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Rampin A, Rossoni A, Chaniotaki L, Gkiatas IS, Tzora A, Skoufos I, Diakakis N, Prassinos N, Zeugolis DI. Xenogeneic versus allogeneic serum and macromolecular crowding in human tenocyte cultures. Eur J Cell Biol 2024; 103:151445. [PMID: 39024989 DOI: 10.1016/j.ejcb.2024.151445] [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: 04/21/2024] [Revised: 07/09/2024] [Accepted: 07/12/2024] [Indexed: 07/20/2024] Open
Abstract
Allogeneic serum and tissue-specific extracellular matrix have been shown to maintain permanently differentiated cell phenotype in culture. This is of particular importance for human tenocytes, a cell population that readily loses its function during ex vivo culture. With these in mind, herein we extracted human tenocytes using either foetal bovine serum or human serum, cultured them in the absence and presence of carrageenan and Ficoll®, the most widely used macromolecular crowding agents (to induce tissue-specific extracellular matrix deposition), and assessed cellular function, via metabolic activity, viability, proliferation and immunofluorescence for collagen related molecules, non-collagenous molecules and transmembrane molecules. At day 7, longest time point assessed, neither carrageenan nor Ficoll® significantly affected metabolic activity, viability and proliferation in either serum and human serum significantly increased metabolic activity and proliferation. At day 7, in the absence of macromolecular crowding, cells in human serum deposited significantly lower collagen type VI, biglycan, versican and tenomodulin than cells in foetal bovine serum. Interestingly, at day 7, in comparison to the no macromolecular crowding group, carrageenan in foetal bovine serum induced the highest effect, as judged by the highest number of significantly increased molecules (collagen type I, collagen type IV, collagen type V, collagen type VI, transforming growth factor β1, matrix metalloproteinase 14, lumican, versican, scleraxis and integrin α2β1). These data, although contradict previous observations where human serum outperformed foetal bovine serum, at the same time, support the use of foetal bovine serum in the development of cell-based medicines.
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Affiliation(s)
- Andrea Rampin
- Department of Agriculture, University of Ioannina, Arta, Greece; School of Veterinary Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece; Regenerative, Modular & Developmental Engineering Laboratory (REMODEL), Charles Institute of Dermatology, Conway Institute of Biomolecular & Biomedical Research and School of Mechanical & Materials Engineering, University College Dublin (UCD), Dublin, Ireland
| | - Andrea Rossoni
- Regenerative, Modular & Developmental Engineering Laboratory (REMODEL), Charles Institute of Dermatology, Conway Institute of Biomolecular & Biomedical Research and School of Mechanical & Materials Engineering, University College Dublin (UCD), Dublin, Ireland
| | - Lefki Chaniotaki
- Regenerative, Modular & Developmental Engineering Laboratory (REMODEL), Charles Institute of Dermatology, Conway Institute of Biomolecular & Biomedical Research and School of Mechanical & Materials Engineering, University College Dublin (UCD), Dublin, Ireland
| | - Ioannis S Gkiatas
- Department of Orthopaedic Surgery, School of Medicine, University of Ioannina, Ioannina, Greece
| | - Athina Tzora
- Department of Agriculture, University of Ioannina, Arta, Greece
| | - Ioannis Skoufos
- Department of Agriculture, University of Ioannina, Arta, Greece
| | - Nikolaos Diakakis
- School of Veterinary Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Nikitas Prassinos
- School of Veterinary Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Dimitrios I Zeugolis
- Regenerative, Modular & Developmental Engineering Laboratory (REMODEL), Charles Institute of Dermatology, Conway Institute of Biomolecular & Biomedical Research and School of Mechanical & Materials Engineering, University College Dublin (UCD), Dublin, Ireland.
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2
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Chen W, Li S, Albahi A, Ye S, Li J, Li B. The effect of konjac glucomannan on enzyme kinetics and fluorescence spectrometry of digestive enzymes: An in vitro research from the perspective of macromolecule crowding. Food Res Int 2024; 184:114247. [PMID: 38609226 DOI: 10.1016/j.foodres.2024.114247] [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: 12/19/2023] [Revised: 03/13/2024] [Accepted: 03/15/2024] [Indexed: 04/14/2024]
Abstract
Konjac glucomannan (KGM) can significantly prolong gastrointestinal digestion. However, it is still worth investigating whether the macromolecular crowding (MMC) induced by KGM is correlated with digestion. In this paper, the MMC effect was quantified by fluorescence resonance energy transfer and microrheology, and the digests of starch, protein, and oil were determined. The digestive enzymes were analyzed by enzyme reaction kinetic and fluorescence quenching. The results showed that higher molecular weight (604.85 ∼ 1002.21 kDa) KGM created a larger MMC (>0.8), and influenced the digestion of macronutrients; the digests of starch, protein, and oil all decreased significantly. MMC induced by KGM decreased the Michaelis-Menten constants (Km and Vmax) of pancreatic α-amylase (PPA), pepsin (PEP), and pancreatic lipase (PPL). The larger MMC (>0.8) induced by KGM resulted in the decrease of fluorescence quenching constants (Ksv) in PPA and PPL, and the increase of Ksv in PEP. Therefore, varying degrees of MMC induced by KGM could play a role in regulating digestion and the inhibitory effect on digestion was more significant in a relatively more crowded environment induced by KGM. This study provides theoretical support for the strategies of nutrient digestion regulation from the perspective of MMC caused by dietary fiber.
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Affiliation(s)
- Wenjing Chen
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen 518000, China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Sha Li
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Amgad Albahi
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Shuxin Ye
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Jing Li
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen 518000, China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China.
| | - Bin Li
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen 518000, China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China.
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Raczyłło E, Gołowicz D, Skóra T, Kazimierczuk K, Kondrat S. Size Sensitivity of Metabolite Diffusion in Macromolecular Crowds. NANO LETTERS 2024; 24. [PMID: 38607288 PMCID: PMC11057039 DOI: 10.1021/acs.nanolett.3c05100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 04/02/2024] [Accepted: 04/03/2024] [Indexed: 04/13/2024]
Abstract
Metabolites play crucial roles in cellular processes, yet their diffusion in the densely packed interiors of cells remains poorly understood, compounded by conflicting reports in existing studies. Here, we employ pulsed-gradient stimulated-echo NMR and Brownian/Stokesian dynamics simulations to elucidate the behavior of nano- and subnanometer-sized tracers in crowded environments. Using Ficoll as a crowder, we observe a linear decrease in tracer diffusivity with increasing occupied volume fraction, persisting─somewhat surprisingly─up to volume fractions of 30-40%. While simulations suggest a linear correlation between diffusivity slowdown and particle size, experimental findings hint at a more intricate relationship, possibly influenced by Ficoll's porosity. Simulations and numerical calculations of tracer diffusivity in the E. coli cytoplasm show a nonlinear yet monotonic diffusion slowdown with particle size. We discuss our results in the context of nanoviscosity and discrepancies with existing studies.
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Affiliation(s)
- Edyta Raczyłło
- Institute
of Physical Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Poland
- Department
of Theoretical Chemistry, Institute of Chemical Sciences, Faculty
of Chemistry, Maria Curie-Skłodowska
University in Lublin, 20-031 Lublin, Poland
| | - Dariusz Gołowicz
- Institute
of Physical Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Poland
| | - Tomasz Skóra
- Institute
of Physical Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Poland
- Scientific
Computing and Imaging Institute, University
of Utah, Salt Lake City, Utah 84112, United States
| | | | - Svyatoslav Kondrat
- Institute
of Physical Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Poland
- Institute
for Computational Physics, University of
Stuttgart 70569, Stuttgart, Germany
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4
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Zhong-Johnson EZL, Dong Z, Canova CT, Destro F, Cañellas M, Hoffman MC, Maréchal J, Johnson TM, Zheng M, Schlau-Cohen GS, Lucas MF, Braatz RD, Sprenger KG, Voigt CA, Sinskey AJ. Analysis of Poly(ethylene terephthalate) degradation kinetics of evolved IsPETase variants using a surface crowding model. J Biol Chem 2024; 300:105783. [PMID: 38395309 PMCID: PMC10963241 DOI: 10.1016/j.jbc.2024.105783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 02/10/2024] [Accepted: 02/19/2024] [Indexed: 02/25/2024] Open
Abstract
Poly(ethylene terephthalate) (PET) is a major plastic polymer utilized in the single-use and textile industries. The discovery of PET-degrading enzymes (PETases) has led to an increased interest in the biological recycling of PET in addition to mechanical recycling. IsPETase from Ideonella sakaiensis is a candidate catalyst, but little is understood about its structure-function relationships with regards to PET degradation. To understand the effects of mutations on IsPETase productivity, we develop a directed evolution assay to identify mutations beneficial to PET film degradation at 30 °C. IsPETase also displays enzyme concentration-dependent inhibition effects, and surface crowding has been proposed as a causal phenomenon. Based on total internal reflectance fluorescence microscopy and adsorption experiments, IsPETase is likely experiencing crowded conditions on PET films. Molecular dynamics simulations of IsPETase variants reveal a decrease in active site flexibility in free enzymes and reduced probability of productive active site formation in substrate-bound enzymes under crowding. Hence, we develop a surface crowding model to analyze the biochemical effects of three hit mutations (T116P, S238N, S290P) that enhanced ambient temperature activity and/or thermostability. We find that T116P decreases susceptibility to crowding, resulting in higher PET degradation product accumulation despite no change in intrinsic catalytic rate. In conclusion, we show that a macromolecular crowding-based biochemical model can be used to analyze the effects of mutations on properties of PETases and that crowding behavior is a major property to be targeted for enzyme engineering for improved PET degradation.
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Affiliation(s)
| | - Ziyue Dong
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Colorado, USA
| | - Christopher T Canova
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Francesco Destro
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | | | - Mikaila C Hoffman
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Jeanne Maréchal
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA; AgroParisTech, Palaiseau, France
| | - Timothy M Johnson
- Plasma Science and Fusion Center, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Maya Zheng
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Gabriela S Schlau-Cohen
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | | | - Richard D Braatz
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Kayla G Sprenger
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Colorado, USA
| | - Christopher A Voigt
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Anthony J Sinskey
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
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5
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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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Barucci A, Flori A, Carpi R, Marchi DD, Esposito M, Menichetti L, Pini R, Ratto F, Belli G, Piazza F. Ficoll as testing material for diffusion weighted imaging-quality assurance phantoms. Magn Reson Imaging 2020; 76:1-7. [PMID: 33161101 DOI: 10.1016/j.mri.2020.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 11/03/2020] [Accepted: 11/03/2020] [Indexed: 10/23/2022]
Abstract
PURPOSE The aim of this work is to test the use of aqueous solutions of Ficoll®**, a highly branched polymer displaying crowding properties, to build a phantom suitable for Diffusion Weighted Imaging (DWI) in Magnetic Resonance Imaging (MRI). METHODS We developed a test object made of a cylindrical plastic container with a precise geometrical arrangement suitable for measuring several samples at the same time. The container was designed to host single vials with variable geometry and number, and to fit inside common commercial head coils for MRI scanners. In our experiments, vials were filled with 8 aqueous solutions of Ficoll 70 and Ficoll 400 spanning a range of polymer concentration from 5 to 30% by weight. Vials containing ultra-pure water were also used as reference. Experiments were performed on both 1.5 and 3 T clinical scanners (GE, Philips and Siemens), under the conditions of a standard clinical examination. RESULTS The geometry of the phantom provided reduced imaging artifacts, especially image distortions at magnetic interfaces. We found that the Apparent Diffusion Coefficient (ADC) varied in the range of 0.00125-0.00223 mm2/s and decreased with Ficoll concentration. ADC vs Ficoll concentration exhibited a linear trend. Results were consistent over time and among different MRI clinical scanners, showing an average variability of 3% at 1.5 T and of 7.5% at 3 T. Moreover, no substantial difference was found between Ficoll 70 and 400. By varying Ficoll concentration, ADC can be modulated to approach tissue-mimicking values. Preliminary results for relaxation measurements proved that both T1 and T2 decreased with Ficoll concentration in the ranges 1.3-2.4 s and 150-800 ms respectively. CONCLUSIONS In this work, we propose a 3D phantom design based on the widespread crowding agent Ficoll, which is suitable for DWI quality assurance purposes in MRI acquisitions. Aqueous Ficoll solutions provide good performance in terms of stability, ease of preparation, and safety.
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Affiliation(s)
- Andrea Barucci
- "Nello Carrara" Institute of Applied Physics, CNR Florence Research Area, Via Madonna del Piano 10, 50019 Sesto Fiorentino, FI, Italy.
| | - Alessandra Flori
- Bioengineering and clinical engineering unit, Fondazione CNR/Regione Toscana G. Monasterio, Via G. Moruzzi 1, 56124 Pisa, Italy
| | - Roberto Carpi
- USL Toscana Centro, Piazza Santa Maria Nuova 1, 50121 Firenze, Italy
| | - Daniele De Marchi
- MRI unit, Fondazione CNR/Regione Toscana G. Monasterio, Via G. Moruzzi 1, 56124 Pisa, Italy
| | - Marco Esposito
- USL Toscana Centro, Piazza Santa Maria Nuova 1, 50121 Firenze, Italy
| | - Luca Menichetti
- Institute of Clinical Physiology, CNR, Via G. Moruzzi 1, 56124 Pisa, Italy
| | - Roberto Pini
- "Nello Carrara" Institute of Applied Physics, CNR Florence Research Area, Via Madonna del Piano 10, 50019 Sesto Fiorentino, FI, Italy
| | - Fulvio Ratto
- "Nello Carrara" Institute of Applied Physics, CNR Florence Research Area, Via Madonna del Piano 10, 50019 Sesto Fiorentino, FI, Italy
| | - Giacomo Belli
- Health Physics Unit, AOU Careggi, Largo Brambilla 3, 50134 Firenze, Italy
| | - Francesco Piazza
- Université d'Orléans and Centre de Biophysique Moléculaire (CBM), CNRS UPR 4301, rue Charles Sadron, 45071 Orléans, France
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7
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Xie Y, Mao Z, Bachman H, Li P, Zhang P, Ren L, Wu M, Huang TJ. Acoustic Cell Separation Based on Density and Mechanical Properties. J Biomech Eng 2020; 142:031005. [PMID: 32006021 PMCID: PMC7104781 DOI: 10.1115/1.4046180] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 12/30/2019] [Indexed: 11/08/2022]
Abstract
Density and mechanical properties (e.g., compressibility or bulk modulus) are important cellular biophysical markers. As such, developing a method to separate cells directly based on these properties can benefit various applications including biological research, diagnosis, prognosis, and therapeutics. As a potential solution, surface acoustic wave (SAW)-based cell separation has demonstrated advantages in terms of biocompatibility and compact device size. However, most SAW-reliant cell separations are achieved using an entangled effect of density, various mechanical properties, and size. In this work, we demonstrate SAW-based separation of cells/particles based on their density and compressibility, irrespective of their sizes, by manipulating the acoustic properties of the fluidic medium. Using our platform, SAW-based separation is achieved by varying the dimensions of the microfluidic channels, the wavelengths of acoustic signals, and the properties of the fluid media. Our method was applied to separate paraformaldehyde-treated and fresh Hela cells based on differences in mechanical properties; a recovery rate of 85% for fixed cells was achieved. It was also applied to separate red blood cells (RBCs) and white blood cells (WBCs) which have different densities. A recovery rate of 80.5% for WBCs was achieved.
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Affiliation(s)
- Yuliang Xie
- Department of Chemical Engineering, The Pennsylvania State
University, University Park, State College, PA
16802
| | - Zhangming Mao
- Department of Engineering Science and Mechanics, The
Pennsylvania State University, University
Park, State College, PA 16802
| | - Hunter Bachman
- Department of Mechanical Engineering and Materials Science,
Duke University, Durham, NC 27708
| | - Peng Li
- Department of Engineering Science and Mechanics, The
Pennsylvania State University, University
Park, State College, PA 16802
| | - Peiran Zhang
- Department of Mechanical Engineering and Materials Science,
Duke University, Durham, NC 27708
| | - Liqiang Ren
- Department of Engineering Science and Mechanics, The
Pennsylvania State University, University
Park, State College, PA 16802
| | - Mengxi Wu
- Department of Mechanical Engineering and Materials Science,
Duke University, Durham, NC 27708
| | - Tony Jun Huang
- Department of Mechanical Engineering and Materials Science,
Duke University, Durham, NC 27708
e-mail:
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8
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Ramberg KO, Antonik PM, Cheung DL, Crowley PB. Measuring the Impact of PEGylation on a Protein-Polysaccharide Interaction. Bioconjug Chem 2019; 30:1162-1168. [PMID: 30869874 DOI: 10.1021/acs.bioconjchem.9b00099] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
PEGylation is the most widely used half-life extension strategy for protein therapeutics. While it imparts a range of attractive attributes PEGylation can impede protein binding and reduce efficacy. A model system to probe the effects of PEGylation on protein binding has practical applications. Here, we present a system based on complex formation between a hexavalent lectin (RSL) and the globular polysaccharide Ficoll PM70 (a type of glycocluster). Mutants of the lectin were used to generate conjugates with 3, 6, or 12 PEG (1 kDa) chains. Using NMR spectroscopy we monitored how the degree of PEGylation impacted the lectin-Ficoll interaction. The binding propensity was observed to decrease with increasing polymer density. Apparently, the extended PEG chains sterically impede the lectin-Ficoll binding. This deduction was supported by molecular dynamics simulations of the protein-polymer conjugates. The implications for protein-surface interactions are discussed.
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Affiliation(s)
- Kiefer O Ramberg
- School of Chemistry , National University of Ireland Galway , University Road , Galway , H91 TK33 , Ireland
| | - Paweł M Antonik
- School of Chemistry , National University of Ireland Galway , University Road , Galway , H91 TK33 , Ireland
| | - David L Cheung
- School of Chemistry , National University of Ireland Galway , University Road , Galway , H91 TK33 , Ireland
| | - Peter B Crowley
- School of Chemistry , National University of Ireland Galway , University Road , Galway , H91 TK33 , Ireland
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9
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Anomalous Dense Liquid Condensates Host the Nucleation of Tumor Suppressor p53 Fibrils. iScience 2019; 12:342-355. [PMID: 30739016 PMCID: PMC6369220 DOI: 10.1016/j.isci.2019.01.027] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 01/03/2019] [Accepted: 01/16/2019] [Indexed: 01/09/2023] Open
Abstract
About half of human cancers are associated with mutations of the tumor suppressor p53. Gained oncogenic functions of the mutants have been related to aggregation behaviors of wild-type and mutant p53. The thermodynamic and kinetic mechanisms of p53 aggregation are poorly understood. Here we find that wild-type p53 forms an anomalous liquid phase. The liquid condensates exhibit several behaviors beyond the scope of classical phase transition theories: their size, ca. 100 nm, is independent of the p53 concentration and decoupled from the protein mass held in the liquid phase. Furthermore, the liquid phase lacks constant solubility. The nucleation of p53 fibrils deviates from the accepted mechanism of sequential association of single solute molecules. We find that the liquid condensates serve as pre-assembled precursors of high p53 concentration that facilitate fibril assembly. Fibril nucleation hosted by precursors represents a novel biological pathway, which opens avenues to suppress protein fibrillation in aggregation diseases.
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10
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Influence of carboxymethylcellulose (NaCMC) on the aggregation and micellization behaviors in aqueous cethylpyridinium chloride solutions: Thermodynamic study and effect of polymer concentration. J Mol Liq 2018. [DOI: 10.1016/j.molliq.2018.06.037] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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11
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12
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Palit S, Yethiraj A. Dynamics and cluster formation in charged and uncharged Ficoll70 solutions. J Chem Phys 2017; 147:074901. [DOI: 10.1063/1.4986366] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Swomitra Palit
- Department of Physics and Physical Oceanography, Memorial University, St. John’s, Newfoundland and Labrador A1B3X7, Canada
| | - Anand Yethiraj
- Department of Physics and Physical Oceanography, Memorial University, St. John’s, Newfoundland and Labrador A1B3X7, Canada
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13
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Kis M, Sipka G, Ayaydin F, Maróti P. The biophysics of a critical phenomenon: colonization and sedimentation of the photosynthetic bacteria Rubrivivax gelatinosus. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2017; 47:139-149. [PMID: 28685171 DOI: 10.1007/s00249-017-1236-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 05/13/2017] [Accepted: 06/26/2017] [Indexed: 11/28/2022]
Abstract
In response to environmental changes, the photosynthetic bacterium Rubrivivax gelatinosus (Rvx.) can switch from a planktonic lifestyle to a phototrophic biofilm. Like in critical phenomena, the colonization and sedimentation of the cells is abrupt and hard to predict causally, and the underlying biophysics of the mechanisms involved is not known. Herein, we report basic experimental observations and quantitative explanations as keys to understanding microbial turnover of aggregates. (1) The moment of sedimentation can be controlled by the height of the tube of cultivation, by the concentrations of externally added Ficoll (a highly branched polymer) and/or of internally produced polysaccharides (constituents of the biofilm). (2) The observed translational diffusion coefficient of the planktonic bacteria is the sum of diffusion coefficients coming from random Brownian and twitching movements of the bacteria and amounts to 14 (μm)2/s. (3) This value drops hyperbolically with the association number of the cell aggregates and with the concentration of the exopolysaccharides in the biofilm. In the experiments described herein, their effects could be separated. (4) The critical conditions of colonization and sinking of the cells will be achieved if the height of the tube meets the scale height that is proportional to the ratio of the diffusion coefficient and the net mass of the bacterium. The decisive role of the web-like structure of a biofilm, the organization of bacteria from loose cooperativity to solid aggregation, and the possible importance of similar controls in other phototrophic microorganisms are discussed.
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Affiliation(s)
- Mariann Kis
- Institute of Medical Physics, University of Szeged, Rerrich Béla tér 1, Szeged, 6720, Hungary
| | - Gábor Sipka
- Institute of Medical Physics, University of Szeged, Rerrich Béla tér 1, Szeged, 6720, Hungary.,Biological Research Center, Hungarian Academy of Sciences, Szeged, 6726, Hungary
| | - Ferhan Ayaydin
- Biological Research Center, Hungarian Academy of Sciences, Szeged, 6726, Hungary
| | - Péter Maróti
- Institute of Medical Physics, University of Szeged, Rerrich Béla tér 1, Szeged, 6720, Hungary.
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14
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Rusinga FI, Weis DD. Soft interactions and volume exclusion by polymeric crowders can stabilize or destabilize transient structure in disordered proteins depending on polymer concentration. Proteins 2017; 85:1468-1479. [PMID: 28425679 DOI: 10.1002/prot.25307] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2017] [Revised: 04/07/2017] [Accepted: 04/17/2017] [Indexed: 01/19/2023]
Abstract
The effects of macromolecular crowding on the transient structure of intrinsically disordered proteins is not well-understood. Crowding by biological molecules inside cells could modulate transient structure and alter IDP function. Volume exclusion theory and observations of structured proteins suggest that IDP transient structure would be stabilized by macromolecular crowding. Amide hydrogen exchange (HX) of IDPs in highly concentrated polymer solutions would provide valuable insights into IDP transient structure under crowded conditions. Here, we have used mass spectrometry to measure HX by a transiently helical random coil domain of the activator of thyroid and retinoid receptor (ACTR) in solutions containing 300 g L-1 and 400 g L-1 of Ficoll, a synthetic polysaccharide, using a recently-developed strong cation exchange-based cleanup method [Rusinga, et al., Anal Chem 2017;89:1275-1282]. Transiently helical regions of ACTR exchanged faster in 300 g L-1 Ficoll than in dilute buffer. In contrast, one transient helix exchanged more slowly in 400 g L-1 Ficoll. Nonspecific interactions destabilize ACTR helicity in 300 g L-1 Ficoll because ACTR engages with the Ficoll polymer mesh. In contrast, 400 g L-1 Ficoll is a semi-dilute solution where ACTR cannot engage the Ficoll mesh. At this higher concentration, volume exclusion stabilizes ACTR helicity because ACTR is compacted in interstitial spaces between Ficoll molecules. Our results suggest that the interplay between nonspecific interactions and volume exclusion in different cellular compartments could modulate IDP function by altering the stability of IDP transient structures. Proteins 2017; 85:1468-1479. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Farai I Rusinga
- Department of Chemistry and R. N. Adams Institute for Bioanalytical Chemistry, University of Kansas, Lawrence, Kansas, USA
| | - David D Weis
- Department of Chemistry and R. N. Adams Institute for Bioanalytical Chemistry, University of Kansas, Lawrence, Kansas, USA
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Kis M, Sipka G, Maróti P. Stoichiometry and kinetics of mercury uptake by photosynthetic bacteria. PHOTOSYNTHESIS RESEARCH 2017; 132:197-209. [PMID: 28260133 DOI: 10.1007/s11120-017-0357-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2016] [Accepted: 02/13/2017] [Indexed: 05/27/2023]
Abstract
Mercury adsorption on the cell surface and intracellular uptake by bacteria represent the key first step in the production and accumulation of highly toxic mercury in living organisms. In this work, the biophysical characteristics of mercury bioaccumulation are studied in intact cells of photosynthetic bacteria by use of analytical (dithizone) assay and physiological photosynthetic markers (pigment content, fluorescence induction, and membrane potential) to determine the amount of mercury ions bound to the cell surface and taken up by the cell. It is shown that the Hg(II) uptake mechanism (1) has two kinetically distinguishable components, (2) includes co-opted influx through heavy metal transporters since the slow component is inhibited by Ca2+ channel blockers, (3) shows complex pH dependence demonstrating the competition of ligand binding of Hg(II) ions with H+ ions (low pH) and high tendency of complex formation of Hg(II) with hydroxyl ions (high pH), and (4) is not a passive but an energy-dependent process as evidenced by light activation and inhibition by protonophore. Photosynthetic bacteria can accumulate Hg(II) in amounts much (about 105) greater than their own masses by well-defined strong and weak binding sites with equilibrium binding constants in the range of 1 (μM)-1 and 1 (mM)-1, respectively. The strong binding sites are attributed to sulfhydryl groups as the uptake is blocked by use of sulfhydryl modifying agents and their number is much (two orders of magnitude) smaller than the number of weak binding sites. Biofilms developed by some bacteria (e.g., Rvx. gelatinosus) increase the mercury binding capacity further by a factor of about five. Photosynthetic bacteria in the light act as a sponge of Hg(II) and can be potentially used for biomonitoring and bioremediation of mercury-contaminated aqueous cultures.
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Affiliation(s)
- Mariann Kis
- Institute of Medical Physics, University of Szeged, Rerrich Béla tér 1, Szeged, 6720, Hungary
| | - Gábor Sipka
- Institute of Medical Physics, University of Szeged, Rerrich Béla tér 1, Szeged, 6720, Hungary
| | - Péter Maróti
- Institute of Medical Physics, University of Szeged, Rerrich Béla tér 1, Szeged, 6720, Hungary.
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Pérez Santero S, Favretto F, Zanzoni S, Chignola R, Assfalg M, D'Onofrio M. Effects of macromolecular crowding on a small lipid binding protein probed at the single-amino acid level. Arch Biochem Biophys 2016; 606:99-110. [DOI: 10.1016/j.abb.2016.07.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 07/16/2016] [Accepted: 07/21/2016] [Indexed: 11/29/2022]
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Yoshitake T, Toyooka T, Nakasone Y, Zikihara K, Tokutomi S, Terazima M. Macromolecular crowding effect for photoreactions of LOV2 domains of Arabidopsis thaliana phototropin 1. J Mol Liq 2016. [DOI: 10.1016/j.molliq.2015.08.030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Nimdeo YM, Joshi YM, Muralidhar K. Measurement of mass diffusivity by light streak imaging. Chem Eng Res Des 2015. [DOI: 10.1016/j.cherd.2015.06.023] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Öberg CM, Rippe B. A distributed two-pore model: theoretical implications and practical application to the glomerular sieving of Ficoll. Am J Physiol Renal Physiol 2014; 306:F844-54. [DOI: 10.1152/ajprenal.00366.2013] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
In the present study, an extended two-pore theory is presented where the porous pathways are continuously distributed according to small- and large-pore mean radii and SDs. Experimental glomerular sieving data for Ficoll were analyzed using the model. In addition, several theoretical findings are presented along with analytic solutions to many of the equations used in distributed pore modeling. The results of the data analysis revealed a small-pore population in the glomerular capillary wall with a mean radius of 36.6 Å having a wide arithmetic SD of ∼5 Å and a large-pore radius of 98.6 Å with an even wider SD of ∼44 Å. The small-pore radius obtained in the analysis was close to that of human serum albumin (35.5 Å). By reanalyzing the data and setting the distribution spread of the model constant, we discovered that a narrow distribution is compensated by an increased mean pore radius and a decreased pore area-to-diffusion length ratio. The wide distribution of pore sizes obtained in the present analysis, even when considering electrostatic hindrance due to the negatively charged barrier, is inconsistent with the high selectivity to proteins typically characterizing the glomerular filtration barrier. We therefore hypothesize that a large portion of the variance in the distribution of pore sizes obtained is due to the molecular “flexibility” of Ficoll, implying that the true variance of the pore system is lower than that obtained using flexible probes. This would also, in part, explain the commonly noted discrepancy between the pore area-to-diffusion length ratio and the filtration coefficient.
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Affiliation(s)
- Carl M. Öberg
- Department of Nephrology, University Hospital of Lund, Lund University, Lund, Sweden
| | - Bengt Rippe
- Department of Nephrology, University Hospital of Lund, Lund University, Lund, Sweden
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Georgalis Y, Braun N, Peschek J, Appavou MS. RETRACTED ARTICLE: Human recombinant α-crystallins: temperature dependence of diffusion coefficients. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2013; 42:417. [PMID: 23306588 DOI: 10.1007/s00249-012-0882-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2012] [Revised: 11/26/2012] [Accepted: 12/11/2012] [Indexed: 06/01/2023]
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