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Uversky VN, Madeira PP, Zaslavsky BY. What Can Be Learned from the Partitioning Behavior of Proteins in Aqueous Two-Phase Systems? Int J Mol Sci 2024; 25:6339. [PMID: 38928046 PMCID: PMC11203663 DOI: 10.3390/ijms25126339] [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: 04/16/2024] [Revised: 05/31/2024] [Accepted: 06/03/2024] [Indexed: 06/28/2024] Open
Abstract
This review covers the analytical applications of protein partitioning in aqueous two-phase systems (ATPSs). We review the advancements in the analytical application of protein partitioning in ATPSs that have been achieved over the last two decades. Multiple examples of different applications, such as the quality control of recombinant proteins, analysis of protein misfolding, characterization of structural changes as small as a single-point mutation, conformational changes upon binding of different ligands, detection of protein-protein interactions, and analysis of structurally different isoforms of a protein are presented. The new approach to discovering new drugs for a known target (e.g., a receptor) is described when one or more previous drugs are already available with well-characterized biological efficacy profiles.
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Affiliation(s)
- Vladimir N. Uversky
- Department of Molecular Medicine, Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA;
| | - Pedro P. Madeira
- Centro de Investigacao em Materiais Ceramicos e Compositos, Department of Chemistry, 3810-193 Aveiro, Portugal;
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Shibata C, Iwashita K, Shiraki K. Salt-containing aqueous two-phase system shows predictable partition of proteins with surface amino acids residues. Int J Biol Macromol 2019; 133:1182-1186. [PMID: 31055113 DOI: 10.1016/j.ijbiomac.2019.04.185] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 04/28/2019] [Accepted: 04/28/2019] [Indexed: 11/24/2022]
Abstract
Aqueous two-phase system (ATPS) containing salts has been used for protein purification and enrichment. However, it is unclear how proteins are partitioned in the top or bottom phases of the system. In this study, we demonstrate that the partition of proteins in salt-containing ATPS (SATPS) depends only on the relation between the protein-surface amino acids and the type of salt using SATPS. The partition coefficients of four proteins changed depending on the kind of salt, according to the Hofmeister series. Interestingly, the partition coefficients of the proteins correlated to those of the combination of the amino acids in the surface of the protein with the correlation coefficients of >0.9. The results suggest that the interaction between the protein surface and aqueous ions plays an indispensable role for the partition of proteins in SATPS that can help in the design of protein partition in ATPS for purification and enrichment.
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Affiliation(s)
- Chika Shibata
- Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8573, Japan
| | - Kazuki Iwashita
- Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8573, Japan
| | - Kentaro Shiraki
- Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8573, Japan.
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Sun Z, Liu Q, Qu G, Feng Y, Reetz MT. Utility of B-Factors in Protein Science: Interpreting Rigidity, Flexibility, and Internal Motion and Engineering Thermostability. Chem Rev 2019; 119:1626-1665. [PMID: 30698416 DOI: 10.1021/acs.chemrev.8b00290] [Citation(s) in RCA: 292] [Impact Index Per Article: 58.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Zhoutong Sun
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West Seventh Avenue, Tianjin Airport Economic Area, Tianjin 300308, China
| | - Qian Liu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ge Qu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West Seventh Avenue, Tianjin Airport Economic Area, Tianjin 300308, China
| | - Yan Feng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Manfred T. Reetz
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West Seventh Avenue, Tianjin Airport Economic Area, Tianjin 300308, China
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
- Chemistry Department, Philipps-University, Hans-Meerwein-Strasse 4, 35032 Marburg, Germany
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da Silva NR, Ferreira LA, Teixeira JA, Uversky VN, Zaslavsky BY. Effects of sodium chloride and sodium perchlorate on properties and partition behavior of solutes in aqueous dextran-polyethylene glycol and polyethylene glycol-sodium sulfate two-phase systems. J Chromatogr A 2019; 1583:28-38. [DOI: 10.1016/j.chroma.2018.11.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 11/01/2018] [Accepted: 11/08/2018] [Indexed: 11/25/2022]
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Torres-Acosta MA, Mayolo-Deloisa K, González-Valdez J, Rito-Palomares M. Aqueous Two-Phase Systems at Large Scale: Challenges and Opportunities. Biotechnol J 2018; 14:e1800117. [PMID: 29878648 DOI: 10.1002/biot.201800117] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 05/10/2018] [Indexed: 11/06/2022]
Abstract
Aqueous two-phase systems (ATPS) have proved to be an efficient and integrative operation to enhance recovery of industrially relevant bioproducts. After ATPS discovery, a variety of works have been published regarding their scaling from 10 to 1000 L. Although ATPS have achieved high recovery and purity yields, there is still a gap between their bench-scale use and potential industrial applications. In this context, this review paper critically analyzes ATPS scale-up strategies to enhance the potential industrial adoption. In particular, large-scale operation considerations, different phase separation procedures, the available optimization techniques (univariate, response surface methodology, and genetic algorithms) to maximize recovery and purity and economic modeling to predict large-scale costs, are discussed. ATPS intensification to increase the amount of sample to process at each system, developing recycling strategies and creating highly efficient predictive models, are still areas of great significance that can be further exploited with the use of high-throughput techniques. Moreover, the development of novel ATPS can maximize their specificity increasing the possibilities for the future industry adoption of ATPS. This review work attempts to present the areas of opportunity to increase ATPS attractiveness at industrial levels.
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Affiliation(s)
- Mario A Torres-Acosta
- Tecnologico de Monterrey, Escuela de Ingeniería y Ciencias, Av. Eugenio Garza Sada 2501 Sur, Monterrey, NL, 64849, México
| | - Karla Mayolo-Deloisa
- Tecnologico de Monterrey, Escuela de Ingeniería y Ciencias, Av. Eugenio Garza Sada 2501 Sur, Monterrey, NL, 64849, México
| | - José González-Valdez
- Tecnologico de Monterrey, Escuela de Ingeniería y Ciencias, Av. Eugenio Garza Sada 2501 Sur, Monterrey, NL, 64849, México
| | - Marco Rito-Palomares
- Tecnologico de Monterrey, Escuela de Ingeniería y Ciencias, Av. Eugenio Garza Sada 2501 Sur, Monterrey, NL, 64849, México.,Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Av. Morones Prieto 3000 Pte, Col. Los Doctores, Monterrey, NL, 64710, México
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Ferreira LA, Uversky VN, Zaslavsky BY. Phase equilibria, solvent properties, and protein partitioning in aqueous polyethylene glycol-600-trimethylamine N-oxide and polyethylene glycol-600-choline chloride two-phase systems. J Chromatogr A 2018; 1535:154-161. [DOI: 10.1016/j.chroma.2018.01.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 12/27/2017] [Accepted: 01/03/2018] [Indexed: 12/21/2022]
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Predicting protein partition coefficients in aqueous two phase system. J Chromatogr A 2016; 1470:50-58. [DOI: 10.1016/j.chroma.2016.09.072] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 07/01/2016] [Accepted: 09/30/2016] [Indexed: 01/22/2023]
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Ferreira LA, Loureiro JA, Gomes J, Uversky VN, Madeira PP, Zaslavsky BY. Why physicochemical properties of aqueous solutions of various compounds are linearly interrelated. J Mol Liq 2016. [DOI: 10.1016/j.molliq.2016.05.068] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Zaslavsky BY, Uversky VN, Chait A. Analytical applications of partitioning in aqueous two-phase systems: Exploring protein structural changes and protein–partner interactions in vitro and in vivo by solvent interaction analysis method. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:622-44. [DOI: 10.1016/j.bbapap.2016.02.017] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Revised: 02/16/2016] [Accepted: 02/21/2016] [Indexed: 12/29/2022]
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Interrelationship between partition behavior of organic compounds and proteins in aqueous dextran-polyethylene glycol and polyethylene glycol-sodium sulfate two-phase systems. J Chromatogr A 2016; 1443:21-5. [DOI: 10.1016/j.chroma.2016.03.032] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 03/14/2016] [Accepted: 03/14/2016] [Indexed: 01/01/2023]
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Ferreira LA, Uversky VN, Zaslavsky BY. Analysis of the distribution of organic compounds and drugs between biological tissues in the framework of solute partitioning in aqueous two-phase systems. MOLECULAR BIOSYSTEMS 2016; 12:3567-3575. [DOI: 10.1039/c6mb00608f] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Distribution of organic compounds between different biological tissues may be considered in the framework of solute partitioning in aqueous two-phase systems.
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Affiliation(s)
| | - 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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Effect of sodium chloride on solute–solvent interactions in aqueous polyethylene glycol–sodium sulfate two-phase systems. J Chromatogr A 2015; 1425:51-61. [PMID: 26615710 DOI: 10.1016/j.chroma.2015.11.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 11/04/2015] [Accepted: 11/05/2015] [Indexed: 01/01/2023]
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Zaslavsky BY, Uversky VN, Chait A. Solvent interaction analysis as a proteomic approach to structure-based biomarker discovery and clinical diagnostics. Expert Rev Proteomics 2015; 13:9-17. [PMID: 26558960 DOI: 10.1586/14789450.2016.1116945] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Proteins have several measurable features in biological fluids that may change under pathological conditions. The current disease biomarker discovery is mostly based on protein concentration in the sample as the measurable feature. Changes in protein structures, such as post-translational modifications and in protein-partner interactions are known to accompany pathological processes. Changes in glycosylation profiles are well-established for many plasma proteins in various types of cancer and other diseases. The solvent interaction analysis method is based on protein partitioning in aqueous two-phase systems and is highly sensitive to changes in protein structure and protein-protein- and protein-partner interactions while independent of the protein concentration in the biological sample. It provides quantitative index: partition coefficient representing changes in protein structure and interactions with partners. The fundamentals of the method are presented with multiple examples of applications of the method to discover and monitor structural protein biomarkers as disease-specific diagnostic indicators.
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Affiliation(s)
- Boris Y Zaslavsky
- a Cleveland Diagnostics , 3615 Superior Avenue, Suite 4407B, Cleveland , OH 44114 , USA
| | - Vladimir N Uversky
- b Department of Molecular Medicine and Byrd Alzheimer's Research Institute, Morsani College of Medicine , University of South Florida , Tampa , FL 33612 , USA
| | - Arnon Chait
- a Cleveland Diagnostics , 3615 Superior Avenue, Suite 4407B, Cleveland , OH 44114 , USA
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da Silva NR, Ferreira LA, Madeira PP, Teixeira JA, Uversky VN, Zaslavsky BY. Analysis of partitioning of organic compounds and proteins in aqueous polyethylene glycol-sodium sulfate aqueous two-phase systems in terms of solute-solvent interactions. J Chromatogr A 2015; 1415:1-10. [PMID: 26342872 DOI: 10.1016/j.chroma.2015.08.053] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Revised: 08/21/2015] [Accepted: 08/24/2015] [Indexed: 12/30/2022]
Abstract
Partition behavior of nine small organic compounds and six proteins was examined in poly(ethylene glycol)-8000-sodium sulfate aqueous two-phase systems containing 0.5M osmolyte (sorbitol, sucrose, trehalose, TMAO) and poly(ethylene glycol)-10000-sodium sulfate system, all in 0.01M sodium phosphate buffer, pH 6.8. The differences between the solvent properties of the coexisting phases (solvent dipolarity/polarizability, hydrogen bond donor acidity, and hydrogen bond acceptor basicity) were characterized with solvatochromic dyes using the solvatochromic comparison method. Differences between the electrostatic properties of the phases were determined by analysis of partitioning of sodium salts of dinitrophenylated (DNP-) amino acids with aliphatic alkyl side-chain. It was found out that the partition coefficient of all compounds examined (including proteins) may be described in terms of solute-solvent interactions. The results obtained in the study show that solute-solvent interactions of nonionic organic compounds and proteins in polyethylene glycol-sodium sulfate aqueous two-phase system differ from those in polyethylene glycol-dextran system.
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Affiliation(s)
- Nuno R da Silva
- IBB-Institute for Biotechnology and Bioengineering, Centre of Biological Engineering, Universidade do Minho, Campus de Gualtar, 4710-057 Braga, Portugal; Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia
| | - Luisa A Ferreira
- Analiza, Inc., 3615 Superior Ave., Cleveland, OH 44114, USA; Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia
| | - Pedro P Madeira
- Laboratory of Separation and Reaction Engineering, Department of Chemical Engineering, Faculty of Engineering of the University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal; Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia
| | - José A Teixeira
- IBB-Institute for Biotechnology and Bioengineering, Centre of Biological Engineering, Universidade do Minho, Campus de Gualtar, 4710-057 Braga, Portugal; Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia
| | - Vladimir N Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA; Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia
| | - Boris Y Zaslavsky
- Analiza, Inc., 3615 Superior Ave., Cleveland, OH 44114, USA; Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia.
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Madeira PP, Bessa A, Loureiro JA, Álvares-Ribeiro L, Rodrigues AE, Zaslavsky BY. Cooperativity between various types of polar solute–solvent interactions in aqueous media. J Chromatogr A 2015; 1408:108-17. [DOI: 10.1016/j.chroma.2015.07.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Revised: 06/29/2015] [Accepted: 07/01/2015] [Indexed: 01/01/2023]
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16
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Ferreira LA, Fedotoff O, Uversky VN, Zaslavsky BY. Effects of osmolytes on protein–solvent interactions in crowded environments: study of sucrose and trehalose effects on different proteins by solvent interaction analysis. RSC Adv 2015. [DOI: 10.1039/c5ra02997j] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The logarithms of the partition coefficients of proteins in the presence of 0.5 M sucrose and trehalose are linearly interrelated.
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Affiliation(s)
| | | | - Vladimir N. Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute
- Morsani College of Medicine
- University of South Florida
- Tampa
- USA
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