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Priyanka, Kaur M, Maiti S. Substrate-induced assembly of cascade enzymes and catalytic surfactants: nanoarchitectonics at the oil-in-water droplet interface. Chem Commun (Camb) 2024; 60:9101-9104. [PMID: 39109397 DOI: 10.1039/d4cc03243h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/21/2024]
Abstract
The heterogeneous distribution of lipids and lipid-bound proteins in a plasma membrane has functional advantages. Herein, in a synthetic system, we demonstrate the assembly of three enzymes involved in cascade reactions, in response to the substrate of the first enzyme at the oil-water interface being stabilized by a Zn(II)-metallosurfactant. Then we show substrate-mediated catalytically-active cluster formation of the metallosurfactant in a binary mixture with another non-catalytic surfactant at the interface. The catalytic ability can be tuned by controlling clustering through the addition of phosphate ions. Overall this work demonstrates functionally diverse supramolecular nanoarchitectonics at the oil-water interface.
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Affiliation(s)
- Priyanka
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Manauli 140306, India.
| | - Manpreet Kaur
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Manauli 140306, India.
| | - Subhabrata Maiti
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Manauli 140306, India.
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2
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Sivoria N, Mahato RR, Priyanka, Saini A, Maiti S. Enzymatic Dissociation of DNA-Histone Condensates in an Electrophoretic Setting: Modulating DNA Patterning and Hydrogel Viscoelasticity. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:13505-13514. [PMID: 38896798 DOI: 10.1021/acs.langmuir.4c00939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Development of an energy-driven self-assembly process is a matter of interest for understanding and mimicking diverse ranges of biological and environmental patterns in a synthetic system. In this article, first we demonstrate transient and temporally controlled self-assembly of a DNA-histone condensate where trypsin (already present in the system) hydrolyzes histone, resulting in disassembly. Upon performing this dynamic self-assembly process in a gel matrix under an electric field, we observe diverse kinds of DNA patterning across the gel matrix depending on the amount of trypsin, incubation time of the reaction mixture, and gel porosity. Notably, here, the micrometer-sized DNA-histone condensate does not move through the gel and only free DNA can pass; therefore, transport and accumulation of DNA at different zones depend on the release rate of DNA by trypsin. Furthermore, we show that the viscoelasticity of the native gel increases in the presence of DNA and a pattern over gel viscoelasticity at different zones can be achieved by tuning the amount of enzyme, i.e., the dissociation rate of the DNA-histone condensate. We believe enabling spatiotemporally controlled DNA patterning by applying an electric field will be potentially important in designing different kinds of spatiotemporally distinct dynamic materials.
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Affiliation(s)
- Neetu Sivoria
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Manauli 140306, India
| | - Rishi Ram Mahato
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Manauli 140306, India
| | - Priyanka
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Manauli 140306, India
| | - Aman Saini
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Manauli 140306, India
| | - Subhabrata Maiti
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Manauli 140306, India
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3
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Shandilya E, Rallabandi B, Maiti S. In situ enzymatic control of colloidal phoresis and catalysis through hydrolysis of ATP. Nat Commun 2024; 15:3603. [PMID: 38684662 PMCID: PMC11059368 DOI: 10.1038/s41467-024-47912-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 04/16/2024] [Indexed: 05/02/2024] Open
Abstract
The ability to sense chemical gradients and respond with directional motility and chemical activity is a defining feature of complex living systems. There is a strong interest among scientists to design synthetic systems that emulate these properties. Here, we realize and control such behaviors in a synthetic system by tailoring multivalent interactions of adenosine nucleotides with catalytic microbeads. We first show that multivalent interactions of the bead with gradients of adenosine mono-, di- and trinucleotides (AM/D/TP) control both the phoretic motion and a proton-transfer catalytic reaction, and find that both effects are diminished greatly with increasing valence of phosphates. We exploit this behavior by using enzymatic hydrolysis of ATP to AMP, which downregulates multivalent interactivity in situ. This produces a sudden increase in transport of the catalytic microbeads (a phoretic jump), which is accompanied by increased catalytic activity. Finally, we show how this enzymatic activity can be systematically tuned, leading to simultaneous in situ spatial and temporal control of the location of the microbeads, as well as the products of the reaction that they catalyze. These findings open up new avenues for utilizing multivalent interaction-mediated programming of complex chemo-mechanical behaviors into active systems.
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Affiliation(s)
- Ekta Shandilya
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER), Mohali, Knowledge City, Manauli, 140306, India
| | - Bhargav Rallabandi
- Department of Mechanical Engineering, University of California, Riverside, CA, 92521, USA.
| | - Subhabrata Maiti
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER), Mohali, Knowledge City, Manauli, 140306, India.
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4
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Priyanka, Maiti S. Co-assembly-mediated biosupramolecular catalysis: thermodynamic insights into nucleobase specific (oligo)nucleotide attachment and cleavage. J Mater Chem B 2023; 11:10383-10394. [PMID: 37874292 DOI: 10.1039/d3tb01747h] [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: 10/25/2023]
Abstract
Gaining control over the stability and cleavage of phosphoester and phosphodiester remains a matter of interest for their application in biotechnology to oligonucleotide-based therapeutics. Herein, we report an efficient unactivated phosphoester hydrolysis (stable mono/di/tri/cyclic nucleotide to nucleoside conversion) via a biosupramolecular system comprising of a non-covalent complex of enzyme, alkaline phosphatase (ALP), and Zn(II)-metallosurfactant. We also demonstrate the nucleobase selective activation or inhibition of ALP-mediated oligonucleotide digestion process using that complex. The higher binding affinity of Zn(II)-containing headgroup with phosphate-containing substrate enhanced the effective substrate concentration surrounding the enzyme, which, in turn, results in a drastic decrease in the Michaelis constant (KM), along with an increase in the turnover (kcat). The catalytic activation or inhibition of nucleobase-specific oligonucleotide digestion depends on the hydration, localization of the substrates, and viscosity of the resultant co-assembly upon substrate binding with the enzyme-metallosurfactant complex. Additionally, through isothermal titration calorimetry experiment, we demonstrate enthalpy-entropy change during both the supramolecular binding of (oligo)nucleotides and simultaneous activation/inhibition in catalytic cleavage. Overall, it showed the possible modularity of Zn(II)-mediated biosupramolecular interaction, describing intrinsic thermodynamic aspects in developing complex biocatalytic circuits with nucleobase-specific oligonucleotides inputs, which are relevant in designing nucleic acid-based cargo for drug delivery and bioimaging.
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Affiliation(s)
- Priyanka
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Manauli 140306, India.
| | - Subhabrata Maiti
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Manauli 140306, India.
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5
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Maiti T, Ghosh P. Unravelling diverse spatiotemporal orders in chlorine dioxide-iodine-malonic acid reaction-diffusion system through circularly polarized electric field and photo-illumination. J Chem Phys 2023; 159:174902. [PMID: 37909457 DOI: 10.1063/5.0171763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 10/16/2023] [Indexed: 11/03/2023] Open
Abstract
Designing and predicting self-organized pattern formation in out-of-equilibrium chemical and biochemical reactions holds fundamental significance. External perturbations like light and electric fields exert a crucial influence on reaction-diffusion systems involving ionic species. While the separate impacts of light and electric fields have been extensively studied, comprehending their combined effects on spatiotemporal dynamics is paramount for designing versatile spatial orders. Here, we theoretically investigate the spatiotemporal dynamics of chlorine dioxide-iodine-malonic acid reaction-diffusion system under photo-illumination and circularly polarized electric field (CPEF). By applying CPEF at varying intensities and frequencies, we observe the predominant emergence of oscillating hexagonal spot-like patterns from homogeneous stable steady states. Furthermore, our study unveils a spectrum of intriguing spatiotemporal instabilities, encompassing stripe-like patterns, oscillating dumbbell-shaped patterns, spot-like instabilities with square-based symmetry, and irregular chaotic patterns. However, when we introduce periodic photo-illumination to the hexagonal spot-like instabilities induced by CPEF in homogeneous steady states, we observe periodic size fluctuations. Additionally, the stripe-like instabilities undergo alternating transitions between hexagonal spots and stripes. Notably, within the Turing region, the interplay between these two external influences leads to the emergence of distinct superlattice patterns characterized by hexagonal-and square-based symmetry. These patterns include parallel lines of spots, target-like formations, black-eye patterns, and other captivating structures. Remarkably, the simple perturbation of the system through the application of these two external fields offers a versatile tool for generating a wide range of pattern-forming instabilities, thereby opening up exciting possibilities for future experimental validation.
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Affiliation(s)
- Tarpan Maiti
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram, Kerala 695551, India
| | - Pushpita Ghosh
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram, Kerala 695551, India
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6
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Maiti S. Simultaneous quantification of serum albumin and gamma globulin using Zn(II)-metallosurfactant via a coffee ring pattern. Chem Commun (Camb) 2023; 59:6536-6539. [PMID: 37161733 DOI: 10.1039/d3cc01221b] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Herein, we report interactivity and conjugate formation ability between a Zn(II)-metallosurfactant and two clinically relevant serum proteins, albumin (ALB) and γ-globulin (GGB). We found that the surfactant-ALB conjugate promotes coffee ring formation, whereas with GGB it gets suppressed, which is due to the difference in structural anisotropy and hydrophobicity of the conjugates. Additionally, validation of this biosensing platform has been established in human serum samples, and it has potential applications for on-spot rapid diagnostics in remote areas.
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Affiliation(s)
- Subhabrata Maiti
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Manauli 140306, India.
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7
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Shandilya E, Maiti S. Self-Regulatory Micro- and Macroscale Patterning of ATP-Mediated Nanobioconjugate. ACS NANO 2023; 17:5108-5120. [PMID: 36827433 DOI: 10.1021/acsnano.3c00431] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Directional interactions and the assembly of a nanobioconjugate in clusters at a specific location are important for patterning and microarrays in biomedical research. Herein, we report that self-assembly and spatial control in surface patterning of the surfactant-functionalized nanoparticles can be governed in micro- and macroscale environments by two factors, synergistic enzyme-substrate-nanoparticle affinity and the phoretic effect. First, we show that aggregation of cationic gold nanoparticles (GNP) can be modulated by multivalent anionic nanoparticle binding of an adenosine-based nucleotide and enzyme, alkaline phosphatase. We further demonstrate two different types of their autonomous aggregation pattern: (i) by introducing an enzyme gradient that modulates the synergistic nonequilibrium interactivity of the nanoparticle, nucleotide, and enzyme both in microfluidic conditions and at the macroscale; and (ii) the surface deposition pattern from evaporating droplets via the coffee ring effect. Here, temporal control over the width and site of the patterning area inside the microfluidic channel under catalytic and noncatalytic conditions has also been demonstrated. Finally, we show a change in capillary phoresis parameters responsible for the coffee ring due to introduction of ATP-loaded GNP in the blood serum, showing applicability in low-cost disease diagnostics. Overall, an enzyme-actuated surface nanobiopatterning method has been demonstrated that has potential application in controlled micro- and macroscale area patterning with a diverse cascade catalytic surface and spatiotemporal multisensory-based application.
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Affiliation(s)
- Ekta Shandilya
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Manauli 140306, India
| | - Subhabrata Maiti
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Manauli 140306, India
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Cao Y, Gabrielli L, Frezzato D, Prins LJ. Persistent ATP-Concentration Gradients in a Hydrogel Sustained by Chemical Fuel Consumption. Angew Chem Int Ed Engl 2023; 62:e202215421. [PMID: 36420591 DOI: 10.1002/anie.202215421] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 11/19/2022] [Accepted: 11/23/2022] [Indexed: 11/25/2022]
Abstract
We show the formation of macroscopic ATP-concentrations in an agarose gel and demonstrate that these gradients can be sustained in time at the expense of the consumption of a chemical fuel. The approach relies on the spatially controlled activation of ATP-producing and ATP-consuming reactions through the local injection of enzymes in the matrix. The reaction-diffusion system is maintained in a stationary non-equilibrium state as long as chemical fuel, phosphocreatine, is present. The reaction-diffusion system is coupled to a supramolecular system composed of monolayer protected gold nanoparticles and a fluorescent probe. As a result of this coupling, fluorescence signals emerge spontaneously in response to the ATP-concentration gradients. We show that the approach permits the rational formation of complex fluorescence patterns that change over time as a function of the evolution of the ATP-concentrations present in the system.
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Affiliation(s)
- Yingjuan Cao
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131, Padova, Italy
| | - Luca Gabrielli
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131, Padova, Italy
| | - Diego Frezzato
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131, Padova, Italy
| | - Leonard J Prins
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131, Padova, Italy
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Mahato RR, Shandilya E, Not Applicable S, Maiti S. Regulating Spatial Localization and Reactivity Biasness of DNAzymes by Metal Ions and Oligonucleotides. Chembiochem 2022; 23:e202200154. [PMID: 35762518 DOI: 10.1002/cbic.202200154] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 06/08/2022] [Indexed: 11/09/2022]
Abstract
Chemical gradient sensing behavior of catalytically active colloids and enzymes is an area of immense interest owing to their importance in understanding fundamental spatiotemporal complexity pattern in living systems and designing of dynamic materials. Herein, we have shown peroxidase activity of DNAzyme (G-quadruplex-hemin complex tagged in a micron-sized glass bead) can be modulated by metal ions and metal ion-binding oligonucleotides. Next we demonstrated both experimentally and theoretically that the localization and product formation ability of the DNAzyme containing particle remains biased to the more catalytically active zone where concentration of metal ion (Hg2+) inhibitor is low. Interestingly, this biased localization can be broken by introduction of Hg2+ binding oligonucleotide in the system. Additionally, macroscopically asymmetric catalytic product distributed zone has also been achieved on this process, showing possibility in regulation in autonomous spatially controlled chemical process. This demonstration of autonomous modulation of the localization pattern and spatially specific enhanced product forming ability of DNAzymes will further enable in designing of responsive nucleic acid-based motile materials and surfaces.
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Affiliation(s)
- Rishi Ram Mahato
- Indian Institute of Science Education and Research Mohali, Chemical Sciences, INDIA
| | - Ekta Shandilya
- Indian Institute of Science Education and Research Mohali, Chemical Sciences, INDIA
| | | | - Subhabrata Maiti
- Indian Institute of Science Education and Research Mohali, Chemical Sciences, Knowledge City, Sector-81, S.A.S. Nagar, Manauli P.O., 140306, Mohali, INDIA
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10
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Mahato RR, Shandilya E, Maiti S. Perpetuating enzymatically-induced spatiotemporal pH and catalytic heterogeneity of a hydrogel by nanoparticles. Chem Sci 2022; 13:8557-8566. [PMID: 35974757 PMCID: PMC9337733 DOI: 10.1039/d2sc02317b] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 06/20/2022] [Indexed: 11/22/2022] Open
Abstract
The attainment of spatiotemporally inhomogeneous chemical and physical properties within a system is gaining attention across disciplines due to the resemblance to environmental and biological heterogeneity. Notably, the origin of natural pH gradients and how they have been incorporated in cellular systems is one of the most important questions in understanding the prebiotic origin of life. Herein, we have demonstrated a spatiotemporal pH gradient formation pattern on a hydrogel surface by employing two different enzymatic reactions, namely, the reactions of glucose oxidase (pH decreasing) and urease (pH increasing). We found here a generic pattern of spatiotemporal change in pH and proton transfer catalytic activity that was completely altered in a cationic gold nanoparticle containing hydrogel. In the absence of nanoparticles, the gradually generated macroscopic pH gradient slowly diminished with time, whereas the presence of nanoparticles helped to perpetuate the generated gradient effect. This behavior is due to the differential responsiveness of the interface of the cationic nanoparticle in temporally changing surroundings with increasing or decreasing pH or ionic contents. Moreover, the catalytic proton transfer ability of the nanoparticle showed a concerted kinetic response following the spatiotemporal pH dynamics in the gel matrix. Notably, this nanoparticle-driven spatiotemporally resolved gel matrix will find applicability in the area of the membrane-free generation and control of spatially segregated chemistry at the macroscopic scale. This work reports perpetuating effect in enzymatically generated spatiotemporal pH gradient across a hydrogel in presence of cationic gold nanoparticle; showing a new route in spatially resolved chemistry in a membrane-free environment.![]()
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Affiliation(s)
- Rishi Ram Mahato
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali Knowledge City, Manauli 140306 India
| | - Ekta Shandilya
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali Knowledge City, Manauli 140306 India
| | - Subhabrata Maiti
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali Knowledge City, Manauli 140306 India
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11
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Shikha, Shandilya E, Priyanka, Maiti S. Directional migration propensity of calf thymus DNA in a gradient of metal ions. Chem Commun (Camb) 2022; 58:9353-9356. [DOI: 10.1039/d2cc03160d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The migration propensity and spatially modulated surface deposition of calf thymus DNA have been reported in response to gradients of different monovalent and divalent ions.
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Affiliation(s)
- Shikha
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Manauli 140306, India
| | - Ekta Shandilya
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Manauli 140306, India
| | - Priyanka
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Manauli 140306, India
| | - Subhabrata Maiti
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Manauli 140306, India
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12
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Deshwal A, Shikha, Maiti S. Trade-off between carbohydrates and metal ions regulates the chemotactic directionality of alkaline phosphatase. Chem Commun (Camb) 2022; 58:12851-12854. [DOI: 10.1039/d2cc04360b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The role of the Hofmeister interaction in governing the chemotactic behavior of alkaline phosphatase in the presence of carbohydrate and metal ion gradients has been established.
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Affiliation(s)
- Akshi Deshwal
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Manauli 140306, India
| | - Shikha
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Manauli 140306, India
| | - Subhabrata Maiti
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Manauli 140306, India
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