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Sharafeldin M, Davis JJ. Characterising the biosensing interface. Anal Chim Acta 2022; 1216:339759. [DOI: 10.1016/j.aca.2022.339759] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 02/08/2022] [Accepted: 03/22/2022] [Indexed: 12/19/2022]
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2
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Kavitha E, Devaraj Stephen L, Brishti FH, Karthikeyan S. Two-trace two-dimensional (2T2D) correlation infrared spectral analysis of Spirulina platensis and its commercial food products coupled with chemometric analysis. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130964] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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3
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Jeanne Dit Fouque K, Fernandez-Lima F. Following Structural Changes by Thermal Denaturation Using Trapped Ion Mobility Spectrometry-Mass Spectrometry. J Phys Chem B 2020; 124:6257-6265. [PMID: 32560586 PMCID: PMC8341290 DOI: 10.1021/acs.jpcb.0c04276] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The behavior of biomolecules as a function of the solution temperature is often crucial to assessing their biological activity and function. While heat-induced changes of biomolecules are traditionally monitored using optical spectroscopy methods, their conformational changes and unfolding transitions remain challenging to interpret. In the present work, the structural transitions of bovine serum albumin (BSA) in native conditions (100 mM aqueous ammonium acetate) were investigated as a function of the starting solution temperature (T ∼ 23-70 °C) using a temperature-controlled nanoelectrospray ionization source (nESI) coupled to a trapped ion mobility spectrometry-mass spectrometry (TIMS-MS) instrument. The charge state distribution of the monomeric BSA changed from a native-like, narrow charge state ([M + 12H]12+ to [M + 16H]16+ at ∼23 °C) and narrow mobility distribution toward an unfolded-like, broad charge state (up to [M + 46H]46+ at ∼70 °C) and broad mobility distribution. Inspection of the average charge state and collision cross section (CCS) distribution suggested a two-state unfolding transition with a melting temperature Tm ∼ 56 ± 1 °C; however, the inspection of the CCS profiles at the charge state level as a function of the solution temperature showcases at least six structural transitions (T1-T7). If the starting solution concentration is slightly increased (from 2 to 25 μM), this method can detect nonspecific BSA dimers and trimers which dissociate early (Td ∼ 34 ± 1 °C) and may disturb the melting curve of the BSA monomer. In a single experiment, this technology provides a detailed view of the solution, protein structural landscape (mobility vs solution temperature vs relative intensity for each charge state).
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Affiliation(s)
- Kevin Jeanne Dit Fouque
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States
| | - Francisco Fernandez-Lima
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States
- Biomolecular Sciences Institute, Florida International University, Miami, Florida 33199, United States
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4
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Keiderling TA. Structure of Condensed Phase Peptides: Insights from Vibrational Circular Dichroism and Raman Optical Activity Techniques. Chem Rev 2020; 120:3381-3419. [DOI: 10.1021/acs.chemrev.9b00636] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Timothy A. Keiderling
- Department of Chemistry, University of Illinois at Chicago 845 West Taylor Street m/c 111, Chicago, Illinois 60607-7061, United States
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5
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Degueldre M, Wielant A, Girot E, Burkitt W, O'Hara J, Debauve G, Gervais A, Jone C. Native peptide mapping - A simple method to routinely monitor higher order structure changes and relation to functional activity. MAbs 2019; 11:1391-1401. [PMID: 31223055 PMCID: PMC6816347 DOI: 10.1080/19420862.2019.1634460] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
In the biopharmaceutical environment, controlling the Critical Quality Attributes (CQA) of a product is essential to prevent changes that affect its safety or efficacy. Physico-chemical techniques and bioassays are used to screen and monitor these CQAs. The higher order structure (HOS) is a CQA that is typically studied using techniques that are not commonly considered amenable to quality control laboratories. Here, we propose a peptide mapping-based method, named native peptide mapping, which could be considered as straightforward for HOS analysis and applicable for IgG4 and IgG1 antibodies. The method was demonstrated to be fit-for-purpose as a stability-indicating assay by showing differences at the peptide level between stressed and unstressed material. The unfolding pathway induced by a heat stress was also studied via native peptide mapping assay. Furthermore, we demonstrated the structure–activity relationship between HOS and biological activity by analyzing different types of stressed samples with a cell-based assay and the native peptide mapping. The correlation between both sets of results was highlighted by monitoring peptides located in the complementary-determining regions and the relative potency of the biotherapeutic product. This relationship represents a useful approach to interrogate the criticality of HOS as a CQA of a drug.
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Affiliation(s)
- Michel Degueldre
- Department of Analytical Science Biologicals, UCB , Braine L'Alleud , Belgium
| | - Annemie Wielant
- Department of Analytical Science Biologicals, UCB , Braine L'Alleud , Belgium
| | - Eglantine Girot
- Department of Analytical Science Biologicals, UCB , Braine L'Alleud , Belgium
| | - Will Burkitt
- Department of Analytical Science Biologicals, UCB , Slough , UK
| | - John O'Hara
- Department of Analytical Science Biologicals, UCB , Slough , UK
| | - Gaël Debauve
- Department of Analytical Science Biologicals, UCB , Braine L'Alleud , Belgium
| | - Annick Gervais
- Department of Analytical Science Biologicals, UCB , Braine L'Alleud , Belgium
| | - Carl Jone
- Department of Analytical Science Biologicals, UCB , Braine L'Alleud , Belgium
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6
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Kessler J, Andrushchenko V, Kapitán J, Bouř P. Insight into vibrational circular dichroism of proteins by density functional modeling. Phys Chem Chem Phys 2018; 20:4926-4935. [PMID: 29384537 DOI: 10.1039/c7cp08016f] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Vibrational circular dichroism (VCD) spectroscopy is an excellent method to determine the secondary structure of proteins in solution. Comparison of experimental spectra with quantum-chemical simulations represents a convenient and objective way to extract information on the structure. This has been difficult for such large molecules where approximate theoretical models have to be used. In the present study we applied the Cartesian-coordinate based tensor transfer (CCT) making it possible to extend the density functional theory (DFT) and model spectral intensities of large globular proteins nearly at quantum-chemical precision. Indeed, comparison with experiment provided a better understanding of the dependence of VCD spectral shapes on the geometry, their sensitivity to fine structural details and interactions with the environment. On a model set of globular proteins the simulated spectra correlated well with experimental data and revealed which structural information can (and cannot) be obtained from this kind of spectroscopy. Although the VCD technique has been regarded as being rather insensitive to side-chain variations, we found that the spectra of human and hen lysozyme differing by a few amino acids only are quite distinct. This has been explained by long-distance coupling of the amide vibrations. Likewise, the modeling reproduced some spectral changes caused by protein deuteration even when the protein structure was conserved.
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Affiliation(s)
- Jiří Kessler
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, 16610 Prague, Czech Republic.
| | - Valery Andrushchenko
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, 16610 Prague, Czech Republic.
| | - Josef Kapitán
- Department of Optics, Palacký University, 17. listopadu 12, 77146 Olomouc, Czech Republic
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, 16610 Prague, Czech Republic.
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7
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Park Y, Park Y, Jin S, Kim JW, Jung YM. Formation mechanism of BAMLET by 2D Raman correlation analysis. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2018.05.066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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8
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Tao Y, Wu Y, Zhang L. Advancements of two dimensional correlation spectroscopy in protein researches. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 197:185-193. [PMID: 29409703 DOI: 10.1016/j.saa.2018.01.039] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Revised: 01/09/2018] [Accepted: 01/13/2018] [Indexed: 05/26/2023]
Abstract
The developments of two-dimensional correlation spectroscopy (2DCOS) applications in protein studies are discussed, especially for the past two decades. The powerful utilities of 2DCOS combined with various analytical techniques in protein studies are summarized. The emphasis is on the vibration spectroscopic techniques including IR, NIR, Raman and optical activity (ROA), as well as vibration circular dichroism (VCD) and fluorescence spectroscopy. In addition, some new developments, such as hetero-spectral 2DCOS, moving-window correlation, and model based correlation, are also reviewed for their utility in the investigation of the secondary structure, denaturation, folding and unfolding changes of protein. Finally, the new possibility and challenges of 2DCOS in protein research are highlighted as well.
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Affiliation(s)
- Yanchun Tao
- State Key Laboratory of Supramolecular Structure and Materials, Institute of Theoretical Chemistry, Jilin University, No. 2699 Qianjin Street, Changchun 130012, China
| | - Yuqing Wu
- State Key Laboratory of Supramolecular Structure and Materials, Institute of Theoretical Chemistry, Jilin University, No. 2699 Qianjin Street, Changchun 130012, China.
| | - Liping Zhang
- Department of Foundation, Jilin Business and Technology College, No. 1666 Kalunhu Street, Changchun 130507, China.
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Motoyama M, Vénien A, Loison O, Sandt C, Watanabe G, Sicard J, Sasaki K, Astruc T. In situ characterization of acidic and thermal protein denaturation by infrared microspectroscopy. Food Chem 2018; 248:322-329. [DOI: 10.1016/j.foodchem.2017.11.031] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 11/08/2017] [Accepted: 11/08/2017] [Indexed: 01/13/2023]
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10
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Noda I. Vibrational two-dimensional correlation spectroscopy (2DCOS) study of proteins. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2017; 187:119-129. [PMID: 28675821 DOI: 10.1016/j.saa.2017.06.034] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2017] [Revised: 06/22/2017] [Accepted: 06/26/2017] [Indexed: 06/07/2023]
Abstract
A tutorial is provided for the generalized two-dimensional correlation spectroscopy (2DCOS), which is applicable to the vibrational spectroscopic study of proteins and related systems. In 2DCOS, similarity or dissimilarity among variations of spectroscopic intensities, which are induced by applying an external perturbation to the sample, is examined by constructing correlation spectra defined by two independent spectral variable axes. By spreading congested or overlapped peaks along the second dimension, apparent spectral resolution is enhanced and interpretation of complex spectra becomes simplified. A set of simple rules for the intensities and signs of correlation peaks is used to extract insightful information. Simulated IR spectra for a model protein are used to demonstrate the specific utility of 2DCOS. Additional tools useful in the 2DCOS analysis of proteins, such as data segmentation assisted with moving-window analysis, 2D codistribution analysis, Pareto scaling, and null-space projection are also discussed.
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Affiliation(s)
- Isao Noda
- University of Delaware, Newark, DE 19716, USA.
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11
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Park Y, Kim Y, Park Y, Jin S, Hwang H, Jung YM. Formation mechanism of α-lactalabumin/oleic acid complex characterized by 2D correlation analysis. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2017; 185:93-97. [PMID: 28549296 DOI: 10.1016/j.saa.2017.05.028] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 05/14/2017] [Indexed: 06/07/2023]
Abstract
Partially unfolded α-lactalbumin (ALA) forms a complex with oleic acid (OA) that exhibits cytotoxic activity. In this study, for the first time, the pH-induced formation mechanism for ALA/OA complexes with two different molar ratios was investigated at the molecular level. For a deeper understanding of the formation mechanism of the two different ALA/OA complexes with decreasing pH, principal component analysis (PCA) and two-dimensional (2D) correlation spectroscopy were used to examine the pH-dependent IR spectra of ALA/OA complexes. By tracking the secondary structural variations in the ALA/OA complexes with decreasing pH, we successfully elucidated the formation mechanism of the ALA/OA complexes at the molecular level. The results showed that the secondary structures of theses complexes exhibited the greatest change between pH4 and pH3.5 and that the components that mainly contributed to the pH-induced transition from the N-state to the A-state were dissimilar in the two different ALA/OA complexes.
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Affiliation(s)
- Yeonju Park
- Department of Chemistry, Institute for Molecular Science and Fusion Technology, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Yeseul Kim
- Department of Chemistry, Institute for Molecular Science and Fusion Technology, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Yujeong Park
- Department of Chemistry, Institute for Molecular Science and Fusion Technology, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Sila Jin
- Department of Chemistry, Institute for Molecular Science and Fusion Technology, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Hoon Hwang
- Department of Chemistry, Institute for Molecular Science and Fusion Technology, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Young Mee Jung
- Department of Chemistry, Institute for Molecular Science and Fusion Technology, Kangwon National University, Chuncheon 24341, Republic of Korea.
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12
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Dasgupta M, Kishore N. Characterization and analysis of binding of Thioflavin T with partially folded and native states of α–lactalbumin protein by calorimetric and spectroscopic techniques. Int J Biol Macromol 2017; 95:376-384. [DOI: 10.1016/j.ijbiomac.2016.11.069] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Revised: 10/25/2016] [Accepted: 11/20/2016] [Indexed: 11/29/2022]
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13
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14
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Park Y, Kim Y, Vikram K, Czarnik-Matusewicz B, Jung YM. Two-Dimensional Correlation Analysis of pH-induced Raman Spectral Changes of α-Lactalbumin. B KOREAN CHEM SOC 2016. [DOI: 10.1002/bkcs.10763] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Yeonju Park
- Department of Chemistry, Institute for Molecular Science and Fusion Technology; Kangwon National University; Chuncheon 24341 Korea
| | - Yeseul Kim
- Department of Chemistry, Institute for Molecular Science and Fusion Technology; Kangwon National University; Chuncheon 24341 Korea
| | - Kunwar Vikram
- Department of Chemistry, Institute for Molecular Science and Fusion Technology; Kangwon National University; Chuncheon 24341 Korea
| | | | - Young Mee Jung
- Department of Chemistry, Institute for Molecular Science and Fusion Technology; Kangwon National University; Chuncheon 24341 Korea
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15
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Sales AE, Breydo L, Porto TS, Porto ALF, Uversky VN. Hydrophobicity-dependent effects of polymers on different protein conformations. RSC Adv 2016. [DOI: 10.1039/c6ra07910e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Polymers can either induce or disrupt secondary and tertiary structure in partially disordered protein conformations. The balance of the forces driving these structural changes depends on the polymer hydrophobicity and protein sequence and structure.
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Affiliation(s)
- Amanda E. Sales
- Department of Molecular Medicine and Byrd Alzheimer's Research Institute
- Morsani College of Medicine
- University of South Florida
- Tampa
- USA
| | - Leonid Breydo
- Department of Molecular Medicine and Byrd Alzheimer's Research Institute
- Morsani College of Medicine
- University of South Florida
- Tampa
- USA
| | - Tatiana S. Porto
- Academic Unit of Garanhuns
- Federal Rural University of Pernambuco
- Garanhuns
- Brazil
| | - Ana L. F. Porto
- Department of Morphology and Animal Physiology
- Federal Rural University of Pernambuco
- 52171-900 Recife
- Brazil
| | - Vladimir N. Uversky
- Department of Molecular Medicine and Byrd Alzheimer's Research Institute
- Morsani College of Medicine
- University of South Florida
- Tampa
- USA
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16
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Lee JW, Kim HI. Investigating acid-induced structural transitions of lysozyme in an electrospray ionization source. Analyst 2015; 140:661-9. [PMID: 25429398 DOI: 10.1039/c4an01794c] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The effect of acids on the structure of lysozyme (Lyz) during electrospray ionization (ESI) was studied by comparing the solution and gas-phase structures of Lyz. Investigation using circular dichroism spectroscopy and small-angle X-ray scattering demonstrated that the folded conformation of Lyz was maintained in pH 2.2 solutions containing different acids. On the other hand, analysis of the charge state distributions and ion mobility (IM) distributions, combined with molecular dynamics simulations, demonstrated that the gas phase structures of Lyz depend on the pKa of the acid used to acidify the protein solution. Formic acid and acetic acid, which are weak acids (pKa > 3.5), induce unfolding of Lyz during ESI, presumably because the undissociated weak acids provide protons to maintain the acidic groups within Lyz protonated and prevent the formation of salt bridges. However, HCl suppressed the formation of the unfolded conformers because the acid is already dissociated in solution, and chloride anions within the ESI droplet can interact with Lyz to reduce the intramolecular electrostatic repulsion. These trends in the IM distributions are observed for all charge states, demonstrating the significance of the acid effect on the structure of Lyz during ESI.
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Affiliation(s)
- Jong Wha Lee
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang, 790-784, South Korea.
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Lee JW, Kim HI. Solvent-induced structural transitions of lysozyme in an electrospray ionization source. Analyst 2015; 140:3573-80. [PMID: 25854591 DOI: 10.1039/c5an00235d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The structural characterization of proteins using electrospray ionization mass spectrometry (ESI-MS) has become an important method for understanding protein structural dynamics. The correlation between the structures of proteins in solution and gas phase needs to be understood for the application of ESI-MS to protein structural studies. Hen egg white lysozyme (Lyz) is a small protein with a stable compact structure in solution. Although it was known that denatured Lyz in solution undergoes compaction during transfer into the gas phase via ESI, detailed characterization of the process was not available. In the present study, we show that the organic cosolvent, which denatures Lyz in solution, induces the collapse of the extended Lyz structure into compact structures during ESI. This process is further facilitated by the presence of acids, whose conjugate bases can interact with Lyz to reduce its charge state and the electrostatic repulsion between its charged residues (Analyst, 2015, 140, 661-669). Exposure of ESI droplets to acid and solvent vapors confirms that the overall process most probably occurs in the charged droplets from ESI. This study provides a detailed understanding of the possible influence of the solvent environment on protein structure during transfer into the gas phase.
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Affiliation(s)
- Jong Wha Lee
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang, 790-784, South Korea
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Park Y, Seo Y, Chae B, Pyo D, Chung H, Hwang H, Jung YM. Understanding the Structural Differences between Spherical and Rod-Shaped Human Insulin Nanoparticles Produced by Supercritical Fluids Precipitation. Chemphyschem 2014; 16:476-82. [DOI: 10.1002/cphc.201402504] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Indexed: 11/10/2022]
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19
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Kang D, Ryu SR, Park Y, Czarnik-Matusewicz B, Jung YM. pH-induced structural changes of ovalbumin studied by 2D correlation IR spectroscopy. J Mol Struct 2014. [DOI: 10.1016/j.molstruc.2014.02.061] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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