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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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2
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Ahmed T, Yamanishi C, Kojima T, Takayama S. Aqueous Two-Phase Systems and Microfluidics for Microscale Assays and Analytical Measurements. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2021; 14:231-255. [PMID: 33950741 DOI: 10.1146/annurev-anchem-091520-101759] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Phase separation is a common occurrence in nature. Synthetic and natural polymers, salts, ionic liquids, surfactants, and biomacromolecules phase separate in water, resulting in an aqueous two-phase system (ATPS). This review discusses the properties, handling, and uses of ATPSs. These systems have been used for protein, nucleic acid, virus, and cell purification and have in recent years found new uses for small organics, polysaccharides, extracellular vesicles, and biopharmaceuticals. Analytical biochemistry applications such as quantifying protein-protein binding, probing for conformational changes, or monitoring enzyme activity have been performed with ATPSs. Not only are ATPSs biocompatible, they also retain their properties at the microscale, enabling miniaturization experiments such as droplet microfluidics, bacterial quorum sensing, multiplexed and point-of-care immunoassays, and cell patterning. ATPSs include coacervates and may find wider interest in the context of intracellular phase separation and origin of life. Recent advances in fundamental understanding and in commercial application are also considered.
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Affiliation(s)
- Tasdiq Ahmed
- Walter H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory School of Medicine, Atlanta, Georgia 30332, USA;
| | - Cameron Yamanishi
- Walter H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory School of Medicine, Atlanta, Georgia 30332, USA;
| | - Taisuke Kojima
- Walter H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory School of Medicine, Atlanta, Georgia 30332, USA;
| | - Shuichi Takayama
- Walter H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory School of Medicine, Atlanta, Georgia 30332, USA;
- Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
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3
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Dumas F, Roger E, Rodriguez J, Benyahia L, Benoit JP. Aqueous Two-Phase Systems: simple one-step process formulation and phase diagram for characterisation. Colloid Polym Sci 2020. [DOI: 10.1007/s00396-020-04748-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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4
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Shibata C, Iwashita K, Shiraki K. Selective separation method of aggregates from IgG solution by aqueous two-phase system. Protein Expr Purif 2019; 161:57-62. [PMID: 31054316 DOI: 10.1016/j.pep.2019.05.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 04/16/2019] [Accepted: 05/01/2019] [Indexed: 11/17/2022]
Abstract
Aggregation of immunoglobulin G (IgG) is a serious concern that results in immunogenicity in pharmaceutical applications. Removal of the small and soluble aggregates in protein solutions through a simple method remains challenging. Here we show that an aqueous two-phase system (ATPS) can be used for the elimination of soluble aggregates from IgG solution. Polyethylene glycol (PEG) and dextran (DEX) were selected as components of the ATPS. As expected, IgG monomers were partitioned into the top or bottom phases of ATPS. Interestingly, almost all the small and soluble aggregates of IgG were extracted to the interface between top and bottom phases, rather than in the liquid phases. The partitioning of monomers and aggregates of IgG can be attributed to the solubility of these protein states in PEG and DEX. Thus, ATPS using PEG and DEX can be employed for the simple removal method of soluble aggregates from IgG solution.
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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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Madeira PP, Loureiro JA, Freire MG, Coutinho JAP. Solvatochromism as a new tool to distinguish structurally similar compounds. J Mol Liq 2019; 274:740-745. [PMID: 30936594 DOI: 10.1016/j.molliq.2018.11.050] [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] [Indexed: 10/27/2022]
Abstract
It is here reported a new concept based on solvatochromism to distinguish structurally similar compounds in aqueous solutions by the analysis of the stabilization of electronic excited states. The sensitivity of this approach to differentiate similar organic compounds, such as structural isomers or compound differing in the number of methylene groups, or proteins with conformational changes induced by being or not bound to cofactors, differing in two amino acids substitutions, or differing in their glycosylation profile, is demonstrated. The sensitivity of the proposed approach, based on the solvatochromic method, opens the path to its use as an auxiliary analytical tool in biomedical diagnosis/prognosis or in quality control of biologic-based drugs.
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Affiliation(s)
- Pedro P Madeira
- CICECO - Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Joana A Loureiro
- LEPABE, Department of Chemical Engineering, Faculty of Engineering of the University of Porto, Porto 4500-465, Portugal
| | - Mara G Freire
- CICECO - Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - João A P Coutinho
- CICECO - Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
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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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The solvent side of proteinaceous membrane-less organelles in light of aqueous two-phase systems. Int J Biol Macromol 2018; 117:1224-1251. [PMID: 29890250 DOI: 10.1016/j.ijbiomac.2018.06.030] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 06/07/2018] [Indexed: 12/29/2022]
Abstract
Water represents a common denominator for liquid-liquid phase transitions leading to the formation of the polymer-based aqueous two-phase systems (ATPSs) and a set of the proteinaceous membrane-less organelles (PMLOs). ATPSs have a broad range of biotechnological applications, whereas PMLOs play a number of crucial roles in cellular compartmentalization and often represent a cellular response to the stress. Since ATPSs and PMLOs contain high concentrations of polymers (such as polyethylene glycol (PEG), polypropylene glycol (PPG), Ucon, and polyvinylpyrrolidone (PVP), Dextran, or Ficoll) or biopolymers (peptides, proteins and nucleic acids), it is expected that the separated phases of these systems are characterized by the noticeable changes in the solvent properties of water. These changes in solvent properties can drive partitioning of various compounds (proteins, nucleic acids, organic low-molecular weight molecules, metal ions, etc.) between the phases of ATPSs or between the PMLOs and their surroundings. Although there is a sizable literature on the properties of the ATPS phases, much less is currently known about PMLOs. In this perspective article, we first represent liquid-liquid phase transitions in water, discuss different types of biphasic (or multiphasic) systems in water, and introduce various PMLOs and some of their properties. Then, some basic characteristics of polymer-based ATPSs are presented, with the major focus being on the current understanding of various properties of ATPS phases and solvent properties of water inside them. Finally, similarities and differences between the polymer-based ATPSs and biological PMLOs are discussed.
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Zaslavsky BY, Uversky VN. In Aqua Veritas: The Indispensable yet Mostly Ignored Role of Water in Phase Separation and Membrane-less Organelles. Biochemistry 2018; 57:2437-2451. [PMID: 29303563 DOI: 10.1021/acs.biochem.7b01215] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Despite the common practice of presenting structures of biological molecules on an empty background and the assumption that interactions between biological macromolecules take place within the inert solvent, water represents an active component of various biological processes. This Perspective addresses indispensable, yet mostly ignored, roles of water in biological liquid-liquid phase transitions and in the biogenesis of various proteinaceous membrane-less organelles. We point out that changes in the structure of water reflected in the changes in its abilities to donate and/or accept hydrogen bonds and participate in dipole-dipole and dipole-induced dipole interactions in the presence of various solutes (ranging from small molecules to synthetic polymers and biological macromolecules) might represent a driving force for the liquid-liquid phase separation, define partitioning of various solutes in formed phases, and define the exceptional ability of intrinsically disordered proteins to be engaged in the formation of proteinaceous membrane-less organelles.
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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 , Florida 33612 , United States.,Laboratory of New Methods in Biology , Institute for Biological Instrumentation of the Russian Academy of Sciences , Pushchino , Moscow Region 142290 , Russia
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Practical aspects of the automated preparation of aqueous two phase systems for the analysis of biological macromolecules. J Chromatogr B Analyt Technol Biomed Life Sci 2017; 1073:60-68. [PMID: 29241086 DOI: 10.1016/j.jchromb.2017.09.048] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 09/25/2017] [Accepted: 09/29/2017] [Indexed: 11/22/2022]
Abstract
A robust strategy for the automated preparation of aqueous two-phase systems (ATPS) using a liquid handling sample processor was developed using gravimetric methods: to determine the accuracy of preparation. The major robotic control parameters requiring adjustment were; speed of aspiration and dispense; delay times following aspiration and dispense alongside measures to control cross-contamination during phase sampling. In general mixture compositions of both polymer/polymer and polymer/salt mixtures could be prepared with a target bias accuracy of less than 5%. However, we found that the bias accuracy with which systems of defined TLL and MR could be constructed was highly dependent on the tie line length of the ATPS and the geometrical form of the ATPS co-existence curve. For systems with a very low degree of curvature (PEG/salt systems here) increases in bias (accuracy) are appreciable at relatively long tie line lengths. Where the degree of curvature is more pronounced (PEG/dextran systems) closer approach to the critical point was possible without major effect on bias/accuracy. Application of the strategy to the measurement of the partitioning of phosphorylated and dephosphorylated forms of the model protein ovalbumin are reported. Differences in partition of phosphorylated (native) forms and dephosphorylated forms could be demonstrated. In a PEG/salt system this was manifest as a substantial decrease in solubility based on overall protein recovery derived from accurate knowledge of the system mass ratio. In a PEG/dextran system differences in partition coefficient could be demonstrated between phosphorylated and dephosphorylated forms.
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Ferreira LA, Gusev NB, Uversky VN, Zaslavsky BY. Effect of human heat shock protein HspB6 on the solvent features of water in aqueous solutions. J Biomol Struct Dyn 2017; 36:1520-1528. [DOI: 10.1080/07391102.2017.1328316] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Luisa A. Ferreira
- Cleveland Diagnostics, 3615 Superior Ave., Suite 4407B, Cleveland, OH 44114, USA
| | - Nikolai B. Gusev
- Department of Biochemistry, School of Biology, Moscow State University, Moscow 119991, Russia
| | - Vladimir N. Uversky
- Department of Molecular Medicine and Byrd Alzheimer’s Research Institute, 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
- Cleveland Diagnostics, 3615 Superior Ave., Suite 4407B, Cleveland, OH 44114, USA
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What are the structural features that drive partitioning of proteins in aqueous two-phase systems? BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:113-120. [DOI: 10.1016/j.bbapap.2016.09.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2016] [Revised: 08/26/2016] [Accepted: 09/18/2016] [Indexed: 02/07/2023]
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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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13
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Stepanenko OV, Povarova OI, Sulatskaya AI, Ferreira LA, Zaslavsky BY, Kuznetsova IM, Turoverov KK, Uversky VN. Protein unfolding in crowded milieu: what crowding can do to a protein undergoing unfolding? J Biomol Struct Dyn 2016; 34:2155-70. [PMID: 26474212 DOI: 10.1080/07391102.2015.1109554] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The natural environment of a protein inside a cell is characterized by the almost complete lack of unoccupied space, limited amount of free water, and the tightly packed crowd of various biological macromolecules, such as proteins, nucleic acids, polysaccharides, and complexes thereof. This extremely crowded natural milieu is poorly mimicked by slightly salted aqueous solutions containing low concentrations of a protein of interest. The accepted practice is to model crowded environments by adding high concentrations of various polymers that serve as model "crowding agents" to the solution of a protein of interest. Although studies performed under these model conditions revealed that macromolecular crowding might have noticeable influence on various aspects related to the protein structure, function, folding, conformational stability, and aggregation propensity, the complete picture describing conformational behavior of a protein under these conditions is missing as of yet. Furthermore, there is an accepted belief that the conformational stability of globular proteins increases in the presence crowding agents due to the excluded volume effects. The goal of this study was to conduct a systematic analysis of the effect of high concentrations of PEG-8000 and Dextran-70 on the unfolding behavior of eleven globular proteins belonging to different structural classes.
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Affiliation(s)
- Olga V Stepanenko
- a Laboratory of Structural Dynamics, Stability and Folding of Proteins , Institute of Cytology, Russian Academy of Sciences , St. Petersburg , Russia
| | - Olga I Povarova
- a Laboratory of Structural Dynamics, Stability and Folding of Proteins , Institute of Cytology, Russian Academy of Sciences , St. Petersburg , Russia
| | - Anna I Sulatskaya
- a Laboratory of Structural Dynamics, Stability and Folding of Proteins , Institute of Cytology, Russian Academy of Sciences , St. Petersburg , Russia
| | - Luisa A Ferreira
- b Cleveland Diagnostics , 3615 Superior Ave., Suite 4407B, Cleveland , OH 44114 , USA
| | - Boris Y Zaslavsky
- b Cleveland Diagnostics , 3615 Superior Ave., Suite 4407B, Cleveland , OH 44114 , USA
| | - Irina M Kuznetsova
- a Laboratory of Structural Dynamics, Stability and Folding of Proteins , Institute of Cytology, Russian Academy of Sciences , St. Petersburg , Russia
| | - Konstantin K Turoverov
- a Laboratory of Structural Dynamics, Stability and Folding of Proteins , Institute of Cytology, Russian Academy of Sciences , St. Petersburg , Russia.,c Department of Biophysics , Peter the Great St. Petersburg Polytechnic University , St. Petersburg , 195251 , Russia
| | - Vladimir N Uversky
- a Laboratory of Structural Dynamics, Stability and Folding of Proteins , Institute of Cytology, Russian Academy of Sciences , St. Petersburg , Russia.,d Department of Molecular Medicine and Byrd Alzheimer's Research Institute, Morsani College of Medicine , University of South Florida , Tampa , FL 33612 , USA
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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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15
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Responses of proteins to different ionic environment are linearly interrelated. J Chromatogr A 2015; 1387:32-41. [DOI: 10.1016/j.chroma.2015.02.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Revised: 01/30/2015] [Accepted: 02/03/2015] [Indexed: 01/03/2023]
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16
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Breydo L, Sales AE, Ferreira L, Fedotoff O, Shevelyova MP, Permyakov SE, Kroeck KG, Permyakov EA, Zaslavsky BY, Uversky VN. Effects of osmolytes on protein-solvent interactions in crowded environment: Analyzing the effect of TMAO on proteins in crowded solutions. Arch Biochem Biophys 2015; 570:66-74. [PMID: 25712220 DOI: 10.1016/j.abb.2015.02.021] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Revised: 02/10/2015] [Accepted: 02/13/2015] [Indexed: 11/20/2022]
Abstract
We analyzed the effect of a natural osmolyte, trimethylamine N-oxide (TMAO), on structural properties and conformational stabilities of several proteins under macromolecular crowding conditions by a set of biophysical techniques. We also used the solvent interaction analysis method to look at the peculiarities of the TMAO-protein interactions under crowded conditions. To this end, we analyzed the partitioning of these proteins in TMAO-free and TMAO-containing aqueous two-phase systems (ATPSs). These ATPSs had the same polymer composition of 6.0 wt.% PEG-8000 and 12.0 wt.% dextran-75, and same ionic composition of 0.01 M K/NaPB, pH 7.4. These analyses revealed that there is no direct interaction of TMAO with proteins, suggesting that the TMAO effects on the protein structure in crowded solutions occur via the effects of this osmolyte on solvent properties of aqueous media. The effects of TMAO on protein structure in the presence of polymers were rather complex and protein-specific. Curiously, our study revealed that in highly concentrated polymer solutions, TMAO does not always act to promote further protein folding.
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Affiliation(s)
- Leonid Breydo
- Department of Molecular Medicine, University of South Florida, Tampa, FL 33612, USA; Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Amanda E Sales
- Department of Molecular Medicine, University of South Florida, Tampa, FL 33612, USA; Department of Morphology and Animal Physiology, Federal Rural University of Pernambuco, 52171-900 Recife, PE, Brazil
| | - Luisa Ferreira
- Analiza, Inc., 3516 Superior Ave., Suite 4407B, Cleveland, USA
| | - Olga Fedotoff
- Analiza, Inc., 3516 Superior Ave., Suite 4407B, Cleveland, USA
| | - Marina P Shevelyova
- Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia
| | - Sergei E Permyakov
- Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia
| | - Kyle G Kroeck
- Department of Molecular Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Eugene A Permyakov
- Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia
| | | | - Vladimir N Uversky
- Department of Molecular Medicine, University of South Florida, Tampa, FL 33612, USA; Byrd Alzheimer's Research Institute, 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; Department of Biological Science, Faculty of Science, King Abdulaziz University, PO Box 80203, Jeddah 21589, Saudi Arabia; Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia.
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Kuznetsova IM, Zaslavsky BY, Breydo L, Turoverov KK, Uversky VN. Beyond the excluded volume effects: mechanistic complexity of the crowded milieu. Molecules 2015; 20:1377-409. [PMID: 25594347 PMCID: PMC6272634 DOI: 10.3390/molecules20011377] [Citation(s) in RCA: 135] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 01/09/2015] [Indexed: 11/16/2022] Open
Abstract
Macromolecular crowding is known to affect protein folding, binding of small molecules, interaction with nucleic acids, enzymatic activity, protein-protein interactions, and protein aggregation. Although for a long time it was believed that the major mechanism of the action of crowded environments on structure, folding, thermodynamics, and function of a protein can be described in terms of the excluded volume effects, it is getting clear now that other factors originating from the presence of high concentrations of “inert” macromolecules in crowded solution should definitely be taken into account to draw a more complete picture of a protein in a crowded milieu. This review shows that in addition to the excluded volume effects important players of the crowded environments are viscosity, perturbed diffusion, direct physical interactions between the crowding agents and proteins, soft interactions, and, most importantly, the effects of crowders on solvent properties.
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Affiliation(s)
- Irina M. Kuznetsova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Ave., St. Petersburg 194064, Russia; E-Mails: (I.M.K.); (K.K.T.)
- St. Petersburg State Polytechnical University, 29 Polytechnicheskaya st., St. Petersburg 195251, Russia
| | - Boris Y. Zaslavsky
- Cleveland Diagnostics, 3615 Superior Ave., Suite 4407B, Cleveland, OH 44114, USA; E-Mail:
| | - Leonid Breydo
- Department of Molecular Medicine and USF Health Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Blvd. MDC07, Tampa, FL 33612, USA; E-Mails:
| | - Konstantin K. Turoverov
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Ave., St. Petersburg 194064, Russia; E-Mails: (I.M.K.); (K.K.T.)
- St. Petersburg State Polytechnical University, 29 Polytechnicheskaya st., St. Petersburg 195251, Russia
| | - Vladimir N. Uversky
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Ave., St. Petersburg 194064, Russia; E-Mails: (I.M.K.); (K.K.T.)
- Department of Molecular Medicine and USF Health Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Blvd. MDC07, Tampa, FL 33612, USA; E-Mails:
- Biology Department, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +1-813-974-5816; Fax: +1-813-974-7357
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18
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Ferreira LA, Madeira PP, Uversky VN, Zaslavsky BY. Analyzing the effects of protecting osmolytes on solute–water interactions by solvatochromic comparison method: I. Small organic compounds. RSC Adv 2015. [DOI: 10.1039/c5ra08610h] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Solvent properties of water in aqueous solutions of osmolytes (sorbitol, sucrose, trehalose, and trimethylamine N-oxide (TMAO)) were studied at different concentrations using the solvatochromic comparison method.
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Affiliation(s)
| | - 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
- Porto
| | - Vladimir N. Uversky
- Department of Molecular Medicine
- Morsani College of Medicine
- University of South Florida
- Tampa
- USA
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Ferreira LA, Chervenak A, Placko S, Kestranek A, Madeira PP, Zaslavsky BY. Effect of ionic composition on the partitioning of organic compounds in octanol–buffer systems. RSC Adv 2015. [DOI: 10.1039/c5ra01402f] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The ionic composition of octanol–buffer systems might have significant effects on the distribution of organic compounds. Their responses to ionic environments follow the relationships established previously in organic solvent-free aqueous solutions.
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Affiliation(s)
| | | | | | | | - Pedro P. Madeira
- Laboratory of Separation and Reaction Engineering
- Dpt. de Engenharia Química
- Faculdade de Engenharia da Universidade do Porto
- Porto
- Portugal
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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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Ferreira LA, Chervenak A, Placko S, Kestranek A, Madeira PP, Zaslavsky BY. Responses of polar organic compounds to different ionic environments in aqueous media are interrelated. Phys Chem Chem Phys 2014; 16:23347-54. [DOI: 10.1039/c4cp02084g] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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da Silva NR, Ferreira LA, Mikheeva LM, Teixeira JA, Zaslavsky BY. Origin of salt additive effect on solute partitioning in aqueous polyethylene glycol-8000-sodium sulfate two-phase system. J Chromatogr A 2014; 1337:3-8. [PMID: 24613040 DOI: 10.1016/j.chroma.2014.02.031] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Revised: 01/31/2014] [Accepted: 02/03/2014] [Indexed: 11/29/2022]
Abstract
Partitioning of a homologous series of dinitrophenylted (DNP-) amino acids with aliphatic side chains was examined in aqueous polyethylene glycol (PEG)-8000-sodium sulfate two-phase systems (ATPS) with the additives NaSCN, NaClO4, and NaH2PO4 at concentrations varied from 0.025M up to 0.54M. The differences between the relative hydrophobicities and electrostatic properties of the two phases in all ATPS were estimated. Partitioning of adenine, adenosine mono-, di- and tri-phosphates was also examined in all ATPSs, including those with NaCl additive. Partition coefficients for these compounds and for nonionic organic compounds previously reported [L.A. Ferreira, P. Parpot, J.A. Teixeira, L.M. Mikheeva, B.Y. Zaslavsky, J. Chromatogr. A 1220 (2012) 14.] were analyzed in terms of linear solvent regression relationship. The results obtained suggest that the effects of the salts additives are related to their influence on the water structure.
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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
| | - Luisa A Ferreira
- IBB-Institute for Biotechnology and Bioengineering, Centre of Biological Engineering, Universidade do Minho, Campus de Gualtar, 4710-057 Braga, Portugal; Analiza, Inc., 3615 Superior Ave., Cleveland, OH 44114, USA
| | | | - José A Teixeira
- IBB-Institute for Biotechnology and Bioengineering, Centre of Biological Engineering, Universidade do Minho, Campus de Gualtar, 4710-057 Braga, Portugal
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Structural features important for differences in protein partitioning in aqueous dextran-polyethylene glycol two-phase systems of different ionic compositions. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:694-704. [PMID: 24486798 DOI: 10.1016/j.bbapap.2014.01.016] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Revised: 01/07/2014] [Accepted: 01/24/2014] [Indexed: 11/23/2022]
Abstract
Partitioning of 15 proteins in dextran-70-polyethylene glycol (PEG)-8000 aqueous two-phase systems (ATPSs) in the presence of 0.01M sodium phosphate buffer, pH7.4 was studied. The effect of salt additives (NaCl, CsCl, Na2SO4, NaClO4 and NaSCN) at different concentrations on the protein partition behavior was examined. The salt effects on protein partitioning were analyzed by using the Collander solvent regression relationship between the protein partition coefficients in ATPSs with and without salt additives. The results obtained show that the presence and concentration of salt additives affect the protein partition behavior. Analysis of ATPSs in terms of the differences between the relative hydrophobicity and electrostatic properties of the phases does not explain the protein partition behavior. The differences between protein partitioning could not be explained by the protein size. The structural signatures for the proteins were constructed from partition coefficient values in four ATPSs with different salt additives, and the structural distances were calculated using cytochrome c as the reference structure. The structural distances for all the examined proteins (except lysozyme) were found to be interrelated. Analysis of about 50 different descriptors of the protein structures revealed that the partition behavior of proteins is determined by the peculiarities of their surfaces (e.g., the number of water-filled cavities and the averaged hydrophobicity of the surface residues) and by the intrinsic flexibility of the protein structure measured in terms of the B-factor (or temperature factor).
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Ferreira L, Madeira PP, Mikheeva L, Uversky VN, Zaslavsky B. Effect of salt additives on protein partition in polyethylene glycol–sodium sulfate aqueous two-phase systems. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:2859-66. [DOI: 10.1016/j.bbapap.2013.07.014] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Revised: 07/23/2013] [Accepted: 07/29/2013] [Indexed: 11/16/2022]
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25
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Breydo L, Mikheeva LM, Madeira PP, Zaslavsky BY, Uversky VN. Solvent interaction analysis of intrinsically disordered proteins in aqueous two-phase systems. MOLECULAR BIOSYSTEMS 2013; 9:3068-79. [PMID: 24072065 DOI: 10.1039/c3mb70329k] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
In an aqueous two-phase system (ATPS), the partitioning of a protein is defined by the differential interactions of the protein with aqueous media in the two phases. Our study shows that partitioning of proteins in a set of ATPSs of different ionic compositions can be used to quantify structural differences between α-synuclein, its variants and several globular proteins. Since application of ATPSs implies the use of high concentrations of two polymers in water when a certain threshold concentration of the polymers is exceeded, and since these levels of polymer concentrations are similar to those commonly used to mimic the effects of macromolecular crowding on proteins, we used circular dichroism spectroscopy to evaluate the structural consequences of placing proteins in solutions with high polymer concentrations and various ionic compositions.
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Affiliation(s)
- Leonid Breydo
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA.
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