 03/17/2022] [Accepted: 03/25/2022] [Indexed: 02/06/2023]
Abstract
The applications of lipases in esterification, amidation, and transesterification have broadened their potential in the production of fine compounds with high cumulative values. Mostly, the catalytic triad of lipases is covered by either one or two mobile peptides called the "lid" that control the substrate channel to the catalytic center. The lid holds unique conformational allostery via interfacial activation to regulate the dynamics and catalytic functions of lipases, thereby highlighting its importance in redesigning these enzymes for industrial applications. The structural characteristic of lipase, the dynamics of lids, and the roles of lid in lipase catalysis were summarized, providing opportunities for rebuilding lid region by biotechniques (e.g., metagenomic technology and protein engineering) and enzyme immobilization. The review focused on the advantages and disadvantages of strategies rebuilding the lid region. The main shortcomings of biotechnologies on lid rebuilding were discussed such as negative effects on lipase (e.g., a decrease of activity). Additionally, the main shortcomings (e.g., enzyme desorption at high temperatre) in immobilization on hydrophobic supports via interfacial action were presented. Solutions to the mentioned problems were proposed by combinations of computational design with biotechnologies, and improvements of lipase immobilization (e.g., immobilization protocols and support design). Finally, the review provides future perspectives about designing hyperfunctional lipases as biocatalysts in the food industry based on lid conformation and dynamics.
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Affiliation(s)
- Gang Chen
- College of Food and Health, Zhejiang Agriculture and Forest University, Hangzhou, China.,State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Imran Mahmood Khan
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Wensen He
- School of Food Science and Technology, Jiangsu University, Zhenjiang, China
| | - Yongxin Li
- College of Food and Health, Zhejiang Agriculture and Forest University, Hangzhou, China
| | - Peng Jin
- College of Food and Health, Zhejiang Agriculture and Forest University, Hangzhou, China
| | - Osvaldo H Campanella
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,Department of Food Science and Technology, Ohio State University, Columbus, Ohio, USA
| | - Haihua Zhang
- College of Food and Health, Zhejiang Agriculture and Forest University, Hangzhou, China
| | - Yanrong Huo
- College of Food and Health, Zhejiang Agriculture and Forest University, Hangzhou, China
| | - Yang Chen
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Huqing Yang
- College of Food and Health, Zhejiang Agriculture and Forest University, Hangzhou, China
| | - Ming Miao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
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Shobhna, Kumari M, Kashyap HK. Mechanistic Insight on BioIL-Induced Structural Alterations in DMPC Lipid Bilayer. J Phys Chem B 2021; 125:11955-11966. [PMID: 34672578 DOI: 10.1021/acs.jpcb.1c06218] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The emerging application risks of traditional ionic liquids (ILs) toward the ecosystem have changed the perception regarding their greenness. This resulted in the exploration of their more biocompatible alternatives known as biocompatible ILs (BioILs). Here, we have investigated the impact of two such biocompatible cholinium amino acid-based ILs on the structural behavior of model homogeneous DMPC (1,2-dimyristoyl-sn-glycero-3-phosphocholine) lipid bilayer using all-atom molecular dynamics simulation technique. Two classic cholinium-amino acid-based ILs, cholinium glycinate ([Ch][Gly]) and cholinium phenylalaninate ([Ch][Phe]), which differ only by the side chain lengths and hydrophobicity of the anions, have been utilized in the present work. Simultaneous analysis of the bilayer structural properties reveals that the existence of [Ch][Gly] BioIL above a particular concentration induces phase transition from fluid phase to gel phase in the DMPC lipid bilayer. Such a freezing of lipid bilayer upon the exposure to concentrated aqueous solution of [Ch][Gly] BioIL indicates the harmfulness of this BioIL toward the cell membranes majorly containing DMPC lipids, as the cell freezing can negatively affect its stability and functionality. Despite having a more hydrophobic amino acid side chain of [Phe]- anion in [Ch][Phe], in the case of bilayer-[Ch][Phe] systems we observe the minimal impact of [Ch][Phe] BioIL on the DMPC bilayer properties up to 10 mol % concentration. In the presence of these BioIL, we observe the thickening of the bilayer and accumulation of the cations and anions of the BioILs at the interface of DMPC lipid heads and tails. The transfer free-energy profile of a [Phe]- anion from aqueous phase to membrane center also indicates the anion partitioning at lipid head-tail interface and its inability to penetrate in the lipid membrane tail region. In contrast, the free-energy profile for a [Gly]- anion offers a very high energy barrier to the insertion of [Gly]- into the membrane interior, leading to accumulation of [Gly]- anions at the lipid head-water region.
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Affiliation(s)
- Shobhna
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Monika 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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Gupta A, Dhattarwal HS, Kashyap HK. Structure of cholinium glycinate biocompatible ionic liquid at graphite electrode interface. J Chem Phys 2021; 154:184702. [PMID: 34241030 DOI: 10.1063/5.0049171] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
We use constant potential molecular dynamics simulations to investigate the interfacial structure of the cholinium glycinate biocompatible ionic liquid (bio-IL) sandwiched between graphite electrodes with varying potential differences. Through number density profiles, we observe that the cation and anion densities oscillate up to ∼1.5 nm from the nearest electrode. The range of these oscillations does not change significantly with increasing electrode potential. However, the amplitudes of the cation (anion) density oscillations show a notable increase with increasing potential at the negative (positive) electrode. At higher potential differences, the bulkier N(CH3)3CH2 group of cholinium cations ([Ch]+) overcomes the steric barrier and comes closer to the negative electrode as compared to oxygen atom (O[Ch]+ ). We observe an increase in the interaction between O[Ch]+ and the positive electrode with a decrease in the distance between them on increasing the potential difference. We also observe hydrogen bonding between the hydroxyl group of [Ch]+ cations and oxygens of glycinate anions through the simulated tangential radial distribution function. Orientational order parameter analysis shows that the cation (anion) prefers to align parallel to the negative (positive) electrode at higher applied potential differences. Charge density profiles show a positive charge density peak near the positive electrode at all the potential differences because of the presence of partially positive charged hydrogen atoms of cations and anions. The differential capacitance (Cd) of the bio-IL shows two constant regimes, one for each electrode. The magnitude of these Cd values clearly suggests potential application of such bio-ILs as promising battery electrolytes.
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Affiliation(s)
- Aditya Gupta
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Harender S Dhattarwal
- 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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Wang A, Chen X, Yu J, Li N, Li H, Yin Y, Xie T, Wu SG. Green preparation of lipase@Ca3(PO4)2 hybrid nanoflowers using bone waste from food production for efficient synthesis of clindamycin palmitate. J IND ENG CHEM 2020. [DOI: 10.1016/j.jiec.2020.06.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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Kumari M, Gupta A, Shobhna, Kashyap HK. Molecular Dynamics Evaluation of the Effect of Cholinium Phenylalaninate Biocompatible Ionic Liquid on Biomimetic Membranes. J Phys Chem B 2020; 124:6748-6762. [PMID: 32786926 DOI: 10.1021/acs.jpcb.0c03433] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Toward the search of sustainable green solvents, choline amino acid ([Ch][AA]) ionic liquids (ILs), mainly derived from renewable feedstocks, have emerged as a promising atoxic alternative to the conventional solvents. Recent studies have shown the remarkably benign nature of cholinium-based ILs against biomimetic phospholipid membranes. However, few of the contemporaneous experimental studies have contradicted the aforesaid ecofriendly nature of these ILs with anions comprising longer alkyl or aromatic tails. Aiming to understand the influence of amino acid side-chain variation in a particular bio-IL on biomembranes, herein, we have evaluated the effect of cholinium phenylalaninate ([Ch][Phe]) IL on the structural stability of homogeneous biomimetic 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine (POPE) lipid bilayers using atomistic molecular dynamics simulations. Although we observe spontaneous intercalation of aromatic rings of [Phe]- anions in the hydrophobic region of the bilayers, the polar backbone of the anion remains coordinated with the lipid polar part through strong electrostatic and H-bonding interactions. Besides, the [Ch]+ cations get accumulated at the lipid-water interface to counter the excess negative charge density. The intercalation of the anionic rings causes significant perturbations in the lipid structural arrangement while still maintaining the bilayer integrity. The quantitative evaluation to probe the deteriorating effect of this bio-IL application establishes anions as the principal component causing the observed structural perturbations. The analysis of the structural properties along with the free energy assessment reveals the higher efficacy of [Ch][Phe] bio-IL to perturb the POPE bilayer structure than the POPC bilayer.
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Affiliation(s)
- Monika Kumari
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Aditya Gupta
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Shobhna
- 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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Susceptibility of biomembrane structure towards amphiphiles, ionic liquids, and deep eutectic solvents. ADVANCES IN BIOMEMBRANES AND LIPID SELF-ASSEMBLY 2020. [DOI: 10.1016/bs.abl.2020.02.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Jumina J, Lavendi W, Singgih T, Triono S, Steven Kurniawan Y, Koketsu M. Preparation of Monoacylglycerol Derivatives from Indonesian Edible Oil and Their Antimicrobial Assay against Staphylococcus aureus and Escherichia coli. Sci Rep 2019; 9:10941. [PMID: 31358890 PMCID: PMC6662904 DOI: 10.1038/s41598-019-47373-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 07/09/2019] [Indexed: 11/30/2022] Open
Abstract
In the present work, linoleic acid and oleic acid were isolated from Indonesian corn oil and palm oil and they were used to prepare monoacylglycerol derivatives as the antibacterial agent. Indonesian corn oil contains 57.74% linoleic acid, 19.88% palmitic acid, 11.84% oleic acid and 3.02% stearic acid. While Indonesian palm oil contains 44.72% oleic acid, 39.28% palmitic acid, 4.56% stearic acid and 1.54% myristic acid. The oleic acid was purified by using Urea Inclusion Complex (UIC) method and its purity was significantly increased from 44.72% to 94.71%. Meanwhile, with the UIC method, the purity of ethyl linoleate was increased from 57.74% to 72.14%. 1-Monolinolein and 2-monoolein compounds were synthesized via two-step process from the isolated linoleic acid and oleic acid, respectively. The preliminary antibacterial assay shows that the 1-monolinolein did not give any antibacterial activity against Staphylococcus aureus and Escherichia coli, while 2-monoolein showed weak antibacterial activity against Staphylococcus aureus.
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Affiliation(s)
- Jumina Jumina
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Gadjah Mada, Yogyakarta, 55281, Indonesia.
| | - Wenggi Lavendi
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Gadjah Mada, Yogyakarta, 55281, Indonesia
| | - Tubagus Singgih
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Gadjah Mada, Yogyakarta, 55281, Indonesia
| | - Sugeng Triono
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Gadjah Mada, Yogyakarta, 55281, Indonesia
| | - Yehezkiel Steven Kurniawan
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Gadjah Mada, Yogyakarta, 55281, Indonesia
| | - Mamoru Koketsu
- Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University, Gifu, 501-1112, Japan
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Kumari P, Kashyap HK. Sensitivity and Resilience of Phosphatidylcholine and Phosphatidylethanolamine Lipid Membranes against Cholinium Glycinate Biocompatible Ionic Liquid. J Phys Chem B 2019; 123:4550-4561. [DOI: 10.1021/acs.jpcb.9b02800] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- 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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Gupta A, Kaur S, Kashyap HK. How Water Permutes the Structural Organization and Microscopic Dynamics of Cholinium Glycinate Biocompatible Ionic Liquid. J Phys Chem B 2019; 123:2057-2069. [DOI: 10.1021/acs.jpcb.8b10235] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Aditya Gupta
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Supreet Kaur
- 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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Das S, Balasubramanian S. pH-Induced Rotation of Lidless Lipase LipA from Bacillus subtilis at Lipase-Detergent Interface. J Phys Chem B 2018; 122:4802-4812. [PMID: 29623706 DOI: 10.1021/acs.jpcb.8b02296] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Lipases exhibit a unique process during the catalysis of the hydrolysis of triglyceride substrates called interfacial activation. Surfactants are used as cosolvents with water not only to offer a less polar environment to the lipases needed for their interfacial activation but also to solvate the substrate which are poorly soluble in water. However, the presence of detergent in the medium can affect both the lipase and the substrate, making the construction of a microkinetic model for lipase activity in the presence of the detergent difficult. Herein, we study the interfacial activation of a lidless lipase LipA from Bacillus subtilis using extensive atomistic molecular dynamics simulations at different concentrations of the surfactant, Thesit (C12E8), at two pH values. Residues which bind to the monomeric detergent are found to be the same as the ones which have been reported earlier to bind to the substrate. Very importantly, a pH-induced rotation of the enzyme with respect to surfactant aggregate has been observed which not only explains the experimentally observed pH-dependent enzymatic activity of this lidless lipase, but also suggests its reorientation at an aqueous-lipodophilic interface.
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Affiliation(s)
- Sudip Das
- Chemistry and Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research , Bangalore 560 064 , India
| | - Sundaram Balasubramanian
- Chemistry and Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research , Bangalore 560 064 , India
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