1
|
Raghunath M, Zeugolis DI. Transforming eukaryotic cell culture with macromolecular crowding. Trends Biochem Sci 2021; 46:805-811. [PMID: 33994289 DOI: 10.1016/j.tibs.2021.04.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 04/07/2021] [Accepted: 04/16/2021] [Indexed: 01/10/2023]
Abstract
In multicellular organisms, the intracellular and extracellular spaces are considerably packed with a diverse range of macromolecular species. Yet, standard eukaryotic cell culture is performed in dilute, and deprived of macromolecules culture media, that barely imitate the density and complex macromolecular composition of tissues. Essentially, we drown cells in a sea of media and then expect them to perform physiologically. Herein, we argue the use of macromolecular crowding (MMC) in eukaryotic cell culture for regenerative medicine and drug discovery purposes.
Collapse
Affiliation(s)
- Michael Raghunath
- Center for Cell Biology and Tissue Engineering, Institute for Chemistry and Biotechnology, Zurich University of Applied Sciences, Wädenswil, Switzerland
| | - Dimitrios I Zeugolis
- Regenerative, Modular, and Developmental Engineering Laboratory (REMODEL), National University of Ireland Galway (NUI Galway), Galway, Ireland; Science Foundation Ireland (SFI) Centre for Research in Medical Devices (CÚRAM), National University of Ireland Galway (NUI Galway), Galway, Ireland; Regenerative, Modular, and Developmental Engineering Laboratory (REMODEL), Faculty of Biomedical Sciences, Università della Svizzera Italiana (USI), Lugano, Switzerland; Regenerative, Modular, and Developmental Engineering Laboratory (REMODEL), School of Mechanical and Materials Engineering, University College Dublin (UCD), Dublin, Ireland.
| |
Collapse
|
2
|
Garnica-Galvez S, Korntner SH, Skoufos I, Tzora A, Diakakis N, Prassinos N, Zeugolis DI. Hyaluronic Acid as Macromolecular Crowder in Equine Adipose-Derived Stem Cell Cultures. Cells 2021; 10:859. [PMID: 33918830 PMCID: PMC8070604 DOI: 10.3390/cells10040859] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 04/02/2021] [Accepted: 04/07/2021] [Indexed: 01/10/2023] Open
Abstract
The use of macromolecular crowding in the development of extracellular matrix-rich cell-assembled tissue equivalents is continuously gaining pace in regenerative engineering. Despite the significant advancements in the field, the optimal macromolecular crowder still remains elusive. Herein, the physicochemical properties of different concentrations of different molecular weights hyaluronic acid (HA) and their influence on equine adipose-derived stem cell cultures were assessed. Within the different concentrations and molecular weight HAs, the 10 mg/mL 100 kDa and 500 kDa HAs exhibited the highest negative charge and hydrodynamic radius, and the 10 mg/mL 100 kDa HA exhibited the lowest polydispersity index and the highest % fraction volume occupancy. Although HA had the potential to act as a macromolecular crowding agent, it did not outperform carrageenan and Ficoll®, the most widely used macromolecular crowding molecules, in enhanced and accelerated collagen I, collagen III and collagen IV deposition.
Collapse
Affiliation(s)
- Sergio Garnica-Galvez
- Laboratory of Animal Science, Nutrition and Biotechnology, Department of Agriculture, University of Ioannina, 47100 Arta, Greece; (S.G.-G.); (I.S.); (A.T.)
- School of Veterinary Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (N.D.); (N.P.)
- Regenerative, Modular & Developmental Engineering Laboratory (REMODEL), Biomedical Sciences Building, National University of Ireland Galway (NUI Galway), H92 W2TY Galway, Ireland;
| | - Stefanie H. Korntner
- Regenerative, Modular & Developmental Engineering Laboratory (REMODEL), Biomedical Sciences Building, National University of Ireland Galway (NUI Galway), H92 W2TY Galway, Ireland;
- Science Foundation Ireland (SFI) Centre for Research in Medical Devices (CÚRAM), Biomedical Sciences Building, National University of Ireland Galway (NUI Galway), H92 W2TY Galway, Ireland
| | - Ioannis Skoufos
- Laboratory of Animal Science, Nutrition and Biotechnology, Department of Agriculture, University of Ioannina, 47100 Arta, Greece; (S.G.-G.); (I.S.); (A.T.)
| | - Athina Tzora
- Laboratory of Animal Science, Nutrition and Biotechnology, Department of Agriculture, University of Ioannina, 47100 Arta, Greece; (S.G.-G.); (I.S.); (A.T.)
| | - Nikolaos Diakakis
- School of Veterinary Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (N.D.); (N.P.)
| | - Nikitas Prassinos
- School of Veterinary Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (N.D.); (N.P.)
| | - Dimitrios I. Zeugolis
- Regenerative, Modular & Developmental Engineering Laboratory (REMODEL), Biomedical Sciences Building, National University of Ireland Galway (NUI Galway), H92 W2TY Galway, Ireland;
- Science Foundation Ireland (SFI) Centre for Research in Medical Devices (CÚRAM), Biomedical Sciences Building, National University of Ireland Galway (NUI Galway), H92 W2TY Galway, Ireland
- Regenerative, Modular & Developmental Engineering Laboratory (REMODEL), Faculty of Biomedical Sciences, Università della Svizzera Italiana (USI), 6904 Lugano, Switzerland
- Regenerative, Modular & Developmental Engineering Laboratory (REMODEL), School of Mechanical and Materials Engineering, University College Dublin (UCD), D04 V1W8 Dublin, Ireland
| |
Collapse
|
3
|
Wilcox XE, Chung CB, Slade KM. Macromolecular crowding effects on the kinetics of opposing reactions catalyzed by alcohol dehydrogenase. Biochem Biophys Rep 2021; 26:100956. [PMID: 33665382 PMCID: PMC7905371 DOI: 10.1016/j.bbrep.2021.100956] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 01/03/2021] [Accepted: 02/09/2021] [Indexed: 12/01/2022] Open
Abstract
In order to better understand how the complex, densely packed, heterogeneous milieu of a cell influences enzyme kinetics, we exposed opposing reactions catalyzed by yeast alcohol dehydrogenase (YADH) to both synthetic and protein crowders ranging from 10 to 550 kDa. The results reveal that the effects from macromolecular crowding depend on the direction of the reaction. The presence of the synthetic polymers, Ficoll and dextran, decrease Vmax and Km for ethanol oxidation. In contrast, these crowders have little effect or even increase these kinetic parameters for acetaldehyde reduction. This increase in Vmax is likely due to excluded volume effects, which are partially counteracted by viscosity hindering release of the NAD+ product. Macromolecular crowding is further complicated by the presence of a depletion layer in solutions of dextran larger than YADH, which diminishes the hindrance from viscosity. The disparate effects from 25 g/L dextran or glucose compared to 25 g/L Ficoll or sucrose reveals that soft interactions must also be considered. Data from binary mixtures of glucose, dextran, and Ficoll support this “tuning” of opposing factors. While macromolecular crowding was originally proposed to influence proteins mainly through excluded volume effects, this work compliments the growing body of evidence revealing that other factors, such as preferential hydration, chemical interactions, and the presence of a depletion layer also contribute to the overall effect of crowding. Yeast alcohol dehydrogenase reduction of acetaldehyde is enhanced by crowding. Crowding effects on YADH kinetics depend on the direction of the reaction. Crowders like dextran can be used as a tool to elucidate enzyme mechanism. Excluded volume optimizes YADH hydride transfer; viscosity hinders product release. The presence of a depletion layer with large crowders mitigates their effects.
Collapse
Affiliation(s)
- Xander E Wilcox
- Department of Chemistry, University of California at Davis, CA, 95616, USA
| | - Charmaine B Chung
- Department of Chemistry, Hobart and William Smith Colleges, 300 Pulteney St, Geneva, NY, 14456, USA
| | - Kristin M Slade
- Department of Chemistry, Hobart and William Smith Colleges, 300 Pulteney St, Geneva, NY, 14456, USA
| |
Collapse
|
4
|
Influence of crowding agents on the dynamics of a multidomain protein in its denatured state: a solvation approach. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2020; 49:289-305. [PMID: 32399581 DOI: 10.1007/s00249-020-01435-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 03/26/2020] [Accepted: 04/28/2020] [Indexed: 01/01/2023]
Abstract
It is now well appreciated that the crowded intracellular environment significantly modulates an array of physiological processes including protein folding-unfolding, aggregation, and dynamics to name a few. In this work we have studied the dynamics of domain I of the protein human serum albumin (HSA) in its urea-induced denatured states, in the presence of a series of commonly used macromolecular crowding agents. HSA was labeled at Cys-34 (a free cysteine) in domain I with the fluorophore 6-bromoacetyl-2-dimethylaminonaphthalene (BADAN) to act as a solvation probe. In partially denatured states (2-6 M urea), lower crowder concentrations (~ < 125 g/L) induced faster dynamics, while the dynamics became slower beyond 150 g/L of crowders. We propose that this apparent switch in dynamics is an evidence of a crossover from soft (enthalpic) to hard-core (entropic) interactions between the protein and crowder molecules. That soft interactions are also important for the crowders used here was further confirmed by the appreciable shift in the wavelength of the emission maximum of BADAN, in particular for PEG8000 and Ficoll 70 at concentrations where the excluded volume effect is not dominant.
Collapse
|
5
|
Chen E, Esquerra RM, Meléndez PA, Chandrasekaran SS, Kliger DS. Microviscosity in E. coli Cells from Time-Resolved Linear Dichroism Measurements. J Phys Chem B 2018; 122:11381-11389. [PMID: 30118225 DOI: 10.1021/acs.jpcb.8b07362] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A protein's folding or function depends on its mobility through the viscous environment that is defined by the presence of macromolecules throughout the cell. The relevant parameter for this mobility is microviscosity-the viscosity on a time and distance scale that is important for protein folding/function movements. A quasi-null, ultrasensitive time-resolved linear dichroism (TRLD) spectroscopy is proving to be a useful tool for measurements of viscosity on this scale, with previous in vitro studies reporting on the microviscosities of crowded environments mimicked by high concentrations of different macromolecules. This study reports the microviscosity experienced by myoglobin in the E. coli cell's heterogeneous cytoplasm by using TRLD to measure rotational diffusion times. The results show that photolyzed deoxyMb ensembles randomize through environment-dependent rotational diffusion with a lifetime of 34 ± 6 ns. This value corresponds to a microviscosity of 2.82 ± 0.42 cP, which is consistent with previous reports of cytoplasmic viscosity in E. coli. The results of these TRLD studies in E. coli (1) provide a measurement of myoglobin mobility in the cytoplasm, (2) taken together with in vitro TRLD studies yield new insights into the nature of the cytoplasmic environment in cells, and (3) demonstrate the feasibility of TRLD as a probe of intracellular viscosity.
Collapse
Affiliation(s)
- Eefei Chen
- Department of Chemistry and Biochemistry , University of California , Santa Cruz , California 95064 , United States
| | - Raymond M Esquerra
- Department of Chemistry and Biochemistry , San Francisco State University , San Francisco , California 94132 , United States
| | - Philipp A Meléndez
- Department of Chemistry and Biochemistry , San Francisco State University , San Francisco , California 94132 , United States
| | - Sita S Chandrasekaran
- Department of Chemistry and Biochemistry , San Francisco State University , San Francisco , California 94132 , United States
| | - David S Kliger
- Department of Chemistry and Biochemistry , University of California , Santa Cruz , California 95064 , United States
| |
Collapse
|
6
|
Behavior of bovine serum albumin in the presence of locust bean gum. Int J Biol Macromol 2018; 111:1-10. [DOI: 10.1016/j.ijbiomac.2017.12.139] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 12/23/2017] [Accepted: 12/25/2017] [Indexed: 12/16/2022]
|