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Singh A, Gupta M, Rastogi H, Khare K, Chowdhury PK. Deeper Insights into Mixed Crowding through Enzyme Activity, Dynamics, and Crowder Diffusion. J Phys Chem B 2024; 128:5293-5309. [PMID: 38808573 DOI: 10.1021/acs.jpcb.4c00337] [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: 05/30/2024]
Abstract
Given the fact that the cellular interior is crowded by many different kinds of macromolecules, it is important that in vitro studies be carried out in the presence of mixed crowder systems. In this regard, we have used binary crowders formed by the combination of some of the commonly used crowding agents, namely, Ficoll 70, Dextran 70, Dextran 40, and PEG 8000 (PEG 8), to study how these affect enzyme activity, dynamics, and crowder diffusion. The enzyme chosen is AK3L1, an isoform of adenylate kinase. To investigate its dynamics, we have carried out three single point mutations (A74C, A132C, and A209C) with the cysteine residues being labeled with a coumarin-based solvatochromic probe [CPM: (7-diethylamino-3-(4-maleimido-phenyl)-4-methylcoumarin)]. Both enzyme activity and dynamics decreased in the binary mixtures as compared with the sum of the individual crowders, suggesting a reduction in excluded volume (in the mixture). To gain deeper insights into the binary mixtures, fluorescence correlation spectroscopy studies were carried out using fluorescein isothiocyanate-labeled Dextran 70 and tetramethylrhodamine-labeled AK3L1 as the diffusion probes. Diffusion in binary mixtures was observed to be much more constrained (relative to the sum of the individual crowders) for the labeled enzyme as compared to the labeled crowder showing different environments being faced by the two species. This was further confirmed during imaging of the phase-separated droplets formed in the binary mixtures having PEG as one of the crowding agents. The interior of these droplets was found to be rich in crowders and densely packed, as shown by confocal and digital holographic microscopy images, with the enzymes predominantly residing outside these droplets, that is, in the relatively less crowded regions. Taken together, our data provide important insights into various aspects of the simplest form of mixed crowding, that is, composed of just two components, and also hint at the enhanced complexity that the cellular interior presents toward having a detailed and comprehensive understanding of the same.
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Affiliation(s)
- Arvind Singh
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Monika Gupta
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Harshita Rastogi
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Kedar Khare
- Optics and Photonics Centre, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Pramit K Chowdhury
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
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2
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Bharmoria P, Tietze AA, Mondal D, Kang TS, Kumar A, Freire MG. Do Ionic Liquids Exhibit the Required Characteristics to Dissolve, Extract, Stabilize, and Purify Proteins? Past-Present-Future Assessment. Chem Rev 2024; 124:3037-3084. [PMID: 38437627 PMCID: PMC10979405 DOI: 10.1021/acs.chemrev.3c00551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 02/08/2024] [Accepted: 02/19/2024] [Indexed: 03/06/2024]
Abstract
Proteins are highly labile molecules, thus requiring the presence of appropriate solvents and excipients in their liquid milieu to keep their stability and biological activity. In this field, ionic liquids (ILs) have gained momentum in the past years, with a relevant number of works reporting their successful use to dissolve, stabilize, extract, and purify proteins. Different approaches in protein-IL systems have been reported, namely, proteins dissolved in (i) neat ILs, (ii) ILs as co-solvents, (iii) ILs as adjuvants, (iv) ILs as surfactants, (v) ILs as phase-forming components of aqueous biphasic systems, and (vi) IL-polymer-protein/peptide conjugates. Herein, we critically analyze the works published to date and provide a comprehensive understanding of the IL-protein interactions affecting the stability, conformational alteration, unfolding, misfolding, and refolding of proteins while providing directions for future studies in view of imminent applications. Overall, it has been found that the stability or purification of proteins by ILs is bispecific and depends on the structure of both the IL and the protein. The most promising IL-protein systems are identified, which is valuable when foreseeing market applications of ILs, e.g., in "protein packaging" and "detergent applications". Future directions and other possibilities of IL-protein systems in light-harvesting and biotechnology/biomedical applications are discussed.
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Affiliation(s)
- Pankaj Bharmoria
- CICECO
- Aveiro Institute of Materials, Chemistry Department, University of Aveiro, 3810-193 Aveiro, Portugal
- Department
of Smart Molecular, Inorganic and Hybrid Materials, Institute of Materials Science of Barcelona (ICMAB-CSIC), 08193 Bellaterra, Barcelona, Spain
- Department
of Chemistry and Molecular Biology, Wallenberg Centre for Molecular
and Translational Medicine, University of
Gothenburg, SE-412 96 Göteborg, Sweden
| | - Alesia A. Tietze
- Department
of Chemistry and Molecular Biology, Wallenberg Centre for Molecular
and Translational Medicine, University of
Gothenburg, SE-412 96 Göteborg, Sweden
| | - Dibyendu Mondal
- CICECO
- Aveiro Institute of Materials, Chemistry Department, University of Aveiro, 3810-193 Aveiro, Portugal
- Institute
of Plant Genetics (IPG), Polish Academy of Sciences, Strzeszyńska 34, 60-479 Poznań, Poland
- Centre
for Nano and Material Sciences, JAIN (Deemed-to-be
University), Jain Global
Campus, Bangalore 562112, India
| | - Tejwant Singh Kang
- Department
of Chemistry, UGC Center for Advance Studies-II,
Guru Nanak Dev University (GNDU), Amritsar 143005, Punjab, India
| | - Arvind Kumar
- Salt
and Marine Chemicals Division, CSIR-Central
Salt and Marine Chemicals Research Institute, G. B. Marg, Bhavnagar 364002, Gujarat, India
| | - Mara G Freire
- CICECO
- Aveiro Institute of Materials, Chemistry Department, University of Aveiro, 3810-193 Aveiro, Portugal
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Khan T, Das N, Negi KS, Bhowmik S, Sen P. Understanding the intricacy of protein in hydrated deep eutectic solvent: Solvation dynamics, conformational fluctuation dynamics, and stability. Int J Biol Macromol 2023; 253:127100. [PMID: 37778586 DOI: 10.1016/j.ijbiomac.2023.127100] [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: 05/22/2023] [Revised: 09/21/2023] [Accepted: 09/25/2023] [Indexed: 10/03/2023]
Abstract
Deep eutectic solvents (DESs) are potential biocatalytic media due to their easy preparation, fine-tuneability, biocompatibility, and most importantly, due to their ability to keep protein stable and active. However, there are many unanswered questions and gaps in our knowledge about how proteins behave in these alternate media. Herein, we investigated solvation dynamics, conformational fluctuation dynamics, and stability of human serum albumin (HSA) in 0.5 Acetamide/0.3 Urea/0.2 Sorbitol (0.5Ac/0.3Ur/0.2Sor) DES of varying concentrations to understand the intricacy of protein behaviour in DES. Our result revealed a gradual decrease in the side-chain flexibility and thermal stability of HSA beyond 30 % DES. On the other hand, the associated water dynamics around domain-I of HSA decelerate only marginally with increasing DES content, although viscosity rises considerably. We propose that even though macroscopic solvent properties are altered, a protein feels only an aqueous type of environment in the presence of DES. This is probably the first experimental study to delineate the role of the associated water structure of the enzyme for maintaining its stability inside DES. Although considerable effort is necessary to generalize such claims, it might serve as the basis for understanding why proteins remain stable and active in DES.
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Affiliation(s)
- Tanmoy Khan
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208 016, UP, India
| | - Nilimesh Das
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208 016, UP, India
| | - Kuldeep Singh Negi
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208 016, UP, India
| | - Suman Bhowmik
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208 016, UP, India
| | - Pratik Sen
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208 016, UP, India.
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4
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Barik S, Mahapatra A, Preeyanka N, Sarkar M. Assessing the impact of choline chloride and benzyltrimethylammonium chloride-based deep eutectic solvents on the structure and conformational dynamics of bovine serum albumin: a combined steady-state, time-resolved fluorescence and fluorescence correlation spectroscopic study. Phys Chem Chem Phys 2023; 25:20093-20108. [PMID: 37462948 DOI: 10.1039/d3cp01380d] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2023]
Abstract
Although deep eutectic solvents (DESs) are regarded as useful substitutes for both ionic liquids and common organic solvents for storage and applications of biomolecules, it is still unclear whether all DESs or only specific types of DESs will be suitable for the said purpose. In view of this, the current study aims to report on the structure and conformational dynamics of BSA in the presence of two DESs, namely ethaline (choline chloride:ethylene glycol) and BMEG (benzyltrimethyl ammonium chloride:ethylene glycol), having the same hydrogen bond donor but with a distinct hydrogen bond acceptor, so that how small changes in one constituent of a DES alter the protein-DES interaction at the molecular level can be understood. The protein-DES interaction is investigated by exploiting both ensemble-averaged measurements like steady-state and time-resolved fluorescence spectroscopy, circular dichroism (CD) spectroscopy, and single-molecule sensitive techniques based on fluorescence correlation spectroscopy (FCS). Interestingly, the results obtained from these studies have demonstrated that while a very small quantity of BMEG completely unfolds the native structure of the protein, it remains in a partially unfolded state even at very high ethaline content. More interestingly, it has been found that at very high concentrations of BMEG, the unfolded protein undergoes enhanced protein-protein interaction resulting in the aggregation of BSA. All of the results obtained from these investigations have essentially suggested that both protein-DES interaction and interspecies interaction among the constituent of DESs play a crucial role in governing the overall stability and conformational dynamics of the protein in DESs.
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Affiliation(s)
- Sahadev Barik
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), An OCC of Homi Bhabha National Institute, Jatni, Khurda, Bhubaneswar 752050, Odisha, India.
- Centre of Interdisciplinary Science (CIS), NISER, Bhubaneswar, Jatni, Khurda, 752050, Odisha, India
| | - Amita Mahapatra
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), An OCC of Homi Bhabha National Institute, Jatni, Khurda, Bhubaneswar 752050, Odisha, India.
- Centre of Interdisciplinary Science (CIS), NISER, Bhubaneswar, Jatni, Khurda, 752050, Odisha, India
| | - Naupada Preeyanka
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), An OCC of Homi Bhabha National Institute, Jatni, Khurda, Bhubaneswar 752050, Odisha, India.
- Centre of Interdisciplinary Science (CIS), NISER, Bhubaneswar, Jatni, Khurda, 752050, Odisha, India
| | - Moloy Sarkar
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), An OCC of Homi Bhabha National Institute, Jatni, Khurda, Bhubaneswar 752050, Odisha, India.
- Centre of Interdisciplinary Science (CIS), NISER, Bhubaneswar, Jatni, Khurda, 752050, Odisha, India
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Mahapatra A, Barik S, Satish L, Chakraborty M, Sarkar M. Assessing the Suitability of a Dicationic Ionic Liquid as a Stabilizing Material for the Storage of DNA in Aqueous Medium. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:14857-14868. [PMID: 36394977 DOI: 10.1021/acs.langmuir.2c02530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The present study has been undertaken with an objective to find out a suitable medium for the long-term stability and storage of the ct-DNA structure in aqueous solution. For this purpose, the potential of a pyrrolidinium-based dicationic ionic liquid (DIL) in stabilizing ct-DNA structure has been investigated by following the DNA-DIL interaction. Additionally, in order to understand the fundamental aspects regarding the DNA-DIL interaction in a comprehensive manner, studies are also done by employing structurally similar monocationic ionic liquids (MILs). The investigations have been carried out both at ensemble-average and single molecular level by using various spectroscopic techniques. The molecular docking study has also been performed to throw more light into the experimental observations. The combined steady-state and time-resolved fluorescence, fluorescence correlation spectroscopy, and circular dichroism measurements have demonstrated that DILs can effectively be used as better storage media for ct-DNA as compared to MILs. Investigations have also shown that the extra electrostatic interaction between the cationic head group of DIL and the phosphate backbone of DNA is primarily responsible for providing better stabilization to ct-DNA, retaining its native structure in aqueous medium. The outcomes of the present study are also expected to provide valuable insights in designing new polycationic IL systems that can be used in nucleic acid-based applications.
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Affiliation(s)
- Amita Mahapatra
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), Jatni, Khurda, Bhubaneswar752050, Odisha, India
- Homi Bhabha National Institute (HBNI), Mumbai400094, India
- Centre for Interdisciplinary Sciences (CIS), NISER, Jatni, Khurda, Bhubaneswar752050, Odisha, India
| | - Sahadev Barik
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), Jatni, Khurda, Bhubaneswar752050, Odisha, India
- Homi Bhabha National Institute (HBNI), Mumbai400094, India
- Centre for Interdisciplinary Sciences (CIS), NISER, Jatni, Khurda, Bhubaneswar752050, Odisha, India
| | - Lakkoji Satish
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), Jatni, Khurda, Bhubaneswar752050, Odisha, India
- Homi Bhabha National Institute (HBNI), Mumbai400094, India
- Centre for Interdisciplinary Sciences (CIS), NISER, Jatni, Khurda, Bhubaneswar752050, Odisha, India
| | - Manjari Chakraborty
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), Jatni, Khurda, Bhubaneswar752050, Odisha, India
- Homi Bhabha National Institute (HBNI), Mumbai400094, India
- Centre for Interdisciplinary Sciences (CIS), NISER, Jatni, Khurda, Bhubaneswar752050, Odisha, India
| | - Moloy Sarkar
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), Jatni, Khurda, Bhubaneswar752050, Odisha, India
- Homi Bhabha National Institute (HBNI), Mumbai400094, India
- Centre for Interdisciplinary Sciences (CIS), NISER, Jatni, Khurda, Bhubaneswar752050, Odisha, India
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6
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Ionic liquids as protein stabilizers for biological and biomedical applications: A review. Biotechnol Adv 2022; 61:108055. [DOI: 10.1016/j.biotechadv.2022.108055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 10/13/2022] [Accepted: 10/23/2022] [Indexed: 11/22/2022]
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7
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Sarkar N, Levinger NE, Datta A. Tribute to Professor Kankan Bhattacharyya. J Phys Chem B 2022; 126:3461-3463. [PMID: 35586923 DOI: 10.1021/acs.jpcb.2c02491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Nilmoni Sarkar
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721 302, West Bengal, India
| | - Nancy E Levinger
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Anindya Datta
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400 076, India
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8
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Tarannum A, Rao JR, Fathima NN. Insights into protein-ionic liquid interaction: A comprehensive overview on theoretical and experimental approaches. Int J Biol Macromol 2022; 209:498-505. [PMID: 35413321 DOI: 10.1016/j.ijbiomac.2022.04.050] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 03/29/2022] [Accepted: 04/06/2022] [Indexed: 01/19/2023]
Abstract
Owing to highly tunable nature, ionic liquids are nesting stance in the scientific community for a wide variety of applications ranging from electrochemistry to product purification, from chemical and biomedical applications to biotechnological interventions and proteomics. Proteins are unstable in its native form and several attempts have been made to stabilize them by addition of various additives. This review focusses on the studies conducted to improve protein stability with ionic liquids along with an emphasis on the mechanism of interaction. This review also specifies and discusses about the brief introduction to ionic liquids, evolution of first-, second-, and third generation of liquids over the years and their selection criterion and applications. Though, there are several elegant reviews available on proteins-ionic liquids interaction, this review systematically highlights the effect of ionic liquids viz., imidazolium, ammonium, phosphonium and choline-based ionic liquids (amino acid-based anions & classical anions) on fibrous proteins viz., collagen and keratin and globular proteins viz., bovine serum albumin and cytochrome c. Thus, this review elaborates the thorough investigations conducted to explore the stabilizing properties of ionic liquids over fibrous and globular proteins.
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Affiliation(s)
- Aafiya Tarannum
- Inorganic and Physical Chemistry Laboratory, CSIR-Central Leather Research Institute, Sardar Patel Road, Adyar, Chennai - 600 020, India
| | - J Raghava Rao
- Inorganic and Physical Chemistry Laboratory, CSIR-Central Leather Research Institute, Sardar Patel Road, Adyar, Chennai - 600 020, India
| | - N Nishad Fathima
- Inorganic and Physical Chemistry Laboratory, CSIR-Central Leather Research Institute, Sardar Patel Road, Adyar, Chennai - 600 020, India.
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9
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Mondal S, Bobbili KB, Paul S, Swamy MJ. DSC and FCS Studies Reveal the Mechanism of Thermal and Chemical Unfolding of CIA17, a Polydisperse Oligomeric Protein from Coccinia Indica. J Phys Chem B 2021; 125:7117-7127. [PMID: 34167304 DOI: 10.1021/acs.jpcb.1c02120] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The mechanism of thermal and chemical unfolding of Coccinia indica agglutinin (CIA17), a chitooligosacharide-specific phloem exudate lectin, was investigated by biophysical approaches. DSC studies revealed that the unfolding thermogram of CIA17 consists of three components (Tm ∼ 98, 106, and 109 °C), which could be attributed to the dissociation of protein oligomers into constituent dimers, dissociation of the dimers into monomers, and unfolding of the monomers. Intrinsic fluorescence studies on the chemical denaturation by guanidinium thiocyanate and guanidinium chloride indicated the presence of two distinct steps in the unfolding pathway, which could be assigned to dissociation of the dimeric protein into monomers and unfolding of the monomers. Results of fluorescence correlation spectroscopic studies could be interpreted in terms of the following model: CIA17 forms oligomeric structures in a concentration dependent manner, with the protein existing as a monomer below 1 nM concentration but associating to form dimers at higher concentrations (KD ≈ 2.9 nM). The dimers associate to yield tetramers with a KD of ∼50 μM, which further associate to form higher oligomers with further increase in concentration. These results are consistent with the proposed role of CIA17 as a key player in the defense response of the plant against microbes and insects.
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Affiliation(s)
- Saradamoni Mondal
- School of Chemistry, University of Hyderabad, Hyderabad-500 046, India
| | | | - Sumanta Paul
- School of Chemistry, University of Hyderabad, Hyderabad-500 046, India
| | - Musti J Swamy
- School of Chemistry, University of Hyderabad, Hyderabad-500 046, India
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10
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Hossain SS, Paul S, Samanta A. Structural Stability and Conformational Dynamics of Cytochrome c in Hydrated Deep Eutectic Solvents. J Phys Chem B 2021; 125:5757-5765. [PMID: 34042450 DOI: 10.1021/acs.jpcb.1c01975] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Many deep eutectic solvents (DESs) are currently being explored as environment-friendly media for biorelated applications. As an understanding of the effect of these solvents on the structure of biomolecules is crucial for these applications, we study how two DESs comprising trimethylglycine (TMG) and ethylene glycol (EG) or glycerol (GL) influence the structural stability and conformational dynamics of cytochrome c (Cytc) using single-molecule-based fluorescence correlation spectroscopy (FCS) technique and several other ensemble-based biophysical methods. The FCS studies on A488-labeled Cytc enable an estimation of the size (20.5 ± 1.5 Å) of the protein and capture its conformational dynamics (54 ± 2 μs) in aqueous buffered solution. It is observed that both size and conformational dynamics of the protein are influenced in the presence of the DESs, but this effect is more pronounced in the case of TMG-EG. The ensemble measurements on both labeled and wild-type Cytc reveal that the protein structure is unfolded completely by TMG-EG, whereas the structure is slightly altered by TMG-GL. The results suggest that the behavior of Cytc in hydrated DESs is determined by the strength of interactions between the DES constituents as well as that between the constituents and the water molecules present in the system.
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Affiliation(s)
- Sk Saddam Hossain
- School of Chemistry, University of Hyderabad, Hyderabad 500046, India
| | - Sneha Paul
- School of Chemistry, University of Hyderabad, Hyderabad 500046, India
| | - Anunay Samanta
- School of Chemistry, University of Hyderabad, Hyderabad 500046, India
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Das N, Khan T, Subba N, Sen P. Correlating Bromelain's activity with its structure and active-site dynamics and the medium's physical properties in a hydrated deep eutectic solvent. Phys Chem Chem Phys 2021; 23:9337-9346. [PMID: 33885064 DOI: 10.1039/d1cp00046b] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Deep eutectic solvents (DESs) are emerging as new media of choice for biocatalysis due to their environmentally friendly nature, fine-tunability, and potential biocompatibility. This work deciphers the behaviour of bromelain in a ternary DES composed of acetamide, urea, and sorbitol at mole fractions of 0.5, 0.3, and 0.2, respectively (0.5Ac/0.3Ur/0.2Sor), with various degrees of hydration. Bromelain is an essential industrial proteolytic enzyme, and the chosen DES is non-ionic and liquid at room temperature. This provides us with a unique opportunity to contemplate protein behaviour in a non-ionic DES for the very first time. Our results infer that at a low DES concentration (up to 30% V/V DES), bromelain adopts a more compact structural conformation, whereas at higher DES concentrations, it becomes somewhat elongated. The microsecond conformational fluctuation time around the active site of bromelain gradually increases with increasing DES concentration, especially beyond 30% V/V. Interestingly, bromelain retains most of its enzymatic activity in the DES, and at some concentrations, the activity is even higher compared with its native state. Furthermore, we correlate the activity of bromelain with its structure, its active-site dynamics, and the physical properties of the medium. Our results demonstrate that the compact structural conformation and flexibility of the active site of bromelain favour its proteolytic activity. Similarly, a medium with increased polarity and decreased viscosity is favourable for its activity. The presented physical insights into how enzymatic activity depends on the protein structure and dynamics and the physical properties of the medium might provide useful guidelines for the rational design of DESs as biocatalytic media.
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Affiliation(s)
- Nilimesh Das
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur - 208 016, UP, India.
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12
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Pramanik U, Chakraborty S, Bhattacharyya K, Mukherjee S. An intrinsically disordered protein in F127 hydrogel: Fluorescence correlation spectroscopy and structural diversity of beta casein. Chem Phys Lett 2021. [DOI: 10.1016/j.cplett.2020.138105] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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13
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Pabbathi A, Samanta A. On the Stability and Conformational Dynamics of Cytochrome c in Ammonium Ionic Liquids. J Phys Chem B 2020; 124:8132-8140. [PMID: 32830967 DOI: 10.1021/acs.jpcb.0c05633] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Owing to their potential applications in the extraction, purification, and preservation of biomolecules and biocatalysis, ionic liquids (ILs) have gained great attention in biotechnology. Although it is known that the structure and dynamics of proteins in ILs depend on the nature of both proteins and ILs, the biophysical mechanism governing the protein-IL interaction, which determines the stability of proteins or the activity of an enzyme in these nonconventional media, is yet to be understood clearly. Herein, we study the effect of two ammonium ILs, triethylammonium dihydrogen phosphate (TEAP) and tributylammonium dihydrogen phosphate (TBAP), on the stability and conformational dynamics of cytochrome c (Cyt c) in its native and unfolded states, employing primarily the single molecule-based fluorescence correlation spectroscopy (FCS) technique. The results show that the native structure of Cyt c is not significantly altered by TEAP, but the tertiary structure is perturbed to a great extent by TBAP, which comprises a longer alkyl chain. Fluctuations of the fluorescence intensity of Alexa488 dye-labeled Cyt c in FCS measurements reveal conformational dynamics (67 ± 10 μs) in the native state of Cyt c that is accelerated in the presence of both ILs but not affected when Cyt c is in its unfolded state. The present findings demonstrate how the stability of this protein can be modulated by using ammonium ILs of different alkyl chain lengths.
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Affiliation(s)
- Ashok Pabbathi
- School of Chemistry, University of Hyderabad, Hyderabad 500046, India
| | - Anunay Samanta
- School of Chemistry, University of Hyderabad, Hyderabad 500046, India
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14
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Samant V, Dey A, Naresh Patwari G. Probing the interaction between human serum albumin and the sodium dodecyl sulphate with fluorescence correlation spectroscopy. J CHEM SCI 2020. [DOI: 10.1007/s12039-020-01816-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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15
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Swain BC, Subadini S, Rout J, Sakshi, Mishra PP, Sahoo H, Tripathy U. Biophysical study on complex formation between β-Lactoglobulin and vitamin B12. Food Chem 2020; 312:126064. [DOI: 10.1016/j.foodchem.2019.126064] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 12/03/2019] [Accepted: 12/14/2019] [Indexed: 01/27/2023]
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16
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A spectroscopic and computational intervention of interaction of lysozyme with 6-mercaptopurine. Anal Bioanal Chem 2020; 412:2565-2577. [DOI: 10.1007/s00216-020-02483-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 01/09/2020] [Accepted: 02/03/2020] [Indexed: 12/26/2022]
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17
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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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18
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Takekiyo T, Miyazaki K, Watanabe Y, Uesugi Y, Tanaka S, Ishikawa Y, Yoshimura Y. Solubilization and recovery of heat-aggregated cytochrome c using alkylammonium nitrate. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.111239] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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19
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Nandy A, Chakraborty S, Nandi S, Bhattacharyya K, Mukherjee S. Structure, Activity, and Dynamics of Human Serum Albumin in a Crowded Pluronic F127 Hydrogel. J Phys Chem B 2019; 123:3397-3408. [DOI: 10.1021/acs.jpcb.9b00219] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Atanu Nandy
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhopal 462066, Madhya Pradesh, India
| | - Subhajit Chakraborty
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhopal 462066, Madhya Pradesh, India
| | - Somen Nandi
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Kankan Bhattacharyya
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhopal 462066, Madhya Pradesh, India
| | - Saptarshi Mukherjee
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhopal 462066, Madhya Pradesh, India
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Zhang R, Wu H, He M, Zhang W, Xu W. Mobility Capillary Electrophoresis-Restrained Modeling Method for Protein Structure Analysis in Mixtures. J Phys Chem B 2019; 123:2335-2341. [PMID: 30807169 DOI: 10.1021/acs.jpcb.9b01148] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Protein stereostructure analysis in mixtures still remains challenging, especially large-scale analysis such as in proteomics. With the capability of measuring the hydrodynamic radius of ions in the liquid phase, mobility capillary electrophoresis (MCE) has been applied to study the structure of peptides. In this study, MCE was extended for protein mixture separation and their corresponding hydrodynamic radius analyses. After ellipsoid approximation, the results obtained by MCE experiments were then used as a restraint in molecular dynamics simulations to predict the most probable structure of each protein. Besides a three-protein mixture, a mixture of disulfide bond reduced insulin was also studied by this MCE-restrained modeling method. The results obtained by this method agree with literature studies, and mass spectrometry experiments were also carried out to confirm our findings.
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Affiliation(s)
- Rongkai Zhang
- School of Life Science , Beijing Institute of Technology , Beijing 100081 , China
| | - Haimei Wu
- School of Life Science , Beijing Institute of Technology , Beijing 100081 , China
| | - Muyi He
- School of Life Science , Beijing Institute of Technology , Beijing 100081 , China
| | - Wenjing Zhang
- School of Life Science , Beijing Institute of Technology , Beijing 100081 , China
| | - Wei Xu
- School of Life Science , Beijing Institute of Technology , Beijing 100081 , China
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Roy S, Mandal S, Banerjee P, Sarkar N. Modification of fatty acid vesicle using an imidazolium-based surface active ionic liquid: a detailed study on its modified properties using spectroscopy and microscopy techniques
$$^{\S }$$
§. J CHEM SCI 2018. [DOI: 10.1007/s12039-018-1532-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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22
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Ionic Liquid: Complexity in Structure and Dynamics, Interaction with Proteins and In Situ Generation of Metal Nano-clusters for Live Cell Imaging. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES INDIA SECTION A-PHYSICAL SCIENCES 2018. [DOI: 10.1007/s40010-018-0516-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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23
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Nandi S, Parui S, Halder R, Jana B, Bhattacharyya K. Interaction of proteins with ionic liquid, alcohol and DMSO and in situ generation of gold nano-clusters in a cell. Biophys Rev 2018; 10:757-768. [PMID: 29147940 PMCID: PMC5988615 DOI: 10.1007/s12551-017-0331-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2017] [Accepted: 10/23/2017] [Indexed: 12/27/2022] Open
Abstract
In this review, we give a brief overview on how the interaction of proteins with ionic liquids, alcohols and dimethyl sulfoxide (DMSO) influences the stability, conformational dynamics and function of proteins/enzymes. We present experimental results obtained from fluorescence correlation spectroscopy on the effect of ionic liquid or alcohol or DMSO on the size (more precisely, the diffusion constant) and conformational dynamics of lysozyme, cytochrome c and human serum albumin in aqueous solution. The interaction of ionic liquid with biomolecules (e.g. protein, DNA etc.) has emerged as a current frontier. We demonstrate that ionic liquids are excellent stabilizers of protein and DNA and, in some cases, cause refolding of a protein already denatured by chemical denaturing agents. We show that in ethanol-water binary mixture, proteins undergo non-monotonic changes in size and dynamics with increasing ethanol content. We also discuss the effect of water-DMSO mixture on the stability of proteins. We demonstrate how large-scale molecular dynamics simulations have revealed the molecular origin of this observed phenomenon and provide a microscopic picture of the immediate environment of the biomolecules. Finally, we describe how favorable interactions of ionic liquids may be utilized for in situ generation of fluorescent gold nano-clusters for imaging a live cell.
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Affiliation(s)
- Somen Nandi
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata, 700 032, India
| | - Sridip Parui
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata, 700 032, India
| | - Ritaban Halder
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata, 700 032, India
| | - Biman Jana
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata, 700 032, India.
| | - Kankan Bhattacharyya
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata, 700 032, India.
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal, Madhya Pradesh, 462 066, India.
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24
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Innovative aspects of protein stability in ionic liquid mixtures. Biophys Rev 2018; 10:841-846. [PMID: 29549586 DOI: 10.1007/s12551-018-0411-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 03/05/2018] [Indexed: 10/17/2022] Open
Abstract
Mixtures of ionic liquids (ILs) have attracted our attention because of their extraordinary performances in extraction technologies and in absorbing large amount of CO2 gas. It has been observed that when two or more ILs are mixed in different proportions, a new solvent is obtained which is much better than that of each component of ILs from which the mixture is obtained. Within a mixture of ILs, several unidentified interactions occur among several ions which give rise to unique solvent properties to the mixture. Herein, in this review, we have highlighted the utilization of the advantageous properties of the IL mixtures in protein stability studies. This approach is exceptional and opens new directions to the use of ILs in biotechnology.
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Aghevlian S, Lu Y, Winnik MA, Hedley DW, Reilly RM. Panitumumab Modified with Metal-Chelating Polymers (MCP) Complexed to 111In and 177Lu-An EGFR-Targeted Theranostic for Pancreatic Cancer. Mol Pharm 2018; 15:1150-1159. [PMID: 29314858 DOI: 10.1021/acs.molpharmaceut.7b01000] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
A metal-chelating polymer (MCP) with a polyglutamide (PGlu) backbone presenting on average 13 DOTA (tetraazacyclododecane-1,4,7,10-tetraacetic acid) chelators for complexing 111In or 177Lu and 10 polyethylene glycol (PEG) chains to minimize liver and spleen uptake was conjugated to antiepidermal growth factor receptor (EGFR) monoclonal antibody (mAb), panitumumab. Because panitumumab-MCP may be dual-labeled with 111In and 177Lu for SPECT, or radioimmunotherapy (RIT) exploiting the Auger electrons or β-particle emissions, respectively, we propose that panitumumab-MCP could be a useful theranostic agent for EGFR-positive PnCa. Bioconjugation was achieved by reaction of a hydrazine nicotinamide (HyNIC) group on the MCP with an aryl aromatic aldehyde introduced into panitumumab by reaction with succinimidyl-4-formylbenzamide (S-4FB). The conjugation reaction was monitored by measurement of the chromophoric bis-aryl hydrazone bond formed (ε350 nm = 24 500 M-1 cm-1) to achieve two MCPs/panitumumab. Labeling of panitumumab-MCP with 111In or 177Lu demonstrated that masses as small as 0.1 μg were labeled to >90% labeling efficiency (L.E.) and a specific activity (SA) of >70 MBq/μg. Panitumumab-DOTA incorporating two DOTA per mAb was labeled with 111In or 177Lu to a maximum SA of 65 MBq/μg and 46 MBq/μg, respectively. Panitumumab-MCP-177Lu exhibited saturable binding to EGFR-overexpressing MDA-MB-468 human breast cancer cells. The Kd for binding of panitumumab-MCP-177Lu to EGFR (2.2 ± 0.6 nmol/L) was not significantly different than panitumumab-DOTA-177Lu (1.0 ± 0.4 nmol/L). 111In and 177Lu were stably complexed to panitumumab-MCP. Panitumumab-MCP-111In exhibited similar whole body retention (55-60%) as panitumumab-DOTA-111In in NOD-scid mice up to 72 h postinjection (p.i.) and equivalent excretion of radioactivity into the urine and feces. The uptake of panitumumab-MCP-111In in most normal tissues in NOD-scid mice with EGFR-positive PANC-1 human pancreatic cancer (PnCa) xenografts at 72 h p.i. was not significantly different than panitumumab-DOTA-111In, except for the liver which was 3-fold greater for panitumumab-MCP-111In. Tumor uptake of panitumumab-MCP-111In (6.9 ± 1.3%ID/g) was not significantly different than panitumumab-DOTA-11In (6.6 ± 3.3%ID/g). Tumor uptake of panitumumab-MCP-111In and panitumumab-DOTA-111In were reduced by preadministration of excess panitumumab, suggesting EGFR-mediated uptake. Tumor uptake of nonspecific IgG-MCP (5.4 ± 0.3%ID/g) was unexpectedly similar to panitumumab-MCP-111In. An increased hydrodynamic radius of IgG when conjugated to an MCP may encourage tumor uptake via the enhanced permeability and retention (EPR) effect. Tumor uptake of panitumumab-DOTA-111In was 3.5-fold significantly higher than IgG-DOTA-111In. PANC-1 tumors were imaged by microSPECT/CT at 72 h p.i. of panitumumab-MCP-111In or panitumumab-DOTA-111In. Tumors were not visualized with preadministration of excess panitumumab to block EGFR, or with nonspecific IgG radioimmunoconjugates. We conclude that linking panitumumab to an MCP enabled higher SA labeling with 111In and 177Lu than DOTA-conjugated panitumumab, with preserved EGFR binding in vitro and comparable tumor localization in vivo in mice with s.c. PANC-1 human PnCa xenografts. Normal tissue distribution was similar except for the liver which was higher for the polymer radioimmunoconjugates.
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Affiliation(s)
- Sadaf Aghevlian
- Department of Pharmaceutical Sciences , University of Toronto , 144 College Street , Toronto , ON M5S 3M2 , Canada
| | - Yijie Lu
- Department of Chemistry , University of Toronto , 80 St. George Street , Toronto , ON M5S 3H6 , Canada
| | - Mitchell A Winnik
- Department of Chemistry , University of Toronto , 80 St. George Street , Toronto , ON M5S 3H6 , Canada
| | - David W Hedley
- Department of Medical Oncology, Princess Margaret Cancer Centre , 610 University Avenue , Toronto , ON M5G 2M9 , Canada
| | - Raymond M Reilly
- Department of Pharmaceutical Sciences , University of Toronto , 144 College Street , Toronto , ON M5S 3M2 , Canada.,Department of Medical Imaging , University of Toronto , 263 McCaul Street , Toronto , ON M5T 1W7 , Canada.,Toronto General Research Institute and Joint Department of Medical Imaging , University Health Network , 200 Elizabeth Street , Toronto , ON M5G 2C4 , Canada
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26
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Takekiyo T, Ishikawa Y, Yoshimura Y. Cryopreservation of Proteins Using Ionic Liquids: A Case Study of Cytochrome c. J Phys Chem B 2017; 121:7614-7620. [DOI: 10.1021/acs.jpcb.7b05158] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Takahiro Takekiyo
- Department of Applied Chemistry, National Defense Academy, 1-10-20, Hashirimizu, Yokosuka,
Kanagawa 239-8686, Japan
| | - Yuka Ishikawa
- Department of Applied Chemistry, National Defense Academy, 1-10-20, Hashirimizu, Yokosuka,
Kanagawa 239-8686, Japan
| | - Yukihiro Yoshimura
- Department of Applied Chemistry, National Defense Academy, 1-10-20, Hashirimizu, Yokosuka,
Kanagawa 239-8686, Japan
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27
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Amin MA, Halder R, Ghosh C, Jana B, Bhattacharyya K. Effect of alcohol on the structure of cytochrome C: FCS and molecular dynamics simulations. J Chem Phys 2017; 145:235102. [PMID: 28010091 DOI: 10.1063/1.4972065] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Effect of ethanol on the size and structure of a protein cytochrome C (Cyt C) is investigated using fluorescence correlation spectroscopy (FCS) and molecular dynamics (MD) simulations. For FCS studies, Cyt C is covalently labeled with a fluorescent probe, alexa 488. FCS studies indicate that on addition of ethanol, the size of the protein varies non-monotonically. The size of Cyt C increases (i.e., the protein unfolds) on addition of alcohol (ethanol) up to a mole fraction of 0.2 (44.75% v/v) and decreases at higher alcohol concentration. In order to provide a molecular origin of this structural transition, we explore the conformational free energy landscape of Cyt C as a function of radius of gyration (Rg) at different compositions of water-ethanol binary mixture using MD simulations. Cyt C exhibits a minimum at Rg ∼ 13 Å in bulk water (0% alcohol). Upon increasing ethanol concentration, a second minimum appears in the free energy surface with gradually larger Rg up to χEtOH ∼ 0.2 (44.75% v/v). This suggests gradual unfolding of the protein. At a higher concentration of alcohol (χEtOH > 0.2), the minimum at large Rg vanishes, indicating compaction. Analysis of the contact map and the solvent organization around protein indicates a preferential solvation of the hydrophobic residues by ethanol up to χEtOH = 0.2 (44.75% v/v) and this causes the gradual unfolding of the protein. At high concentration (χEtOH = 0.3 (58% v/v)), due to structural organization in bulk water-ethanol binary mixture, the extent of preferential solvation by ethanol decreases. This causes a structural transition of Cyt C towards a more compact state.
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Affiliation(s)
- Md Asif Amin
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Ritaban Halder
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Catherine Ghosh
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Biman Jana
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Kankan Bhattacharyya
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
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28
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Kundu S, Banerjee C, Sarkar N. Inhibiting the Fibrillation of Serum Albumin Proteins in the Presence of Surface Active Ionic Liquids (SAILs) at Low pH: Spectroscopic and Microscopic Study. J Phys Chem B 2017; 121:7550-7560. [DOI: 10.1021/acs.jpcb.7b03457] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Sangita Kundu
- Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, WB, India
| | - Chiranjib Banerjee
- Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, WB, India
| | - Nilmoni Sarkar
- Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, WB, India
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29
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30
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GHOSH CATHERINE, ASIF AMIN MD, JANA BIMAN, BHATTACHARYYA KANKAN. Size and Structure of Cytochrome-c bound to Gold nano-clusters: Effect of Ethanol. J CHEM SCI 2017. [DOI: 10.1007/s12039-017-1239-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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31
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Roy A, Kundu S, Dutta R, Sarkar N. Influence of bile salt on vitamin E derived vesicles involving a surface active ionic liquid and conventional cationic micelle. J Colloid Interface Sci 2017; 501:202-214. [PMID: 28456104 DOI: 10.1016/j.jcis.2017.04.051] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 04/17/2017] [Accepted: 04/18/2017] [Indexed: 11/30/2022]
Abstract
This study has been actually performed with the aim to develop vitamin E derived vesicles individually from a surface active ionic liquid (1-Hexadecyl-3-Methylimidazolium chloride ([C16mim]Cl)) and a common cationic amphiphile (benzyldimethylhexadecylammonium chloride (BHDC)) and also to investigate their consequent breakdown in presence of bile salt molecule. From this study, it is revealed that the rotational motion of coumarin 153 (C153) molecule is hindered as the vitamin E content is increased in the individual micellar solution of [C16mim]Cl and BHDC. The extent of enhancement in rotational relaxation time is more pronounced in case of [C16mim]Cl-vitamin E solutions than in the BHDC-vitamin E vesicular aggregates which confirms the greater rigidity of the former vesicular system than the later one. Moreover, the effect of bile salt in the vitamin E forming vesicular assemblies have also been unravelled. It is found that the large area occupancy by the steroidal backbone of the bile salt plays a crucial role towards the enlargement of the average surfactant head group area. This results in disintegration of the vesicles composed of vitamin E and consequently, vesicles are transformed into mixed micellar aggregates. From the anisotropy measurement it is found that the rotational motion of C153 is more hindered in the [C16mim]Cl/BHDC-NaCh mixed micelles compared to that inside the individual vesicles. The fluorescence correlation spectroscopic (FCS) study also confirms that the mixed micelles have a more compact structure than that of the [C16mim]Cl-vitamin E and BHDC-vitamin E vesicles. Altogether, the micelle to vesicle transition involving any vitamin and their disruption by bile salt would be an interesting investigation both from the view point of basic colloidal chemistry and towards the generation of new drug delivery vehicle due to their unique microenvironment. Therefore, in future, these systems can be utilised as vehicle for the transport and as well as delivery of drugs and as probable reactor in nanomaterial synthesis.
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Affiliation(s)
- Arpita Roy
- Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, WB, India
| | - Sangita Kundu
- Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, WB, India
| | - Rupam Dutta
- Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, WB, India
| | - Nilmoni Sarkar
- Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, WB, India.
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Kumar A, Bisht M, Venkatesu P. Biocompatibility of ionic liquids towards protein stability: A comprehensive overview on the current understanding and their implications. Int J Biol Macromol 2017; 96:611-651. [DOI: 10.1016/j.ijbiomac.2016.12.005] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 12/02/2016] [Accepted: 12/04/2016] [Indexed: 10/20/2022]
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Roy A, Dutta R, Banerjee P, Kundu S, Sarkar N. 5-Methyl Salicylic Acid-Induced Thermo Responsive Reversible Transition in Surface Active Ionic Liquid Assemblies: A Spectroscopic Approach. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:7127-37. [PMID: 27345738 DOI: 10.1021/acs.langmuir.6b01287] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
This article describes the formation of stable unilamellar vesicles involving surface active ionic liquid (SAIL), 1-hexadecyl-3-methylimidazolium chloride (C16mimCl), and 5-methyl salicylic acid (5mS). Turbidity, dynamic light scattering (DLS), transmission electron microscopy (TEM), and viscosity measurements suggest that C16mimCl containing micellar aggregates are transformed to elongated micelle and finally into vesicular aggregates with the addition of 5mS. Besides, we have also investigated the photophysical aspects of a hydrophobic (coumarin 153, C153) and a hydrophilic molecule (rhodamine 6G (R6G) perchlorate) during 5mS-induced micelle to vesicle transition. The rotational motion of C153 becomes slower, whereas faster motion is observed for R6G during micelle to vesicle transition. Moreover, the fluorescence correlation spectroscopy (FCS) measurements suggest that the translational diffusion of hydrophobic probe becomes slower in C16mimCl-5mS aggregates in comparison to C16mimCl micelle. However, a reverse trend in translational diffusion motion of hydrophilic molecule has been observed in C16mimCl-5mS aggregates. Moreover, we have also found that the C16mimCl-5mS containing vesicles are transformed into micelles upon enhanced temperature, and it is further confirmed by turbidity, DLS measurements that this transition is a reversible one. Finally, temperature-induced rotational motion of C153 and R6G has been monitored in C16mimCl-5mS aggregates to get a complete scenario regarding the temperature-induced vesicle to micelle transition.
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Affiliation(s)
- Arpita Roy
- Department of Chemistry, Indian Institute of Technology , Kharagpur 721302, WB, India
| | - Rupam Dutta
- Department of Chemistry, Indian Institute of Technology , Kharagpur 721302, WB, India
| | - Pavel Banerjee
- Department of Chemistry, Indian Institute of Technology , Kharagpur 721302, WB, India
| | - Sangita Kundu
- Department of Chemistry, Indian Institute of Technology , Kharagpur 721302, WB, India
| | - Nilmoni Sarkar
- Department of Chemistry, Indian Institute of Technology , Kharagpur 721302, WB, India
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Bhunia D, Chowdhury R, Bhattacharyya K, Ghosh S. Fluorescence fluctuation of an antigen-antibody complex: circular dichroism, FCS and smFRET of enhanced GFP and its antibody. Phys Chem Chem Phys 2016; 17:25250-9. [PMID: 26353083 DOI: 10.1039/c5cp04908c] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The structure and dynamics of an antigen-antibody complex are monitored by circular dichroism (CD) spectroscopy, fluorescence correlation spectroscopy (FCS) and single molecule FRET (smFRET). In this work, the antigen is enhanced GFP (EGFP) and the antibody is anti-EGFP VHH-His6. From FCS measurements, the hydrodynamic radius (rH) of EGFP and its antibody (VHH-His6) is found to be 24 ± 2 Å and 18 ± 2 Å, respectively. For the antigen-antibody complex (EGFP:anti-EGFP VHH-His6), rH is 41 ± 3 Å. CD spectra indicate that the addition of guanidium hydrochloride (GdnHCl) causes unfolding of the antigen, its antibody and their complex, and a consequent increase in size is observed from FCS data. smFRET between EGFP (donor, D) and Alexa 594 (acceptor, A) bound to anti-EGFP VHH-His6 reveals a time dependent fluctuation in donor-acceptor distances. This suggests that the structure of the antigen-antibody complex is dynamic in nature and is not rigid.
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Affiliation(s)
- Debmalya Bhunia
- Organic & Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, Jadavpur, Kolkata-700032, India.
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35
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Ghosh C, Bhunia D, Ghosh S, Jana B, Ghosh S, Bhattacharyya K. Fluorescence Probing of Fluctuating Microtubule using a Covalent Fluorescent Probe: Effect of Taxol. ChemistrySelect 2016. [DOI: 10.1002/slct.201600353] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Catherine Ghosh
- Department of Physical Chemistry; Indian Association for the Cultivation of Science; Jadavpur Kolkata- 700032 India
| | - Debmalya Bhunia
- Organic & Medicinal Chemistry Division; CSIR-Indian Institute of Chemical Biology; Jadavpur Kolkata- 700032 India
| | - Shirsendu Ghosh
- Department of Physical Chemistry; Indian Association for the Cultivation of Science; Jadavpur Kolkata- 700032 India
| | - Batakrishna Jana
- Organic & Medicinal Chemistry Division; CSIR-Indian Institute of Chemical Biology; Jadavpur Kolkata- 700032 India
| | - Surajit Ghosh
- Organic & Medicinal Chemistry Division; CSIR-Indian Institute of Chemical Biology; Jadavpur Kolkata- 700032 India
| | - Kankan Bhattacharyya
- Department of Physical Chemistry; Indian Association for the Cultivation of Science; Jadavpur Kolkata- 700032 India
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Chattoraj S, Amin MA, Bhattacharyya K. Cytochrome c-Capped Fluorescent Gold Nanoclusters: Imaging of Live Cells and Delivery of Cytochrome c. Chemphyschem 2016; 17:2088-95. [PMID: 27028215 DOI: 10.1002/cphc.201501163] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Indexed: 01/09/2023]
Abstract
Cytochrome c-capped fluorescent gold nanoclusters (Au-NCs) are used for imaging of live lung and breast cells. Delivery of cytochrome c inside the cells is confirmed by covalently attaching a fluorophore (Alexa Fluor 594) to cytochrome c-capped Au-NCs and observing fluorescence from Alexa 594 inside the cell. Mass spectrometry studies suggest that in bulk water, addition of glutathione (GSH) to cytochrome c-capped Au-NCs results in the formation of glutathione-capped Au-NCs and free apo-cytochrome c. Thus glutathione displaces cytochrome c as a capping agent. Using confocal microscopy, the emission spectra and decay of Au-NCs are measured in live cells. From the position of the emission maximum it is shown that the Au-NCs exist as Au8 in bulk water and as Au13 inside the cells. Fluorescence resonance energy transfer from cytochrome c-Au-NC (donor) to Mitotracker Orange (acceptor) indicates that the Au-NCs localise in the mitochondria of live cells.
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Affiliation(s)
- Shyamtanu Chattoraj
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata, 700 032, India), Fax: (91)-33-2473-2805
| | - Md Asif Amin
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata, 700 032, India), Fax: (91)-33-2473-2805
| | - Kankan Bhattacharyya
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata, 700 032, India), Fax: (91)-33-2473-2805.
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37
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Khan MF, Singh MK, Sen S. Measuring Size, Size Distribution, and Polydispersity of Water-in-Oil Microemulsion Droplets using Fluorescence Correlation Spectroscopy: Comparison to Dynamic Light Scattering. J Phys Chem B 2016; 120:1008-20. [DOI: 10.1021/acs.jpcb.5b09920] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Mohammad Firoz Khan
- Spectroscopy Laboratory,
School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Moirangthem Kiran Singh
- Spectroscopy Laboratory,
School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Sobhan Sen
- Spectroscopy Laboratory,
School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
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38
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Ghosh S, Bhattacharyya K. Single-molecule Spectroscopy: Exploring Heterogeneity in Chemical and Biological Systems. CHEM REC 2016; 16:601-13. [DOI: 10.1002/tcr.201500214] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Indexed: 11/08/2022]
Affiliation(s)
- Shirsendu Ghosh
- Department of Physical Chemistry; Indian Association for the Cultivation of Science; 2A and 2B, Raja Subodh Chandra Mullick Rd Jadavpur, Kolkata West Bengal 700032 India
| | - Kankan Bhattacharyya
- Department of Physical Chemistry; Indian Association for the Cultivation of Science; 2A and 2B, Raja Subodh Chandra Mullick Rd Jadavpur, Kolkata West Bengal 700032 India
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39
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Sengupta B, Yadav R, Sen P. Startling temperature effect on proteins when confined: single molecular level behaviour of human serum albumin in a reverse micelle. Phys Chem Chem Phys 2016; 18:14350-8. [DOI: 10.1039/c6cp00452k] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The present work reports the effect of confinement, and temperature therein, on the conformational fluctuation dynamics of domain-I of human serum albumin (HSA) by fluorescence correlation spectroscopy (FCS).
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Affiliation(s)
- Bhaswati Sengupta
- Department of Chemistry, Indian Institute of Technology Kanpur
- Kanpur
- India
| | - Rajeev Yadav
- Department of Chemistry, Indian Institute of Technology Kanpur
- Kanpur
- India
| | - Pratik Sen
- Department of Chemistry, Indian Institute of Technology Kanpur
- Kanpur
- India
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40
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Sil P, Paul SS, Silvio ED, Travaglini-Allocatelli C, Chattopadhyay K. Studies of cytochrome c-551 unfolding using fluorescence correlation spectroscopy and other biophysical techniques. Phys Chem Chem Phys 2016; 18:24537-48. [DOI: 10.1039/c6cp04819f] [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
Fluorescence correlation spectroscopy studies with a bacterial cytochrome c labeled at different positions complement NMR hydrogen exchange results.
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Affiliation(s)
- Pallabi Sil
- Structural Biology and Bioinformatics Division
- CSIR-Indian Institute of Chemical Biology
- Kolkata 700032
- India
| | - Simanta Sarani Paul
- Structural Biology and Bioinformatics Division
- CSIR-Indian Institute of Chemical Biology
- Kolkata 700032
- India
| | - Eva Di Silvio
- Department of Biochemical Sciences
- University of Rome “La Sapienza”
- Rome
- Italy
| | | | - Krishnananda Chattopadhyay
- Structural Biology and Bioinformatics Division
- CSIR-Indian Institute of Chemical Biology
- Kolkata 700032
- India
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41
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Banerjee C, Roy A, Kundu N, Banik D, Sarkar N. A new strategy to prepare giant vesicles from surface active ionic liquids (SAILs): a study of protein dynamics in a crowded environment using a fluorescence correlation spectroscopic technique. Phys Chem Chem Phys 2016; 18:14520-30. [DOI: 10.1039/c5cp07225e] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
A simple procedure for the preparation of giant vesicles using surface active ionic liquids (SAILs) has been provided in this paper.
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Affiliation(s)
- Chiranjib Banerjee
- Department of Chemistry
- Indian Institute of Technology
- Kharagpur 721302
- India
| | - Arpita Roy
- Department of Chemistry
- Indian Institute of Technology
- Kharagpur 721302
- India
| | - Niloy Kundu
- Department of Chemistry
- Indian Institute of Technology
- Kharagpur 721302
- India
| | - Debasis Banik
- Department of Chemistry
- Indian Institute of Technology
- Kharagpur 721302
- India
| | - Nilmoni Sarkar
- Department of Chemistry
- Indian Institute of Technology
- Kharagpur 721302
- India
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42
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Kuchlyan J, Kundu N, Banik D, Roy A, Sarkar N. Spectroscopy and Fluorescence Lifetime Imaging Microscopy To Probe the Interaction of Bovine Serum Albumin with Graphene Oxide. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:13793-13801. [PMID: 26646418 DOI: 10.1021/acs.langmuir.5b03648] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The interaction of graphene oxide (GO) with bovine serum albumin (BSA) in aqueous buffer solution has been investigated with various spectroscopic and imaging techniques. At single molecular resolution this interaction has been performed using fluorescence correlation spectroscopy (FCS) and fluorescence lifetime imaging microscopy (FLIM) techniques. The conformational dynamics of BSA on GO's influence have been explored by FCS and circular dichroism (CD) spectroscopy. For the FCS studies BSA was labeled covalently by a fluorophore, Alexa Fluor 488. On the addition of GO in phosphate buffer of 10 mM at pH 7.4 the diffusion time (τD) and the hydrodynamic radius (Rh) of BSA increase due to adsorption of BSA. Conformational relaxation time components of native BSA drastically vary with the addition of GO, signifying the change of conformational dynamics of BSA after addition of GO. The adsorption isotherm also indicates significant adsorption of BSA on the GO surface. Adsorption of BSA on the GO surface has shown in direct images of atomic force microscopy (AFM) and FLIM. Fluorescence quenching study of BSA with addition of GO also indicates that there is strong interaction between BSA and GO.
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Affiliation(s)
- Jagannath Kuchlyan
- Department of Chemistry, Indian Institute of Technology , Kharagpur 721302, WB, India
| | - Niloy Kundu
- Department of Chemistry, Indian Institute of Technology , Kharagpur 721302, WB, India
| | - Debasis Banik
- Department of Chemistry, Indian Institute of Technology , Kharagpur 721302, WB, India
| | - Arpita Roy
- Department of Chemistry, Indian Institute of Technology , Kharagpur 721302, WB, India
| | - Nilmoni Sarkar
- Department of Chemistry, Indian Institute of Technology , Kharagpur 721302, WB, India
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43
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Ghosh S, Parui S, Jana B, Bhattacharyya K. Ionic liquid induced dehydration and domain closure in lysozyme: FCS and MD simulation. J Chem Phys 2015; 143:125103. [DOI: 10.1063/1.4931974] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Shirsendu Ghosh
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700 032, India
| | - Sridip Parui
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700 032, India
| | - Biman Jana
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700 032, India
| | - Kankan Bhattacharyya
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700 032, India
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44
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Haldar S, Sil P, Thangamuniyandi M, Chattopadhyay K. Conversion of amyloid fibrils of cytochrome c to mature nanorods through a honeycomb morphology. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:4213-23. [PMID: 25338286 DOI: 10.1021/la5029993] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Amyloid species with various morphologies have been found for different proteins and disease systems. In this article, we aim to ask if these morphologies are unique to a particular protein or if they convert from one to another. Using a heme protein containing iron as the transition-metal activator of aggregation and a negatively charged surfactant, partial unfolding of the protein and its aggregation have been induced. In the pathway of aggregation, we have observed the formation of several morphological structures of a single protein, which were visualized directly using atomic force microscopy (AFM). These structures have been found to appear and disappear with time, and their formation could be monitored under normal buffer conditions and at room temperature without requiring any sophisticated chemical or biological methodologies. In addition, we have observed the formation of honeycomb-shaped morphology, which may serve as an intermediate. These amyloid-based nanostructures may have the potential to be explored in therapeutics delivery and other biomedical applications.
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Affiliation(s)
- Shubhasis Haldar
- Protein Folding and Dynamics Laboratory, Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata 700032, India
| | - Pallabi Sil
- Protein Folding and Dynamics Laboratory, Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata 700032, India
| | - Muruganandan Thangamuniyandi
- Protein Folding and Dynamics Laboratory, Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata 700032, India
| | - Krishnananda Chattopadhyay
- Protein Folding and Dynamics Laboratory, Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata 700032, India
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45
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Paul SS, Sil P, Haldar S, Mitra S, Chattopadhyay K. Subtle Change in the Charge Distribution of Surface Residues May Affect the Secondary Functions of Cytochrome c. J Biol Chem 2015; 290:14476-90. [PMID: 25873393 DOI: 10.1074/jbc.m114.607010] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Indexed: 11/06/2022] Open
Abstract
Although the primary function of cytochrome c (cyt c) is electron transfer, the protein caries out an additional secondary function involving its interaction with membrane cardiolipin (CDL), its peroxidase activity, and the initiation of apoptosis. Whereas the primary function of cyt c is essentially conserved, its secondary function varies depending on the source of the protein. We report here a detailed experimental and computational study, which aims to understand, at the molecular level, the difference in the secondary functions of cyt c obtained from horse heart (mammalian) and Saccharomyces cerevisiae (yeast). The conformational landscape of cyt c has been found to be heterogeneous, consisting of an equilibrium between the compact and extended conformers as well as the oligomeric species. Because the determination of relative populations of these conformers is difficult to obtain by ensemble measurements, we used fluorescence correlation spectroscopy (FCS), a method that offers single-molecule resolution. The population of different species is found to depend on multiple factors, including the protein source, the presence of CDL and urea, and their concentrations. The complex interplay between the conformational distribution and oligomerization plays a crucial role in the variation of the pre-apoptotic regulation of cyt c observed from different sources. Finally, computational studies reveal that the variation in the charge distribution at the surface and the charge reversal sites may be the key determinant of the conformational stability of cyt c.
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Affiliation(s)
- Simanta Sarani Paul
- From the Protein Folding and Dynamics Laboratory, Structural Biology and Bioinformatics Division, Council of Scientific and Industrial Research (CSIR)-Indian Institute of Chemical Biology, Kolkata 700032, India
| | - Pallabi Sil
- From the Protein Folding and Dynamics Laboratory, Structural Biology and Bioinformatics Division, Council of Scientific and Industrial Research (CSIR)-Indian Institute of Chemical Biology, Kolkata 700032, India
| | - Shubhasis Haldar
- From the Protein Folding and Dynamics Laboratory, Structural Biology and Bioinformatics Division, Council of Scientific and Industrial Research (CSIR)-Indian Institute of Chemical Biology, Kolkata 700032, India
| | - Samaresh Mitra
- From the Protein Folding and Dynamics Laboratory, Structural Biology and Bioinformatics Division, Council of Scientific and Industrial Research (CSIR)-Indian Institute of Chemical Biology, Kolkata 700032, India
| | - Krishnananda Chattopadhyay
- From the Protein Folding and Dynamics Laboratory, Structural Biology and Bioinformatics Division, Council of Scientific and Industrial Research (CSIR)-Indian Institute of Chemical Biology, Kolkata 700032, India
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46
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Jaganathan M, Ramakrishnan C, Velmurugan D, Dhathathreyan A. Understanding ethylammonium nitrate stabilized cytochrome c – Molecular dynamics and experimental approach. J Mol Struct 2015. [DOI: 10.1016/j.molstruc.2014.10.049] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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47
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Ghosh S, Ghosh C, Nandi S, Bhattacharyya K. Unfolding and refolding of a protein by cholesterol and cyclodextrin: a single molecule study. Phys Chem Chem Phys 2015; 17:8017-27. [DOI: 10.1039/c5cp00385g] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Cholesterol induced unfolding of a globular protein, human serum albumin (HSA), and β-cyclodextrin induced refolding of the unfolded protein is demonstrated in this study.
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Affiliation(s)
- Shirsendu Ghosh
- Department of Physical Chemistry
- Indian Association For The cultivation of Science
- Kolkata 700 032
- India
| | - Catherine Ghosh
- Department of Physical Chemistry
- Indian Association For The cultivation of Science
- Kolkata 700 032
- India
| | - Somen Nandi
- Department of Physical Chemistry
- Indian Association For The cultivation of Science
- Kolkata 700 032
- India
| | - Kankan Bhattacharyya
- Department of Physical Chemistry
- Indian Association For The cultivation of Science
- Kolkata 700 032
- India
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48
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Chakrabarty S, Kaur H, Pal T, Kar S, Ghosh S, Ghosh S. Morphology dependent photoinduced electron transfer from N,N-dimethylaniline to semiconductor cadmium sulfide. RSC Adv 2014. [DOI: 10.1039/c4ra05498a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
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49
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Yadav R, Sengupta B, Sen P. Conformational Fluctuation Dynamics of Domain I of Human Serum Albumin in the Course of Chemically and Thermally Induced Unfolding Using Fluorescence Correlation Spectroscopy. J Phys Chem B 2014; 118:5428-38. [DOI: 10.1021/jp502762t] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Rajeev Yadav
- Department
of Chemistry Indian Institute of Technology Kanpur, Kanpur 208 016, UP, India
| | - Bhaswati Sengupta
- Department
of Chemistry Indian Institute of Technology Kanpur, Kanpur 208 016, UP, India
| | - Pratik Sen
- Department
of Chemistry Indian Institute of Technology Kanpur, Kanpur 208 016, UP, India
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50
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Chattoraj S, Mandal AK, Bhattacharyya K. Effect of ethanol-water mixture on the structure and dynamics of lysozyme: A fluorescence correlation spectroscopy study. J Chem Phys 2014; 140:115105. [DOI: 10.1063/1.4868642] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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