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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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2
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Sarhangi SM, Matyushov DV. Anomalously Small Reorganization Energy of the Half Redox Reaction of Azurin. J Phys Chem B 2022; 126:3000-3011. [DOI: 10.1021/acs.jpcb.2c00338] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Setare M. Sarhangi
- Department of Physics, Arizona State University, P.O. Box 871504, Tempe, Arizona 85287-1504, United States
| | - Dmitry V. Matyushov
- School of Molecular Sciences and Department of Physics, Arizona State University, P.O. Box 871504, Tempe, Arizona 85287-1504, United States
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3
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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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4
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Pradhan B, Engelhard C, Van Mulken S, Miao X, Canters GW, Orrit M. Single electron transfer events and dynamical heterogeneity in the small protein azurin from Pseudomonas aeruginosa. Chem Sci 2019; 11:763-771. [PMID: 34123050 PMCID: PMC8146731 DOI: 10.1039/c9sc05405g] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 11/25/2019] [Indexed: 01/07/2023] Open
Abstract
Monitoring the fluorescence of single-dye-labeled azurin molecules, we observed the reaction of azurin with hexacyanoferrate under controlled redox potential yielding data on the timing of individual (forward and backward) electron transfer (ET) events. Change-point analysis of the time traces demonstrates significant fluctuations of ET rates and of mid-point potential E 0. These fluctuations are a signature of dynamical heterogeneity, here observed on a 14 kDa protein, the smallest to date. By correlating changes in forward and backward reaction rates we found that 6% of the observed change events could be explained by a change in midpoint potential, while for 25% a change of the donor-acceptor coupling could explain the data. The remaining 69% are driven by variations in complex association constants or structural changes that cause forward and back ET rates to vary independently. Thus, the observed spread in individual ET rates could be related in a unique way to variations in molecular parameters. The relevance for the understanding of metabolic processes is briefly discussed.
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Affiliation(s)
- Biswajit Pradhan
- Huygens-Kamerlingh Onnes Laboratory, Leiden University 2300 RA Leiden Netherlands
| | | | | | - Xueyan Miao
- School of Public Health, Guilin Medical University 541004 Guilin China
| | - Gerard W Canters
- Huygens-Kamerlingh Onnes Laboratory, Leiden University 2300 RA Leiden Netherlands
| | - Michel Orrit
- Huygens-Kamerlingh Onnes Laboratory, Leiden University 2300 RA Leiden Netherlands
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5
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Andreoni A, Sen S, Hagedoorn PL, Buma WJ, Aartsma TJ, Canters GW. Fluorescence Correlation Spectroscopy of Labeled Azurin Reveals Photoinduced Electron Transfer between Label and Cu Center. Chemistry 2018; 24:646-654. [PMID: 29064125 DOI: 10.1002/chem.201703733] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Indexed: 11/06/2022]
Abstract
Fluorescent labeling of biomacromolecules enjoys increasing popularity for structural, mechanistic, and microscopic investigations. Its success hinges on the ability of the dye to alternate between bright and dark states. Förster resonance energy transfer (FRET) is an important source of fluorescence modulation. Photo-induced electron transfer (PET) may occur as well, but is often considered only when donor and acceptor are in van der Waals contact. In this study, PET is shown between a label and redox centers in oxidoreductases, which may occur over large distances. In the small blue copper protein azurin, labeled with ATTO655, PET is observed when the label is at 18.5 Å, but not when it is at 29.1 Å from the Cu. For CuII , PET from label to Cu occurs at a rate of (4.8±0.3)×104 s-1 and back at (0.7±0.1)×103 s-1 . With CuI the numbers are (3.3±0.7)×106 s-1 and (1.0±0.1)×104 s-1 . Reorganization energies and electronic coupling elements are in the range of 0.8-1.2 eV and 0.02-0.5 cm-1 , respectively. These data are compatible with electron transfer (ET) along a through-bond pathway although transient complex formation followed by ET cannot be ruled out. The outcome of this study is a useful guideline for experimental designs in which oxidoreductases are labelled with fluorescent dyes, with particular attention to single molecule investigations. The labelling position for FRET can be optimized to avoid reactions like PET by evaluating the structure and thermodynamics of protein and label.
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Affiliation(s)
- Alessio Andreoni
- Leiden Institute of Physics, Leiden University, Niels Bohrweg 2, 2333CC, Leiden, The Netherlands.,Present address: National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Saptaswa Sen
- Leiden Institute of Physics, Leiden University, Niels Bohrweg 2, 2333CC, Leiden, The Netherlands.,Present address: AlbaNova University Center, Department of Applied Physics, KTH-Royal Institute of, Technology, 10691, Stockholm, Sweden
| | - Peter-Leon Hagedoorn
- TU Delft, Applied Sciences, Biotechnology, Building 58, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Wybren J Buma
- Van't Hoff Institute for Molecular Sciences, Science Park 904, P.O. Box 94157, 1090 GD, Amsterdam, The Netherlands
| | - Thijs J Aartsma
- Leiden Institute of Physics, Leiden University, Niels Bohrweg 2, 2333CC, Leiden, The Netherlands
| | - Gerard W Canters
- Leiden Institute of Physics, Leiden University, Niels Bohrweg 2, 2333CC, Leiden, The Netherlands
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Affiliation(s)
- Chao Ji
- School of Chemical Engineering The University of New South Wales Australia
- Cooperative Research Centre for Polymers Australia
| | - Jingwei Hou
- School of Chemical Engineering The University of New South Wales Australia
| | - Kai Wang
- School of Civil and Environmental Engineering The University of New South Wales Australia
| | - Yun Hau Ng
- School of Chemical Engineering The University of New South Wales Australia
| | - Vicki Chen
- School of Chemical Engineering The University of New South Wales Australia
- Cooperative Research Centre for Polymers Australia
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7
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Affiliation(s)
- Chao Ji
- School of Chemical Engineering The University of New South Wales Australia
- Cooperative Research Centre for Polymers Australia
| | - Jingwei Hou
- School of Chemical Engineering The University of New South Wales Australia
| | - Kai Wang
- School of Civil and Environmental Engineering The University of New South Wales Australia
| | - Yun Hau Ng
- School of Chemical Engineering The University of New South Wales Australia
| | - Vicki Chen
- School of Chemical Engineering The University of New South Wales Australia
- Cooperative Research Centre for Polymers Australia
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8
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Sekretaryova AN, Vagin MY, Turner APF, Eriksson M. Electrocatalytic Currents from Single Enzyme Molecules. J Am Chem Soc 2016; 138:2504-7. [DOI: 10.1021/jacs.5b13149] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Alina N. Sekretaryova
- Department
of Physics, Chemistry and Biology, Linköping University, SE-581 83, Linköping, Sweden
| | - Mikhail Yu. Vagin
- Department
of Physics, Chemistry and Biology, Linköping University, SE-581 83, Linköping, Sweden
- Department
of Science and Technology, Linköping University, SE-601 74, Norrköping, Sweden
| | - Anthony P. F. Turner
- Department
of Physics, Chemistry and Biology, Linköping University, SE-581 83, Linköping, Sweden
| | - Mats Eriksson
- Department
of Physics, Chemistry and Biology, Linköping University, SE-581 83, Linköping, Sweden
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9
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Heppner D, Kjaergaard CH, Solomon EI. Mechanism of the reduction of the native intermediate in the multicopper oxidases: insights into rapid intramolecular electron transfer in turnover. J Am Chem Soc 2014; 136:17788-801. [PMID: 25490729 PMCID: PMC4291763 DOI: 10.1021/ja509150j] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Indexed: 12/20/2022]
Abstract
The multicopper oxidases (MCOs) are the family of enzymes that catalyze the 4-electron reduction of O2 to H2O coupled to the four 1-electron oxidations of substrate. In the catalytic cycle electrons are transferred intramolecularly over ∼13 Å from a Type 1 (T1) Cu site that accepts electrons from substrate to a trinuclear Cu cluster (TNC) where O2 is reduced to H2O at rapid rates consistent with turnover (560 s(-1)). The oxygen reduction mechanism for the MCOs is well-characterized, whereas the rereduction is less understood. Our initial study of Rhus vernicifera Laccase (Heppner et al. J. Am. Chem. Soc. 2013, 135, 12212) experimentally established that the native intermediate (NI), the species formed upon O-O bond cleavage, is reduced with an IET rate >700 s(-1) and is the catalytically relevant fully oxidized form of the enzyme, rather than the resting state. In this report, we present kinetic and spectroscopic results coupled to DFT calculations that evaluate the mechanism of the 3 e(-)/3 H(+) reduction of NI, where all three catalytically relevant intramolecular electron transfer (IET) steps are rapid and involve three different structural changes. These three rapid IET processes reflect the sophisticated mechanistic control of the TNC to enable rapid turnover. All three IET processes are fast due to the associated protonation of the bridging oxo and hydroxo ligands, generated by O-O cleavage, to form water products that are extruded from the TNC upon full reduction, thereby defining a unifying mechanism for oxygen reduction and rapid IET by the TNC in the catalytic cycle of the MCOs.
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Affiliation(s)
- David
E. Heppner
- Department of Chemistry, Stanford University, 333 Campus Drive, Stanford, California 94305-5080, United States
| | - Christian H. Kjaergaard
- Department of Chemistry, Stanford University, 333 Campus Drive, Stanford, California 94305-5080, United States
| | - Edward I. Solomon
- Department of Chemistry, Stanford University, 333 Campus Drive, Stanford, California 94305-5080, United States
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10
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Tabares LC, Gupta A, Aartsma TJ, Canters GW. Tracking electrons in biological macromolecules: from ensemble to single molecule. Molecules 2014; 19:11660-78. [PMID: 25102116 PMCID: PMC6271485 DOI: 10.3390/molecules190811660] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Revised: 07/23/2014] [Accepted: 07/25/2014] [Indexed: 11/29/2022] Open
Abstract
Nature utilizes oxido-reductases to cater to the energy demands of most biochemical processes in respiratory species. Oxido-reductases are capable of meeting this challenge by utilizing redox active sites, often containing transition metal ions, which facilitate movement and relocation of electrons/protons to create a potential gradient that is used to energize redox reactions. There has been a consistent struggle by researchers to estimate the electron transfer rate constants in physiologically relevant processes. This review provides a brief background on the measurements of electron transfer rates in biological molecules, in particular Cu-containing enzymes, and highlights the recent advances in monitoring these electron transfer events at the single molecule level or better to say, at the individual event level.
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Affiliation(s)
- Leandro C Tabares
- Commissariat à l'Energie Atomique, Institut de Biologie et de Technologies de Saclay, Service de Bioénergétique, Biologie Structurale et Mécanismes (CNRS UMR-8221), Gif-sur-Yvette Cedex 91191, France
| | - Ankur Gupta
- Leiden Institute of Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, Niels Bohrweg 2, PO Box 9504, RA Leiden 2300, The Netherlands
| | - Thijs J Aartsma
- Leiden Institute of Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, Niels Bohrweg 2, PO Box 9504, RA Leiden 2300, The Netherlands
| | - Gerard W Canters
- Leiden Institute of Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, Niels Bohrweg 2, PO Box 9504, RA Leiden 2300, The Netherlands.
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Akkilic N, van der Grient F, Kamran M, Sanghamitra NJM. Chemically-induced redox switching of a metalloprotein reveals thermodynamic and kinetic heterogeneity, one molecule at a time. Chem Commun (Camb) 2014; 50:14523-6. [DOI: 10.1039/c4cc06334a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
FRET-based detection of individual azurin–Cy5 molecules shows an on (reduction)–off (oxidation) fluorescence switching, reveals the redox parameters.
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Affiliation(s)
- Namik Akkilic
- Biological and Soft Matter Physics
- LION
- Leiden University
- 2333 CA Leiden, The Netherlands
| | - Fenna van der Grient
- Biological and Soft Matter Physics
- LION
- Leiden University
- 2333 CA Leiden, The Netherlands
| | - Muhammad Kamran
- Biological and Soft Matter Physics
- LION
- Leiden University
- 2333 CA Leiden, The Netherlands
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