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Singh A, Gupta M, Rastogi H, Khare K, Chowdhury PK. Deeper Insights into Mixed Crowding through Enzyme Activity, Dynamics, and Crowder Diffusion. J Phys Chem B 2024; 128:5293-5309. [PMID: 38808573 DOI: 10.1021/acs.jpcb.4c00337] [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: 05/30/2024]
Abstract
Given the fact that the cellular interior is crowded by many different kinds of macromolecules, it is important that in vitro studies be carried out in the presence of mixed crowder systems. In this regard, we have used binary crowders formed by the combination of some of the commonly used crowding agents, namely, Ficoll 70, Dextran 70, Dextran 40, and PEG 8000 (PEG 8), to study how these affect enzyme activity, dynamics, and crowder diffusion. The enzyme chosen is AK3L1, an isoform of adenylate kinase. To investigate its dynamics, we have carried out three single point mutations (A74C, A132C, and A209C) with the cysteine residues being labeled with a coumarin-based solvatochromic probe [CPM: (7-diethylamino-3-(4-maleimido-phenyl)-4-methylcoumarin)]. Both enzyme activity and dynamics decreased in the binary mixtures as compared with the sum of the individual crowders, suggesting a reduction in excluded volume (in the mixture). To gain deeper insights into the binary mixtures, fluorescence correlation spectroscopy studies were carried out using fluorescein isothiocyanate-labeled Dextran 70 and tetramethylrhodamine-labeled AK3L1 as the diffusion probes. Diffusion in binary mixtures was observed to be much more constrained (relative to the sum of the individual crowders) for the labeled enzyme as compared to the labeled crowder showing different environments being faced by the two species. This was further confirmed during imaging of the phase-separated droplets formed in the binary mixtures having PEG as one of the crowding agents. The interior of these droplets was found to be rich in crowders and densely packed, as shown by confocal and digital holographic microscopy images, with the enzymes predominantly residing outside these droplets, that is, in the relatively less crowded regions. Taken together, our data provide important insights into various aspects of the simplest form of mixed crowding, that is, composed of just two components, and also hint at the enhanced complexity that the cellular interior presents toward having a detailed and comprehensive understanding of the same.
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Affiliation(s)
- Arvind Singh
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Monika Gupta
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Harshita Rastogi
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Kedar Khare
- Optics and Photonics Centre, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Pramit K Chowdhury
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
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2
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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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3
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Trosel Y, Gregory LP, Booth VK, Yethiraj A. Diffusion NMR and Rheology of a Model Polymer in Bacterial Cell Lysate Crowders. Biomacromolecules 2023. [PMID: 37216308 DOI: 10.1021/acs.biomac.2c01534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The intracellular milieu is crowded and heterogeneous, and this can have profound consequences for biomolecule motions and biochemical kinetics. Macromolecular crowding has been traditionally studied in artificial crowders like Ficoll and dextran or globular proteins such as bovine serum albumin. It is, however, not clear if the effects of artificial crowders on such phenomena are the same as the crowding that is experienced in a heterogeneous biological environment. Bacterial cells, for example, are composed of heterogeneous biomolecules with different sizes, shapes, and charges. Using crowders composed of one of three different pretreatments of bacterial cell lysate (unmanipulated, ultracentrifuged, and anion exchanged), we examine the effects of crowding on the diffusivity of a model polymer. We measure the translational diffusivity, via diffusion NMR, of the test polymer polyethylene glycol (PEG) in these bacterial cell lysates. We show that the small (Rg ∼ 5 nm) test polymer shows a modest decrease in self-diffusivity with increasing crowder concentration for all lysate treatments. The corresponding self-diffusivity decrease in the artificial Ficoll crowder is much more pronounced. Moreover, a comparison of the rheological response of biological and artificial crowders shows that while the artificial crowder Ficoll exhibits a Newtonian response even at high concentrations, the bacterial cell lysate is markedly non-Newtonian; it behaves like a shear-thinning fluid with a yield stress. While at any concentration the rheological properties are sensitive to both lysate pretreatment and batch-to-batch variations, the PEG diffusivity is nearly unaffected by the type of lysate pretreatment.
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Affiliation(s)
- Yanitza Trosel
- Department of Physics and Physical Oceanography, Memorial University of Newfoundland, St. John's, Newfoundland A1B 3X9, Canada
| | - Liam P Gregory
- Department of Biochemistry, Memorial University of Newfoundland, St. John's, Newfoundland A1B 3X9, Canada
| | - Valerie K Booth
- Department of Physics and Physical Oceanography, Memorial University of Newfoundland, St. John's, Newfoundland A1B 3X9, Canada
- Department of Biochemistry, Memorial University of Newfoundland, St. John's, Newfoundland A1B 3X9, Canada
| | - Anand Yethiraj
- Department of Physics and Physical Oceanography, Memorial University of Newfoundland, St. John's, Newfoundland A1B 3X9, Canada
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Cammarata M, Piazza F, Rivas G, Schirò G, Temussi PA, Pastore A. Revitalizing an important field in biophysics: The new frontiers of molecular crowding. Front Mol Biosci 2023; 10:1153996. [PMID: 36923640 PMCID: PMC10010569 DOI: 10.3389/fmolb.2023.1153996] [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: 01/30/2023] [Accepted: 02/13/2023] [Indexed: 03/02/2023] Open
Abstract
Taking into account the presence of the crowded environment of a macromolecule has been an important goal of biology over the past 20 years. Molecular crowding affects the motions, stability and the kinetic behaviour of proteins. New powerful approaches have recently been developed to study molecular crowding, some of which make use of the synchrotron radiation light. The meeting "New Frontiers in Molecular Crowding" was organized in July 2022at the European Synchrotron Radiation facility of Grenoble to discuss the new frontiers of molecular crowding. The workshop brought together researchers from different disciplines to highlight the new developments of the field, including areas where new techniques allow the scientists to gain unprecedently expected information. A key conclusion of the meeting was the need to build an international and interdisciplinary research community through enhanced communication, resource-sharing, and educational initiatives that could let the molecular crowding field flourish further.
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Affiliation(s)
- Marco Cammarata
- Experiment Division, European Synchrotron Radiation Facility, 71 Ave des Martyrs, Grenoble, France
| | - Francesco Piazza
- Department of Physics & Astronomy, University of Florence and INFN Sezione di Firenze, Sesto Fiorentino, Italy
| | - Germán Rivas
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Giorgio Schirò
- CNRS, CEA, IBS, University Grenoble Alpes, Grenoble, France
| | - Piero Andrea Temussi
- Dipartimento di Scienze Chimiche, University "Federico II" of Naples, via Cynthia, Naples, Italy
| | - Annalisa Pastore
- Experiment Division, European Synchrotron Radiation Facility, 71 Ave des Martyrs, Grenoble, France
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Ranganathan VT, Bazmi S, Wallin S, Liu Y, Yethiraj A. Is Ficoll a Colloid or Polymer? A Multitechnique Study of a Prototypical Excluded-Volume Macromolecular Crowder. Macromolecules 2022. [DOI: 10.1021/acs.macromol.2c00677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Saman Bazmi
- Department of Physics and Physical Oceanography, Memorial University, St. John’s, NLA1B 3X7, Canada
| | - Stefan Wallin
- Department of Physics and Physical Oceanography, Memorial University, St. John’s, NLA1B 3X7, Canada
| | - Yun Liu
- Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland20899, United States
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware19716, United States
| | - Anand Yethiraj
- Department of Physics and Physical Oceanography, Memorial University, St. John’s, NLA1B 3X7, Canada
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Rastogi H, Chowdhury PK. Correlating the Local and Global Dynamics of an Enzyme in the Crowded Milieu. J Phys Chem B 2022; 126:3208-3223. [PMID: 35442681 DOI: 10.1021/acs.jpcb.1c09759] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Enzymes are dynamic biological macromolecules, with their catalytic function(s) being largely influenced by the changes in local fluctuations of amino acid side chains as well as global structural modulations that the enzyme undergoes. Such local and global motions can be highly affected inside the crowded physiological interior of the cell. Here, we have addressed the role of dynamic structural flexibility in affecting the activation energy barrier of a flexible multidomain enzyme adenylate kinase (AK3L1, UniProtKB: Q9UIJ7). Activation energy profiles of both local (at three different sites along the polypeptide backbone) and global dynamics of the enzyme have been monitored using solvation studies on the subnanosecond time scale and tryptophan quenching studies over the temperature range of 278-323 K, respectively, under crowded conditions (Ficoll 70, Dextran 40, Dextran 70, and PEG 8). This study not only provides the site-specific mapping of dynamics but reveals that the activation energies associated with these local motions undergo a significant decrease in the presence of macromolecular crowders, providing new insights into how crowding affects internal protein dynamics. The crowded scenario also aids in enhancing the coupling between the local and global motions of the enzyme. Moreover, select portions/regions of the enzyme when taken together can well mirror the overall dynamics of the biomolecule, showing possible energy hotspots along the polypeptide backbone.
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Affiliation(s)
- Harshita Rastogi
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India 110016
| | - Pramit K Chowdhury
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India 110016
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Gupta M, Chowdhury PK. Protein dynamics as a sensor for macromolecular crowding: Insights into mixed crowding. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2021.117969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Rastogi H, Chowdhury PK. Understanding enzyme behavior in a crowded scenario through modulation in activity, conformation and dynamics. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2021; 1869:140699. [PMID: 34298166 DOI: 10.1016/j.bbapap.2021.140699] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/08/2021] [Accepted: 07/19/2021] [Indexed: 01/25/2023]
Abstract
Macromolecular crowding, inside the physiological interior, modulates the energy landscape of biological macromolecules in multiple ways. Amongst these, enzymes occupy a special place and hence understanding the function of the same in the crowded interior is of utmost importance. In this study, we have investigated the manner in which the multidomain enzyme, AK3L1 (PDB ID: 1ZD8), an isoform of adenylate kinase, has its features affected in presence of commonly used crowders (PEG 8, Dextran 40, Dextran 70, and Ficoll 70). Michaelis Menten plots reveal that the crowders in general enhance the activity of the enzyme, with the Km and Vmax values showing significant variations. Ficoll 70, induced the maximum activity for AK3L1 at 100 g/L, beyond which the activity reduced. Ensemble FRET studies were performed to provide insights into the relative domain (LID and CORE) displacements in presence of the crowders. Solvation studies reveal that the protein matrix surrounding the probe CPM (7-diethylamino-3-(4-maleimido-phenyl)-4-methylcoumarin) gets restricted in presence of the crowders, with Ficoll 70 providing the maximum rigidity, the same being linked to the decrease in the activity of the enzyme. Through our multipronged approach, we have observed a distinct correlation between domain displacement, enzyme activity and associated dynamics. Thus, keeping in mind the complex nature of enzyme activity and the surrounding bath of dense soup that the biological entity remains immersed in, indeed more such approaches need to be undertaken to have a better grasp of the "enzymes in the crowd".
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Affiliation(s)
- Harshita Rastogi
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Pramit K Chowdhury
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India.
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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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Confinement Effects on Glass-Forming Aqueous Dimethyl Sulfoxide Solutions. Molecules 2020; 25:molecules25184127. [PMID: 32917011 PMCID: PMC7570821 DOI: 10.3390/molecules25184127] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 09/04/2020] [Accepted: 09/05/2020] [Indexed: 11/17/2022] Open
Abstract
Combining broadband dielectric spectroscopy and nuclear magnetic resonance studies, we analyze the reorientation dynamics and the translational diffusion associated with the glassy slowdown of the eutectic aqueous dimethyl sulfoxide solution in nano-sized confinements, explicitly, in silica pores with different diameters and in ficoll and lysozyme matrices at different concentrations. We observe that both rotational and diffusive dynamics are slower and more heterogeneous in the confinements than in the bulk but the degree of these effects depends on the properties of the confinement and differs for the components of the solution. For the hard and the soft matrices, the slowdown and the heterogeneity become more prominent when the size of the confinement is reduced. In addition, the dynamics are more retarded for dimethyl sulfoxide than for water, implying specific guest-host interactions. Moreover, we find that the temperature dependence of the reorientation dynamics and of the translational diffusion differs in severe confinements, indicating a breakdown of the Stokes–Einstein–Debye relation. It is discussed to what extent these confinement effects can be rationalized in the framework of core-shell models, which assume bulk-like and slowed-down motions in central and interfacial confinement regions, respectively.
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Palit S, He L, Hamilton WA, Yethiraj A, Yethiraj A. The effect of crowder charge in a model polymer–colloid system for macromolecular crowding: Polymer structure and dynamics. J Chem Phys 2017; 147:114902. [DOI: 10.1063/1.4986353] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [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
| | - Lilin He
- Biology and Soft Matter Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - William A. Hamilton
- Instrument and Source Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Arun Yethiraj
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
| | - Anand Yethiraj
- Department of Physics and Physical Oceanography, Memorial University, St. John’s, Newfoundland and Labrador A1B3X7, Canada
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