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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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Titus AR, Herron P, Streletzky KA, Madeira PP, Uversky VN, Zaslavsky BY. Effect of trimethylamine- N-oxide on the phase separation of aqueous polyethylene glycol-600-Dextran-75 two-phase systems. Phys Chem Chem Phys 2024; 26:10546-10556. [PMID: 38506647 DOI: 10.1039/d3cp06200g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
The emergence of phase separation in both intracellular biomolecular condensates (membrane-less organelles) and in vitro aqueous two-phase systems (ATPS) relies on the formation of immiscible water-based phases/domains. The solvent properties and arrangement of hydrogen bonds within these domains have been shown to differ and can be modulated with the addition of various inorganic salts and osmolytes. The naturally occuring osmolyte, trimethylamine-N-oxide (TMAO), is well established as a biological condensate stabilizer whose presence results in enhanced phase separation of intracellular membrane-less compartments. Here, we show the unique effect of TMAO on the mechanism of phase separation in model PEG-600-Dextran-75 ATPS using dynamic and static light scattering in conjunction with ATR-FTIR and solvatochromic analysis. We observe that the presence of TMAO may enhance or destabilize phase separation depending on the concentration of phase forming components. Additionally, the behavior and density of mesoscopic polymer agglomerates, which arise prior to macroscopic phase separation, are altered by the presence and concentration of TMAO.
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Affiliation(s)
- Amber R Titus
- Cleveland Diagnostics, 3615 Superior Ave., Cleveland, OH 44114, USA.
| | - Patrick Herron
- Department of Physics, Cleveland State University, Cleveland, Ohio 44115, USA.
| | - Kiril A Streletzky
- Department of Physics, Cleveland State University, Cleveland, Ohio 44115, USA.
| | - Pedro P Madeira
- Centro de Investigacao em Materiais Ceramicos e Compositos, Department of Chemistry, 3810-193 Aveiro, Portugal.
| | - 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.
| | - Boris Y Zaslavsky
- Cleveland Diagnostics, 3615 Superior Ave., Cleveland, OH 44114, USA.
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Dutta P, Roy P, Sengupta N. Effects of External Perturbations on Protein Systems: A Microscopic View. ACS OMEGA 2022; 7:44556-44572. [PMID: 36530249 PMCID: PMC9753117 DOI: 10.1021/acsomega.2c06199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 11/14/2022] [Indexed: 06/17/2023]
Abstract
Protein folding can be viewed as the origami engineering of biology resulting from the long process of evolution. Even decades after its recognition, research efforts worldwide focus on demystifying molecular factors that underlie protein structure-function relationships; this is particularly relevant in the era of proteopathic disease. A complex co-occurrence of different physicochemical factors such as temperature, pressure, solvent, cosolvent, macromolecular crowding, confinement, and mutations that represent realistic biological environments are known to modulate the folding process and protein stability in unique ways. In the current review, we have contextually summarized the substantial efforts in unveiling individual effects of these perturbative factors, with major attention toward bottom-up approaches. Moreover, we briefly present some of the biotechnological applications of the insights derived from these studies over various applications including pharmaceuticals, biofuels, cryopreservation, and novel materials. Finally, we conclude by summarizing the challenges in studying the combined effects of multifactorial perturbations in protein folding and refer to complementary advances in experiment and computational techniques that lend insights to the emergent challenges.
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Affiliation(s)
- Pallab Dutta
- Department
of Biological Sciences, Indian Institute
of Science Education and Research (IISER) Kolkata, Mohanpur741246, India
| | - Priti Roy
- Department
of Biological Sciences, Indian Institute
of Science Education and Research (IISER) Kolkata, Mohanpur741246, India
- Department
of Chemistry, Oklahoma State University, Stillwater, Oklahoma74078, United States
| | - Neelanjana Sengupta
- Department
of Biological Sciences, Indian Institute
of Science Education and Research (IISER) Kolkata, Mohanpur741246, India
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4
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Mechanism of Phase Separation in Aqueous Two-Phase Systems. Int J Mol Sci 2022; 23:ijms232214366. [PMID: 36430844 PMCID: PMC9697872 DOI: 10.3390/ijms232214366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 11/15/2022] [Accepted: 11/16/2022] [Indexed: 11/22/2022] Open
Abstract
Liquid-liquid phase separation underlies the formation of membrane-less organelles inside living cells. The mechanism of this process can be examined using simple aqueous mixtures of two or more solutes, which are able to phase separate at specific concentration thresholds. This work presents the first experimental evidence that mesoscopic changes precede visually detected macroscopic phase separation in aqueous mixtures of two polymers and a single polymer and salt. Dynamic light scattering (DLS) analysis indicates the formation of mesoscopic polymer agglomerates in these systems. These agglomerates increase in size with increasing polymer concentrations prior to visual phase separation. Such mesoscopic changes are paralleled by changes in water structure as evidenced by Attenuated Total Reflection-Fourier Transform Infrared (ATR-FTIR) spectroscopic analysis of OH-stretch bands. Through OH-stretch band analysis, we obtain quantitative estimates of the relative fractions of four subpopulations of water structures coexisting in aqueous solutions. These estimates indicate that abrupt changes in hydrogen bond arrangement take place at concentrations below the threshold of macroscopic phase separation. We used these experimental observations to develop a model of phase separation in aqueous media.
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Bhattacharjee S, Pandit S, Seth D. How Kosmotropic and Chaotropic Osmolytes Perturb the Properties of an Aqueous Solution of a Pluronic Block Copolymer? LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:9347-9362. [PMID: 35868256 DOI: 10.1021/acs.langmuir.2c01207] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Poloxamer 407 (P-407) composed of a poly(ethylene glycol)-block-poly(propylene glycol)-block-poly(ethylene glycol) (PEG-PPG-PEG) unit has two distinct microenvironments: the interior core formed by the PPG unit and the exterior shell formed by the PEG unit. In this work, we have used two fluorescent molecules coumarin-153 and 8-anilino-1-naphthalene sulfonic acid (ANS) of contrasting natures to characterize and probe the water dynamics in the core and corona regions of the copolymer by means of spectroscopic techniques, namely, absorption, fluorescence, and time-resolved fluorescence emission spectroscopy and Fourier transform infrared (FTIR) spectroscopy. Changes in the surface morphologies were characterized by using microscopic techniques. Further, two classes of osmolytes kosmotropic (betaine and sarcosine) and chaotropic (urea) known to perturb the water structure were added to aqueous solutions of P-407. Our studies reveal that the addition of kosmotropes decreases the critical micelle temperature (CMT) of the copolymer, whereas the chaotropic osmolyte increases the CMT. Steady-state studies reveal that the addition of the osmolytes to the copolymer increases the polarity of the micelle formed and hence results in the red shift in the ANS absorbance maximum. FTIR spectroscopy reveals that kosmotropes interact with the PEG moiety of the copolymer, whereas the chaotrope interacts with both the PEG and PPG moieties of the copolymer. Solvent relaxation studies produced less changes upon the addition of the kosmotropes, whereas a greater change in the relaxation time was observed in the presence of the chaotrope.
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Affiliation(s)
- Sanyukta Bhattacharjee
- Department of Chemistry, Indian Institute of Technology Patna, Patna, Bihar 801103, India
| | - Souvik Pandit
- Department of Chemistry, Indian Institute of Technology Patna, Patna, Bihar 801103, India
| | - Debabrata Seth
- Department of Chemistry, Indian Institute of Technology Patna, Patna, Bihar 801103, India
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Titus AR, Kooijman EE. Current methods for studying intracellular liquid-liquid phase separation. CURRENT TOPICS IN MEMBRANES 2021; 88:55-73. [PMID: 34862032 DOI: 10.1016/bs.ctm.2021.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Liquid-liquid phase separation (LLPS) is a ubiquitous process that drives the formation of membrane-less intracellular compartments. This compartmentalization contains vastly different protein/RNA/macromolecule concentrations compared to the surrounding cytosol despite the absence of a lipid boundary. Because of this, LLPS is important for many cellular signaling processes and may play a role in their dysregulation. This chapter highlights recent advances in the understanding of intracellular phase transitions along with current methods used to identify LLPS in vitro and model LLPS in situ.
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Affiliation(s)
- Amber R Titus
- Department of Biological Sciences, Kent State University, Kent, OH, United States.
| | - Edgar E Kooijman
- Department of Biological Sciences, Kent State University, Kent, OH, United States
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Logan Howard R, Wang Y, Allbritton NL. Use of liquid lithography to form in vitro intestinal crypts with varying microcurvature surrounding the stem cell niche. JOURNAL OF MICROMECHANICS AND MICROENGINEERING : STRUCTURES, DEVICES, AND SYSTEMS 2021; 31:125006. [PMID: 35241878 PMCID: PMC8887876 DOI: 10.1088/1361-6439/ac2d9c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
BACKGROUND AND AIMS The role of the crypt microarchitecture and surrounding tissue curvature on intestinal stem/proliferative cell physiology is unknown. The utility of liquid lithography in creating polydimethylsiloxane (PDMS) micropillar stamps with controlled tip curvature was assessed. Using these stamps, the impact of microcurvature at the crypt base on intestinal cell and cytoskeletal behavior was studied. METHODS An SU-8 master mold as a support, polyols of varying surface energies as sacrificial liquids, and liquid PDMS as the solidifiable material were combined using liquid lithography to form PDMS micropillar arrays. Vapor phase deposition of organosilane onto the master mold was used to modify the surface energy of the master mold to shape the micropillar tips. Collagen was molded using the micropillar arrays forming a scaffold for culture of human primary colonic epithelial cells. Cell proliferation and cytoskeletal properties were assessed using fluorescent stains. RESULTS Liquid lithography using low surface energy polyols (<55 dynes/cm) generated convex-tipped PDMS micropillars, while polyols with higher surface energies (>55 dynes/cm) yielded concave-tipped PDMS micropillars. Gradients of octyltrichlorosilane deposition across a master mold with an array of microwells yielded a PDMS micropillar array with a range of tip curvatures. Human primary colonic epithelial cells cultured on micropillar-molded collagen scaffolds demonstrated a stem/proliferative cell compartment at the crypt base. Crypts with a convex base demonstrated significantly lower cell proliferation at the crypt base than that of cells in crypts with either flat or concave bases. Crypts with a convex base also displayed higher levels of G-actin activity compared to that of crypts with flat or concave bases. CONCLUSIONS Liquid lithography enabled creation of arrays of in vitro colonic crypts with programmable curvature. Primary cells at the crypt base sensed and responded to surface curvature by altering their proliferation and cytoskeletal properties.
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Affiliation(s)
- R Logan Howard
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Cystic Fibrosis and Pulmonary Diseases Research and Treatment Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Yuli Wang
- Department of Bioengineering, University of Washington, Seattle, Washington
| | - Nancy L Allbritton
- Department of Bioengineering, University of Washington, Seattle, Washington
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da Silva N, Ferreira LA, Belgovskiy AI, Madeira PP, Teixeira JA, Mann EK, Adin Mann J, Meyer WV, Smart AE, Chernyak VY, Uversky VN, Zaslavsky BY. Effects of different solutes on the physical chemical properties of aqueous solutions via rearrangement of hydrogen bonds in water. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116288] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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9
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Joshi PU, Turpeinen DG, Schroeder M, Jones B, Lyons A, Kriz S, Khaksari M, O'Hagan D, Nikam S, Heldt CL. Osmolyte enhanced aqueous two-phase system for virus purification. Biotechnol Bioeng 2021; 118:3251-3262. [PMID: 34129733 DOI: 10.1002/bit.27849] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 05/26/2021] [Accepted: 06/02/2021] [Indexed: 01/15/2023]
Abstract
Due to the high variation in viral surface properties, a platform method for virus purification is still lacking. A potential alternative to the high-cost conventional methods is aqueous two-phase systems (ATPSs). However, optimizing virus purification in ATPS requires a large experimental design space, and the optimized systems are generally found to operate at high ATPS component concentrations. The high concentrations capitalize on hydrophobic and electrostatic interactions to obtain high viral particle yields. This study investigated using osmolytes as driving force enhancers to reduce the high concentration of ATPS components while maintaining high yields. The partitioning behavior of porcine parvovirus (PPV), a nonenveloped mammalian virus, and human immunodeficiency virus-like particle (HIV-VLP), a yeast-expressed enveloped VLP, were studied in a polyethylene glycol (PEG) 12 kDa-citrate system. The partitioning of the virus modalities was enhanced by osmoprotectants glycine and betaine, while trimethylamine N-oxide was ineffective for PPV. The increased partitioning to the PEG-rich phase pertained only to viruses, resulting in high virus purification. Recoveries were 100% for infectious PPV and 92% for the HIV-VLP, with high removal of the contaminant proteins and more than 60% DNA removal when glycine was added. The osmolyte-induced ATPS demonstrated a versatile method for virus purification, irrespective of the expression system.
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Affiliation(s)
- Pratik U Joshi
- Department of Chemical Engineering, Michigan Technological University, Houghton, Michigan, USA.,Health Research Institute, Michigan Technological University, Houghton, Michigan, USA
| | - Dylan G Turpeinen
- Department of Chemical Engineering, Michigan Technological University, Houghton, Michigan, USA.,Health Research Institute, Michigan Technological University, Houghton, Michigan, USA
| | - Michael Schroeder
- Department of Chemical Engineering, Michigan Technological University, Houghton, Michigan, USA
| | - Bianca Jones
- Department of Biochemistry, University of Detroit-Mercy, Detroit, Michigan, USA
| | - Audrey Lyons
- Department of Chemical Engineering, Michigan Technological University, Houghton, Michigan, USA
| | - Seth Kriz
- Department of Chemical Engineering, Michigan Technological University, Houghton, Michigan, USA.,Health Research Institute, Michigan Technological University, Houghton, Michigan, USA
| | - Maryam Khaksari
- Great Lakes Research Center, Michigan Technological University, Houghton, Michigan, USA
| | | | | | - Caryn L Heldt
- Department of Chemical Engineering, Michigan Technological University, Houghton, Michigan, USA.,Health Research Institute, Michigan Technological University, Houghton, Michigan, USA
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Titus AR, Ferreira LA, Belgovskiy AI, Kooijman EE, Mann EK, Mann JA, Meyer WV, Smart AE, Uversky VN, Zaslavsky BY. Interfacial tension and mechanism of liquid-liquid phase separation in aqueous media. Phys Chem Chem Phys 2020; 22:4574-4580. [PMID: 32048659 DOI: 10.1039/c9cp05810a] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The organization of multiple subcellular compartments is controlled by liquid-liquid phase separation. Phase separation of this type occurs with the emergence of interfacial tension. Aqueous two-phase systems formed by two non-ionic polymers can be used to separate and analyze biological macromolecules, cells and viruses. Phase separation in these systems may serve as the simple model of phase separation in cells also occurring in aqueous media. To better understand liquid-liquid phase separation mechanisms, interfacial tension was measured in aqueous two-phase systems formed by dextran and polyethylene glycol and by polyethylene glycol and sodium sulfate in the presence of different additives. Interfacial tension values depend on differences between the solvent properties of the coexisting phases, estimated experimentally by parameters representing dipole-dipole, ion-dipole, ion-ion, and hydrogen bonding interactions. Based on both current and literature data, we propose a mechanism for phase separation in aqueous two-phase systems. This mechanism is based on the fundamental role of intermolecular forces. Although it remains to be confirmed, it is possible that these may underlie all liquid-liquid phase separation processes in biology.
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Affiliation(s)
- Amber R Titus
- Department of Biological Sciences, Kent State University, OH, Kent, USA
| | | | | | - Edgar E Kooijman
- Department of Biological Sciences, Kent State University, OH, Kent, USA
| | | | - J Adin Mann
- Department of Chemical and Biomolecular Engineering, Case Western Reserve University, Cleveland, OH, USA
| | | | | | - Vladimir N Uversky
- Department of Molecular Medicine and Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA and Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Pushchino, Moscow region, Russia
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Madadlou A, Saint-Jalmes A, Guyomarc'h F, Floury J, Dupont D. Development of an aqueous two-phase emulsion using hydrophobized whey proteins and erythritol. Food Hydrocoll 2019. [DOI: 10.1016/j.foodhyd.2019.02.031] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Martins PAT, Domingues N, Pires C, Alves AM, Palmeira T, Samelo J, Cardoso R, Velazquez-Campoy A, Moreno MJ. Molecular crowding effects on the distribution of amphiphiles in biological media. Colloids Surf B Biointerfaces 2019; 180:319-325. [PMID: 31071572 DOI: 10.1016/j.colsurfb.2019.04.065] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 03/23/2019] [Accepted: 04/29/2019] [Indexed: 12/01/2022]
Abstract
Biological systems are the result of the interactions established among their many distinct molecules and molecular assemblies. The high concentration of small molecules dissolved in the aqueous media alter the water properties with important consequences in the interactions established. In this work, the effects of high concentrations of the disaccharide trehalose on the solubility of a homologous series of fluorescent amphiphiles (NBD-Cn, n=4-16) and on their interaction with a lipid bilayer and a serum protein are quantitatively characterized. Both kinetic and equilibrium aspects are reported for a better understanding of the effects observed. The aqueous solubility of the most hydrophobic amphiphiles (n ≥ 8) is strongly increased by 1 M trehalose, while no signifcant effect is observed for the most polar amphiphile (n = 4). This results from a decrease in the magnitude of the hydrophobic effect at molecular crowding conditions. A small decrease is observed on the equilibrium association with serum albumin. This is most significant for amphiphiles with longer alkyl chains, in agreement with their increased solubility in the aqueous media containing trehalose. The effects on the association of the amphiphiles with lipid bilayers are influenced by both equilibrium and kinetic aspects. On the one hand, the decreased magnitude of the hydrophobic effect leads to a decrease in the affinity of the amphiphiles towards the membrane. However, this tendency may be overbalanced by the effects on the kinetics of the interaction (insertion/desorption) due to the increase in the viscosity of the aqueous media. It is shown that the distribution of amphiphilic drugs in the crowded biological media is significantly different from that predicted from studies in dilute solutions and that the effects are dependent on the solute's hydrophobicity.
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Affiliation(s)
- Patrícia A T Martins
- CQC-Biological Chemistry Group, Chemistry Department FCTUC, Largo D. Dinis, Rua Larga, 3004-535, Coimbra, Portugal
| | - Neuza Domingues
- CQC-Biological Chemistry Group, Chemistry Department FCTUC, Largo D. Dinis, Rua Larga, 3004-535, Coimbra, Portugal; CEDOC, NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, 1169-056, Lisboa, Portugal
| | - Cristiana Pires
- CQC-Biological Chemistry Group, Chemistry Department FCTUC, Largo D. Dinis, Rua Larga, 3004-535, Coimbra, Portugal
| | - Ana Maria Alves
- CQC-Biological Chemistry Group, Chemistry Department FCTUC, Largo D. Dinis, Rua Larga, 3004-535, Coimbra, Portugal
| | - Tiago Palmeira
- CQC-Biological Chemistry Group, Chemistry Department FCTUC, Largo D. Dinis, Rua Larga, 3004-535, Coimbra, Portugal; CQFM-IN and IBB-Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal
| | - Jaime Samelo
- CQC-Biological Chemistry Group, Chemistry Department FCTUC, Largo D. Dinis, Rua Larga, 3004-535, Coimbra, Portugal
| | - Renato Cardoso
- CQC-Biological Chemistry Group, Chemistry Department FCTUC, Largo D. Dinis, Rua Larga, 3004-535, Coimbra, Portugal; Exogenus Therapeutics S.A, Biocant Park, 3060-197, Cantanhede, Portugal
| | - Adrian Velazquez-Campoy
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Units IQFR-CSIC-BIFI and GBsC-CSIC-BIFI, and Department of Biochemistry and Molecular and Cell Biology, Universidad de Zaragoza, 50018, Zaragoza, Spain; Aragon Institute for Health Research (IIS Aragon), 50009, Zaragoza, Spain; Biomedical Research Networking Centre for Liver and Digestive Diseases (CIBERehd), Madrid, Spain; Fundacion ARAID, Government of Aragon, 50018, Zaragoza, Spain
| | - Maria João Moreno
- CQC-Biological Chemistry Group, Chemistry Department FCTUC, Largo D. Dinis, Rua Larga, 3004-535, Coimbra, Portugal.
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Intrinsic Disorder-Based Emergence in Cellular Biology: Physiological and Pathological Liquid-Liquid Phase Transitions in Cells. Polymers (Basel) 2019; 11:polym11060990. [PMID: 31167414 PMCID: PMC6631845 DOI: 10.3390/polym11060990] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 05/29/2019] [Accepted: 05/31/2019] [Indexed: 12/14/2022] Open
Abstract
The visible outcome of liquid-liquid phase transitions (LLPTs) in cells is the formation and disintegration of various proteinaceous membrane-less organelles (PMLOs). Although LLPTs and related PMLOs have been observed in living cells for over 200 years, the physiological functions of these transitions (also known as liquid-liquid phase separation, LLPS) are just starting to be understood. While unveiling the functionality of these transitions is important, they have come into light more recently due to the association of abnormal LLPTs with various pathological conditions. In fact, several maladies, such as various cancers, different neurodegenerative diseases, and cardiovascular diseases, are known to be associated with either aberrant LLPTs or some pathological transformations within the resultant PMLOs. Here, we will highlight both the physiological functions of cellular liquid-liquid phase transitions as well as the pathological consequences produced through both dysregulated biogenesis of PMLOs and the loss of their dynamics. We will also discuss the potential downstream toxic effects of proteins that are involved in pathological formations.
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Salvi N, Abyzov A, Blackledge M. Solvent-dependent segmental dynamics in intrinsically disordered proteins. SCIENCE ADVANCES 2019; 5:eaax2348. [PMID: 31259246 PMCID: PMC6598773 DOI: 10.1126/sciadv.aax2348] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 05/22/2019] [Indexed: 05/04/2023]
Abstract
Protein and water dynamics have a synergistic relationship, which is particularly important for intrinsically disordered proteins (IDPs), although the details of this coupling remain poorly understood. Here, we combine temperature-dependent molecular dynamics simulations using different water models with extensive nuclear magnetic resonance (NMR) relaxation to examine the importance of distinct modes of solvent and solute motion for the accurate reproduction of site-specific dynamics in IDPs. We find that water dynamics play a key role in motional processes internal to "segments" of IDPs, stretches of primary sequence that share dynamic properties and behave as discrete dynamic units. We identify a relationship between the time scales of intrasegment dynamics and the lifetime of hydrogen bonds in bulk water. Correct description of these motions is essential for accurate reproduction of protein relaxation. Our findings open important perspectives for understanding the role of hydration water on the behavior and function of IDPs in solution.
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15
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Understanding the Role of Preferential Exclusion of Sugars and Polyols from Native State IgG1 Monoclonal Antibodies and its Effect on Aggregation and Reversible Self-Association. Pharm Res 2019; 36:109. [DOI: 10.1007/s11095-019-2642-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Accepted: 05/07/2019] [Indexed: 11/27/2022]
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17
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Hosseiniyan Khatibi SM, Zununi Vahed F, Sharifi S, Ardalan M, Mohajel Shoja M, Zununi Vahed S. Osmolytes resist against harsh osmolarity: Something old something new. Biochimie 2019; 158:156-164. [PMID: 30629975 DOI: 10.1016/j.biochi.2019.01.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 01/03/2019] [Indexed: 12/14/2022]
Abstract
From the halophilic bacteria to human, cells have to survive under the stresses of harsh environments. Hyperosmotic stress is a process that triggers cell shrinkage, oxidative stress, DNA damage, and apoptosis and it potentially contributes to a number of human diseases. Remarkably, by high salts and organic solutes concentrations, a variety of organisms struggle with these conditions. Different strategies have been developed for cellular osmotic adaptations among which organic osmolyte synthesis/accumulation is a conserved once. Osmolytes are naturally occurring solutes used by cells of several halophilic (micro) organisms to preserve cell volume and function. In this review, the osmolytes diversity and their protective roles in harsh hyperosmolar environments from bacteria to human cells are highlighted. Moreover, it provides a close look at mammalian kidney osmoregulation at a molecular level. This review provides a concise view on the recent developments and advancements on the applications of osmolytes. Identification of disease-related osmolytes and their targeted-delivery may be used as a therapeutic measurement for treatment of the pathological conditions and the inherited diseases related to protein misfolding and aggregation. The molecular and cellular aspects of cell adaptation against harsh environmental osmolarity will benefit the development of effective drugs for many diseases.
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Affiliation(s)
| | | | - Simin Sharifi
- Dental and Periodontal Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
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Whittington AC, Rokyta DR. Biophysical Spandrels form a Hot-Spot for Kosmotropic Mutations in Bacteriophage Thermal Adaptation. J Mol Evol 2018; 87:27-36. [PMID: 30564861 DOI: 10.1007/s00239-018-9882-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 12/15/2018] [Indexed: 12/18/2022]
Abstract
Temperature plays a dominating role in protein structure and function, and life has evolved myriad strategies to adapt proteins to environmental thermal stress. Cellular systems can utilize kosmotropic osmolytes, the products of complex biochemical pathways, to act as chemical chaperones. These extrinsic molecules, e.g., trehalose, alter local water structure to modulate the strength of the hydrophobic effect and increase protein stability. In contrast, simpler genetic systems must rely on intrinsic mutation to affect protein stability. In naturally occurring microvirid bacteriophages of the subfamily Bullavirinae, capsid stability is randomly distributed across the phylogeny, suggesting it is not phylogenetically linked and could be altered through adaptive mutation. We hypothesized that these phages could utilize an adaptive mechanism that mimics the stabilizing effects of the kosmotrope trehalose through mutation. Kinetic stability of wild-type ID8, a relative of ΦX174, displays a saturable response to trehalose. Thermal adaptation mutations in ID8 improve capsid stability and reduce responsiveness to trehalose suggesting the mutations move stability closer to the kosmotropic saturation point, mimicking the kosmotropic effect of trehalose. These mutations localize to and modulate the hydrophobicity of a cavern formation at the interface of phage coat and spike proteins-an evolutionary spandrel. Across a series of genetically distinct phages, responsiveness to trehalose correlates positively with cavern hydrophobicity suggesting that the level of hydrophobicity of the cavern may provide a biophysical gating mechanism constraining or permitting adaptation in a lineage-specific manner. Our results demonstrate that a single mutation can exploit pre-existing, non-adaptive structural features to mimic the adaptive effects of complex biochemical pathways.
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Affiliation(s)
- A Carl Whittington
- Department of Biological Science, Florida State University, 319 Stadium Dr., Tallahassee, FL, 32306, USA.
| | - Darin R Rokyta
- Department of Biological Science, Florida State University, 319 Stadium Dr., Tallahassee, FL, 32306, USA
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19
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Ferreira LA, Walczyk Mooradally A, Zaslavsky B, Uversky VN, Graether SP. Effect of an Intrinsically Disordered Plant Stress Protein on the Properties of Water. Biophys J 2018; 115:1696-1706. [PMID: 30297135 DOI: 10.1016/j.bpj.2018.09.014] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 09/09/2018] [Accepted: 09/18/2018] [Indexed: 11/19/2022] Open
Abstract
Dehydrins are plant proteins that are able to protect plants from various forms of dehydrative stress such as drought, cold, and high salinity. Dehydrins can prevent enzymes from losing activity after freeze/thaw treatments. Previous studies had suggested that the dehydrins function by a molecular shield effect, essentially preventing a denatured enzyme from aggregating with another enzyme. Therefore, the larger the dehydrin, the larger the shield and theoretically the more effective the protection. Although this relationship holds for smaller dehydrins, it fails to explain why larger dehydrins are less efficient than would be predicted from their size. Using solvatochromic dyes to probe the solvent features of water, we first confirm that the dehydrins do not bind the dyes, which would interfere with interpretation of the data. We then show that the dehydrins have an effect on three solvent properties of water (dipolarity/polarizability, hydrogen-bond donor acidity and hydrogen-bond acceptor basicity), which can contribute to the protective mechanism of these proteins. Interpretation of these data suggests that although polyethylene glycol and dehydrins have similar protective effects, dehydrins may more efficiently modify the hydrogen-bonding ability of bulk water to prevent enzyme denaturation. This possibly explains why dehydrins recover slightly more enzyme activity than polyethylene glycol.
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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, Florida; Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, Moscow Region, Russian Federation.
| | - Steffen P Graether
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada.
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20
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Bayat M, Gourabi H, khammari A, Ahmad F, Saboury AA. A comparative study of structure, stability and function of sc-tenecteplase in the presence of stabilizing osmolytes. J Biotechnol 2018; 280:1-10. [DOI: 10.1016/j.jbiotec.2018.05.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 05/17/2018] [Accepted: 05/24/2018] [Indexed: 01/29/2023]
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21
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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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22
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Alvarado YJ, Ferrebuz A, Paz JL, Rodríguez-Lugo P, Restrepo J, Romero F, Fernández-Acuña J, Williams YO, Toro-Mendoza J. Surface Behavior of BSA/Water/Carbohydrate Systems from Molecular Polarizability Measurements. J Phys Chem B 2018; 122:4231-4238. [PMID: 29582658 DOI: 10.1021/acs.jpcb.7b11998] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The effect of the presence of glucose and sucrose on the nonintrinsic contribution to partial molar volume ⟨Θ⟩ni of bovine serum albumin (BSA) is determined by means of static and dynamic electronic polarizability measurements. For that aim, a combined strategy based on high-resolution refractometry, high exactitude densitometry, and synchronous fluorescence spectroscopy is applied. Both static and dynamic mean electronic molecular polarizability values are found to be sensitive to the presence of glucose. In the case of sucrose, the polarizability of BSA is not appreciably affected. In fact, our results revealed that the electronic changes observed occurred without a modification of the native conformation of BSA. On the contrary, a nonmonotonous behavior with the concentration is observed in presence of glucose. These results advocate the influence of the electronic polarization on the repulsive and attractive protein-carbohydrate interactions. An analysis using the scaled particle theory indicates that the accumulation of glucose on the protein surface promotes dehydration. Inversely, hydration and preferential exclusion occur in the vicinity of the protein surface for sucrose-enriched systems.
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Affiliation(s)
| | | | - Jose Luis Paz
- Departamento de Física , Escuela Politécnica Nacional , Ladron de Guevara , Quito 170517 , Ecuador
| | - Patricia Rodríguez-Lugo
- Laboratorio de Electrónica Molecular, Facultad Experimental de Ciencias, Departamento de Química , Universidad del Zulia , Maracaibo 4001 , Venezuela
| | | | - Freddy Romero
- Center for Translational Medicine and Korman Lung Center , Thomas Jefferson University , Philadelphia , Pennsylvania 19107 , United States
| | - Jaqueline Fernández-Acuña
- Centro de Estudios Interdisciplinarios de la Física , Instituto Venezolano de Investigaciones Científicas (IVIC) , Caracas 1020A , Venezuela
| | - Yhan O'Neil Williams
- Centro de Estudios Interdisciplinarios de la Física , Instituto Venezolano de Investigaciones Científicas (IVIC) , Caracas 1020A , Venezuela
| | - Jhoan Toro-Mendoza
- Centro de Estudios Interdisciplinarios de la Física , Instituto Venezolano de Investigaciones Científicas (IVIC) , Caracas 1020A , Venezuela
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23
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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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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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25
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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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26
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Ferreira LA, Uversky VN, Zaslavsky BY. Role of solvent properties of water in crowding effects induced by macromolecular agents and osmolytes. MOLECULAR BIOSYSTEMS 2017; 13:2551-2563. [DOI: 10.1039/c7mb00436b] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Dipolarity/polarizability of water in polymer mixtures may be additive, reduced or enhanced depending on the composition of the mixture.
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Affiliation(s)
| | - V. N. Uversky
- Department of Molecular Medicine
- Morsant College of Medicine
- University of South Florida
- Tampa
- USA
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