Interaction of KMP-11 and its mutants with ionic liquid choline dihydrogen phosphate: Multispectroscopic studies aided by docking and molecular dynamics simulations

Saha, Saumen; Sannigrahi, Achinta; Chattopadhyay, Krishnananda; Chowdhury, Joydeep

doi:10.1016/j.molliq.2020.112475

Cited by 7 publications

(12 citation statements)

References 39 publications

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“…The changes in the molar Gibbs energy (Δ G 0 ) and entropy contribution to the binding ( T Δ S 0 ) were then determined easily from the following equations. 49 Δ G 0 = −RT ln K b Δ G 0 = Δ H 0 − T Δ S 0 where R represents the universal gas constant, and T symbolizes the temperature measured in Kelvin.…”

Section: Methodsmentioning

confidence: 99%

Interaction of plant alkaloid berberine with β-lactoglobulin: an account from spectroscopic, thermodynamic, and small-angle X-ray scattering studies aided by theoretical calculations

Saha,

Bhattacharjee,

Chowdhury

2023

New J. Chem.

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Section: Methodsmentioning

confidence: 99%

Interaction of plant alkaloid berberine with β-lactoglobulin: an account from spectroscopic, thermodynamic, and small-angle X-ray scattering studies aided by theoretical calculations

Saha,

Bhattacharjee,

Chowdhury

2023

New J. Chem.

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“…In 2020, Bunagan and co-workers determined that [Chn][Cl] interacts favorably with the polyproline II (PPII) helix structure of late embryogenesis abundant protein thus imparting structural stability to the protein . One more aspect of [Chn][DHP] effects toward protein was studied by Saha et al Through multispectroscopic studies, they revealed that there was no sign of an effect of [Chn][DHP] toward KMP-11. This was supported by docking and molecular dynamics simulations studies .…”

Section: Recent Advances In Exploring Cholinium-based Ionic Liquids F...mentioning

confidence: 99%

“…One more aspect of [Chn][DHP] effects toward protein was studied by Saha et al Through multispectroscopic studies, they revealed that there was no sign of an effect of [Chn][DHP] toward KMP-11. This was supported by docking and molecular dynamics simulations studies . In a recent work by Hallett and co-workers, thermal stability and conformational transitions of avidin protein in different Chn ILs were examined using DLS, SAXS, DSF, CD spectroscopy, and binding experiments.…”

Section: Recent Advances In Exploring Cholinium-based Ionic Liquids F...mentioning

confidence: 99%

“…Effect of Cholinium-Based ILs on the Structural Features of Some Other Proteins. In this section, discussion of the literature on the impact of Chn ILs on some uncommon yet biologically significant proteins such as keratin, 189,190 horseadish peroxidase (HRP), 191 ascorbate oxidase from Cucurbita (AOC), 191 azurin, 191 D-fructose dehydrogenase (FDH), 191 L-asparaginase, 192 alkaline protease alcalase (APA), 193 lactate oxidase, 194 laccase, 195 concanavalin A (Con A), 196 aggregated recombinant proteins expressed in Escherichia coli, 197 hemocyanins, 198 herceptin, 199 late embryogenesis abundant protein, 200 kinetoplastid membrane protein-11 (KMP-11), 201 avidin, 202 and green fluorescent protein 203 is provided. Idris et al 189 conducted experiments on the dissolution of turkey feather keratin in cholinium thioglycolate [Chn][Thg] and two imidazolium-based ILs under nitrogen pressure.…”

Section: Effect Of Cholinium-based Ils On the Structuralmentioning

confidence: 99%

“…This was supported by docking and molecular dynamics simulations studies. 201 In a recent work by Hallett and co-workers, 202 A comprehensive evaluation of the current literature suggests that Chn ILs have profound importance for biomolecules, owing to their designability and miscibility in water. Certainly, the nontoxic behavior of cholinium cation exerts very low impact on the biocompatibility with proteins.…”

Section: Effect Of Cholinium-based Ils On the Structuralmentioning

confidence: 99%

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Contemporary Advancement of Cholinium-Based Ionic Liquids for Protein Stability and Long-Term Storage: Past, Present, and Future Outlook

Sindhu

Kumar

Venkatesu

2022

ACS Sustainable Chem. Eng.

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In the past two decades, ionic liquids (ILs) have been acknowledged as potentially attractive “green” and “designer” solvents since their broader chemical space and the tunable nature of the diverse ions can finely modulate their physiochemical properties while enabling task-specific optimization. They have found numerous applications in fields ranging from enzymatic reactions to protein preservation, which focused on the development of various types of ILs and their application for providing protein stability in vitro. Among various families of ILs, some of them have serious limitations similar to organic solvents; they cause environmental toxicity as they are non-biodegradable. In other words, some of the ILs impart stress to biomolecules and ultimately denature the protein. In this regard, the need for biocompatible ILs has come to the light and cholinium-based ILs (Chn ILs) have proved themselves as the most promising ILs to support the structure of biomolecules. The family of Chn ILs has only taken growth in recent years. Despite the numerous studies, more exhaustive research in the field of Chn ILs and biomolecules still needs acceleration. Herein, we review the strategies and current progress on Chn ILs for protein and enzyme-based applications keeping in mind all crucial past and present research outcomes. Furthermore, we elucidate an overview of the various ways to enhance enzymatic activity, structural stability, and long-term storage of proteins in the presence of Chn ILs. We believe these insights will be fruitful for designing various processes based on ILs in the diverse field of biotechnology and ILs will serve as novel solvents for protein stability and enzymatic reactions, maintaining their utility in industrial and biomedical based applications. The huge varieties of biobased Chn ILs hold the promise of recent advances and developments for the correct selection of long-term storage of enzymes.

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Interaction between Halogenated Phenols and Thyroxine‐Binding Protein: A Multispectral and Computational Approach

Liang,

Chen,

Huang

et al. 2024

ChemistrySelect

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The aim of this study was to understand the interaction between transthyretin (TTR) and halogenated phenols (HPs) including 2,4‐dichlorophenol (DCP), 2,4,6‐trichlorophenol (TCP), pentachlorophenol (PCP), 2‐bromophenol (2‐BP), 2,4‐dibromophenol (DBP) and 2,4,6‐tribromophenol (TBP). Computer simulation and multi‐spectroscopy techniques were used to investigate the interaction. The fluorescence of TTR was found to be quenched through static quenching and non‐radiative energy transfer by HPs, suggesting that the binding process between HPs and TTR was primarily influenced by van der Waals forces and hydrogen bonds. ANS substitution experiments indicated that HPs interacted with TTR at the T4 binding site. Three‐dimensional fluorescence spectra and Fourier transform infrared spectroscopy were used to investigate the conformational and microenvironmental changes of TTR resulting from the interactions with HPs. Additionally, molecular docking and reduced density gradient analysis were used to identify the specific residues and binding forces involved in the interaction between HPs and TTR binding sites. The findings were subsequently validated through quantum chemical analysis. This research integrates state‐of‐the‐art multispectral analytical methodologies with sophisticated computational modeling to introduce an innovative approach for dissecting the interactions between halogenated phenols (HPs) and transthyretin (TTR). This methodology offers a novel avenue for investigating the molecular interplay between HPs and TTR, thereby providing critical insights that are instrumental in assessing the latent toxicity of these compounds.

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Interaction of KMP-11 and its mutants with ionic liquid choline dihydrogen phosphate: Multispectroscopic studies aided by docking and molecular dynamics simulations

Cited by 7 publications

References 39 publications

Interaction of plant alkaloid berberine with β-lactoglobulin: an account from spectroscopic, thermodynamic, and small-angle X-ray scattering studies aided by theoretical calculations

Interaction of plant alkaloid berberine with β-lactoglobulin: an account from spectroscopic, thermodynamic, and small-angle X-ray scattering studies aided by theoretical calculations

Contemporary Advancement of Cholinium-Based Ionic Liquids for Protein Stability and Long-Term Storage: Past, Present, and Future Outlook

Interaction between Halogenated Phenols and Thyroxine‐Binding Protein: A Multispectral and Computational Approach

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