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Ray D, Chamlagai D, Kumar S, Mukhopadhyay S, Chakrabarty S, Aswal VK, Mitra S. Molecular Insights into the Conformational and Binding Behaviors of Human Serum Albumin Induced by Surface-Active Ionic Liquids. J Phys Chem B 2024; 128:6622-6637. [PMID: 38937939 DOI: 10.1021/acs.jpcb.4c01915] [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: 06/29/2024]
Abstract
Extensive research has been carried out to investigate the stability and function of human serum albumin (HSA) when exposed to surface-active ionic liquids (SAILs) with different head groups (imidazolium, morpholinium, and pyridinium) and alkyl chain lengths (ranging from decyl to tetradecyl). Analysis of the protein fluorescence spectra indicates noticeable changes in the secondary structure of HSA with varying concentrations of all SAILs tested. Helicity calculations based on the Fourier transform infrared (FTIR) data show that HSA becomes more organized at the micellar concentration of SAILs, leading to an increased protein activity at this level. Small-angle neutron scattering (SANS) data confirm the formation of a bead-necklace structure between the SAILs and HSA. Atomistic molecular dynamics (MD) simulation results identify several hotspots on the protein surface for interaction with SAIL, which results in the modulation of protein conformational fluctuation and stability. Furthermore, fluorescence resonance energy transfer (FRET) experiments with the intramolecular charge transfer (ICT) probe trans-ethyl p-(dimethylamino) cinnamate (EDAC) demonstrate that higher alkyl chain lengths and SAIL concentrations result in a significantly increased energy transfer efficiency. The findings of this study provide a detailed molecular-level understanding of how the protein structure and function are affected by the presence of SAILs, with potential implications for a wide range of applications involving protein-SAIL composite systems.
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Affiliation(s)
- Dhiman Ray
- Department of Chemistry, North-Eastern Hill University, Shillong 793 022, India
| | - Dipak Chamlagai
- Department of Chemistry, North-Eastern Hill University, Shillong 793 022, India
| | - Sugam Kumar
- Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai 400085, India
| | - Sutanu Mukhopadhyay
- Department of Chemical and Biological Sciences, S. N. Bose National Centre for Basic Sciences, Kolkata 700106, India
| | - Suman Chakrabarty
- Department of Chemical and Biological Sciences, S. N. Bose National Centre for Basic Sciences, Kolkata 700106, India
| | - Vinod K Aswal
- Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai 400085, India
| | - Sivaprasad Mitra
- Department of Chemistry, North-Eastern Hill University, Shillong 793 022, India
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Hu Y, Xing Y, Yue H, Chen T, Diao Y, Wei W, Zhang S. Ionic liquids revolutionizing biomedicine: recent advances and emerging opportunities. Chem Soc Rev 2023; 52:7262-7293. [PMID: 37751298 DOI: 10.1039/d3cs00510k] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
Abstract
Ionic liquids (ILs), due to their inherent structural tunability, outstanding miscibility behavior, and excellent electrochemical properties, have attracted significant research attention in the biomedical field. As the application of ILs in biomedicine is a rapidly emerging field, there is still a need for systematic analyses and summaries to further advance their development. This review presents a comprehensive survey on the utilization of ILs in the biomedical field. It specifically emphasizes the diverse structures and properties of ILs with their relevance in various biomedical applications. Subsequently, we summarize the mechanisms of ILs as potential drug candidates, exploring their effects on various organisms ranging from cell membranes to organelles, proteins, and nucleic acids. Furthermore, the application of ILs as extractants and catalysts in pharmaceutical engineering is introduced. In addition, we thoroughly review and analyze the applications of ILs in disease diagnosis and delivery systems. By offering an extensive analysis of recent research, our objective is to inspire new ideas and pathways for the design of innovative biomedical technologies based on ILs.
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Affiliation(s)
- Yanhui Hu
- Beijing Key Laboratory of Ionic Liquids Clean Process, CAS Key Laboratory of Green Process and Engineering, State Key Laboratory of Multiphase Complex Systems, State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China.
- Innovation Academy for Green Manufacture, Chinese Academy of Sciences, Beijing 100190, China
- College of Chemical and Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
- Chengdu Institute of Organic Chemistry, Chinese Academy of Sciences, Chengdu 610041, China
| | - Yuyuan Xing
- Beijing Key Laboratory of Ionic Liquids Clean Process, CAS Key Laboratory of Green Process and Engineering, State Key Laboratory of Multiphase Complex Systems, State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China.
- Innovation Academy for Green Manufacture, Chinese Academy of Sciences, Beijing 100190, China
- College of Chemical and Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hua Yue
- Beijing Key Laboratory of Ionic Liquids Clean Process, CAS Key Laboratory of Green Process and Engineering, State Key Laboratory of Multiphase Complex Systems, State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China.
- College of Chemical and Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tong Chen
- College of Chemical and Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
- Chengdu Institute of Organic Chemistry, Chinese Academy of Sciences, Chengdu 610041, China
| | - Yanyan Diao
- Beijing Key Laboratory of Ionic Liquids Clean Process, CAS Key Laboratory of Green Process and Engineering, State Key Laboratory of Multiphase Complex Systems, State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China.
- Innovation Academy for Green Manufacture, Chinese Academy of Sciences, Beijing 100190, China
- College of Chemical and Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Wei
- Beijing Key Laboratory of Ionic Liquids Clean Process, CAS Key Laboratory of Green Process and Engineering, State Key Laboratory of Multiphase Complex Systems, State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China.
- College of Chemical and Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Suojiang Zhang
- Beijing Key Laboratory of Ionic Liquids Clean Process, CAS Key Laboratory of Green Process and Engineering, State Key Laboratory of Multiphase Complex Systems, State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China.
- Innovation Academy for Green Manufacture, Chinese Academy of Sciences, Beijing 100190, China
- College of Chemical and Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
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Cytochrome c in cancer therapy and prognosis. Biosci Rep 2022; 42:232225. [PMID: 36479932 PMCID: PMC9780037 DOI: 10.1042/bsr20222171] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 12/01/2022] [Accepted: 12/08/2022] [Indexed: 12/13/2022] Open
Abstract
Cytochrome c (cyt c) is an electron transporter of the mitochondrial respiratory chain. Upon permeabilization of the mitochondrial outer membrane, cyt c is released into the cytoplasm, where it triggers the intrinsic pathway of apoptosis. Cytoplasmic cyt c can further reach the bloodstream. Apoptosis inhibition is one of the hallmarks of cancer and its induction in tumors is a widely used therapeutic approach. Apoptosis inhibition and induction correlate with decreased and increased serum levels of cyt c, respectively. The quantification of cyt c in the serum is useful in the monitoring of patient response to chemotherapy, with potential prognosis value. Several highly sensitive biosensors have been developed for the quantification of cyt c levels in human serum. Moreover, the delivery of exogenous cyt c to the cytoplasm of cancer cells is an effective approach for inducing their apoptosis. Similarly, several protein-based and nanoparticle-based systems have been developed for the therapeutic delivery of cyt c to cancer cells. As such, cyt c is a human protein with promising value in cancer prognosis and therapy. In addition, its thermal stability can be extended through PEGylation and ionic liquid storage. These processes could contribute to enhancing its therapeutic exploitation in clinical facilities with limited refrigeration conditions. Here, I discuss these research lines and how their timely conjunction can advance cancer therapy and prognosis.
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Garg M, Sharma D, Kumar R. Analysis of the effect of 1-Allyl-3-Methylimidazolium chloride on thermodynamic stability, folding kinetics, and motional dynamics of horse cytochrome c. Biophys Chem 2022; 290:106892. [PMID: 36115294 DOI: 10.1016/j.bpc.2022.106892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 09/03/2022] [Accepted: 09/04/2022] [Indexed: 11/02/2022]
Abstract
1-allyl-3-methylimidazolium chloride (AMIMCl) acts as a potential green solvent for proteins. The present work provides a possible pathway by which the structural, kinetic, thermodynamic, and folding properties of horse cytochrome c (cyt c) are affected in green aqueous-AMIMCl systems. Analysis of the effect of AMIMCl on thermodynamic stability, refolding/unfolding kinetics, and motional dynamics of cyt c provided important information, (i) AMIMCl decreases the thermodynamic stability of reduced cyt c and also strengthens the guanidinium chloride (GdmCl)-mediated decrease in thermodynamic stability of protein, (ii) AMIMCl reduces the thermal-fluctuation of Met80-containing omega-loop of natively-folded compact state of carbonmonoxycytochrome c (MCO-state) due to polyfunctional interactions between the AMIM+ and different groups of protein, (iii) AMIMCl shifts the kinetic chevron plot, ln kobs[GdmCl] to the lower concentration of GdmCl, (iv) AMIMCl shifts the refolding and unfolding limps to vertically downwards and upwards, respectively, and (v) AMIMCl reducing the unfolding free energy estimated by both thermodynamic and kinetic analysis.
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Affiliation(s)
- Mansi Garg
- Department of Chemistry, Central University of Punjab, Bathinda 151001, India
| | - Deepak Sharma
- Council of Scientific and Industrial Research- Institute of Microbial Technology, Sector 39A, Chandigarh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Rajesh Kumar
- Department of Chemistry, Central University of Punjab, Bathinda 151001, India.
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Tulsiyan K, Jena S, González-Viegas M, Kar RK, Biswal HS. Structural Dynamics of RNA in the Presence of Choline Amino Acid Based Ionic Liquid: A Spectroscopic and Computational Outlook. ACS CENTRAL SCIENCE 2021; 7:1688-1697. [PMID: 34729412 PMCID: PMC8554839 DOI: 10.1021/acscentsci.1c00768] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Indexed: 05/03/2023]
Abstract
Ribonucleic acid (RNA) is exceedingly sensitive to degradation compared to DNA. The current protocol for storage of purified RNA requires freezing conditions below -20 °C. Recent advancements in biological chemistry have identified amino acid-based ionic liquids as suitable preservation media for RNA, even in the presence of degrading enzymes. However, the mechanistic insight into the interaction between ILs and RNA is unclear. To the best of our knowledge, no attempts are made so far to provide a molecular view. This work aims to establish a detailed understanding of how ILs enable structural stability to RNA sourced from Torula yeast. Herein, we manifest the hypothesis of multimodal binding of IL and its minimal perturbation to the macromolecular structure, with several spectroscopic techniques such as time-resolved fluorescence and fluorescence correlation spectroscopy (FCS) aided with molecular dynamics at microsecond time scales. Relevant structural and thermodynamic details from biophysical experiments confirm that even long-term RNA preservation with ILs is a possible alternative devoid of any structural deformation. These results establish a unifying mechanism of how ILs are maintaining conformational integrity and thermal stability. The atomistic insights are transferable for their potential applications in drug delivery and biomaterials by considering the advantages of having maximum structural retention and minimum toxicity.
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Affiliation(s)
- Kiran
Devi Tulsiyan
- School
of Chemical Sciences, National Institute
of Science Education and Research (NISER), Bhimpur-Padanpur, Via-Jatni, District, Khurda, 752050, Bhubaneswar, India
- Homi
Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Subhrakant Jena
- School
of Chemical Sciences, National Institute
of Science Education and Research (NISER), Bhimpur-Padanpur, Via-Jatni, District, Khurda, 752050, Bhubaneswar, India
- Homi
Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - María González-Viegas
- Institut
für Biologie, Humboldt Universität zu Berlin, Invalidenstraße 42, 10115 Berlin, Germany
| | - Rajiv K. Kar
- Faculty
II-Mathematics and Natural Sciences, Technische
Universität Berlin, Sekr. PC 14, Strasse des 17, Juni 135, D-10623 Berlin, Germany
| | - Himansu S. Biswal
- School
of Chemical Sciences, National Institute
of Science Education and Research (NISER), Bhimpur-Padanpur, Via-Jatni, District, Khurda, 752050, Bhubaneswar, India
- Homi
Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
- . Phone: +91-674-2494 185/186
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Affiliation(s)
- Michael Feig
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, United States
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Effect of Hydrated Ionic Liquid on Photocycle and Dynamics of Photoactive Yellow Protein. Molecules 2021; 26:molecules26154554. [PMID: 34361707 PMCID: PMC8348629 DOI: 10.3390/molecules26154554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 07/15/2021] [Accepted: 07/23/2021] [Indexed: 12/03/2022] Open
Abstract
The mechanism by which proteins are solvated in hydrated ionic liquids remains an open question. Herein, the photoexcitation dynamics of photoactive yellow protein dissolved in hydrated choline dihydrogen phosphate (Hy[ch][dhp]) were studied by transient absorption and transient grating spectroscopy. The photocyclic reaction of the protein in Hy[ch][dhp] was similar to that observed in the buffer solution, as confirmed by transient absorption spectroscopy. However, the structural change of the protein during the photocycle in Hy[ch][dhp] was found to be different from that observed in the buffer solution. The known change in the diffusion coefficient of the protein was apparently suppressed in high concentrations of [ch][dhp], plausibly due to stabilization of the secondary structure.
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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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Effect of imidazolium based ionic liquids on CO-association dynamics and thermodynamic stability of Ferrocytochrome c. Biophys Chem 2020; 268:106497. [PMID: 33212391 DOI: 10.1016/j.bpc.2020.106497] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 11/01/2020] [Accepted: 11/01/2020] [Indexed: 11/20/2022]
Abstract
Analysis of kinetic and thermodynamic parameters measured for CO-association reaction of Ferrocytochrome c (Ferrocyt c) under variable concentrations of 1-butyl-3-methylimidazolium with varying anion ([Bmim]X) (X = Cl-, I-, Br-, HSO4-) at pH 7 revealed that the low concentration of [Bmim]X (≤0.5 M) constrains the CO-association dynamics of Ferrocyt c and typically follows the order: [Bmim]HSO4 > [Bmim]Cl > [Bmim]Br > [Bmim]I. At relatively higher concentrations (>0.5), the chaotropic action of [Bmim]+ dominates which consequently increases the thermal-fluctuations responsible to denature the protein and thus accelerates the speed of CO-association reaction. Analysis of thermal denaturation curves of Ferrocyt c measured at different concentrations of [Bmim]X revealed that the [Bmim]X decreases the thermodynamic stability of protein and typically follows the order: [Bmim]I > [Bmim]Br > [Bmim]Cl > [Bmim]CH3COO > [Bmim]HSO4, demonstrating that the effect of [Bmim]X on thermodynamic stability of protein is not in accordance to Hofmeister series effect of anions because instead of increasing the kosmotropic anion carrying [Bmim]X ([Bmim]CH3COO and [Bmim]HSO4) also decreases the thermodynamic stability of protein.
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