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Chun SY, Son MK, Park CR, Lim C, Kim HI, Kwak K, Cho M. Direct observation of protein structural transitions through entire amyloid aggregation processes in water using 2D-IR spectroscopy. Chem Sci 2022; 13:4482-4489. [PMID: 35656138 PMCID: PMC9020176 DOI: 10.1039/d1sc06047c] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 03/18/2022] [Indexed: 12/02/2022] Open
Abstract
Amyloid proteins that undergo self-assembly to form insoluble fibrillar aggregates have attracted much attention due to their role in biological and pathological significance in amyloidosis. This study aims to understand the amyloid aggregation dynamics of insulin (INS) in H2O using two-dimensional infrared (2D-IR) spectroscopy. Conventional IR studies have been performed in D2O to avoid spectral congestion despite distinct H–D isotope effects. We observed a slowdown of the INS fibrillation process in D2O compared to that in H2O. The 2D-IR results reveal that different quaternary structures of INS at the onset of the nucleation phase caused the distinct fibrillation pathways of INS in H2O and D2O. A few different biophysical analysis, including solution-phase small-angle X-ray scattering combined with molecular dynamics simulations and other spectroscopic techniques, support our 2D-IR investigation results, providing insight into mechanistic details of distinct structural transition dynamics of INS in water. We found the delayed structural transition in D2O is due to the kinetic isotope effect at an early stage of fibrillation of INS in D2O, i.e., enhanced dimer formation of INS in D2O. Our 2D-IR and biophysical analysis provide insight into mechanistic details of structural transition dynamics of INS in water. This study demonstrates an innovative 2D-IR approach for studying protein dynamics in H2O, which will open the way for observing protein dynamics under biological conditions without IR spectroscopic interference by water vibrations. This study aims to understand the structural transition dynamics of INS during amyloid aggregation in H2O using 2D-IR spectroscopy. The results show that distinct fibrillations in D2O and H2O originated from different quaternary structures of INS.![]()
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Affiliation(s)
- So Yeon Chun
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS) Seoul 02841 Republic of Korea
- Department of Chemistry, Korea University Seoul 02841 Republic of Korea
| | - Myung Kook Son
- Department of Chemistry, Korea University Seoul 02841 Republic of Korea
- Center for Proteogenome Research, Korea University Seoul 02841 Republic of Korea
- Single Cell Analysis Laboratory, Korea University Seoul 02841 Republic of Korea
| | - Chae Ri Park
- Department of Chemistry, Korea University Seoul 02841 Republic of Korea
- Center for Proteogenome Research, Korea University Seoul 02841 Republic of Korea
- Single Cell Analysis Laboratory, Korea University Seoul 02841 Republic of Korea
| | - Chaiho Lim
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS) Seoul 02841 Republic of Korea
- Department of Chemistry, Korea University Seoul 02841 Republic of Korea
| | - Hugh I Kim
- Department of Chemistry, Korea University Seoul 02841 Republic of Korea
- Center for Proteogenome Research, Korea University Seoul 02841 Republic of Korea
- Single Cell Analysis Laboratory, Korea University Seoul 02841 Republic of Korea
| | - Kyungwon Kwak
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS) Seoul 02841 Republic of Korea
- Department of Chemistry, Korea University Seoul 02841 Republic of Korea
| | - Minhaeng Cho
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS) Seoul 02841 Republic of Korea
- Department of Chemistry, Korea University Seoul 02841 Republic of Korea
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Arkell K, Breil MP, Frederiksen SS, Nilsson B. Mechanistic Modeling of Reversed-Phase Chromatography of Insulins with Potassium Chloride and Ethanol as Mobile-Phase Modulators. ACS OMEGA 2017; 2:136-146. [PMID: 30023511 PMCID: PMC6044668 DOI: 10.1021/acsomega.6b00248] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 12/23/2016] [Indexed: 05/28/2023]
Abstract
The purpose of this study was to investigate the adsorption mechanism in reversed-phase chromatography (RPC) of proteins and to develop a model for the effect of dual mobile phase modulators-a salt and an organic solvent-on this process. Two different adsorption mechanisms were considered: (1) pure association of a protein molecule and one or more ligands and (2) displacement of the organic modulator, with which the adsorbent is saturated, by the protein upon association with one or more ligands. One model was then derived from each of the two considered mechanisms, combining thermodynamic theories on salting-in, RPC, and the solubility of proteins. The model was then applied to chromatographic data from an earlier report as well as supplementary data for solubility and vapor-liquid equilibria, and case-specific simplifications were made. We found that an adaptation of Kirkwood's electrostatic theories to hydrophobic interaction chromatography describes the observed effect of KCl well. Combining chromatographic and solubility data for one of the insulins, we concluded that the variation in the activity coefficient of the insulin with respect to the concentration of ethanol alone cannot describe its effect on retention. Consequently, one or more other phenomena must affect the adsorption process. Our second model fits the retention data well, supporting the hypothesis that ethanol is directly involved in the adsorption mechanism in this case. Using additional experiments at a high-protein load, we extended the linear-range equilibrium model into a dynamic model for preparative conditions. This model shows good agreement with the high-load data for one of the insulin variants, without any additional effects of the modulator concentrations on the adsorption capacity.
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Affiliation(s)
- Karolina Arkell
- Department
of Chemical Engineering, Faculty of Engineering, Lund University, P.O. Box 124, SE-21100 Lund, Sweden
| | - Martin P. Breil
- Modelling and Optimization and Mathematical Modelling, Novo Nordisk A/S, Smørmosevej 17-19, DK-2880 Bagsværd, Denmark
| | - Søren S. Frederiksen
- Modelling and Optimization and Mathematical Modelling, Novo Nordisk A/S, Smørmosevej 17-19, DK-2880 Bagsværd, Denmark
| | - Bernt Nilsson
- Department
of Chemical Engineering, Faculty of Engineering, Lund University, P.O. Box 124, SE-21100 Lund, Sweden
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Verma R, Daya K. Understanding the decay of proteins: A method to study time dependent response of pM concentration of insulin at microwave frequencies. MethodsX 2017; 4:35-41. [PMID: 28116247 PMCID: PMC5233787 DOI: 10.1016/j.mex.2016.11.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 11/30/2016] [Indexed: 11/29/2022] Open
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Ivanov IT, Paarvanova B. Dielectric relaxations on erythrocyte membrane as revealed by spectrin denaturation. Bioelectrochemistry 2016; 110:59-68. [PMID: 27071054 DOI: 10.1016/j.bioelechem.2016.03.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Revised: 03/25/2016] [Accepted: 03/26/2016] [Indexed: 11/30/2022]
Abstract
We studied the effect of spectrin denaturation at 49.5°C (TA) on the dielectric relaxations and related changes in the complex impedance, Z*, complex capacitance, C*, and dielectric loss curve of suspensions containing human erythrocytes, erythrocyte ghost membranes (EMs) and Triton-X-100 residues of EMs. The loss curve prior to, minus the loss curve after TA, resulted in a bell-shaped peak at 1.5MHz. The changes in the real and imaginary components of Z* and C* at TA, i.e., ΔZre, ΔZim, ΔCre and ΔCim, calculated in the same way, strongly varied with frequency. Between 1.0 and 12MHz the -ΔZim vs ΔZre, and ΔCim vs ΔCre plots depicted semicircles with critical frequencies, fcr, at 2.5MHz expressing recently reported relaxation of spectrin dipoles. Between 0.02 and 1.0MHz the -ΔZim vs ΔZre plot exhibited another relaxation whose fcr mirrored that of beta relaxation. This relaxation was absent on Triton-X-shells, while on erythrocytes and EMs it was inhibited by selective dissociation of either attachment sites between spectrin and bilayer. Considering above findings and inaccessibility of cytosole to outside field at such frequencies, the latter relaxation was assumed originating from a piezoelectric effect on the highly deformable spectrin filaments.
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Affiliation(s)
- I T Ivanov
- Dept. of Physics, Biophysics, Reontgenology and Radiology, Medical Faculty, Thracian University, Stara Zagora 6000, Bulgaria.
| | - B Paarvanova
- Dept. of Physics, Biophysics, Reontgenology and Radiology, Medical Faculty, Thracian University, Stara Zagora 6000, Bulgaria
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Koizumi H, Uda S, Fujiwara K, Tachibana M, Kojima K, Nozawa J. Crystallization of high-quality protein crystals using an external electric field. J Appl Crystallogr 2015. [DOI: 10.1107/s1600576715015885] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The effect of a 20 kHz external electric field on the quality of tetragonal hen egg white (HEW) lysozyme crystals was investigated using X-ray diffraction rocking-curve measurements. The full width at half-maximum was found to be larger for high-order reflections but smaller for low-order reflections. In particular, it was revealed that a large amount of local strain is accumulated in tetragonal HEW lysozyme crystals grown under an applied field at 20 kHz. Comparison with previous results obtained for crystals grown with an applied field at 1 MHz [Koizumi, Uda, Fujiwara, Tachibana, Kojima & Nozawa (2013).J. Appl. Cryst.46, 25–29] indicated that improvement of the protein crystal quality could be achieved by selection of an appropriate frequency for the applied electric field, which has a significant effect on the growth of the solid.
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Tomita Y, Koizumi H, Uda S, Fujiwara K, Nozawa J. Control of Gibbs free energy relationship between hen egg white lysozyme polymorphs under application of an external alternating current electric field. J Appl Crystallogr 2012. [DOI: 10.1107/s002188981200249x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The distribution of phases between bulk (tetragonal structure) and spherulitic crystals for hen egg white lysozyme was controlled under application of an external alternating current electric field. The distribution of phases differed depending on differences in the magnitude of the electrostatic energy contribution to the respective chemical potentials of the two solid phases. Therefore, the Gibbs free energy relationship between the two solid phases could be controlled by changing the frequency of the applied external electric field. Such a method of controlling the Gibbs free energy relationship among polymorphs would be adaptable to many kinds of protein.
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Laogun AA, Agba EH, Ajayi NO. A comparison of the dielectric behaviour of human haemoglobin SC with SS and AA in solution. Phys Med Biol 1997; 42:707-15. [PMID: 9127446 DOI: 10.1088/0031-9155/42/4/007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Haemoglobin (Hb) SC is one of the most prevalent sickle-cell disorders. Patients with Hb SC are known to inherit a befa(S)-globin gene from one parent and a beta(C)-globin gene from the other. The radiofrequency dielectric properties of heterozygous Hb SC have been investigated and compared with those of homozygous Hb SS and AA in solution. The relative permittivity, epsilon', the dielectric loss factor, epsilon", and the energy dissipation factor, tan delta, of the different haemoglobin samples have been measured in the frequency range 0.1-50.0 MHz using a TF1245 Marconi Q-meter working in conjunction with a TF1246 oscillator at a room temperature of 26.0 +/- 0.5 degrees C. The Hb SC samples were found to exhibit dielectric dispersions distinctly different from those of Hb SS and AA. The dielectric data were fitted to the Cole-Cole structural equation and the fitted parameters are presented. The results are discussed on the basis of the molecular structure and polymerization characteristics of the haemoglobins in solution.
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Affiliation(s)
- A A Laogun
- International Centre for Theoretical Physics, Trieste, Italy
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Pethig R, Kell DB. The passive electrical properties of biological systems: their significance in physiology, biophysics and biotechnology. Phys Med Biol 1987; 32:933-70. [PMID: 3306721 DOI: 10.1088/0031-9155/32/8/001] [Citation(s) in RCA: 612] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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Abstract
The dielectric dispersion of human breast milk has been investigated by means of a resonance technique over the frequency range 0.1-100 MHz and at six temperatures from 10 to 60 degrees C. A computer analysis of the data was carried out on the basis of the Cole-Cole structural model and the fitted parameters have been presented. The dependence on temperature of both the viscosity of the human milk and its dielectric relaxation has been discussed. The heat of activation delta H of the milk, calculated in accordance with Eyring's theory of rate processes was found to be 19.5 +/- 0.6 kJ mol-1 for the dielectric relaxation process and 20.2 +/- 0.8 kJ mol-1 for viscous flow.
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Abstract
The relative permittivity and AC conductivity of breast milk have been investigated in four different mammalian species, human, cow, goat and sheep, in the frequency range 0.1-100 MHz and at a room temperature of 26.5 +/- 0.5 degrees C. The results showed that the sheep milk exhibited the largest dielectric dispersion, followed in decreasing order by milks from the goat, cow and human. The dielectric data were fitted to the Debye and Cole-Cole structural equations and the fitted parameters have been presented for the different species. The curve-fitting analysis has shown that for all the milk samples the Cole-Cole model gave a better fit to the dielectric data than the Debye model, thus suggesting heterogeneity of structure in milk. On the basis of the Cole-Cole model, the relaxation times in the mammalian milks were found to be distributed about the mean values of 162 +/- 10, 171 +/- 9, 177 +/- 14 and 192 +/- 12 ns for human, cow, goat and sheep milks, respectively.
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