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Sanchez-Fernandez A, Poon JF, Leung AE, Prévost SF, Dicko C. Stabilization of Non-Native Folds and Programmable Protein Gelation in Compositionally Designed Deep Eutectic Solvents. ACS NANO 2024; 18:18314-18326. [PMID: 38949563 PMCID: PMC11256765 DOI: 10.1021/acsnano.4c01950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 06/17/2024] [Accepted: 06/18/2024] [Indexed: 07/02/2024]
Abstract
Proteins are adjustable units from which biomaterials with designed properties can be developed. However, non-native folded states with controlled topologies are hardly accessible in aqueous environments, limiting their prospects as building blocks. Here, we demonstrate the ability of a series of anhydrous deep eutectic solvents (DESs) to precisely control the conformational landscape of proteins. We reveal that systematic variations in the chemical composition of binary and ternary DESs dictate the stabilization of a wide range of conformations, that is, compact globular folds, intermediate folding states, or unfolded chains, as well as controlling their collective behavior. Besides, different conformational states can be visited by simply adjusting the composition of ternary DESs, allowing for the refolding of unfolded states and vice versa. Notably, we show that these intermediates can trigger the formation of supramolecular gels, also known as eutectogels, where their mechanical properties correlate to the folding state of the protein. Given the inherent vulnerability of proteins outside the native fold in aqueous environments, our findings highlight DESs as tailorable solvents capable of stabilizing various non-native conformations on demand through solvent design.
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Affiliation(s)
- Adrian Sanchez-Fernandez
- Center
for Research in Biological Chemistry and Molecular Materials (CiQUS),
Department of Chemical Engineering, Universidade
de Santiago de Compostela, Santiago de Compostela 15705, Spain
| | - Jia-Fei Poon
- European
Spallation Source, Lund University, Lund SE-22100, Sweden
| | | | | | - Cedric Dicko
- Pure
and Applied Biochemistry, Department of Chemistry, Lund University, Lund SE-22100, Sweden
- Lund
Institute of Advanced Neutron and X-ray Science, Lund SE-22370, Sweden
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2
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Yang L, Zhang W, Xu W. Efficient protein conformation dynamics characterization enabled by mobility-mass spectrometry. Anal Chim Acta 2023; 1243:340800. [PMID: 36697173 DOI: 10.1016/j.aca.2023.340800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 12/25/2022] [Accepted: 01/02/2023] [Indexed: 01/11/2023]
Abstract
Protein structure dynamics in solution and from solution to gas phase are important but challenging topics. Great efforts and advances have been made especially since the wide application of ion mobility mass spectrometry (IM-MS), by which protein collision cross section (CCS) in gas phase could be measured. Due to the lack of efficient experimental methods, protein structures in protein databank are typically referred as their structures in solution. Although conventional structural biology techniques provide high-resolution protein structures, complicated and stringent processes also limit their applicability under different solvent conditions, thus preventing the capture of protein dynamics in solution. Enabled by the combination of mobility capillary electrophoresis (MCE) and IM-MS, an efficient experimental protocol was developed to characterize protein conformation dynamics in solution and from solution to gas phase. As a first attempt, key factors that affecting protein conformations were distinguished and evaluated separately, including pH, temperature, softness of ionization process, presence and specific location of disulfide bonds. Although similar extent of unfolding could be observed for different proteins, in-depth analysis reveals that pH decrease from 7.0 to 3.0 dominates the unfolding of proteins without disulfide bonds in conventional ESI-MS experiments; while harshness of the ionization process dominates the unfolding of proteins with disulfide bonds. Second, disulfide bonds show capability of preserving protein conformations in acidic solution environments. However, by monitoring protein conformation dynamics and comparing results from different proteins, it is also found that their capability is position dependent. Surprisingly, disulfide bonds did not show the capability of preserving protein conformations during ionization processes.
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Affiliation(s)
- Lei Yang
- School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Wenjing Zhang
- School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Wei Xu
- School of Life Science, Beijing Institute of Technology, Beijing, 100081, China.
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3
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Meena P, Kishore N. Synergistic effects of osmolytes on solvent exclusion and resulting protein stabilization: Studies with sucrose, taurine and sorbitol individually and in combination. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.121175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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4
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Abstract
In the past, many intensive attempts failed to capture or underestimated the copopulated intermediate conformers from the protein folding/unfolding reaction. We report a promising approach to kinetically trap, resolve, and quantify protein conformers that evolve during unfolding in solution. We conducted acid-induced unfolding of three model proteins (cytochrome c, myoglobin, and lysozyme), and the corresponding reaction aliquots upon decreasing the pH were electrosprayed for high field asymmetric waveform ion mobility spectrometry (FAIMS) measurements. The copopulated conformers were resolved, visualized, and quantified by a two-dimensional mapping of the FAIMS output. Contrary to expectations, all the above proteins appeared metamorphic (multiple-folded conformations) at the physiological pH, and cytochrome c exhibited an unusual "conformational shuttling" before forming the molten globule state. Thus, in contrast to many previous studies, a wide variety of thermodynamically stable intermediate conformers, including compact, molten globule, and partially unfolded forms, was trapped from solution, probing the unfolding mechanism in detail.
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Affiliation(s)
- Veena Shankar Avadhani
- Department of Chemistry, Indian Institute of Science Education and Research Tirupati, Tirupati 517507, India
| | - Supratim Mondal
- Department of Chemistry, Indian Institute of Science Education and Research Tirupati, Tirupati 517507, India
| | - Shibdas Banerjee
- Department of Chemistry, Indian Institute of Science Education and Research Tirupati, Tirupati 517507, India
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5
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Luan M, Hou Z, Huang G. Suppression of Protein Structural Perturbations in Native Electrospray Ionization during the Final Evaporation Stages Revealed by Molecular Dynamics Simulations. J Phys Chem B 2021; 126:144-150. [PMID: 34964355 DOI: 10.1021/acs.jpcb.1c09130] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Native electrospray ionization was known to preserve the protein structure in solution, which overcame the uncontrollable acidification of droplets during transfer from solution into the gas phase in conventional electrospray ionization. However, detailed experimental studies on when and how could native electrospray ionization minimize structural perturbations remain quite unclear. Herein, we conducted molecular dynamics simulations to investigate the protein structure evolution during electrospray ionization. At a neutral droplet pH, the protein structure in solution could be retained after evaporation, which was in accordance with previous reports. As the droplet pH deviated from neutral, we have found that the compact protein structure would not unfold until the last 10 ns prior to the final desolvation, which demonstrated that the role of native electrospray ionization in preserving the protein structure was mainly reflected on the final evaporation stages. The present study might provide new insights into studying the microscopic biomolecular events occurring during the liquid-gas interface transition and their influence on solution-structure retention.
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Affiliation(s)
- Moujun Luan
- The First Affiliated Hospital of USTC, University of Science and Technology of China, 230001 Hefei, China.,School of Chemistry and Materials Science, University of Science and Technology of China, 230026 Hefei, China
| | - Zhuanghao Hou
- The First Affiliated Hospital of USTC, University of Science and Technology of China, 230001 Hefei, China.,School of Chemistry and Materials Science, University of Science and Technology of China, 230026 Hefei, China.,National Synchrotron Radiation Laboratory, University of Science and Technology of China, 230029 Hefei, China
| | - Guangming Huang
- The First Affiliated Hospital of USTC, University of Science and Technology of China, 230001 Hefei, China.,School of Chemistry and Materials Science, University of Science and Technology of China, 230026 Hefei, China.,National Synchrotron Radiation Laboratory, University of Science and Technology of China, 230029 Hefei, China
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6
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Prasanthan P, Kishore N. Combined effect of equimolal osmolytes trehalose and glycine on stability of hen egg-white lysozyme: Quantitative mechanistic aspects. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.01.071] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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7
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Moldenhauer D, Fuenzalida Werner JP, Strassert CA, Gröhn F. Light-Responsive Size of Self-Assembled Spiropyran-Lysozyme Nanoparticles with Enzymatic Function. Biomacromolecules 2019; 20:979-991. [PMID: 30570257 DOI: 10.1021/acs.biomac.8b01605] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Novel light-responsive nanoassemblies with switchable size and enzymatic activity are built from a protein and a water-soluble spiropyran. Assemblies are created by electrostatic self-assembly in aqueous solution such that the photochromic property of the spiropyran enables light responsiveness. Upon visible light exposure, the aggregate size increases from 200 to 400 nm. The enzyme retains its activity upon aggregation into the assembly, while it decreases through visible light irradiation. Fundamentally, we show how the two different spiropyran isomers, the open-ring merocyanine form and the closed-ring spiropyran form, bind differently to the protein, which triggers the assembly size and use of thermodynamic data to understand the binding process and the size response. Thus, as a proof of concept, a self-assembly driven light-tunable enzyme activity in conjunction with a triggerable assembly size is demonstrated for a model system. The concept bears future potential for various possible biological applications ranging from genetic control over vaccine applications to the detection of certain proteins.
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Affiliation(s)
- Daniel Moldenhauer
- Department of Chemistry and Pharmacy and Interdisciplinary Center for Molecular Materials (ICMM) , Friedrich-Alexander-Universität Erlangen-Nürnberg , Egerlandstraße 3 , D-91058 Erlangen , Germany
| | - Juan Pablo Fuenzalida Werner
- Department of Chemistry and Pharmacy and Interdisciplinary Center for Molecular Materials (ICMM) , Friedrich-Alexander-Universität Erlangen-Nürnberg , Egerlandstraße 3 , D-91058 Erlangen , Germany
| | - Cristian A Strassert
- Institute of Physics and Center for Nanotechnology , Westfälische Wilhelms-Universität Münster , Heisenbergstraße 11 , D-48149 Münster , Germany
| | - Franziska Gröhn
- Department of Chemistry and Pharmacy and Interdisciplinary Center for Molecular Materials (ICMM) , Friedrich-Alexander-Universität Erlangen-Nürnberg , Egerlandstraße 3 , D-91058 Erlangen , Germany
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8
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Corona discharge electrospray ionization of formate-containing solutions enables in-source reduction of disulfide bonds. Anal Bioanal Chem 2018; 411:4729-4737. [PMID: 30397758 DOI: 10.1007/s00216-018-1447-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 10/12/2018] [Accepted: 10/22/2018] [Indexed: 01/05/2023]
Abstract
Disulfide bonds are critical linkages for maintaining protein structure and enzyme activity. These linkages, however, can limit peptide sequencing efforts by mass spectrometry (MS) and often require chemical reduction and alkylation. Under such conditions, information regarding cysteine connectivity is lost. Online partial disulfide reduction within the electrospray (ESI) source has recently been established as a means to identify complex cysteine linkage patterns in a liquid chromatography-MS experiment without the need for sample pre-treatment. Corona discharge (CD) is invoked as the causative factor of this in-source reduction (ISR); however, evidence remains largely circumstantial. In this study, we demonstrate that instrumental factors-nebulizing gas, ESI capillary material, organic solvent content, ESI spray needle-to-MS distance-all modulate the degree of reduction observed for the single disulfide in oxytocin, further implicating CD in ISR. Rigorous analysis of solution conditions, however, reveals that corona discharge alone can induce only minor disulfide reduction. We establish that CD-ESI of peptide solutions containing formic acid or its conjugate base results in a dramatic increase in disulfide reduction. It is also determined that ISR is exacerbated at low pH for complex peptides containing multiple disulfide bonds and possessing higher-order structure, as well as for a small protein. Overall, our results demonstrate that ESI of formate/formic acid-containing solutions under corona discharge conditions facilitates disulfide ISR, likely by a similar reduction pathway measured in γ-radiolysis studies nearly three decades ago.
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9
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Han JY, Choi TS, Kim HI. Molecular Role of Ca 2+ and Hard Divalent Metal Cations on Accelerated Fibrillation and Interfibrillar Aggregation of α-Synuclein. Sci Rep 2018; 8:1895. [PMID: 29382893 PMCID: PMC5789889 DOI: 10.1038/s41598-018-20320-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 01/17/2018] [Indexed: 01/11/2023] Open
Abstract
α-Synuclein (αSyn) is an intrinsically disordered protein, the aggregation of which is highly related to the pathology of diverse α-synucleinopathies. Various hard divalent metal cations have been shown to affect αSyn aggregation. Especially, Ca2+ is suggested to be a crucial ion due to its physiological relevance to α-synucleinopathies. However, the molecular origin of αSyn aggregation mediated by the metal ions is not fully elucidated. In this study, we revealed that hard divalent metal ions had almost identical influences on αSyn aggregation. Based on these similarities, the molecular role of Ca2+ was investigated as a representative metal ion. Herein, we demonstrated that binding of multiple Ca2+ ions induces structural transition of αSyn monomers to extended conformations, which promotes rapid αSyn fibrillation. Additionally, we observed that Ca2+ induced further interfibrillar aggregation via electrostatic and hydrophobic interactions. Our results from multiple biophysical methods, including ion mobility-mass spectrometry (IM-MS), synchrotron small-angle X-ray scattering (SAXS), transmission electron microscopy (TEM), provide detailed information on the structural change of αSyn and the aggregation process mediated by Ca2+. Overall, our study would be valuable for understanding the influence of Ca2+ on the aggregation of αSyn during the pathogenesis of α-synucleinopathies.
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Affiliation(s)
- Jong Yoon Han
- Department of Chemistry, Korea University, Seoul, 02841, Republic of Korea
| | - Tae Su Choi
- Department of Chemistry, Korea University, Seoul, 02841, Republic of Korea
| | - Hugh I Kim
- Department of Chemistry, Korea University, Seoul, 02841, Republic of Korea.
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10
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Choi TS, Lee HJ, Han JY, Lim MH, Kim HI. Molecular Insights into Human Serum Albumin as a Receptor of Amyloid-β in the Extracellular Region. J Am Chem Soc 2017; 139:15437-15445. [DOI: 10.1021/jacs.7b08584] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Tae Su Choi
- Department
of Chemistry, Korea University, Seoul 02841, Republic of Korea
- Department
of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea
| | | | - Jong Yoon Han
- Department
of Chemistry, Korea University, Seoul 02841, Republic of Korea
| | | | - Hugh I. Kim
- Department
of Chemistry, Korea University, Seoul 02841, Republic of Korea
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11
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Konermann L. Addressing a Common Misconception: Ammonium Acetate as Neutral pH "Buffer" for Native Electrospray Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:1827-1835. [PMID: 28710594 DOI: 10.1007/s13361-017-1739-3] [Citation(s) in RCA: 146] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 06/14/2017] [Accepted: 06/15/2017] [Indexed: 05/12/2023]
Abstract
Native ESI-MS involves the transfer of intact proteins and biomolecular complexes from solution into the gas phase. One potential pitfall is the occurrence of pH-induced changes that can affect the analyte while it is still surrounded by solvent. Most native ESI-MS studies employ neutral aqueous ammonium acetate solutions. It is a widely perpetuated misconception that ammonium acetate buffers the analyte solution at neutral pH. By definition, a buffer consists of a weak acid and its conjugate weak base. The buffering range covers the weak acid pKa ± 1 pH unit. NH4+ and CH3-COO- are not a conjugate acid/base pair, which means that they do not constitute a buffer at pH 7. Dissolution of ammonium acetate salt in water results in pH 7, but this pH is highly labile. Ammonium acetate does provide buffering around pH 4.75 (the pKa of acetic acid) and around pH 9.25 (the pKa of ammonium). This implies that neutral ammonium acetate solutions electrosprayed in positive ion mode will likely undergo acidification down to pH 4.75 ± 1 in the ESI plume. Ammonium acetate nonetheless remains a useful additive for native ESI-MS. It is a volatile electrolyte that can mimic the solvation properties experienced by proteins under physiological conditions. Also, a drop from pH 7 to around pH 4.75 is less dramatic than the acidification that would take place in pure water. It is hoped that the habit of referring to pH 7 solutions as ammonium acetate "buffer" will disappear from the literature. Ammonium acetate "solution" should be used instead. Graphical Abstract ᅟ.
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Affiliation(s)
- Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, ON, N6A 5B7, Canada.
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12
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Proof of concept of a “greener” protein purification/enrichment method based on carboxylate-terminated carbosilane dendrimer-protein interactions. Anal Bioanal Chem 2016; 408:7679-7687. [DOI: 10.1007/s00216-016-9864-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 08/04/2016] [Indexed: 10/21/2022]
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13
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Sun Y, Vahidi S, Sowole MA, Konermann L. Protein Structural Studies by Traveling Wave Ion Mobility Spectrometry: A Critical Look at Electrospray Sources and Calibration Issues. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:31-40. [PMID: 26369778 DOI: 10.1007/s13361-015-1244-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Revised: 07/27/2015] [Accepted: 07/29/2015] [Indexed: 06/05/2023]
Abstract
The question whether electrosprayed protein ions retain solution-like conformations continues to be a matter of debate. One way to address this issue involves comparisons of collision cross sections (Ω) measured by ion mobility spectrometry (IMS) with Ω values calculated for candidate structures. Many investigations in this area employ traveling wave IMS (TWIMS). It is often implied that nanoESI is more conducive for the retention of solution structure than regular ESI. Focusing on ubiquitin, cytochrome c, myoglobin, and hemoglobin, we demonstrate that Ω values and collisional unfolding profiles are virtually indistinguishable under both conditions. These findings suggest that gas-phase structures and ion internal energies are independent of the type of electrospray source. We also note that TWIMS calibration can be challenging because differences in the extent of collisional activation relative to drift tube reference data may lead to ambiguous peak assignments. It is demonstrated that this problem can be circumvented by employing collisionally heated calibrant ions. Overall, our data are consistent with the view that exposure of native proteins to electrospray conditions can generate kinetically trapped ions that retain solution-like structures on the millisecond time scale of TWIMS experiments. ᅟ
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Affiliation(s)
- Yu Sun
- Department of Chemistry, The University of Western Ontario, London, ON, N6A 5B7, Canada
| | - Siavash Vahidi
- Department of Chemistry, The University of Western Ontario, London, ON, N6A 5B7, Canada
| | - Modupeola A Sowole
- Department of Chemistry, The University of Western Ontario, London, ON, N6A 5B7, Canada
| | - Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, ON, N6A 5B7, Canada.
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14
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Politis A, Borysik AJ. Assembling the pieces of macromolecular complexes: Hybrid structural biology approaches. Proteomics 2015; 15:2792-803. [DOI: 10.1002/pmic.201400507] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 01/26/2015] [Accepted: 02/24/2015] [Indexed: 01/14/2023]
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15
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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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16
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Abdelhamid HN, Wu HF. Synthesis of a highly dispersive sinapinic acid@graphene oxide (SA@GO) and its applications as a novel surface assisted laser desorption/ionization mass spectrometry for proteomics and pathogenic bacteria biosensing. Analyst 2015; 140:1555-65. [DOI: 10.1039/c4an02158d] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
GO-modified sinapinic acid was synthesized and characterized; it was then investigated for use in SALDI-MS for proteomics and pathogenic bacterial biosensing.
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Affiliation(s)
- Hani Nasser Abdelhamid
- Department of Chemistry
- National Sun Yat-Sen University
- Kaohsiung
- Taiwan
- Department of Chemistry
| | - Hui-Fen Wu
- Department of Chemistry
- National Sun Yat-Sen University
- Kaohsiung
- Taiwan
- School of Pharmacy
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