1
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Ginesi RE, Draper ER. Methods of changing low molecular weight gel properties through gelation kinetics. SOFT MATTER 2024; 20:3887-3896. [PMID: 38691131 DOI: 10.1039/d4sm00238e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2024]
Abstract
Low molecular weight gels continue to attract notable interest, with many potential applications. However, there are still significant gaps in our understanding of these systems and the correlation between the pre-gel and final gel states. The kinetics of the gelation process plays a crucial role in the bulk properties of the hydrogel and presents an opportunity to fine-tune these systems to meet the requirements of the chosen application. Therefore, it is possible to use a single gelator for multiple applications. This review discusses four ways to modify the pre-gelled structures before triggering gelation. Such modifications can enhance the material's intended performance, which may result in significant advancements in high-tech areas, such as drug delivery, cell culturing, electronics, and tissue engineering.
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Affiliation(s)
- Rebecca E Ginesi
- School of Chemistry, University of Glasgow, Glasgow, UK, G12 8QQ, UK.
| | - Emily R Draper
- School of Chemistry, University of Glasgow, Glasgow, UK, G12 8QQ, UK.
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2
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Kölbel J, Anuschek ML, Stelzl I, Santitewagun S, Friess W, Zeitler JA. Dynamical Transition in Dehydrated Proteins. J Phys Chem Lett 2024; 15:3581-3590. [PMID: 38527099 PMCID: PMC11000241 DOI: 10.1021/acs.jpclett.3c03584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 03/16/2024] [Accepted: 03/19/2024] [Indexed: 03/27/2024]
Abstract
Terahertz time-domain spectroscopy and differential scanning calorimetry were used to study the role of the dynamics of biomolecules decoupled from solvent effects. Lyophilized sucrose exhibited steadily increasing absorption with temperature as anharmonic excitations commenced as the system emerged from a deep minimum of the potential energy landscape where harmonic vibrations dominate. The polypeptide bacitracin and two globular proteins, lysozyme and human serum albumin, showed a more complex temperature dependence. Further analysis focused on the spectral signature below and above the boson peak. We found evidence of the onset of anharmonic motions that are characteristic for partial unfolding and molecular jamming in the dry biomolecules. The activation of modes of the protein molecules at temperatures comparable to the protein dynamical transition temperature was observed in the absence of hydration. No evidence of Fröhlich coherence, postulated to facilitate biological function, was found in our experiments.
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Affiliation(s)
- Johanna Kölbel
- Department
of Chemical Engineering, University of Cambridge, Cambridge CB3 0AS, U.K.
| | - Moritz L. Anuschek
- Department
of Chemical Engineering, University of Cambridge, Cambridge CB3 0AS, U.K.
- Department
of Pharmacy - Center for Drug Research, Pharmaceutical Technology
and Biopharmaceutics, Ludwig-Maximilians
Universität, Butenandtstrasse
5, 81377 Munich, Germany
| | - Ivonne Stelzl
- Department
of Pharmacy - Center for Drug Research, Pharmaceutical Technology
and Biopharmaceutics, Ludwig-Maximilians
Universität, Butenandtstrasse
5, 81377 Munich, Germany
| | - Supawan Santitewagun
- Department
of Chemical Engineering, University of Cambridge, Cambridge CB3 0AS, U.K.
| | - Wolfgang Friess
- Department
of Pharmacy - Center for Drug Research, Pharmaceutical Technology
and Biopharmaceutics, Ludwig-Maximilians
Universität, Butenandtstrasse
5, 81377 Munich, Germany
| | - J. Axel Zeitler
- Department
of Chemical Engineering, University of Cambridge, Cambridge CB3 0AS, U.K.
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3
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Maheshwari A, Kishore N. pH-dependent interactions of biologically important metal ions with hen egg white lysozyme based on its hydration properties: Thermodynamic and mechanistic insights. Int J Biol Macromol 2024; 259:129297. [PMID: 38211927 DOI: 10.1016/j.ijbiomac.2024.129297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 12/19/2023] [Accepted: 01/05/2024] [Indexed: 01/13/2024]
Abstract
Importance of metal ion selectivity in biomolecules and their key role in proteins are widely explored. However, understanding the thermodynamics of how hydrated metal ions alter the protein hydration and their conformation is also important. In this study, the interaction of some biologically important Ca2+, Mn2+, Co2+, Cu2+, and Zn2+ ions with hen egg white lysozyme at pH 2.1, 3.0, 4.5 and 7.4 has been investigated. Intrinsic fluorescence studies have been employed for metal ion-induced protein conformational changes analysis. Thermostability based on protein hydration has been investigated using differential scanning calorimetry (DSC). Thermodynamic parameters emphasizing on metal ion-protein binding mechanistic insights have been well discussed using isothermal titration calorimetry (ITC). Overall, these experiments have reported that their interactions are pH-dependent and entropically driven. This research also reports the strongly hydrated metal ions as water structure breaker unlike osmolytes based on DSC studies. These experimental results have highlighted higher concentrations of different metal ions effect on the protein hydration and thermostability which might be helpful in understanding their interactions in aqueous solutions.
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Affiliation(s)
- Anjali Maheshwari
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400 076, India
| | - Nand Kishore
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400 076, India.
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4
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Goktayoglu E, Oztop MH, Ozcan S. Proteomics Approach to Differentiate Protein Extraction Methods in Sugar Beet Leaves. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023. [PMID: 37276611 DOI: 10.1021/acs.jafc.2c09190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Interest in alternative plant-based protein sources is continuously growing. Sugar beet leaves have the potential to satisfy that demand due to their high protein content. They are considered as agricultural waste and utilizing them as protein sources can bring them back to the food chain. In this study, isoelectric-point-precipitation, heat-coagulation, ammonium-sulfate precipitation, high-pressure-assisted isoelectric-point precipitation, and high-pressure-assisted heat coagulation methods were used to extract proteins from sugar beet leaves. A mass spectrometry-based proteomic approach was used for comprehensive protein characterization. The analyses yielded 817 proteins, the most comprehensive protein profile on sugar beet leaves to date. Although the total protein contents were comparable, there was a significant difference between the methods for low-abundance proteins. High-pressure-assisted methods showed elevated levels of proteins predominantly located in the chloroplast. Here we showed for the first time that the extraction/precipitation methods may result in different protein profiles that potentially affect the physical and nutritional properties of functional products.
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Affiliation(s)
- Ece Goktayoglu
- Department of Food Engineering, Middle East Technical University, 06800 Ankara, Turkiye
- Department of Chemical Engineering, University of California Davis, Davis, California 95616, United States
| | - Mecit Halil Oztop
- Department of Food Engineering, Middle East Technical University, 06800 Ankara, Turkiye
| | - Sureyya Ozcan
- Department of Chemistry, Middle East Technical University, 06800 Ankara, Turkiye
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5
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Stephens AD, Kölbel J, Moons R, Chung CW, Ruggiero MT, Mahmoudi N, Shmool TA, McCoy TM, Nietlispach D, Routh AF, Sobott F, Zeitler JA, Kaminski Schierle GS. Decreased Water Mobility Contributes To Increased α-Synuclein Aggregation. Angew Chem Int Ed Engl 2023; 62:e202212063. [PMID: 36316279 PMCID: PMC10107867 DOI: 10.1002/anie.202212063] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 10/24/2022] [Accepted: 10/28/2022] [Indexed: 01/13/2023]
Abstract
The solvation shell is essential for the folding and function of proteins, but how it contributes to protein misfolding and aggregation has still to be elucidated. We show that the mobility of solvation shell H2 O molecules influences the aggregation rate of the amyloid protein α-synuclein (αSyn), a protein associated with Parkinson's disease. When the mobility of H2 O within the solvation shell is reduced by the presence of NaCl, αSyn aggregation rate increases. Conversely, in the presence CsI the mobility of the solvation shell is increased and αSyn aggregation is reduced. Changing the solvent from H2 O to D2 O leads to increased aggregation rates, indicating a solvent driven effect. We show the increased aggregation rate is not directly due to a change in the structural conformations of αSyn, it is also influenced by a reduction in both the H2 O mobility and αSyn mobility. We propose that reduced mobility of αSyn contributes to increased aggregation by promoting intermolecular interactions.
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Affiliation(s)
| | - Johanna Kölbel
- Department of Chemical Engineering and BiotechnologyUniversity of CambridgeUK
| | - Rani Moons
- Department of ChemistryUniversity of AntwerpBelgium
| | - Chyi Wei Chung
- Department of Chemical Engineering and BiotechnologyUniversity of CambridgeUK
| | - Michael T. Ruggiero
- Department of Chemical Engineering and BiotechnologyUniversity of CambridgeUK
- Department of ChemistryUniversity of VermontUSA
| | | | - Talia A. Shmool
- Department of Chemical Engineering and BiotechnologyUniversity of CambridgeUK
| | - Thomas M. McCoy
- Department of Chemical Engineering and BiotechnologyUniversity of CambridgeUK
| | | | - Alexander F. Routh
- Department of Chemical Engineering and BiotechnologyUniversity of CambridgeUK
| | - Frank Sobott
- Department of ChemistryUniversity of AntwerpBelgium
- The Astbury Centre for Structural Molecular BiologyUniversity of LeedsUK
| | - J. Axel Zeitler
- Department of Chemical Engineering and BiotechnologyUniversity of CambridgeUK
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6
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Stephens AD, Kölbel J, Moons R, Chung CW, Ruggiero MT, Mahmoudi N, Shmool TA, McCoy TM, Nietlispach D, Routh AF, Sobott F, Zeitler JA, Kaminski Schierle GS. Decreased Water Mobility Contributes To Increased α-Synuclein Aggregation. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 135:e202212063. [PMID: 38516046 PMCID: PMC10952249 DOI: 10.1002/ange.202212063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Indexed: 03/23/2024]
Abstract
The solvation shell is essential for the folding and function of proteins, but how it contributes to protein misfolding and aggregation has still to be elucidated. We show that the mobility of solvation shell H2O molecules influences the aggregation rate of the amyloid protein α-synuclein (αSyn), a protein associated with Parkinson's disease. When the mobility of H2O within the solvation shell is reduced by the presence of NaCl, αSyn aggregation rate increases. Conversely, in the presence CsI the mobility of the solvation shell is increased and αSyn aggregation is reduced. Changing the solvent from H2O to D2O leads to increased aggregation rates, indicating a solvent driven effect. We show the increased aggregation rate is not directly due to a change in the structural conformations of αSyn, it is also influenced by a reduction in both the H2O mobility and αSyn mobility. We propose that reduced mobility of αSyn contributes to increased aggregation by promoting intermolecular interactions.
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Affiliation(s)
| | - Johanna Kölbel
- Department of Chemical Engineering and BiotechnologyUniversity of CambridgeUK
| | - Rani Moons
- Department of ChemistryUniversity of AntwerpBelgium
| | - Chyi Wei Chung
- Department of Chemical Engineering and BiotechnologyUniversity of CambridgeUK
| | - Michael T. Ruggiero
- Department of Chemical Engineering and BiotechnologyUniversity of CambridgeUK
- Department of ChemistryUniversity of VermontUSA
| | | | - Talia A. Shmool
- Department of Chemical Engineering and BiotechnologyUniversity of CambridgeUK
| | - Thomas M. McCoy
- Department of Chemical Engineering and BiotechnologyUniversity of CambridgeUK
| | | | - Alexander F. Routh
- Department of Chemical Engineering and BiotechnologyUniversity of CambridgeUK
| | - Frank Sobott
- Department of ChemistryUniversity of AntwerpBelgium
- The Astbury Centre for Structural Molecular BiologyUniversity of LeedsUK
| | - J. Axel Zeitler
- Department of Chemical Engineering and BiotechnologyUniversity of CambridgeUK
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7
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Qi Z, Qin Y, Wang J, Zhao M, Yu Z, Xu Q, Nie H, Yan Q, Ge Y. The aqueous supramolecular chemistry of crown ethers. Front Chem 2023; 11:1119240. [PMID: 36742036 PMCID: PMC9895837 DOI: 10.3389/fchem.2023.1119240] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 01/10/2023] [Indexed: 01/22/2023] Open
Abstract
This mini-review summarizes the seminal exploration of aqueous supramolecular chemistry of crown ether macrocycles. In history, most research of crown ethers were focusing on their supramolecular chemistry in organic phase or in gas phase. In sharp contrast, the recent research evidently reveal that crown ethers are very suitable for studying abroad range of the properties and applications of water interactions, from: high water-solubility, control of Hofmeister series, "structural water", and supramolecular adhesives. Key studies revealing more details about the properties of water and aqueous solutions are highlighted.
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Affiliation(s)
- Zhenhui Qi
- Sino-German Joint Research Lab for Space Biomaterials and Translational Technology, Synergetic Innovation Center of Biological Optoelectronics and Healthcare Engineering (BOHE), Shaanxi Provincial Synergistic Innovation Center for Flexible Electronics & Health Sciences (FEHS), School of Life Sciences, Northwestern Polytechnical University, Xi’an, Shaanxi, China,*Correspondence: Zhenhui Qi, ; Qiangqiang Xu, ; Yan Ge,
| | - Yao Qin
- Sino-German Joint Research Lab for Space Biomaterials and Translational Technology, Synergetic Innovation Center of Biological Optoelectronics and Healthcare Engineering (BOHE), Shaanxi Provincial Synergistic Innovation Center for Flexible Electronics & Health Sciences (FEHS), School of Life Sciences, Northwestern Polytechnical University, Xi’an, Shaanxi, China
| | - Jijun Wang
- Sino-German Joint Research Lab for Space Biomaterials and Translational Technology, Synergetic Innovation Center of Biological Optoelectronics and Healthcare Engineering (BOHE), Shaanxi Provincial Synergistic Innovation Center for Flexible Electronics & Health Sciences (FEHS), School of Life Sciences, Northwestern Polytechnical University, Xi’an, Shaanxi, China
| | - Maojin Zhao
- Sino-German Joint Research Lab for Space Biomaterials and Translational Technology, Synergetic Innovation Center of Biological Optoelectronics and Healthcare Engineering (BOHE), Shaanxi Provincial Synergistic Innovation Center for Flexible Electronics & Health Sciences (FEHS), School of Life Sciences, Northwestern Polytechnical University, Xi’an, Shaanxi, China
| | - Zhuo Yu
- Sino-German Joint Research Lab for Space Biomaterials and Translational Technology, Synergetic Innovation Center of Biological Optoelectronics and Healthcare Engineering (BOHE), Shaanxi Provincial Synergistic Innovation Center for Flexible Electronics & Health Sciences (FEHS), School of Life Sciences, Northwestern Polytechnical University, Xi’an, Shaanxi, China
| | - Qiangqiang Xu
- Sino-German Joint Research Lab for Space Biomaterials and Translational Technology, Synergetic Innovation Center of Biological Optoelectronics and Healthcare Engineering (BOHE), Shaanxi Provincial Synergistic Innovation Center for Flexible Electronics & Health Sciences (FEHS), School of Life Sciences, Northwestern Polytechnical University, Xi’an, Shaanxi, China,*Correspondence: Zhenhui Qi, ; Qiangqiang Xu, ; Yan Ge,
| | - Hongqi Nie
- Science and Technology on Combustion, Internal Flow and Thermostructure Laboratory, Northwestern Polytechnical University, Xi’an, China
| | - Qilong Yan
- Science and Technology on Combustion, Internal Flow and Thermostructure Laboratory, Northwestern Polytechnical University, Xi’an, China
| | - Yan Ge
- Sino-German Joint Research Lab for Space Biomaterials and Translational Technology, Synergetic Innovation Center of Biological Optoelectronics and Healthcare Engineering (BOHE), Shaanxi Provincial Synergistic Innovation Center for Flexible Electronics & Health Sciences (FEHS), School of Life Sciences, Northwestern Polytechnical University, Xi’an, Shaanxi, China,*Correspondence: Zhenhui Qi, ; Qiangqiang Xu, ; Yan Ge,
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8
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Guo Y, Nishida N, Hoshino T. Quantifying the Separation of Positive and Negative Areas in Electrostatic Potential for Predicting Feasibility of Ammonium Sulfate for Protein Crystallization. J Chem Inf Model 2021; 61:4571-4581. [PMID: 34565151 DOI: 10.1021/acs.jcim.1c00505] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ammonium sulfate (AS) and poly(ethylene glycol) (PEG) are the most popular precipitants in protein crystallization. Some proteins are preferably crystallized by AS, while some are by PEG. The electrostatic potential is related to the preference of the precipitant agents. The iso-surfaces of the electrostatic potentials for the AS-crystallized proteins display a common shape and a distinct separation between the positive and negative areas. In contrast, the PEG-crystallized proteins show unclear positive and negative separation. In this work, we propose schemes to quantitatively evaluate the separation for predicting which precipitant is favorable for crystal growth between AS or PEG. Three methods were attempted to quantify the amplitude of the separation, separation distance, dipole moment, and shape regularity. The positive and negative areas are approximated to the spherical potentials caused by point charges. The first method is a measurement of the distance between the positive and negative point charges. The second one is an assessment including the quantity of electric charge into the distance. The last one is an approach monitoring the clarity of the positive and negative separation. The average value for 25 kinds of AS-preferring proteins was higher than that for the PEG-preferring ones in all three methods. Therefore, every method can distinguish the proteins preferring AS for crystal growth from those preferring PEG. These methods require an iso-surface of the electrostatic potential depicted at a certain contouring value. The shape of the iso-surface depends on the contouring value. The dependency on contour was examined by depicting the iso-surfaces of electrostatic potential with three values at ±0.8, ±0.5, and ±0.2 kT/e. While reducing the contouring value leads to the increase in separation distance and the decrease in shape regularity, dipole moment is independent of the alteration of contouring value. While the AS-preferring proteins are distinguishable from the PEG-preferring ones in any contouring values, the iso-surface at ±0.5 kT/e seems adequate for regular use. The dipole moment assessment is feasible for the choice of potent precipitants for crystal growth in experiments.
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Affiliation(s)
- Yan Guo
- Graduate School of Pharmaceutical Sciences, Chiba University, Inohana 1-8-1, Chuo-ku, Chiba 260-8675, Japan
| | - Noritaka Nishida
- Graduate School of Pharmaceutical Sciences, Chiba University, Inohana 1-8-1, Chuo-ku, Chiba 260-8675, Japan
| | - Tyuji Hoshino
- Graduate School of Pharmaceutical Sciences, Chiba University, Inohana 1-8-1, Chuo-ku, Chiba 260-8675, Japan
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9
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Yun G, Kang DG, Rheem HB, Lee H, Han SY, Park J, Cho WK, Han SM, Choi IS. Reversed Anionic Hofmeister Effect in Metal-Phenolic-Based Film Formation. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:15552-15557. [PMID: 33325235 DOI: 10.1021/acs.langmuir.0c02928] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Although metal-phenolic species have emerged as one of the versatile material-independent-coating materials, providing attractive tools for interface engineering, mechanistic understanding of their film formation and growth still remains largely unexplored. Especially, the anions have been overlooked despite their high concentration in the coating solution. Considering that the anions are critical in the reactivity of metal-organic complex and the formation and/or property of functional materials, we investigated the anionic effects on the characteristics of film formation, such as film thickness and properties, in the Fe3+-tannic acid coating. We found that the film characteristics were strongly dictated by the counteranions (e.g., SO42-, Cl-, and Br-) of the Fe3+ ion. Specifically, the film thickness and properties (i.e., mechanical modulus, permeability, and stability) followed the reversed anionic Hofmeister series (Br- > Cl- > SO42-). Mechanistic studies suggested that more chaotropic anions, such as Br-, might induce a more widely extended structure of the Fe3+-TA complexes in the coating solution, leading to thicker, harder, but more porous films. The reversed anionic Hofmeister effect was further confirmed by the additive effects of various sodium salts (NaF, NaCl, NaBr, and NaClO4).
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Affiliation(s)
- Gyeongwon Yun
- Center for Cell-Encapsulation Research, Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Dong Gyu Kang
- Department of Materials Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Hyeong Bin Rheem
- Center for Cell-Encapsulation Research, Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Hojae Lee
- Center for Cell-Encapsulation Research, Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Sang Yeong Han
- Center for Cell-Encapsulation Research, Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Joohyouck Park
- Center for Cell-Encapsulation Research, Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Woo Kyung Cho
- Department of Chemistry, Chungnam National University, Daejeon 34134, Korea
| | - Seung Min Han
- Department of Materials Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Insung S Choi
- Center for Cell-Encapsulation Research, Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
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10
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Schewa S, Schroer MA, Zickmantel T, Song YH, Blanchet CE, Gruzinov AY, Katona G, Svergun DI, Roessle M. A THz transparent 3D printed microfluidic cell for small angle x-ray scattering. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2020; 91:084101. [PMID: 32872894 DOI: 10.1063/5.0004706] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 07/09/2020] [Indexed: 06/11/2023]
Abstract
Excitation frequencies in the terahertz (THz) range are expected to lead to functionally relevant domain movements within the biological macromolecules such as proteins. The possibility of examining such movements in an aqueous environment is particularly valuable since here proteins are not deprived of any motional degrees of freedom. Small angle x-ray scattering (SAXS) is a powerful method to study the structure and domain movements of proteins in solution. Here, we present a microfluidic cell for SAXS experiments, which is also transparent for THz radiation. Specifically, cell dimensions and material were optimized for both radiation sources. In addition, the polystyrene cell can be 3D printed and easily assembled. We demonstrate the practicality of our design for SAXS measurements on several proteins in solution.
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Affiliation(s)
- S Schewa
- University of Applied Sciences Lübeck, Mönkhofer Weg 239, 23562 Lübeck, Germany
| | - M A Schroer
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation c/o DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - T Zickmantel
- Physics Institute, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - Y-H Song
- Physics Institute, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - C E Blanchet
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation c/o DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - A Yu Gruzinov
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation c/o DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - G Katona
- Department of Chemistry and Molecular Biology, University of Gothenburg, 41390 Gothenburg, Sweden
| | - D I Svergun
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation c/o DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - M Roessle
- University of Applied Sciences Lübeck, Mönkhofer Weg 239, 23562 Lübeck, Germany
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11
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Abe M, Suzuki R, Kojima K, Tachibana M. Evaluation of crystal quality of thin protein crystals based on the dynamical theory of X-ray diffraction. IUCRJ 2020; 7:761-766. [PMID: 32695422 PMCID: PMC7340263 DOI: 10.1107/s2052252520007393] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 06/03/2020] [Indexed: 06/11/2023]
Abstract
Knowledge of X-ray diffraction in macromolecular crystals is important for not only structural analysis of proteins but also diffraction physics. Dynamical diffraction provides evidence of perfect crystals. Until now, clear dynamical diffraction in protein crystals has only been observed in glucose isomerase crystals. We wondered whether there were other protein crystals with high quality that exhibit dynamical diffraction. Here we report the observation of dynamical diffraction in thin ferritin crystals by rocking-curve measurement and imaging techniques such as X-ray topography. It is generally known that in the case of thin crystals it is difficult to distinguish whether dynamical diffraction occurs from only rocking-curve profiles. Therefore, our results clarified that dynamical diffraction occurs in thin protein crystals because fringe contrasts similar to Pendellösung fringes were clearly observed in the X-ray topographic images. For macromolecular crystallography, it is hard to obtain large crystals because they are difficult to crystallize. For thin crystals, dynamical diffraction can be demonstrated by analysis of the equal-thickness fringes observed by X-ray topography.
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Affiliation(s)
- Marina Abe
- Graduate School of Nanobioscience, Yokohama City University, 22-2 Seto, Kanazawa-ku, Yokohama 236-0027, Japan
| | - Ryo Suzuki
- Graduate School of Nanobioscience, Yokohama City University, 22-2 Seto, Kanazawa-ku, Yokohama 236-0027, Japan
- Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Kenichi Kojima
- Department of Education, Yokohama Soei University, 1 Mihocho, Midori-ku, Yokohama 226-0015, Japan
| | - Masaru Tachibana
- Graduate School of Nanobioscience, Yokohama City University, 22-2 Seto, Kanazawa-ku, Yokohama 236-0027, Japan
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12
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Maser TL, Honarvar E, Venter AR. Delayed Desorption Improves Protein Analysis by Desorption Electrospray Ionization Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:803-811. [PMID: 32157888 DOI: 10.1021/jasms.9b00047] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Protein analysis by desorption electrospray ionization mass spectrometry (DESI-MS) is limited and often accompanied by a mass-dependent loss in sensitivity as protein molecular weight increases. Previously, incomplete dissolution was identified as a potential contributing factor to this limitation for larger proteins. Here, we developed a unique two-step configuration in which a prewetting solvent is applied to the sample surface proximal to DESI analysis by a wetting quill to increase dissolution time and the detection of larger proteins. After optimizing the system with a mixture of proteins containing cytochrome c, myoglobin, and chymotripsinogen, we demonstrate the ability of delayed desorption to improve the analysis of larger proteins such as bovine serum albumin. Albumin and other serum proteins, including even larger ones, were also detected directly from diluted goat serum. An additional feature of this technique is the ability to deliver multiple solvents with potential synergistic or cooperative effects. For example, when using acetonitrile solutions of formic acid and ammonium bicarbonate as the prewetting and DESI spray solvent, respectively, the intensity of chymotrypsinogen improved dramatically compared to controls but less so for smaller proteins such as myoglobin and cytochrome c. Adduct removal was also observed for all proteins. These early results demonstrate the ability of this two-step technique for the use of multiple additives and increased dissolution times compared to standard DESI-MS experiments.
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Affiliation(s)
- Tara L Maser
- Department of Chemistry, Western Michigan University, Kalamazoo, Michigan 49008-5413, United States
| | - Elahe Honarvar
- Department of Chemistry, Western Michigan University, Kalamazoo, Michigan 49008-5413, United States
| | - Andre R Venter
- Department of Chemistry, Western Michigan University, Kalamazoo, Michigan 49008-5413, United States
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Kang B, Tang H, Zhao Z, Song S. Hofmeister Series: Insights of Ion Specificity from Amphiphilic Assembly and Interface Property. ACS OMEGA 2020; 5:6229-6239. [PMID: 32258857 PMCID: PMC7114165 DOI: 10.1021/acsomega.0c00237] [Citation(s) in RCA: 136] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 03/13/2020] [Indexed: 05/04/2023]
Abstract
Hofmeister series (HS), ion specific effect, or lyotropic sequence acts as a pivotal part in a number of biological and physicochemical phenomena, e.g., changing the solubility of hydrophobic solutes, the cloud points of polymers and nonionic surfactants, the activities of various enzymes, the action of ions on an ion-channel, and the surface tension of electrolyte solutions, etc. This review focused on how ion specificity influences the critical micelle concentration (CMC) and how the thermoresponsive behavior of surfactants, and the dynamic transition of the aggregate, controls the aggregate transition and gel formation and tunes the properties of air/water interfaces (Langmuir monolayer and interfacial free energy). Recent progress of the ion specific effect in bulk phase and at interfaces in amphiphilic systems and gels is summarized. Applications and a molecular level theoretical explanation of HS are discussed comprehensively. This review is aimed to supply a fresh and comprehensive understanding of Hofmiester phenomena in surfactants, polymers, colloids, and interface science and to provide a guideline to design the microstructures and templates for preparation of nanomaterials.
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Affiliation(s)
- Beibei Kang
- School of Chemistry and Chemical Engineering, Shandong University of Technology, Zibo 255000, P. R. China
| | - Huicheng Tang
- School of Chemistry and Chemical Engineering, Shandong University of Technology, Zibo 255000, P. R. China
| | - Zengdian Zhao
- School of Chemistry and Chemical Engineering, Shandong University of Technology, Zibo 255000, P. R. China
| | - Shasha Song
- School of Chemistry and Chemical Engineering, Shandong University of Technology, Zibo 255000, P. R. China
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Joti Y, Kitao A. Cancellation between auto- and mutual correlation contributions of protein/water dynamics in terahertz time-domain spectra. Biophys Physicobiol 2019; 16:240-247. [PMID: 31984177 PMCID: PMC6975922 DOI: 10.2142/biophysico.16.0_240] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 07/16/2019] [Indexed: 12/01/2022] Open
Abstract
Terahertz time-domain spectra (THz-TDS) were investigated using the results of molecular dynamics (MD) simulations of Staphylococcal nuclease at two hydration states in the temperature range between 100 and 300 K. The temperature dependence of THz-TDS was found to differ significantly from that of the incoherent neutron scattering spectra (INSS) calculated from the same MD simulation results. We further examined contributions of the mutual and auto-correlations of the atomic fluctuations to THz-TDS and found that the negative value of the former contribution nearly canceled out the positive value of the latter, resulting in a monotonic increase of the reduced absorption cross section. Because of this cancellation, no distinct broad peak was observed in the absorption lineshape function of THz-TDS, whereas the protein boson peak was observed in INSS. The contribution of water molecules to THz-TDS was extremely large for the hydrated protein at temperatures above 200 K, in which large-amplitude motions of water were excited. The combination of THz-TDS, INSS and MD simulations has the potential to extract function-relevant protein dynamics occurring on the picosecond to nanosecond timescale.
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Affiliation(s)
- Yasumasa Joti
- Japan Synchrotron Radiation Research Institute, Sayo-gun, Hyogo 679-5198, Japan
- RIKEN SPring-8 Center, Sayo-gun, Hyogo 679-5148, Japan
| | - Akio Kitao
- School of Life Sciences and Technology, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan
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15
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Kumar A, Bhakuni K, Venkatesu P. Strategic planning of proteins in ionic liquids: future solvents for the enhanced stability of proteins against multiple stresses. Phys Chem Chem Phys 2019; 21:23269-23282. [PMID: 31621726 DOI: 10.1039/c9cp04772g] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Ionic liquids (ILs) present a vast number of solvents capable of replacing toxic organic solvents in chemical, biotechnology and biomedical applications. ILs are inexpensive and environmentally friendly as the materials can be recycled conveniently. Chemists use a variety of cation and anion combinations to produce an IL that fits the requirements of the sustainable future through the pursuit of greener chemical processes. As such, the development of various types of ILs has been recognized as the emergence of environmentally friendly solvents to attain enhanced protein stability in vitro. The literature survey reveals that there exist a large number of scholarly articles as well as elegant reviews on protein stability in ILs. Biomolecules have adapted to antagonistic environmental stresses that normally denature proteins, and the mechanism of adaptation that protects the cellular components against denaturation involves the intracellular concentration of co-solvents. In this regard, recent experimental results distinctly demonstrated that ILs are stabilizing proteins against denaturing stresses, and their presence in the cells does not alter protein functional activities. However, a review focusing particularly on the refolding and counteracting effects of the ILs against denatured proteins by multiple stresses is still missing. This perspective unveils the studies that have been conducted to improve protein stabilities with ILs as well as the refolding and counteracting abilities of these ILs against the denatured proteins under the influence of multiple stresses. We believe that ILs can provide significant environmental and economic advantages for biochemical processes in the near future. Essentially, numerous investigations are required to allow us to further explore the stabilizing properties of ILs over proteins.
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Affiliation(s)
- Awanish Kumar
- Department of Chemistry, University of Delhi, Delhi-110 007, India.
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17
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Niessen KA, Xu M, George DK, Chen MC, Ferré-D'Amaré AR, Snell EH, Cody V, Pace J, Schmidt M, Markelz AG. Protein and RNA dynamical fingerprinting. Nat Commun 2019; 10:1026. [PMID: 30833555 PMCID: PMC6399446 DOI: 10.1038/s41467-019-08926-3] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 02/04/2019] [Indexed: 01/30/2023] Open
Abstract
Protein structural vibrations impact biology by steering the structure to functional intermediate states; enhancing tunneling events; and optimizing energy transfer. Strong water absorption and a broad continuous vibrational density of states have prevented optical identification of these vibrations. Recently spectroscopic signatures that change with functional state were measured using anisotropic terahertz microscopy. The technique however has complex sample positioning requirements and long measurement times, limiting access for the biomolecular community. Here we demonstrate that a simplified system increases spectroscopic structure to dynamically fingerprint biomacromolecules with a factor of 6 reduction in data acquisition time. Using this technique, polarization varying anisotropy terahertz microscopy, we show sensitivity to inhibitor binding and unique vibrational spectra for several proteins and an RNA G-quadruplex. The technique’s sensitivity to anisotropic absorbance and birefringence provides rapid assessment of macromolecular dynamics that impact biology. The characterization of biomacromolecule structural vibrations has been impeded by a broad continuous vibrational density of states obscuring molecule specific vibrations. A terahertz microscopy system using polarization control produces signatures to dynamically fingerprint proteins and a RNA G-quadruplex.
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Affiliation(s)
| | - Mengyang Xu
- Department of Physics, University at Buffalo, SUNY, Buffalo, NY, USA
| | - Deepu K George
- Department of Physics, University at Buffalo, SUNY, Buffalo, NY, USA
| | - Michael C Chen
- National Heart, Lung and Blood Institute, Bethesda, MD, USA
| | | | - Edward H Snell
- Hauptman-Woodward Medical Research Institute & Department of Structural Biology, University at Buffalo, SUNY, Buffalo, NY, USA
| | - Vivian Cody
- Hauptman-Woodward Medical Research Institute & Department of Structural Biology, University at Buffalo, SUNY, Buffalo, NY, USA
| | - James Pace
- Hauptman-Woodward Medical Research Institute & Department of Structural Biology, University at Buffalo, SUNY, Buffalo, NY, USA
| | - Marius Schmidt
- Department of Physics, University of Wisconsin, Milwaukee, WI, USA
| | - Andrea G Markelz
- Department of Physics, University at Buffalo, SUNY, Buffalo, NY, USA. .,Hauptman-Woodward Medical Research Institute & Department of Structural Biology, University at Buffalo, SUNY, Buffalo, NY, USA.
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18
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Francisco OA, Clark CJ, Glor HM, Khajehpour M. Do soft anions promote protein denaturation through binding interactions? A case study using ribonuclease A. RSC Adv 2019; 9:3416-3428. [PMID: 35518962 PMCID: PMC9060304 DOI: 10.1039/c8ra10303h] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Accepted: 01/20/2019] [Indexed: 11/21/2022] Open
Abstract
It has long been known that large soft anions like bromide, iodide and thiocyanate are protein denaturing agents, but their mechanism of action is still unclear. In this work we have investigated the protein denaturing properties of these anions using Ribonuclease A (RNase A) as a model protein system. Salt-induced perturbations to the protein folding free energy were determined using differential scanning calorimetry and the results demonstrate that the addition of sodium iodide and sodium thiocyanate significantly decreases the melting temperature of the protein. In order to account for this reduction in protein stability, we show that the introduction of salts that contain soft anions to the aqueous solvent perturbs the protein unfolding free energy through three mechanisms: (a) screening Coulomb interactions that exist between charged protein residues, (b) Hofmeister effects, and (c) specific anion binding to CH and CH2 moieties in the protein polypeptide backbone. Using the micellization of 1,2-hexanediol as a ruler for hydrophobicity, we have devised a practical methodology that separates the Coulomb and Hofmeister contributions of salts to the protein unfolding free energy. This allowing us to isolate the contribution of soft anion binding interactions to the unfolding process. The analysis shows that binding contributions have the largest magnitude, confirming that it is the binding of soft anions to the polypeptide backbone that is the main promoter of protein unfolding.
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Affiliation(s)
| | | | - Hayden M Glor
- Department of Chemistry, University of Manitoba Canada
| | - Mazdak Khajehpour
- Department of Chemistry, University of Manitoba Canada
- University of Manitoba 468 Parker Bldg. Winnipeg Manitoba R3T2N2 Canada +1-204-2721546
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19
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Friedman R. Simulations of Biomolecules in Electrolyte Solutions. ADVANCED THEORY AND SIMULATIONS 2019. [DOI: 10.1002/adts.201800163] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Ran Friedman
- Department of Chemistry and Biomedical SciencesLinnæus UniversityKalmar SE‐391 82 Sweden
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20
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Honarvar E, Venter AR. Comparing the Effects of Additives on Protein Analysis Between Desorption Electrospray (DESI) and Electrospray Ionization (ESI). JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:2443-2455. [PMID: 30232734 DOI: 10.1007/s13361-018-2058-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2017] [Revised: 08/17/2018] [Accepted: 08/17/2018] [Indexed: 06/08/2023]
Abstract
It is frequently said that DESI-MS follows a similar ionization mechanism as ESI because of similarities usually observed in their respective mass spectra. However, practical use of DESI-MS for protein analysis is limited to proteins with lower molecular weights (< 25 kDa) due to a mass-dependent loss in signal intensity. Here we investigated commonly used volatile acids and their ammonium salt buffers for DESI-MS analysis of protein. We noticed that, surprisingly, some additives influence the analysis differently in DESI compared to ESI. Improved signal intensities with both DESI and ESI were obtained when acetic and formic acid were added into aqueous methanol spray solvents with both DESI and ESI. On the other hand, while with ESI the addition of ammonium salts into spray solutions strongly reduced both signal and S/N, with DESI signal intensities and S/N were improved dramatically. Ammonium bicarbonate when used with DESI reduced the total amount of adduction and delivered excellent signal-to-noise ratios with high intensity; however, it also denatures protein. When native state protein mass spectra are preferred, ammonium acetate would also deliver reasonable adduct removal and improved S/N. The amount of total adduction of individual adducting species and of all species could not be correlated with differences in either solutions pH values or with proton affinities of the anions. An obvious difference between DESI and ESI mass spectrometry is the effects of protein solubility during droplet pickup (desorption), but differences in the sizes, velocities, and composition of ionizing droplets were also discussed as important factors. Graphical Abstract ᅟ.
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Affiliation(s)
- Elahe Honarvar
- Department of Chemistry, Western Michigan University, Kalamazoo, MI, 49008-5413, USA
| | - Andre R Venter
- Department of Chemistry, Western Michigan University, Kalamazoo, MI, 49008-5413, USA.
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21
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Blaffert J, Haeri HH, Blech M, Hinderberger D, Garidel P. Spectroscopic methods for assessing the molecular origins of macroscopic solution properties of highly concentrated liquid protein solutions. Anal Biochem 2018; 561-562:70-88. [PMID: 30243977 DOI: 10.1016/j.ab.2018.09.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Revised: 09/08/2018] [Accepted: 09/17/2018] [Indexed: 01/14/2023]
Abstract
In cases of subcutaneous injection of therapeutic monoclonal antibodies, high protein concentrations (>50 mg/ml) are often required. During the development of these high concentration liquid formulations (HCLF), challenges such as aggregation, gelation, opalescence, phase separation, and high solution viscosities are more prone compared to low concentrated protein formulations. These properties can impair manufacturing processes, as well as protein stability and shelf life. To avoid such unfavourable solution properties, a detailed understanding about the nature of these properties and their driving forces are required. However, the fundamental mechanisms that lead to macroscopic solution properties, as above mentioned, are complex and not fully understood, yet. Established analytical methods for assessing the colloidal stability, i.e. the ability of a native protein to remain dispersed in solution, are restricted to dilute conditions and provide parameters such as the second osmotic virial coefficient, B22, and the diffusion interaction coefficient, kD. These parameters are routinely applied for qualitative estimations and identifications of proteins with challenging solution behaviours, such as high viscosities and aggregation, although the assays are prepared for low protein concentration conditions, typically between 0.1 and 20 mg/ml ("ideal" solution conditions). Quantitative analysis of samples of high protein concentration is difficult and it is hard to obtain information about the driving forces of such solution properties and corresponding protein-protein self-interactions. An advantage of using specific spectroscopic methods is the potential of directly analysing highly concentrated protein solutions at different solution conditions. This allows for collecting/gaining valuable information about the fundamental mechanisms of solution properties of the high protein concentration regime. In addition, the derived parameters might be more predictive as compared to the parameters originating from assays which are optimized for the low protein concentration range. The provided information includes structural data, molecular dynamics at various timescales and protein-solvent interactions, which can be obtained at molecular resolution. Herein, we provide an overview about spectroscopic techniques for analysing the origins of macroscopic solution behaviours in general, with a specific focus on pharmaceutically relevant high protein concentration and formulation conditions.
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Affiliation(s)
- Jacob Blaffert
- Institute of Chemistry, Martin Luther University Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120, Halle/Saale, Germany
| | - Haleh Hashemi Haeri
- Institute of Chemistry, Martin Luther University Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120, Halle/Saale, Germany
| | - Michaela Blech
- Boehringer Ingelheim Pharma GmbH & Co. KG, Protein Science, Birkerndorfer Str. 65, 88397, Biberach/Riß, Germany
| | - Dariush Hinderberger
- Institute of Chemistry, Martin Luther University Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120, Halle/Saale, Germany
| | - Patrick Garidel
- Institute of Chemistry, Martin Luther University Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120, Halle/Saale, Germany; Boehringer Ingelheim Pharma GmbH & Co. KG, Protein Science, Birkerndorfer Str. 65, 88397, Biberach/Riß, Germany.
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22
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Effects of lyotropic anions on thermodynamic stability and dynamics of horse cytochrome c. Biophys Chem 2018; 240:88-97. [DOI: 10.1016/j.bpc.2018.06.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2018] [Revised: 06/09/2018] [Accepted: 06/10/2018] [Indexed: 11/19/2022]
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Prasad A, Sivalingam V, Bharathi V, Girdhar A, Patel BK. The amyloidogenicity of a C-terminal region of TDP-43 implicated in Amyotrophic Lateral Sclerosis can be affected by anions, acetylation and homodimerization. Biochimie 2018; 150:76-87. [PMID: 29751083 DOI: 10.1016/j.biochi.2018.05.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 05/04/2018] [Indexed: 12/11/2022]
Abstract
Amyotrophic Lateral Sclerosis (ALS) is a fatal neurodegenerative disease associated with accumulation of hyper-phosphorylated, and ubiquitinated TAR DNA-binding protein-43 (TDP-43) as inclusion deposits in neuronal cells. Recently, amyloid-like fibrillar aggregates of TDP-43 have been reported from several ALS patients. The C-terminal region of TDP-43 is central to TDP-43's pathological aggregation and most of the familial ALS mutations in the encoding TARDBP gene are located in this domain. Also, aberrant proteolytic cleavages of TDP-43 produce cytotoxic C-terminal fragments of ∼15-35 kDa. The C-terminal end harbours a glycine-rich region and a Q/N rich prion-like aggregation-prone domain which has been shown to form amyloid-like fibrillar aggregates in vitro. Previously, TDP-43 protein has also been shown to undergo several other post-translational modifications such as acetylation and dimerization, however, their effects on TDP-43's amyloid-like in vitro aggregation have not been examined. Towards this, we have here examined effects of anions, acetylation and homodimerization on the in vitro aggregation of a C-terminal fragment (amino acid: 193-414) of TDP-43 termed TDP-432C. We find that kosmotropic anions greatly accelerate whereas chaotropic anions impede its aggregation. Also, we show that acetylation of certain lysines in C-terminal fragments significantly reduces the TDP-432C's amyloid-like aggregation. Furthermore, we separated spontaneously formed cysteine-linked homodimers of the recombinantly purified TDP-432C using size-exclusion chromatography and found that these dimers retain amyloidogenicity. These findings would be of significance to the TDP-43 aggregation-induced pathology in ALS.
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Affiliation(s)
- Archana Prasad
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana, 502285, India
| | - Vishwanath Sivalingam
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana, 502285, India
| | - Vidhya Bharathi
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana, 502285, India
| | - Amandeep Girdhar
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana, 502285, India
| | - Basant K Patel
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana, 502285, India.
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Ferreira LA, Uversky VN, Zaslavsky BY. Effects of the Hofmeister series of sodium salts on the solvent properties of water. Phys Chem Chem Phys 2018; 19:5254-5261. [PMID: 28150000 DOI: 10.1039/c6cp08214a] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The solvent features of water (solvent dipolarity/polarizability, π*, hydrogen bond donor acidity, α, and hydrogen bond acceptor basicity, β) were examined in aqueous solutions of Na2SO4, NaF, CH3COONa, NaCl, NaBr, NaI, and NaClO4 at concentrations of each salt from 0 to 1.0 M (up to 2.0 M for NaClO4). The solvent features of water in solutions of different concentrations for each salt were found to be linearly related as π* = z + aα + bβ. The coefficients of this relationship were suggested to represent the signature of the salt effect on the solvent features of water. The normalized distances for each salt were calculated using glucose as a reference compound. These distances may be used as the relative measures of the salt-water interactions. It is demonstrated that the distances for all salts examined are interrelated with structural water entropies and static polarizabilities of anions. It is shown that the distance may be used as a measure of the relative effects of salts on precipitation of ferric oxide, excessive chemical potential of propanol in salt solutions, surface tension, and viscosity. The distance represents the relative measure of the salt effect on the solvent features of water in a salt solution. The examples presented confirm that the approach used does enable us to characterize the differences between the effects of salts in the Hofmeister series on the properties of water.
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Affiliation(s)
- L A Ferreira
- Cleveland Diagnostics, 3615 Superior Ave., Suite 4407B, Cleveland, Ohio 44114, USA.
| | - V N Uversky
- Department of Molecular Medicine and Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - B Y Zaslavsky
- Cleveland Diagnostics, 3615 Superior Ave., Suite 4407B, Cleveland, Ohio 44114, USA.
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Honarvar E, Venter AR. Ammonium Bicarbonate Addition Improves the Detection of Proteins by Desorption Electrospray Ionization Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:1109-1117. [PMID: 28315234 DOI: 10.1007/s13361-017-1628-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2016] [Revised: 01/26/2017] [Accepted: 02/09/2017] [Indexed: 05/11/2023]
Abstract
The analysis of protein by desorption electrospray ionization mass spectrometry (DESI-MS) is considered impractical due to a mass-dependent loss in sensitivity with increase in protein molecular weights. With the addition of ammonium bicarbonate to the DESI-MS analysis the sensitivity towards proteins by DESI was improved. The signal to noise ratio (S/N) improvement for a variety of proteins increased between 2- to 3-fold relative to solvent systems containing formic acid and more than seven times relative to aqueous methanol spray solvents. Three methods for ammonium bicarbonate addition during DESI-MS were investigated. The additive delivered improvements in S/N whether it was mixed with the analyte prior to sample deposition, applied over pre-prepared samples, or simply added to the desorption spray solvent. The improvement correlated well with protein pI but not with protein size. Other ammonium or bicarbonate salts did not produce similar improvements in S/N, nor was this improvement in S/N observed for ESI of the same samples. As was previously described for ESI, DESI also caused extensive protein unfolding upon the addition of ammonium bicarbonate. Graphical Abstract ᅟ.
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Affiliation(s)
- Elahe Honarvar
- Department of Chemistry, Western Michigan University, Kalamazoo, MI, 49008-5413, USA
| | - Andre R Venter
- Department of Chemistry, Western Michigan University, Kalamazoo, MI, 49008-5413, USA.
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Zhang R, Zhou R, Pan W, Lin W, Zhang X, Li M, Li J, Niu F, Li A. Salting-in effect on muscle protein extracted from giant squid (Dosidicus gigas). Food Chem 2017; 215:256-62. [DOI: 10.1016/j.foodchem.2016.07.177] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 07/28/2016] [Accepted: 07/29/2016] [Indexed: 11/28/2022]
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