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Chullipalliyalil K, Elkassas K, McAuliffe MAP, Vucen S, Crean A. In-Vial Detection of Protein Denaturation Using Intrinsic Fluorescence Anisotropy. Anal Chem 2023; 95:2774-2782. [PMID: 36696963 PMCID: PMC9909669 DOI: 10.1021/acs.analchem.2c03912] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The conventional quality control techniques for identifying the denaturation of biopharmaceuticals includes sodium dodecyl sulfate-polyacrylamide gel electrophoresis for identifying fragmentation, ion exchange chromatography and isoelectric focusing for identifying deamidation, reverse-phase high-performance liquid chromatography (HPLC) for identifying oxidation, and size-exclusion HPLC for identifying aggregation. These stability assessments require essential processes that are destructive to the product tested. All these techniques are lab based and require sample removal from a sealed storage vial, which can breach the sterility. In this work, we investigate the heat- and surfactant-induced denaturation of an in-vial-stored model protein, bovine serum albumin (BSA), by analyzing its intrinsic fluorescence without removing the sample from the vial. A lab-based bespoke setup which can do the measurement in vial is used to demonstrate the change in fluorescence polarization of the protein to determine the denaturation level. The results obtained are compared to circular dichroism and size-exclusion HPLC measurements. The results prove that in-vial fluorescence measurements can be performed to monitor protein denaturation. A cost-effective portable solution to provide a top-level overview of biopharmaceutical product stability from manufacture to the point of patient administration can be further developed using the same technique.
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Affiliation(s)
| | - Khaled Elkassas
- SSPC
Centre for Pharmaceutical Research, School of Pharmacy, University College Cork, CorkT12 YT20, Ireland
| | - Michael A. P. McAuliffe
- Centre
for Advanced Photonics & Process Analysis, Munster Technological University Cork, CorkT12 P928, Ireland
| | - Sonja Vucen
- SSPC
Centre for Pharmaceutical Research, School of Pharmacy, University College Cork, CorkT12 YT20, Ireland
| | - Abina Crean
- SSPC
Centre for Pharmaceutical Research, School of Pharmacy, University College Cork, CorkT12 YT20, Ireland
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2
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Raina N, Hassan MI, Ahmad F, Islam A, Singh AK. PEG mediated destabilization of holo α-lactalbumin probed by in silico and in vitro studies: deviation from excluded volume effect. J Biomol Struct Dyn 2022; 40:13265-13277. [PMID: 34726117 DOI: 10.1080/07391102.2021.1987990] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Crowded and confined macromolecular milieus surround proteins, and both are stabilizing if the nature of the interaction between crowder and proteins are considered hard-core repulsive interactions. However, non-specific chemical interactions between a protein and its surroundings also play a significant role and the sum effect of both hard-core repulsion and soft interaction balances the overall effect of crowding/confinement. Previous studies showing the effect of polyethylene glycol (PEG) on protein and nucleic acid may be interpreted as either primarily excluded volume effect or, in some cases, chemical effect by changing solvent properties. In case of destabilizing interactions, charge-charge and hydrophobic contact have to gain more attention. For instance, in vitro and in vivo studies using protein as crowding agent revealed the destabilization of proteins induced by charge-charge interactions. To investigate the effect of PEG 10 kDa on holo α-lactalbumin (holo α-LA), structure and thermal stability of the protein were measured at different pH values using several techniques. Structural characterization by Trp-fluorescence, near-UV CD and far-UV measurements at different pH values clearly shows perturbation of tertiary and secondary structure of holo α-LA by PEG 10 kDa. Furthermore, the dynamic light scattering measurement shows that the protein is homogeneous under all experimental conditions. Analysis of the heat-induced denaturation profile in the presence of the crowder shows destabilization of the protein in terms of Tm (midpoint of denaturation) and ΔGD0 (Gibbs free energy change at 25 °C). To evaluate the interaction of PEG 10 kDa with holo α-LA and stability of PEG-α-LA complex, docking and molecular dynamic simulation were carried out for 100 ns.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Neha Raina
- Department of Biotechnology, Sharda University, Greater Noida, Uttar Pradesh, India.,Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, Delhi, India
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, Delhi, India
| | - Faizan Ahmad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, Delhi, India
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, Delhi, India
| | - Amit Kumar Singh
- Department of Biotechnology, Sharda University, Greater Noida, Uttar Pradesh, India
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3
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MAREKHA B, Hunger J. A single methyl group drastically changes urea's hydration dynamics. J Chem Phys 2022; 156:164504. [DOI: 10.1063/5.0085461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The amphiphilicity and denaturation efficiency of urea can be tuned via alkylation. Although the interaction of alkylureas with water and proteins has been studied in detail, the hydration of 1-methylurea has remained elusive, precluding the isolation of the effect of an individual methyl group. Here, we study water dynamics in the hydration shell of 1-methylurea (1-MU) using infrared absorption and ultrafast infrared spectroscopies. We find that 1-MU hardly affects the hydrogen-bond distribution of water as probed by the OD stretching vibration of HOD molecules. Polarization resolved infrared pump-probe experiments reveal that 1-MU slows down the rotational dynamics of up to 3 water molecules in its hydration shell. Comparison to earlier results for other alkylureas suggests that further alkylation does not necessarily slow down the rotational dynamics of additional water molecules. Two-dimensional infrared experiments show that 1-MU markedly slows down the hydrogen-bond fluctuation dynamics of water, yet similar to what has been found for urea and dimethylureas. Remarkably, (alkyl-) ureas that share a similar effect on water's hydrogen-bond fluctuation dynamics share a similar (modest) protein denaturation tendency. As such, not only the hydrophobicity but also hydration of hydrophilic fragments of alkylureas may be relevant to explain their function towards biomolecules.
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Affiliation(s)
- Bogdan MAREKHA
- Max-Planck-Institute for Medical Research Department of Biomolecular Mechanisms, Germany
| | - Johannes Hunger
- Molecular Spectroscopy, Max Planck Institute for Polymer Research, Germany
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4
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Kobayashi S, Fujii S, Koga A, Wakai S, Matubayasi N, Sambongi Y. Pseudomonas aeruginosa cytochrome c551 denaturation by five systematic urea derivatives that differ in the alkyl chain length. Biosci Biotechnol Biochem 2017; 81:1274-1278. [DOI: 10.1080/09168451.2017.1303361] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Abstract
Reversible denaturation of Pseudomonas aeruginosa cytochrome c551 (PAc551) could be followed using five systematic urea derivatives that differ in the alkyl chain length, i.e. urea, N-methylurea (MU), N-ethylurea (EU), N-propylurea (PU), and N-butylurea (BU). The BU concentration was the lowest required for the PAc551 denaturation, those of PU, EU, MU, and urea being gradually higher. Furthermore, the accessible surface area difference upon PAc551 denaturation caused by BU was found to be the highest, those by PU, EU, MU, and urea being gradually lower. These findings indicate that urea derivatives with longer alkyl chains are stronger denaturants. In this study, as many as five systematic urea derivatives could be applied for the reversible denaturation of a single protein, PAc551, for the first time, and the effects of the alkyl chain length on protein denaturation were systematically verified by means of thermodynamic parameters.
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Affiliation(s)
- Shinya Kobayashi
- Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Japan
| | - Sotaro Fujii
- Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Japan
| | - Aya Koga
- Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Japan
| | - Satoshi Wakai
- Graduate School of Science Technology and Innovation, Kobe University, Kobe, Japan
| | - Nobuyuki Matubayasi
- Graduate School of Engineering Science, Osaka University, Osaka, Japan
- Elements Strategy Initiative for Catalysts and Batteries, Kyoto University, Kyoto, Japan
| | - Yoshihiro Sambongi
- Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Japan
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5
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Yamamori Y, Matubayasi N. Interaction-component analysis of the effects of urea and its alkylated derivatives on the structure of T4-lysozyme. J Chem Phys 2017; 146:225103. [DOI: 10.1063/1.4985222] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Yu Yamamori
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Nobuyuki Matubayasi
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
- Elements Strategy Initiative for Catalysts and Batteries, Kyoto University, Katsura, Kyoto 615-8520, Japan
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6
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Jain R, Sharma D, Kumar S, Kumar R. Factor Defining the Effects of Glycine Betaine on the Thermodynamic Stability and Internal Dynamics of Horse Cytochrome c. Biochemistry 2014; 53:5221-35. [DOI: 10.1021/bi500356c] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Rishu Jain
- School
of Chemistry and Biochemistry, Thapar University, Patiala 147004, India
| | - Deepak Sharma
- Council
of Scientific and Industrial Research, Institute of Microbial Technology, Sector 39A, Chandigarh, India
| | - Sandeep Kumar
- School
of Chemistry and Biochemistry, Thapar University, Patiala 147004, India
| | - Rajesh Kumar
- School
of Chemistry and Biochemistry, Thapar University, Patiala 147004, India
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7
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Kumar S, Sharma D, Kumar R. Effect of urea and alkylureas on the stability and structural fluctuation of the M80-containing Ω-loop of horse cytochrome c. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:641-55. [DOI: 10.1016/j.bbapap.2014.01.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Revised: 01/10/2014] [Accepted: 01/22/2014] [Indexed: 11/27/2022]
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8
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Lin LS, Kunitani MG, Hora MS. Interferon-β-1b (Betaseron®): A Model for Hydrophobic Therapeutic Proteins. ACTA ACUST UNITED AC 2002. [DOI: 10.1007/0-306-47452-2_6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
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10
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Chalikian TV, Völker J, Anafi D, Breslauer KJ. The native and the heat-induced denatured states of alpha-chymotrypsinogen A: thermodynamic and spectroscopic studies. J Mol Biol 1997; 274:237-52. [PMID: 9398530 DOI: 10.1006/jmbi.1997.1394] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
We report the first protein phase-diagram characterized by a combination of volumetric, calorimetric, and spectroscopic techniques. More specifically, we use ultrasonic velocimetry, densimetry, and differential scanning calorimetry, in conjunction with UV absorbance and CD spectroscopy to detect and to characterize the conformational transitions of alpha-chymotrypsinogen A as a function of both pH and temperature. As judged by the CD spectra, we find that, at room temperature, the protein remains in the native state over the entire pH range investigated (pH 1 to 10). The melting profiles of the native state reveal three distinct pH domains in which protein denaturation produces different final states. Below pH 3.1, we find the heat-induced denatured state of the protein to be molten globule (MG), lacking the native-like tertiary structure, while exhibiting significant secondary structural elements. At neutral and alkaline pH, we find the heat-induced denatured state to be unfolded (U), lacking both tertiary and secondary structures, while being structurally similar to the urea-unfolded state. At intermediate pH values (between pH 3.1 and 7), we find the heat-induced denatured state to exhibit properties characteristic of both the MG and U states. Although at room temperature the protein remains native within the whole pH range studied (pH 1 to 10), our volumetric data reveal that the native state slightly "softens" at low pH, probably, due to pH-induced alterations in electrostatic forces causing the packing of the protein interior at low pH and room temperature to become less "tight". This softening of the protein at low pH is reflected in an 8% increase in the intrinsic compressibility, kM, of the protein "native" state. Our volumetric data also allow us to conclude that the heat-induced MG state retains a liquid-like, water-inaccessible core, with a volume that corresponds to about 40% of the solvent-inaccessible core of the native state. By contrast, our volumetric data are consistent with the U state of the protein being essentially unfolded, with the majority of its constituent atomic groups being solvent exposed and, therefore, strongly hydrated.
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Affiliation(s)
- T V Chalikian
- Department of Chemistry Rutgers, The State University of New Jersey, Piscataway, NJ 08855, USA
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11
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Malavasic M, Poklar N, Macek P, Vesnaver G. Fluorescence studies of the effect of pH, guanidine hydrochloride and urea on equinatoxin II conformation. BIOCHIMICA ET BIOPHYSICA ACTA 1996; 1280:65-72. [PMID: 8634317 DOI: 10.1016/0005-2736(95)00278-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The solvent denaturation of equinatoxin II (EqTxII) in aqueous solutions of urea, guanidine hydrochloride (Gu-HCl) and at various pH values was examined by monitoring changes in the protein intrinsic emission fluorescence spectra and in the fluorescence spectra of the added external probe ANS. It has been observed that EqTxII denaturation is reflected in a strong red shift of intrinsic fluorescence emission maxima accompanied by a simultaneous decrease in fluorescence intensity and that guanidine hydrochloride is significantly more powerful denaturant than urea or changing of pH. Comparison of intrinsic fluorescence spectra of EqTxII denatured by one of the three denaturing agents has shown that the fully denatured states of the protein in Gu-HCl and urea are similar and substantially different from those induced by changing of pH. Furthermore, according to the measurements of the ANS-fluorescence in EqTxII solutions as a function of pH the protein exists at pH values below 2.0 in an acid-denatured compact state.
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Affiliation(s)
- M Malavasic
- Department of Chemistry, University of Ljubljana, Slovenia
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12
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Abstract
Solvation of alpha-chymotrypsinogen A (alpha-ctg A) in aqueous urea, methylurea, N,N'-dimethylurea and ethylurea was studied by density measurements. From the densities at constant molality and at constant chemical potential the preferential solvation parameters were determined. In urea and methylurea preferential solvation was observed, whereas in N,N'-dimethylurea and ethylurea at higher concentration water is preferentially bound. From preferential solvation data Gibbs free energy of transfer of alpha-ctg A from water to urea and alkylurea solutions were calculated. Since the enthalpies of transfer were determined previously, the entropies of transfer could also be obtained so that a complete thermodynamic description is available. An attempt is made to interpret the values of the thermodynamic quantities in terms of various interactions involved in solvation as well as to calculate the exchange constant by using the model of weak interactions. In solvation of alkylureas the hydrophobic nature of the alkyl groups is clearly reflected.
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Affiliation(s)
- N Poklar
- Department of Chemistry, University of Ljubljana, Slovenia
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13
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Poklar N, Vesnaver G, Lapanje S. Thermodynamics of denaturation of alpha-chymotrypsinogen A in aqueous urea and alkylurea solutions. JOURNAL OF PROTEIN CHEMISTRY 1995; 14:709-19. [PMID: 8747432 DOI: 10.1007/bf01886910] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The effects of pH, urea, and alkylureas on the thermal stability of alpha-chymotrypsinogen A (alpha-ctg A) have been investigated by differential scanning calorimetry (DSC) and UV spectroscopy. Heat capacity changes and enthalpies of transition of alpha-ctg A in the presence of urea and alkylureas were measured at the transition temperature. Using these data, the corresponding Gibbs free energies, enthalpies, and entropies of denaturation at 25 degrees C were calculated. Comparison of these values shows that at 25 degrees C denaturation with urea is characterized by a significantly smaller enthalpy and entropy of denaturation. At all denaturant concentrations the enthalpy term slightly dominates the entropy term in the Gibbs free energy function. The most obvious effect of alkylureas was lowering of the temperature of transition, which was increasing with alkylurea concentration and the size of alkyl chain. Destabilization of the folded protein in the presence of alkylureas appears to be primarily the result of the weakening of hydrophobic interactions due to diminished solvent ordering around the protein-molecules. At pH lower than 2.0, alpha-ctg A still exists in a very stable form, probably the acid-denatured from (A-form).
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Affiliation(s)
- N Poklar
- Department of Chemistry, University of Ljubljana, Slovenia
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14
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Zerovnik E, Jerala R, Poklar N, Kroon-Zitko L, Turk V. Compactness of the molten globule in comparison to unfolded states as observed by size-exclusion chromatography. BIOCHIMICA ET BIOPHYSICA ACTA 1994; 1209:140-3. [PMID: 7947976 DOI: 10.1016/0167-4838(94)90149-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The volumes of elution of denatured states of four proteins at high urea (8 M) and ethylurea (6 M) concentration were determined. They were found equally unfolded in both solvents. The volumes of elution of the unfolded states were compared to those of the native states and of some molten globule intermediates. It has been shown that the protein proteinase inhibitor stefin B, exhibits 'molten globule'-like properties on acid denaturation. The high salt acidic intermediate (a molten globule) as well as the native state of stefin B eluted as dimers, at 18 degrees C. On thermal denaturation above 42 degrees C, the intermediate dissociated into compact monomers. The more stable stefin A, which is monomeric and does not transform into molten globule intermediates under similar perturbing conditions, was always used for comparison. The states of both, stefin A and B in 50% methanol were found to be monomeric and of native-like compactness.
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Affiliation(s)
- E Zerovnik
- Department of Biochemistry and Molecular Biology, J. Stefan Institute, Ljubljana, Slovenia
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