1
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Hengardi MT, Liang C, Madivannan K, Yang LK, Koduru L, Kanagasundaram Y, Arumugam P. Reversing the directionality of reactions between non-oxidative pentose phosphate pathway and glycolytic pathway boosts mycosporine-like amino acid production in Saccharomyces cerevisiae. Microb Cell Fact 2024; 23:121. [PMID: 38725068 PMCID: PMC11080194 DOI: 10.1186/s12934-024-02365-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 03/15/2024] [Indexed: 05/13/2024] Open
Abstract
BACKGROUND Mycosporine-like amino acids (MAAs) are a class of strongly UV-absorbing compounds produced by cyanobacteria, algae and corals and are promising candidates for natural sunscreen components. Low MAA yields from natural sources, coupled with difficulties in culturing its native producers, have catalyzed synthetic biology-guided approaches to produce MAAs in tractable microbial hosts like Escherichia coli, Saccharomyces cerevisiae and Corynebacterium glutamicum. However, the MAA titres obtained in these hosts are still low, necessitating a thorough understanding of cellular factors regulating MAA production. RESULTS To delineate factors that regulate MAA production, we constructed a shinorine (mycosporine-glycine-serine) producing yeast strain by expressing the four MAA biosynthetic enzymes from Nostoc punctiforme in Saccharomyces cerevisiae. We show that shinorine is produced from the pentose phosphate pathway intermediate sedoheptulose 7-phosphate (S7P), and not from the shikimate pathway intermediate 3-dehydroquinate (3DHQ) as previously suggested. Deletions of transaldolase (TAL1) and phosphofructokinase (PFK1/PFK2) genes boosted S7P/shinorine production via independent mechanisms. Unexpectedly, the enhanced S7P/shinorine production in the PFK mutants was not entirely due to increased flux towards the pentose phosphate pathway. We provide multiple lines of evidence in support of a reversed pathway between glycolysis and the non-oxidative pentose phosphate pathway (NOPPP) that boosts S7P/shinorine production in the phosphofructokinase mutant cells. CONCLUSION Reversing the direction of flux between glycolysis and the NOPPP offers a novel metabolic engineering strategy in Saccharomyces cerevisiae.
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Affiliation(s)
- Miselle Tiana Hengardi
- Agency for Science, Technology and Research (A*STAR), Singapore Institute of Food and Biotechnology Innovation, 31 Biopolis Way, Singapore, 138869, Singapore.
- NUS Graduate School for Integrated Sciences and Engineering, National University of Singapore, 21 Lower Kent Ridge Road, Singapore, 119077, Singapore.
| | - Cui Liang
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, 1 CREATE Way, Singapore, 138602, Singapore
| | - Keshiniy Madivannan
- Innovation & Enterprise, Agency for Science, Technology and Research (A*STAR), 1 Fusionopolis Way, Singapore, 138632, Singapore
| | - Lay Kien Yang
- Agency for Science, Technology and Research (A*STAR), Singapore Institute of Food and Biotechnology Innovation, 31 Biopolis Way, Singapore, 138869, Singapore
| | - Lokanand Koduru
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Singapore, 138673, Singapore
| | - Yoganathan Kanagasundaram
- Agency for Science, Technology and Research (A*STAR), Singapore Institute of Food and Biotechnology Innovation, 31 Biopolis Way, Singapore, 138869, Singapore
| | - Prakash Arumugam
- Agency for Science, Technology and Research (A*STAR), Singapore Institute of Food and Biotechnology Innovation, 31 Biopolis Way, Singapore, 138869, Singapore.
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore.
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2
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Grassmann G, Miotto M, Desantis F, Di Rienzo L, Tartaglia GG, Pastore A, Ruocco G, Monti M, Milanetti E. Computational Approaches to Predict Protein-Protein Interactions in Crowded Cellular Environments. Chem Rev 2024; 124:3932-3977. [PMID: 38535831 PMCID: PMC11009965 DOI: 10.1021/acs.chemrev.3c00550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 02/20/2024] [Accepted: 02/21/2024] [Indexed: 04/11/2024]
Abstract
Investigating protein-protein interactions is crucial for understanding cellular biological processes because proteins often function within molecular complexes rather than in isolation. While experimental and computational methods have provided valuable insights into these interactions, they often overlook a critical factor: the crowded cellular environment. This environment significantly impacts protein behavior, including structural stability, diffusion, and ultimately the nature of binding. In this review, we discuss theoretical and computational approaches that allow the modeling of biological systems to guide and complement experiments and can thus significantly advance the investigation, and possibly the predictions, of protein-protein interactions in the crowded environment of cell cytoplasm. We explore topics such as statistical mechanics for lattice simulations, hydrodynamic interactions, diffusion processes in high-viscosity environments, and several methods based on molecular dynamics simulations. By synergistically leveraging methods from biophysics and computational biology, we review the state of the art of computational methods to study the impact of molecular crowding on protein-protein interactions and discuss its potential revolutionizing effects on the characterization of the human interactome.
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Affiliation(s)
- Greta Grassmann
- Department
of Biochemical Sciences “Alessandro Rossi Fanelli”, Sapienza University of Rome, Rome 00185, Italy
- Center
for Life Nano & Neuro Science, Istituto
Italiano di Tecnologia, Rome 00161, Italy
| | - Mattia Miotto
- Center
for Life Nano & Neuro Science, Istituto
Italiano di Tecnologia, Rome 00161, Italy
| | - Fausta Desantis
- Center
for Life Nano & Neuro Science, Istituto
Italiano di Tecnologia, Rome 00161, Italy
- The
Open University Affiliated Research Centre at Istituto Italiano di
Tecnologia, Genoa 16163, Italy
| | - Lorenzo Di Rienzo
- Center
for Life Nano & Neuro Science, Istituto
Italiano di Tecnologia, Rome 00161, Italy
| | - Gian Gaetano Tartaglia
- Center
for Life Nano & Neuro Science, Istituto
Italiano di Tecnologia, Rome 00161, Italy
- Department
of Neuroscience and Brain Technologies, Istituto Italiano di Tecnologia, Genoa 16163, Italy
- Center
for Human Technologies, Genoa 16152, Italy
| | - Annalisa Pastore
- Experiment
Division, European Synchrotron Radiation
Facility, Grenoble 38043, France
| | - Giancarlo Ruocco
- Center
for Life Nano & Neuro Science, Istituto
Italiano di Tecnologia, Rome 00161, Italy
- Department
of Physics, Sapienza University, Rome 00185, Italy
| | - Michele Monti
- RNA
System Biology Lab, Department of Neuroscience and Brain Technologies, Istituto Italiano di Tecnologia, Genoa 16163, Italy
| | - Edoardo Milanetti
- Center
for Life Nano & Neuro Science, Istituto
Italiano di Tecnologia, Rome 00161, Italy
- Department
of Physics, Sapienza University, Rome 00185, Italy
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3
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Mersch SA, Bergman S, Sheets ED, Boersma AJ, Heikal AA. Two-photon excited-state dynamics of mEGFP-linker-mScarlet-I crowding biosensor in controlled environments. Phys Chem Chem Phys 2024; 26:3927-3940. [PMID: 38231116 DOI: 10.1039/d3cp04733d] [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: 01/18/2024]
Abstract
Macromolecular crowding affects many cellular processes such as diffusion, biochemical reaction kinetics, protein-protein interactions, and protein folding. Mapping the heterogeneous, dynamic crowding in living cells or tissues requires genetically encoded, site-specific, crowding sensors that are compatible with quantitative, noninvasive fluorescence micro-spectroscopy. Here, we carried out time-resolved 2P-fluorescence measurements of a new mEGFP-linker-mScarlet-I macromolecular crowding construct (GE2.3) to characterize its environmental sensitivity in biomimetic crowded solutions (Ficoll-70, 0-300 g L-1) via Förster resonance energy transfer (FRET) analysis. The 2P-fluorescence lifetime of the donor (mEGFP) was measured under magic-angle polarization, in the presence (intact) and absence (enzymatically cleaved) of the acceptor (mScarlet-I), as a function of the Ficoll-70 concentration. The FRET efficiency was used to quantify the sensitivity of GE2.3 to macromolecular crowding and to determine the environmental dependence of the mEGFP-mScarlet-I distance. We also carried out time-resolved 2P-fluorescence depolarization anisotropy to examine both macromolecular crowding and linker flexibility effects on GE2.3 rotational dynamics within the context of the Stokes-Einstein model as compared with theoretical predictions based on its molecular weight. These time-resolved 2P-fluorescence depolarization measurements and conformational population analyses of GE2.3 were also used to estimate the free energy gain upon the structural collapse in crowded environment. Our results further the development of a rational engineering design for bioenvironmental sensors without the interference of cellular autofluorescence. Additionally, these results in well-defined environments will inform our future in vivo studies of genetically encoded GE2.3 towards the mapping of the crowded intracellular environment under different physiological conditions.
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Affiliation(s)
- Sarah A Mersch
- Department of Chemistry and Biochemistry, Swenson College of Science and Engineering, University of Minnesota Duluth, Duluth, MN 55812, USA.
| | - Sarah Bergman
- Department of Chemistry and Biochemistry, Swenson College of Science and Engineering, University of Minnesota Duluth, Duluth, MN 55812, USA.
| | - Erin D Sheets
- Department of Chemistry and Biochemistry, Swenson College of Science and Engineering, University of Minnesota Duluth, Duluth, MN 55812, USA.
| | - Arnold J Boersma
- Cellular Protein Chemistry, Bijvoet Centre for Biomolecular Research, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Ahmed A Heikal
- Department of Chemistry and Biochemistry, Swenson College of Science and Engineering, University of Minnesota Duluth, Duluth, MN 55812, USA.
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4
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Hall D. Biophysical Reviews' "Meet the Editors Series": a profile of Damien Hall. Biophys Rev 2023; 15:1883-1896. [PMID: 38192343 PMCID: PMC10771549 DOI: 10.1007/s12551-023-01176-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/08/2023] [Indexed: 01/10/2024] Open
Abstract
This piece introduces Damien Hall, Chief Editor of the Biophysical Reviews journal since 2019. Currently working as an Assistant Professor at Kanazawa University, the author describes his association with the journal along with some parts of his family history and academic journey.
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Affiliation(s)
- Damien Hall
- WPI Nano Life Science Institute, Kanazawa University, Kakumamachi, Kanazawa, Ishikawa 920-1164 Japan
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5
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Zuev YF, Kusova AM, Sitnitsky AE. Protein translational diffusion as a way to detect intermolecular interactions. Biophys Rev 2023; 15:1111-1125. [PMID: 37975004 PMCID: PMC10643801 DOI: 10.1007/s12551-023-01108-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 07/26/2023] [Indexed: 11/19/2023] Open
Abstract
In this work, we analyze the information on the protein intermolecular interactions obtained from macromolecular diffusion. We have shown that the most hopeful results are given by our approach based on analysis of protein translational self-diffusion and collective diffusion obtained by dynamic light scattering and pulsed-field gradient NMR (PFG NMR) spectroscopy with the help of Vink's approach to analyze diffusion motion of particles by frictional formalism of non-equilibrium thermodynamics and the usage of the Derjaguin-Landau-Verwey-Overbeek (DLVO) theory of colloid particles interactions in electrolyte solutions. Early we have shown that integration of Vink's theory with DLVO provides a reliable basis for uniform interpreting of PFG NMR and DLS experiments on concentration dependence of diffusion coefficients. Basic details of theoretical and mathematical procedures and a broad analysis of experimental attestation of proposed conception on proteins of various structural form, size, and shape are presented. In the present review, the main capabilities of our approach obtain the details of intermolecular interactions of proteins with different shapes, internal structures, and mass. The universality of Vink's approach is experimentally shown, which gives the appropriate description of experimental results for proteins of complicated structure and shape.
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Affiliation(s)
- Yuriy F. Zuev
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Lobachevsky St., 2/31, 420111 Kazan, Russia
| | - Aleksandra M. Kusova
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Lobachevsky St., 2/31, 420111 Kazan, Russia
| | - Aleksandr E. Sitnitsky
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Lobachevsky St., 2/31, 420111 Kazan, Russia
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6
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Dos Santos ACF, Ahmadzadegan A, Ximenes E, Vlachos P, Ardekani A, Kapur S, Corvari V, Ladisch MR. Concentration-dependent diffusion of unlabeled protein within an in vitro hyaluronic acid matrix. Biotechnol Bioeng 2023. [PMID: 37466320 DOI: 10.1002/bit.28505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 06/16/2023] [Accepted: 07/10/2023] [Indexed: 07/20/2023]
Abstract
Diffusion and movement of subcutaneously injected biologics and high-concentration immunoglobulin G (IgG) therapeutics away from the injection site and through the subcutaneous (SC) tissue may be concentration dependent. This possibility was confirmed by in situ measurement of diffusion coefficients of unlabeled bovine IgG in phosphate-buffered saline within an in vitro hyaluronic acid matrix that represents the SC electrostatic environment. Diffusion decreased from 2.67 to 0.05 × 10-7 cm2 /s when IgG concentration increased from 25 to 73 mg/mL. The results demonstrated that in situ detection of unlabeled proteins within an in vitro SC environment provides another useful tool for the preclinical characterization of injectable biologics.
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Affiliation(s)
- Antonio C F Dos Santos
- Department of Agricultural and Biological Engineering, Laboratory of Renewable Resources Engineering, Purdue University, West Lafayette, Indiana, USA
| | - Adib Ahmadzadegan
- School of Mechanical Engineering, Purdue University, West Lafayette, Indiana, USA
| | - Eduardo Ximenes
- Department of Agricultural and Biological Engineering, Laboratory of Renewable Resources Engineering, Purdue University, West Lafayette, Indiana, USA
| | - Pavlos Vlachos
- School of Mechanical Engineering, Purdue University, West Lafayette, Indiana, USA
| | - Arezoo Ardekani
- School of Mechanical Engineering, Purdue University, West Lafayette, Indiana, USA
| | - Shiven Kapur
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana, USA
| | - Vince Corvari
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana, USA
| | - Michael R Ladisch
- Department of Agricultural and Biological Engineering, Laboratory of Renewable Resources Engineering, Purdue University, West Lafayette, Indiana, USA
- Eli Lilly, Indianapolis, Indiana, USA
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7
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Rivas G. Biophysical Reviews' "Meet the Editors Series"-a profile of Germán Rivas. Biophys Rev 2023; 15:151-156. [PMID: 37124917 PMCID: PMC10133429 DOI: 10.1007/s12551-023-01061-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/23/2023] [Indexed: 05/02/2023] Open
Abstract
German Rivas is an executive editor of the IUPAB Biophysical Reviews journal based in Spain. As the head of the Department of Structural and Chemical Biology at the Center for Biological Research (CIB) Margarita Salas (one of the largest research institutes devoted to life sciences of the Spanish National Research Council (CSIC)), he leads a research program aimed at understanding the structure function relationship of large macromolecular complexes (involved in bacterial cell division) when placed in physiologically complex and "crowded" media toward their reconstitution from the bottom up in cell-like compartments. In this "Meet the Editors'" piece, he briefly describes his research interests and history.
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Affiliation(s)
- Germán Rivas
- Systems Biochemistry Lab, Department of Structural and Chemical Biology, CIB Margarita Salas – CSIC, 28040 Madrid, Spain
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8
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Panigrahy S, Sahu R, Reddy SK, Nayar D. Structure, energetics and dynamics in crowded amino acid solutions: a molecular dynamics study. Phys Chem Chem Phys 2023; 25:5430-5442. [PMID: 36744506 DOI: 10.1039/d2cp04238j] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
A comprehensive understanding of crowding effects on biomolecular processes necessitates investigating the bulk thermodynamic and kinetic properties of the solutions with an accurate molecular representation of the crowded milieu. Recent studies have reparameterized the non-bonded dispersion interaction of solutes to precisely model intermolecular interactions, which would circumvent artificial aggregation as shown by the original force-fields. However, the performance of this reparameterization is yet to be assessed for concentrated crowded solutions in terms of investigating the hydration shell structure, energetics and dynamics. In this study, we perform molecular dynamics simulations of crowded aqueous solutions of five zwitterionic neutral amino acids (Gly, Ala, Thr, Pro, and Ser), mimicking the molecular crowding environment, using a modified AMBER ff99SB-ILDN force-field. We systematically examine and show that the reproducibility of the osmotic coefficients, density, viscosity and self-diffusivity of amino acids improves using the modified force-field in crowded concentrations. The modified force-field also improves the structuring of the solute solvation shells, solute interaction energy and convergence of tails of radial distribution functions, indicating reduction in the artificial aggregation. Our results also indicate that the hydrogen bonding network of water weakens and water molecules anomalously diffuse at small time scales in the crowded solutions. These results underscore the significance of examining the solution properties and anomalous hydration behaviour of water in crowded solutions, which have implications in shaping the structure and dynamics of biomolecules. The findings also illustrate the improvement in predicting bulk solution properties using the modified force-field, thereby providing an approach towards accurate modeling of crowded molecular solutions.
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Affiliation(s)
- Sibasankar Panigrahy
- Department of Materials Science and Engineering, Indian Institute of Technology Delhi, New Delhi 110016, India.
| | - Rahul Sahu
- Center for Computational and Data Sciences, Indian Institute of Technology Kharagpur, West Bengal 721302, India
| | - Sandeep K Reddy
- Center for Computational and Data Sciences, Indian Institute of Technology Kharagpur, West Bengal 721302, India
| | - Divya Nayar
- Department of Materials Science and Engineering, Indian Institute of Technology Delhi, New Delhi 110016, India.
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9
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Hvozd T, Kalyuzhnyi YV, Vlachy V. Behaviour of the model antibody fluid constrained by rigid spherical obstacles: Effects of the obstacle-antibody attraction. SOFT MATTER 2022; 18:9108-9117. [PMID: 36426679 DOI: 10.1039/d2sm01258h] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
This study investigates the behaviour of a fluid of monoclonal antibodies (mAbs) when trapped in a confinement represented by rigid spherical obstacles that attract antibodies. The antibody molecule is depicted as an assembly of seven hard spheres (7-bead model), organized to resemble a Y-shaped object. The model antibody has two Fab and one Fc domains located in the corners of letter Y. In this calculation, only the Fab-Fab and Fab-Fc attractive pairs of interactions are effective. The confinement is formed by the randomly distributed hard-spheres fixed in space. The spherical obstacles, besides the size exclusion, interact with beads of the antibody molecules via the Yukawa attractive potential. We applied the combination of the scaled particle theory, replica Ornstein-Zernike equations, Wertheim's thermodynamic perturbation approach and the Flory-Stockmayer theory to calculate: (i) the phase diagram of the liquid-liquid phase separation and the percolation threshold, (ii) the cluster size distributions, and (iii) the second virial coefficient of the protein fluid distributed among the obstacles. All these quantities were calculated as functions of the strength of the attraction between the monoclonal antibodies, and the monoclonal antibodies and obstacles. The conclusion is that while the hard-sphere obstacles decrease the critical density and the critical temperature of the mAbs fluid, the effect of the protein-obstacle attraction is more complex. Adding an attractive potential to the obstacle-mAbs interaction first increases the wideness of the T*-ρ envelope. However, with the further increase of the obstacle-mAbs attraction intensity, we observe reversal of the effect, the T*-ρ curves become narrower. At some point, depending on the obstacle-mAbs interaction, the situation is observed where two different temperatures have the same fluid density (re-entry point). In all the cases shown here the critical point decreases below the value for the neat fluid, but the behaviour with respect to an increase of the strength of the obstacle-mAbs attraction is not monotonic. Yet another interesting phenomenon, known in the literature as an approach toward the "empty liquid" state, is observed. The stability of the "protein droplets", formed by the liquid-liquid phase separation, depends on their local environment and temperature.
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Affiliation(s)
- Taras Hvozd
- Institute for Condensed Matter Physics, National Academy of Sciences of Ukraine, Svientsitskoho 1, Lviv, Ukraine.
| | - Yurij V Kalyuzhnyi
- Institute for Condensed Matter Physics, National Academy of Sciences of Ukraine, Svientsitskoho 1, Lviv, Ukraine.
| | - Vojko Vlachy
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, SI-1000 Ljubljana, Slovenia.
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10
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Parray ZA, Naqvi AAT, Ahanger IA, Shahid M, Ahmad F, Hassan MI, Islam A. Measuring Structural Changes in Cytochrome c under Crowded Conditions Using In Vitro and In Silico Approaches. Polymers (Basel) 2022; 14:polym14224808. [PMID: 36432935 PMCID: PMC9692323 DOI: 10.3390/polym14224808] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 07/26/2022] [Accepted: 07/28/2022] [Indexed: 11/11/2022] Open
Abstract
It is known from in vitro studies that macromolecular crowding in the cell effects protein structure, stability and function; but predictive studies are relatively unexplored. There are few reports where the effect of various crowder mixtures has been exploited to discern their combined effect on the structural stability of proteins. These studies are more significant because their effect can mimicked with in vivo conditions, where the environment is heterogeneous. Effects of two crowders, polyethylene glycol (PEG 400 Da), and its monomer ethylene glycol (EG) alone and in mixture on the structural stability of cytochrome c (cyt c) were determined using various spectroscopic and bioinformatics tools. The main conclusions of our study are (i) the monomer EG has a kosmotropic effect on the protein (stabilizes the protein), and has no significant effect on the tertiary structure; (ii) PEG 400 destabilizes the structure as well as the stability of the protein; and (iii) EG counteracts the destabilizing effect of PEG 400. From this investigation, it seems evident that proteins may fold or unfold in the crowded environment of the cell where various interactions assist them to maintain their structure for their functions. Bioinformatics approaches were also used to support all of the in vitro observations. Cyt c is functional protein; if the structure of the protein is modulated due to change in the environment its nature of function will also change. Our research addresses the question by modulating the environment around the protein, and the macromolecule (protein) conformation dynamics and interaction study via in vitro and in silico approaches which indirectly compares with that of the environment in-cellular milieu, which is highly crowded.
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Affiliation(s)
- Zahoor Ahmad Parray
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
- Department of Chemistry, Indian Institute of Technology Delhi, IIT Campus, Hauz Khas, New Delhi 110016, India
| | - Ahmad Abu Turab Naqvi
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Ishfaq Ahmad Ahanger
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
- Department of Chemistry, Biochemistry and Forensic Science, Amity School of Applied Sciences, Amity University Haryana, Gurugram 122413, India
| | - Mohammad Shahid
- Department of Basic Medical Sciences, College of Medicine, Prince Sattam Bin Abdulaziz University, Al Kharj 11942, Saudi Arabia
| | - Faizan Ahmad
- Department of Biochemistry, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi 110062, India
| | - Md. Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
- Correspondence: ; Tel.: +91-9312812007
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11
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J-aggregation of 5, 10, 15, 20-tetraphenyl-21H, 23H-porphinetetrasulfonic acid in a molecular crowding environment simulated using dextran. ANAL SCI 2022; 38:1505-1512. [PMID: 36050568 DOI: 10.1007/s44211-022-00185-5] [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: 06/30/2022] [Accepted: 08/23/2022] [Indexed: 11/01/2022]
Abstract
In a molecular crowding environment, different thermodynamics is often observed in a dilute solution. One such example is the promotion of the formation of amyloids, which are causal agents of Alzheimer's disease. Although a considerable number of molecular crowding studies have been reported, its effect remains unclear. In this study, we investigated a J-aggregation of a porphyrin derivative, 5, 10, 15, 20-tetraphenyl-21H,23H-porphinetetrasulfonic acid (TPPS), in a molecular crowding environment simulated by dextran (Dex) in HClO4, HCl, and NaCl solutions. The changes in the number of monomers in the J-aggregate (n) with the concentration of Dex (CDex) depended on the type of solution. No change in n was observed in the NaCl solution, which indicated that the Dex solution did not affect the J-aggregation because of the ionic strength effect. In the HCl solution, the aggregation behavior changed with the pH. Further, at a low pH, the electrostatic interactions promoted J-aggregation by the volume exclusion of Dex, while the aggregation was suppressed at a high pH owing to steric hindrance. A different aggregation mechanism, involving the hydrogen bonding between NH in the center of the TPPS macrocyclic frame and the SO3H and ClO4- functional groups, was responsible for the J-aggregation in the HClO4 solution. Moreover, the n value increased owing to the volume exclusion effect. We expect that this study will be useful for further elucidation of the molecular crowding effect.
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12
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Nasralla M, Laurent H, Baker DL, Ries ME, Dougan L. A study of the interaction between TMAO and urea in water using NMR spectroscopy. Phys Chem Chem Phys 2022; 24:21216-21222. [PMID: 36040138 DOI: 10.1039/d2cp02475f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Trimethylamine N-oxide (TMAO) and urea are small organic biological molecules. While TMAO is known as a protective osmolyte that promotes the native form of biomolecules, urea is a denaturant. An understanding of the impact of TMAO and urea on water structure may aid in uncovering the molecular mechanisms that underlie this activity. Here we investigate binary solutions of TMAO-water, urea-water and ternary solutions of TMAO-urea-water using NMR spectroscopy at 300 K. An enhancement of the total hydrogen bonding in water was found upon the addition of TMAO and this effect was neutralised by a mole ratio of 1-part TMAO to 4-parts urea. Urea was found to have little effect on the strength of water's hydrogen bonding network and the dynamics of water molecules. Evidence was found for a weak interaction between TMAO and urea. Taken together, these results suggest that TMAO's function as a protective osmolyte, and its counteraction of urea, may be driven by the strength of its hydrogen bond interactions with water, and by a secondary reinforcement of water's own hydrogen bond network. They also suggest that the TMAO-urea complex forms through the donation of a hydrogen bond by urea.
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Affiliation(s)
- Mazin Nasralla
- School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, UK.
| | - Harrison Laurent
- School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, UK.
| | - Daniel L Baker
- School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, UK.
| | - Michael E Ries
- School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, UK.
| | - Lorna Dougan
- School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, UK.
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13
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Miyagawa A, Komatsu H, Nagatomo S, Nakatani K. Acid Dissociation Behavior of 8-Hydroxyquinoline-5-Sulfonic Acid in Molecular Crowding Environment Modeled Using Polyethylene Glycol. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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14
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15
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Basu M, Mishra PP. Kineto-Mechanistic Investigation of Effect of Macromolecular Crowding on the Breathing of DNA Bubble. J Phys Chem B 2022; 126:1375-1387. [PMID: 35143192 DOI: 10.1021/acs.jpcb.1c08206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Macromolecular crowding along with hydrogen bonding or stacking interactions and hydration reportedly has enormous repercussions on elementary biochemical processes, such as the folding of proteins or nucleic acids involving the stability of DNA base pairing. By using the mismatch-induced DNA bubble as a mesoscopic model, the complex interplay of macromolecular crowding on the dynamical fluctuations at the bubble region within the thermodynamic limit has been monitored using single-molecule fluorescence resonance energy transfer (sm-FRET). These single-molecule experimental results have been further corroborated using physical models such as "scaled particle theory" (SPT) and "Gaussian cloud model" (GCM), to predict the biological activity of DNA. The two-state fluctuation of the DNA bubble has been visualized as a function of the nature, size, and concentration of the crowder. The influence of crowders on the DNA conformation has been investigated with the help of the m-factor, the eccentricity, and the kinetic and thermodynamic parameters without any prior assumption. The clear effect of crowding on the dynamics of such a simple biomolecular system emphasizes the power of single-molecule methods and the dependency of the radius of gyration of the co-solute as well as the preferential interaction with the crowder on the distinct conformational states adopted by the bubble. This study provides an idea and hypothesizes the preferential propensity of the DNA bubble to adopt a conformation with the single-stranded domains being far apart, independent of the crowder size, that may be beneficial for efficient recognition by proteins for an uninterrupted procession of the biological process of the central dogma.
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Affiliation(s)
- Manali Basu
- Single Molecule Biophysics Lab, Chemical Sciences Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India.,Homi Bhaba National Institute, Mumbai, Maharashtra 400094, India
| | - Padmaja Prasad Mishra
- Single Molecule Biophysics Lab, Chemical Sciences Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India.,Homi Bhaba National Institute, Mumbai, Maharashtra 400094, India
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16
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Miyagawa A, Komatsu H, Nagatomo S, Nakatani K. Effect of Molecular Crowding on Complexation of Metal Ions and 8-Quinolinol-5-Sulfonic Acid. J Phys Chem B 2021; 125:9853-9859. [PMID: 34410719 DOI: 10.1021/acs.jpcb.1c05851] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The effect of molecular crowding on macromolecular reactions has been revealed by many researchers. In this study, we investigate the complexation of metal ions (Zn, Co, and Cd) with 8-quinolinol-5-sulfonic acid as a model of small-molecular reactions in molecular crowding. The complexation constants for 1:1, 1:2, and total complexation in the presence of polyethylene glycol (PEG, a molecular crowding reagent) are evaluated based on the increase in the reactant activity by volume exclusion and the decrease in the water activity due to the change in osmotic pressure. All complexation constants are enhanced by increasing the concentration of PEG. Its mechanisms differ for 1:1, 1:2, and total complexation. The 1:1 complexation is promoted only by the influence of the water activity, while the reactant and water activities influence the increase in the 1:2 complexation constant. Increasing the molecular weight of PEG further increases the complexation constants, as dehydration of the complex is promoted by a higher hydration number of PEG. Because this study gives the fundamental knowledge for the protein-metal interaction, in which solvation is an important factor, in molecular crowding, it provides new insights into molecular crowding studies and should attract the attention of a broad spectrum of biochemistry researchers.
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Affiliation(s)
- Akihisa Miyagawa
- Department of Chemistry, Faculty of Pure and Applied Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8571, Japan
| | - Hiroyuki Komatsu
- Department of Chemistry, Faculty of Pure and Applied Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8571, Japan
| | - Shigenori Nagatomo
- Department of Chemistry, Faculty of Pure and Applied Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8571, Japan
| | - Kiyoharu Nakatani
- Department of Chemistry, Faculty of Pure and Applied Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8571, Japan
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17
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Odahara T, Odahara Y. Association of protein–detergent particles in the presence of polymers comprised of different degrees of polymerization of oxyethylene subunits. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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18
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Sugimoto N, Endoh T, Takahashi S, Tateishi-Karimata H. Chemical Biology of Double Helical and Non-Double Helical Nucleic Acids: “To B or Not To B, That Is the Question”. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2021. [DOI: 10.1246/bcsj.20210131] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 17-1-20 Minatojima-minamimachi, Kobe, Hyogo 650-0047, Japan
- Graduate School of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 17-1-20 Minatojima-minamimachi, Kobe, Hyogo 650-0047, Japan
| | - Tamaki Endoh
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 17-1-20 Minatojima-minamimachi, Kobe, Hyogo 650-0047, Japan
| | - Shuntaro Takahashi
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 17-1-20 Minatojima-minamimachi, Kobe, Hyogo 650-0047, Japan
| | - Hisae Tateishi-Karimata
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 17-1-20 Minatojima-minamimachi, Kobe, Hyogo 650-0047, Japan
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19
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Sahu R, Nayar D. Crowding effects on water-mediated hydrophobic interactions. J Chem Phys 2021; 155:024903. [PMID: 34266250 DOI: 10.1063/5.0054410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Understanding the fundamental forces such as hydrophobic interactions in a crowded intracellular environment is necessary to comprehensively decipher the mechanisms of protein folding and biomolecular self-assemblies. The widely accepted entropic depletion view of crowding effects primarily attributes biomolecular compaction to the solvent excluded volume effects exerted by the "inert" crowders, neglecting their soft interactions with the biomolecule. In this study, we examine the effects of chemical nature and soft attractive energy of crowders on the water-mediated hydrophobic interaction between two non-polar neopentane solutes using molecular dynamics simulations. The crowded environment is modeled using dipeptides composed of polar and non-polar amino acids of varying sizes. The results show that amongst the non-polar crowders, Leu2 strengthens the hydrophobic interactions significantly, whereas the polar and small-sized non-polar crowders do not show significant strengthening. Distinct underlying thermodynamic driving forces are illustrated where the small-sized crowders drive hydrophobic interaction via a classic entropic depletion effect and the bulky crowders strengthen it by preferential interaction with the solute. A crossover from energy-stabilized solvent-separated pair to entropy-stabilized contact pair state is observed in the case of bulky non-polar (Leu2) and polar (Lys2) crowders. The influence of solute-crowder energy in affecting the dehydration energy penalty is found to be crucial for determining the neopentane association. The findings demonstrate that along with the entropic (size) effects, the energetic effects also play a crucial role in determining hydrophobic association. The results can be extended and have implications in understanding the impact of protein crowding with varying chemistry in modulating the protein free energy landscapes.
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Affiliation(s)
- Rahul Sahu
- Centre for Computational and Data Sciences, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal 721302, India
| | - Divya Nayar
- Centre for Computational and Data Sciences, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal 721302, India
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20
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Modeling protein association from homogeneous to mixed environments: A reaction-diffusion dynamics approach. J Mol Graph Model 2021; 107:107936. [PMID: 34139641 DOI: 10.1016/j.jmgm.2021.107936] [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: 01/06/2021] [Revised: 03/30/2021] [Accepted: 04/26/2021] [Indexed: 11/21/2022]
Abstract
Protein-protein association in vivo occur in a crowded and complex environment. Theoretical models based on hard-core repulsion predict stabilization of the product under crowded conditions. Soft interactions, on the contrary, can either stabilize or destabilize the product formation. Here we modeled protein association in presence of crowders of varying size, shape, interaction potential and used different mixing parameters for constituent crowders to study the influence on the association reaction. It was found that size is a more dominant factor in crowder-induced stabilization than the shape. Furthermore, in a mixture of crowders having different sizes but identical interaction potential, the change of free energy is additive of the free energy changes produced by individual crowders. However, the free energy change is not additive if two crowders of same size interact via different interaction potentials. These findings provide a systematic understanding of crowding influences in heterogeneous medium.
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21
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Suda K, Suematsu A, Akiyama R. Lateral depletion effect on two-dimensional ordering of bacteriorhodopsins in a lipid bilayer: A theoretical study based on a binary hard-disk model. J Chem Phys 2021; 154:204904. [PMID: 34241177 DOI: 10.1063/5.0044399] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The 2D ordering of bacteriorhodopsins in a lipid bilayer was studied using a binary hard-disk model. The phase diagrams were calculated taking into account the lateral depletion effects. The critical concentrations of the protein ordering for monomers and trimers were obtained from the phase diagrams. The critical concentration ratio agreed well with the experiment when the repulsive core interaction between the depletants, namely, lipids, was taken into account. The results suggest that the depletion effect plays an important role in the association behaviors of transmembrane proteins.
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Affiliation(s)
- Keiju Suda
- Department of Chemistry, Graduate School of Science, Kyushu University, Fukuoka 819-0395, Japan
| | - Ayumi Suematsu
- Faculty of Science and Engineering, Kyushu Sangyo University, Fukuoka 813-8503, Japan
| | - Ryo Akiyama
- Department of Chemistry, Graduate School of Science, Kyushu University, Fukuoka 819-0395, Japan
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22
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Hasan S, Naeem A. The modulation of structural stability of horseradish peroxidase as a consequence of macromolecular crowding. J Mol Recognit 2021; 34:e2902. [PMID: 34013591 DOI: 10.1002/jmr.2902] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 03/24/2021] [Accepted: 04/05/2021] [Indexed: 11/07/2022]
Abstract
Macromolecular crowding plays an inevitable role in all biological processes influencing association, conformation, and other characteristics of proteins. Present study is based on the effect of macromolecular crowding on structure of horseradish peroxidase (HRP) enzyme. Concentration-dependent conformational changes induced by crowding agents, dextran 70 and polyethylene glycol (PEG)-4000, were monitored employing a range of biophysical techniques. The intrinsic fluorescence spectra showed transition of protein from native to unfolded state. Marked increase in 8-Anilino-1-naphthalene-sulphonoic acid and Thioflavin T fluorescence indicated presence of non-native moieties with 80 mg/mL dextran. Enhanced absorbance in turbidity, Soret, and Congo red in corroboration with scattering intensity at 350nm results revealed incidence of HRP aggregates. A new peak around 218 nm in CD spectra pointed towards change in secondary structure towards β-sheets. Significant loss of enzyme activity upon structural disruption was seen. Comet assay demonstrated DNA damage and genotoxic nature of HRP aggregates, supporting spectroscopic, and fluorescence results. The normalized results were obtained with 120 mg/mL PEG-4000 close to that of native HRP implying no disruptive effect on structure. It can be hypothesized that macromolecular crowding is a vital element, which can have diverse effects. In this study, dextran 70 was observed to have pro-aggregatory effect while enhanced stability of native enzyme was witnessed with PEG. Hence, it can be stated that PEG has potentially better crowder as it helps retain the native enzyme structure. Routine addition of crowding agents is recommended if biological molecules are to be studied under more physiologically appropriate environments.
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Affiliation(s)
- Samra Hasan
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, India
| | - Aabgeena Naeem
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, India
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23
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Structural Refolding and Thermal Stability of Myoglobin in the Presence of Mixture of Crowders: Importance of Various Interactions for Protein Stabilization in Crowded Conditions. Molecules 2021; 26:molecules26092807. [PMID: 34068693 PMCID: PMC8126177 DOI: 10.3390/molecules26092807] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 04/26/2021] [Accepted: 04/27/2021] [Indexed: 11/16/2022] Open
Abstract
The intracellular environment is overcrowded with a range of molecules (small and large), all of which influence protein conformation. As a result, understanding how proteins fold and stay functional in such crowded conditions is essential. Several in vitro experiments have looked into the effects of macromolecular crowding on different proteins. However, there are hardly any reports regarding small molecular crowders used alone and in mixtures to observe their effects on the structure and stability of the proteins, which mimics of the cellular conditions. Here we investigate the effect of different mixtures of crowders, ethylene glycol (EG) and its polymer polyethylene glycol (PEG 400 Da) on the structural and thermal stability of myoglobin (Mb). Our results show that monomer (EG) has no significant effect on the structure of Mb, while the polymer disrupts its structure and decreases its stability. Conversely, the additive effect of crowders showed structural refolding of the protein to some extent. Moreover, the calorimetric binding studies of the protein showed very weak interactions with the mixture of crowders. Usually, we can assume that soft interactions induce structural perturbations while exclusion volume effects stabilize the protein structure; therefore, we hypothesize that under in vivo crowded conditions, both phenomena occur and maintain the stability and function of proteins.
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24
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Jia TZ, Caudan M, Mamajanov I. Origin of Species before Origin of Life: The Role of Speciation in Chemical Evolution. Life (Basel) 2021; 11:154. [PMID: 33671365 PMCID: PMC7922636 DOI: 10.3390/life11020154] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 02/11/2021] [Accepted: 02/15/2021] [Indexed: 11/17/2022] Open
Abstract
Speciation, an evolutionary process by which new species form, is ultimately responsible for the incredible biodiversity that we observe on Earth every day. Such biodiversity is one of the critical features which contributes to the survivability of biospheres and modern life. While speciation and biodiversity have been amply studied in organismic evolution and modern life, it has not yet been applied to a great extent to understanding the evolutionary dynamics of primitive life. In particular, one unanswered question is at what point in the history of life did speciation as a phenomenon emerge in the first place. Here, we discuss the mechanisms by which speciation could have occurred before the origins of life in the context of chemical evolution. Specifically, we discuss that primitive compartments formed before the emergence of the last universal common ancestor (LUCA) could have provided a mechanism by which primitive chemical systems underwent speciation. In particular, we introduce a variety of primitive compartment structures, and associated functions, that may have plausibly been present on early Earth, followed by examples of both discriminate and indiscriminate speciation affected by primitive modes of compartmentalization. Finally, we discuss modern technologies, in particular, droplet microfluidics, that can be applied to studying speciation phenomena in the laboratory over short timescales. We hope that this discussion highlights the current areas of need in further studies on primitive speciation phenomena while simultaneously proposing directions as important areas of study to the origins of life.
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Affiliation(s)
- Tony Z. Jia
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan;
- Blue Marble Space Institute of Science, 1001 4th Ave., Suite 3201, Seattle, WA 98154, USA
| | - Melina Caudan
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan;
| | - Irena Mamajanov
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan;
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25
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Glycation of Plant Proteins Via Maillard Reaction: Reaction Chemistry, Technofunctional Properties, and Potential Food Application. Foods 2021; 10:foods10020376. [PMID: 33572281 PMCID: PMC7915956 DOI: 10.3390/foods10020376] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 02/02/2021] [Accepted: 02/05/2021] [Indexed: 12/19/2022] Open
Abstract
Plant proteins are being considered to become the most important protein source of the future, and to do so, they must be able to replace the animal-derived proteins currently in use as techno-functional food ingredients. This poses challenges because plant proteins are oftentimes storage proteins with a high molecular weight and low water solubility. One promising approach to overcome these limitations is the glycation of plant proteins. The covalent bonding between the proteins and different carbohydrates created via the initial stage of the Maillard reaction can improve the techno-functional characteristics of these proteins without the involvement of potentially toxic chemicals. However, compared to studies with animal-derived proteins, glycation studies on plant proteins are currently still underrepresented in literature. This review provides an overview of the existing studies on the glycation of the major groups of plant proteins with different carbohydrates using different preparation methods. Emphasis is put on the reaction conditions used for glycation as well as the modifications to physicochemical properties and techno-functionality. Different applications of these glycated plant proteins in emulsions, foams, films, and encapsulation systems are introduced. Another focus lies on the reaction chemistry of the Maillard reaction and ways to harness it for controlled glycation and to limit the formation of undesired advanced glycation products. Finally, challenges related to the controlled glycation of plant proteins to improve their properties are discussed.
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26
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Taylor MP, Vinci C, Suzuki R. Effects of macromolecular crowding on the folding of a polymer chain: A Wang-Landau simulation study. J Chem Phys 2020; 153:174901. [PMID: 33167653 DOI: 10.1063/5.0025640] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
A flexible polymer chain in the presence of inert macromolecular crowders will experience a loss of configurational entropy due to the crowder excluded volume. This entropy reduction will be most pronounced in good solvent conditions where the chain assumes an expanded coil conformation. For polymers that undergo a folding transition from a coil to a compact ordered state, as is the case for many globular proteins, macromolecular crowding is expected to stabilize the folded state and thereby shift the transition location. Here, we study such entropic stabilization effects for a tangent square-well sphere chain (monomer diameter σ) in the presence of hard-sphere (HS) crowders (diameter D ≥ σ). We use the Wang-Landau simulation algorithm to construct the density of states for this chain in a crowded environment and are thus able to directly compute the reduction in configurational entropy due to crowding. We study both a chain that undergoes all-or-none folding directly from the coil state and a chain that folds via a collapsed-globule intermediate state. In each case, we find an increase in entropic stabilization for the compact states with an increase in crowder density and, for fixed crowder density, with a decrease in crowder size (concentrated, small crowders have the largest effect). The crowder significantly reduces the average size for the unfolded states while having a minimal effect on the size of the folded states. In the athermal limit, our results directly provide the confinement free energy due to crowding for a HS chain in a HS solvent.
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Affiliation(s)
- Mark P Taylor
- Department of Physics, Hiram College, Hiram, Ohio 44234, USA
| | | | - Ryogo Suzuki
- Department of Physics, Hiram College, Hiram, Ohio 44234, USA
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Consequence of macromolecular crowding on aggregation propensity and structural stability of haemoglobin under glycating conditions. Int J Biol Macromol 2020; 162:1044-1053. [PMID: 32553973 DOI: 10.1016/j.ijbiomac.2020.06.127] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 05/31/2020] [Accepted: 06/12/2020] [Indexed: 12/20/2022]
Abstract
Cell interiors are extremely congested with biological macromolecules exerting crowding effect, influencing various physiognomies of protein life. Present work deals with effect of crowding on folding behaviour of haemoglobin (Hb) under glycating conditions. Macromolecular crowding was mimicked by concentrated solutions of dextran 70. Hb with 0.2 M fructose and ribose was incubated separately for 96 h in dilute and crowded solution to analyse conformational changes. Reduced intrinsic and ANS fluorescence, decreased Soret absorbance, enhanced turbidity, browning of protein, red shift in ThT and Congo red spectra significantly unveiled protein aggregation. FTIR and CD results revealed transition from α-helix to β-sheets confirming aggregation. Transmission electron microscopy exhibited incidence of aggregates. Macromolecular crowding was witnessed to defend conformational stability of native Hb under stress condition at 100 mg/ml dextran, noticeably indicating deceleration of aggregation. Stabilising effect of crowding was marginally better in fructosylated Hb than with ribose due to difference in their glycation potential. Contrarily, in over-crowded solution where dextran concentration was 500 mg/ml, heightened aggregation was perceived implying concentration dependant, dual nature of macromolecular crowding. The novelty of this study lies in idea of considering macromolecular crowding as a key player in regulation of protein stability which was safely ignored previously.
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28
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Hvozd T, Kalyuzhnyi YV, Vlachy V. Aggregation, liquid-liquid phase separation, and percolation behaviour of a model antibody fluid constrained by hard-sphere obstacles. SOFT MATTER 2020; 16:8432-8443. [PMID: 32812624 DOI: 10.1039/d0sm01014f] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
This study is concerned with the behaviour of proteins within confinement created by hard-sphere obstacles. An individual antibody molecule is depicted as an assembly of seven hard spheres, organized to resemble a Y-shaped (on average) antibody (7-bead model) protein. For comparison with other studies we, in one case, model the protein as a hard sphere decorated by three short-range attractive sites. The antibody has two Fab and one Fc domains located in the corners of the letter Y. In this calculation, only the Fab-Fab and Fab-Fc attractive pair interactions are possible. The confinement is formed by the randomly distributed hard-sphere obstacles fixed in space. Aside from size exclusion, the obstacles do not interact with antibodies, but they affect the protein-protein correlation. We used a combination of the scaled-particle theory, Wertheim's thermodynamic perturbation theory and the Flory-Stockmayer theory to calculate: (i) the second virial coefficient of the protein fluid, (ii) the percolation threshold, (iii) cluster size distributions, and (iv) the liquid-liquid phase separation as a function of the strength of the various pair interactions of the protein and the model parameters, such as protein concentration and the packing fraction of obstacles. The conclusion is that hard-sphere obstacles strongly decrease the critical density and also, but to a much lesser extent, the critical temperature. Also, the confinement enhances clustering, making the percolating region broader. The effect depends on the model parameters, such as the packing fraction of obstacles η0, the inter-site interaction strength εIJ, and the ratio between the size of the obstacle σ0 and the size of one bead of the model antibody σhs; the value of this ratio is varied here from 2 to 5. Interestingly, at low to moderate packing fractions of obstacles, the second virial coefficient first slightly decreases (destabilization), and the slope depends on the observation temperature, but then at higher values of η0 it increases. The calculated values of the second virial coefficient also depend on the size of the obstacles.
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Affiliation(s)
- Taras Hvozd
- Institute for Condensed Matter Physics, National Academy of Sciences of Ukraine, Svientsitskoho 1, Lviv, Ukraine.
| | - Yurij V Kalyuzhnyi
- Institute for Condensed Matter Physics, National Academy of Sciences of Ukraine, Svientsitskoho 1, Lviv, Ukraine. and Faculty of Science, J. E. Purkinje University, 400 96 Ústí nad Labem, Czech Republic
| | - Vojko Vlachy
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, SI-1000 Ljubljana, Slovenia.
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29
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Liquid-Liquid Phase Separation in Crowded Environments. Int J Mol Sci 2020; 21:ijms21165908. [PMID: 32824618 PMCID: PMC7460619 DOI: 10.3390/ijms21165908] [Citation(s) in RCA: 129] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 08/13/2020] [Indexed: 12/23/2022] Open
Abstract
Biomolecular condensates play a key role in organizing cellular fluids such as the cytoplasm and nucleoplasm. Most of these non-membranous organelles show liquid-like properties both in cells and when studied in vitro through liquid–liquid phase separation (LLPS) of purified proteins. In general, LLPS of proteins is known to be sensitive to variations in pH, temperature and ionic strength, but the role of crowding remains underappreciated. Several decades of research have shown that macromolecular crowding can have profound effects on protein interactions, folding and aggregation, and it must, by extension, also impact LLPS. However, the precise role of crowding in LLPS is far from trivial, as most condensate components have a disordered nature and exhibit multiple weak attractive interactions. Here, we discuss which factors determine the scope of LLPS in crowded environments, and we review the evidence for the impact of macromolecular crowding on phase boundaries, partitioning behavior and condensate properties. Based on a comparison of both in vivo and in vitro LLPS studies, we propose that phase separation in cells does not solely rely on attractive interactions, but shows important similarities to segregative phase separation.
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30
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Collagen hydrogel confinement of Amyloid-β (Aβ) accelerates aggregation and reduces cytotoxic effects. Acta Biomater 2020; 112:164-173. [PMID: 32464268 DOI: 10.1016/j.actbio.2020.05.030] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 05/18/2020] [Accepted: 05/19/2020] [Indexed: 01/09/2023]
Abstract
Alzheimer's disease (AD) is the most common form of dementia and is associated with the accumulation of amyloid-β (Aβ), a peptide whose aggregation has been associated with neurotoxicity. Drugs targeting Aβ have shown great promise in 2D in vitro models and mouse models, yet preclinical and clinical trials for AD have been highly disappointing. We propose that current in vitro culture systems for discovering and developing AD drugs have significant limitations; specifically, that Aβ aggregation is vastly different in these 2D cultures carried out on flat plastic or glass substrates vs. in a 3D environment, such as brain tissue, where Aβ confinement alters aggregation kinetics and thermodynamics. In this work, we identified attenuation of Aβ cytotoxicity in 3D hydrogel culture compared to 2D cell culture. We investigated Aβ structure and aggregation in solution vs. hydrogel using Transmission Electron Microscopy (TEM), Fluorescence Correlation Spectroscopy (FCS), and Thioflavin T (ThT) assays. Our results reveal that the equilibrium is shifted to stable extended β-sheet (ThT positive) aggregates in hydrogels and away from the relatively unstable/unstructured presumed toxic oligomeric Aβ species in solution. Volume exclusion imparted by hydrogel confinement stabilizes unfolded, presumably toxic species, promoting stable extended β-sheet fibrils. STATEMENT OF SIGNIFICANCE: Alzheimer's disease (AD) is a devastating disease and has been studied for over 100 years. Yet, no cure exists and only 5 prescription drugs are FDA-approved to temporarily treat the AD symptoms of declining brain functions related to thinking and memory. Why don't we have more effective treatments to cure AD or relieve AD symptoms? We propose that current culture methods based upon cells cultured on flat, stiff substrates have significant limitations for discovering and developing AD drugs. This study provides strong evidence that AD drugs should be tested in 3D culture systems as a step along the development pathway towards new, more effective drugs to treat AD.
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31
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Davis CM, Gruebele M. Cytoskeletal Drugs Modulate Off-Target Protein Folding Landscapes Inside Cells. Biochemistry 2020; 59:2650-2659. [PMID: 32567840 DOI: 10.1021/acs.biochem.0c00299] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The dynamic cytoskeletal network of microtubules and actin filaments can be disassembled by drugs. Cytoskeletal drugs work by perturbing the monomer-polymer equilibrium, thus changing the size and number of macromolecular crowders inside cells. Changes in both crowding and nonspecific surface interactions ("sticking") following cytoskeleton disassembly can affect the protein stability, structure, and function directly or indirectly by changing the fluidity of the cytoplasm and altering the crowding and sticking of other macromolecules in the cytoplasm. The effect of cytoskeleton disassembly on protein energy landscapes inside cells has yet to be observed. Here we have measured the effect of several cytoskeletal drugs on the folding energy landscape of two FRET-labeled proteins with different in vitro sensitivities to macromolecular crowding. Phosphoglycerate kinase (PGK) was previously shown to be more sensitive to crowding, whereas variable major protein-like sequence expressed (VlsE) was previously shown to be more sensitive to sticking. The in-cell effects of drugs that depolymerize either actin filaments (cytochalasin D and latrunculin B) or microtubules (nocodazole and vinblastine) were compared. The crowding sensor protein CrH2-FRET verified that cytoskeletal drugs decrease the extent of crowding inside cells despite also reducing the overall cell volume. The decreased compactness and folding stability of PGK could be explained by the decreased extent of crowding induced by these drugs. VlsE's opposite response to the drugs shows that depolymerization of the cytoskeleton also changes sticking in the cellular milieu. Our results demonstrate that perturbation of the monomer-polymer cytoskeletal equilibrium, for example, during natural cell migration or stresses from drug treatment, has off-target effects on the energy landscapes of proteins in the cell.
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Simpson LW, Good TA, Leach JB. Protein folding and assembly in confined environments: Implications for protein aggregation in hydrogels and tissues. Biotechnol Adv 2020; 42:107573. [PMID: 32512220 DOI: 10.1016/j.biotechadv.2020.107573] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 05/03/2020] [Accepted: 05/30/2020] [Indexed: 12/20/2022]
Abstract
In the biological milieu of a cell, soluble crowding molecules and rigid confined environments strongly influence whether the protein is properly folded, intrinsically disordered proteins assemble into distinct phases, or a denatured or aggregated protein species is favored. Such crowding and confinement factors act to exclude solvent volume from the protein molecules, resulting in an increased local protein concentration and decreased protein entropy. A protein's structure is inherently tied to its function. Examples of processes where crowding and confinement may strongly influence protein function include transmembrane protein dimerization, enzymatic activity, assembly of supramolecular structures (e.g., microtubules), nuclear condensates containing transcriptional machinery, protein aggregation in the contexts of disease and protein therapeutics. Historically, most protein structures have been determined from pure, dilute protein solutions or pure crystals. However, these are not the environments in which these proteins function. Thus, there has been an increased emphasis on analyzing protein structure and dynamics in more "in vivo-like" environments. Complex in vitro models using hydrogel scaffolds to study proteins may better mimic features of the in vivo environment. Therefore, analytical techniques need to be optimized for real-time analysis of proteins within hydrogel scaffolds.
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Affiliation(s)
- Laura W Simpson
- Department of Chemical, Biochemical and Environmental Engineering, University of Maryland Baltimore County, Eng 314, 1000 Hilltop Circle, Baltimore, MD 21250, USA
| | - Theresa A Good
- Division of Molecular and Cellular Biosciences, National Science Foundation, 2415 Eisenhower Ave, Alexandria, VA 22314, USA
| | - Jennie B Leach
- Department of Chemical, Biochemical and Environmental Engineering, University of Maryland Baltimore County, Eng 314, 1000 Hilltop Circle, Baltimore, MD 21250, USA.
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Smith R, Lebeaupin T, Juhász S, Chapuis C, D'Augustin O, Dutertre S, Burkovics P, Biertümpfel C, Timinszky G, Huet S. Poly(ADP-ribose)-dependent chromatin unfolding facilitates the association of DNA-binding proteins with DNA at sites of damage. Nucleic Acids Res 2020; 47:11250-11267. [PMID: 31566235 PMCID: PMC6868358 DOI: 10.1093/nar/gkz820] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 09/01/2019] [Accepted: 09/26/2019] [Indexed: 12/19/2022] Open
Abstract
The addition of poly(ADP-ribose) (PAR) chains along the chromatin fiber due to PARP1 activity regulates the recruitment of multiple factors to sites of DNA damage. In this manuscript, we investigated how, besides direct binding to PAR, early chromatin unfolding events controlled by PAR signaling contribute to recruitment to DNA lesions. We observed that different DNA-binding, but not histone-binding, domains accumulate at damaged chromatin in a PAR-dependent manner, and that this recruitment correlates with their affinity for DNA. Our findings indicate that this recruitment is promoted by early PAR-dependent chromatin remodeling rather than direct interaction with PAR. Moreover, recruitment is not the consequence of reduced molecular crowding at unfolded damaged chromatin but instead originates from facilitated binding to more exposed DNA. These findings are further substantiated by the observation that PAR-dependent chromatin remodeling at DNA lesions underlies increased DNAse hypersensitivity. Finally, the relevance of this new mode of PAR-dependent recruitment to DNA lesions is demonstrated by the observation that reducing the affinity for DNA of both CHD4 and HP1α, two proteins shown to be involved in the DNA-damage response, strongly impairs their recruitment to DNA lesions.
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Affiliation(s)
- Rebecca Smith
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, F- 35000 Rennes, France
| | - Théo Lebeaupin
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, F- 35000 Rennes, France
| | - Szilvia Juhász
- MTA SZBK Lendület DNA damage and nuclear dynamics research group, Institute of Genetics, Biological Research Center, 6276 Szeged, Hungary
| | - Catherine Chapuis
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, F- 35000 Rennes, France
| | - Ostiane D'Augustin
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, F- 35000 Rennes, France
| | - Stéphanie Dutertre
- Univ Rennes, CNRS, Inserm, BIOSIT (Biologie, Santé, Innovation Technologique de Rennes) - UMS 3480, US 018, F-35000 Rennes, France
| | - Peter Burkovics
- Laboratory of Replication and Genome Stability, Institute of Genetics, Biological Research Center, 6276 Szeged, Hungary
| | - Christian Biertümpfel
- Department of Structural Cell Biology, Molecular Mechanisms of DNA Repair, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Gyula Timinszky
- MTA SZBK Lendület DNA damage and nuclear dynamics research group, Institute of Genetics, Biological Research Center, 6276 Szeged, Hungary
| | - Sébastien Huet
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, F- 35000 Rennes, France
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34
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Andrews SS. Effects of surfaces and macromolecular crowding on bimolecular reaction rates. Phys Biol 2020; 17:045001. [DOI: 10.1088/1478-3975/ab7f51] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Rønnow SR, Dabbagh RQ, Genovese F, Nanthakumar CB, Barrett VJ, Good RB, Brockbank S, Cruwys S, Jessen H, Sorensen GL, Karsdal MA, Leeming DJ, Sand JMB. Prolonged Scar-in-a-Jar: an in vitro screening tool for anti-fibrotic therapies using biomarkers of extracellular matrix synthesis. Respir Res 2020; 21:108. [PMID: 32381012 PMCID: PMC7203825 DOI: 10.1186/s12931-020-01369-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2019] [Accepted: 04/22/2020] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Idiopathic pulmonary fibrosis (IPF) is a rapidly progressing disease with challenging management. To find novel effective therapies, better preclinical models are needed for the screening of anti-fibrotic compounds. Activated fibroblasts drive fibrogenesis and are the main cells responsible for the accumulation of extracellular matrix (ECM). Here, a prolonged Scar-in-a-Jar assay was combined with clinically validated biochemical markers of ECM synthesis to evaluate ECM synthesis over time. To validate the model as a drug screening tool for novel anti-fibrotic compounds, two approved compounds for IPF, nintedanib and pirfenidone, and a compound in development, omipalisib, were tested. METHODS Primary human lung fibroblasts from healthy donors were cultured for 12 days in the presence of ficoll and were stimulated with TGF-β1 with or without treatment with an ALK5/TGF-β1 receptor kinase inhibitor (ALK5i), nintedanib, pirfenidone or the mTOR/PI3K inhibitor omipalisib (GSK2126458). Biomarkers of ECM synthesis were evaluated over time in cell supernatants using ELISAs to assess type I, III, IV, V and VI collagen formation (PRO-C1, PRO-C3, PRO-C4, PRO-C5, PRO-C6), fibronectin (FBN-C) deposition and α-smooth muscle actin (α-SMA) expression. RESULTS TGF-β1 induced synthesis of PRO-C1, PRO-C6 and FBN-C as compared with unstimulated fibroblasts at all timepoints, while PRO-C3 and α-SMA levels were not elevated until day 8. Elevated biomarkers were reduced by suppressing TGF-β1 signalling with ALK5i. Nintedanib and omipalisib were able to reduce all biomarkers induced by TGF-β1 in a concentration dependent manner, while pirfenidone had no effect on α-SMA. CONCLUSIONS TGF-β1 stimulated synthesis of type I, III and VI collagen, fibronectin and α-SMA but not type IV or V collagen. Synthesis was increased over time, although temporal profiles differed, and was modulated pharmacologically by ALK5i, nintedanib, pirfenidone and omipalisib. This prolonged 12-day Scar-in-a-Jar assay utilising biochemical markers of ECM synthesis provides a useful screening tool for novel anti-fibrotic compounds.
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Affiliation(s)
- Sarah Rank Rønnow
- Nordic Bioscience A/S, Herlev, Herlev Hovedgade 205-207, DK-2730, Herlev, Denmark
- Department of Cancer and Inflammation Research, Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Rand Qais Dabbagh
- Nordic Bioscience A/S, Herlev, Herlev Hovedgade 205-207, DK-2730, Herlev, Denmark
| | - Federica Genovese
- Nordic Bioscience A/S, Herlev, Herlev Hovedgade 205-207, DK-2730, Herlev, Denmark
| | | | - Vikki J Barrett
- Department of Fibrosis DPU, Respiratory TA, GlaxoSmithKline, Stevenage, UK
| | - Robert B Good
- Department of Fibrosis DPU, Respiratory TA, GlaxoSmithKline, Stevenage, UK
| | - Sarah Brockbank
- Innovative Medicines Unit, Grünenthal Innovation, Aachen, Germany
- Present Address: Medicines Discovery Catapult, Alderley Edge, Cheshire, UK
| | - Simon Cruwys
- Innovative Medicines Unit, Grünenthal Innovation, Aachen, Germany
- Present Address: TherapeutAix AG, Aachen, Germany
| | - Henrik Jessen
- Nordic Bioscience A/S, Herlev, Herlev Hovedgade 205-207, DK-2730, Herlev, Denmark
| | - Grith Lykke Sorensen
- Department of Cancer and Inflammation Research, Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Morten Asser Karsdal
- Nordic Bioscience A/S, Herlev, Herlev Hovedgade 205-207, DK-2730, Herlev, Denmark
| | - Diana Julie Leeming
- Nordic Bioscience A/S, Herlev, Herlev Hovedgade 205-207, DK-2730, Herlev, Denmark
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36
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Rupprecht N, Vural DC. Depletion force between disordered linear macromolecules. Phys Rev E 2020; 101:022607. [PMID: 32168718 DOI: 10.1103/physreve.101.022607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 01/29/2020] [Indexed: 06/10/2023]
Abstract
When two macromolecules come very near in a fluid, the surrounding molecules, having finite volume, are less likely to get in between. This leads to a pressure difference manifesting as an entropic attraction, called depletion force. Here we calculate the density profile of liquid molecules surrounding a disordered rigid macromolecules modeled as a random arrangement of hard spheres on a linear backbone. We analytically determine the position dependence of the depletion force between two such disordered molecules by calculating the free energy of the system. We then use molecular dynamics simulations to obtain the depletion force between stiff disordered polymers as well as flexible ones and compare the two against each other. We also show how the disorder averaging can be handled starting from the inhomogenous reference interaction site model equations.
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Affiliation(s)
- Nathaniel Rupprecht
- Department of Physics, University of Notre Dame, South Bend, Indiana 46556, USA
| | - Dervis Can Vural
- Department of Physics, University of Notre Dame, South Bend, Indiana 46556, USA
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37
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Gotlib IY, Victorov AI. Association kinetics and equilibrium in solutions of cross-associating chains that contain inactive spacers. POLYMER 2020. [DOI: 10.1016/j.polymer.2019.122085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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38
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Honegger P, Steinhauser O. The protein-water nuclear Overhauser effect (NOE) as an indirect microscope for molecular surface mapping of interaction patterns. Phys Chem Chem Phys 2019; 22:212-222. [PMID: 31799520 DOI: 10.1039/c9cp04752b] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
In this computational study, the intermolecular solute-solvent Nuclear Overhauser Effect (NOE) of the model protein ubiquitin in different chemical environments (free, bound to a partner protein and encapsulated) is investigated. Short-ranged NOE observables such as the NOE/ROE ratio reveal hydration phenomena on absolute timescales such as fast hydration sites and slow water clefts. We demonstrate the ability of solute-solvent NOE differences measured of the same protein in different chemical environments to reveal hydration changes on the relative timescale. The resulting NOE/ROE-surface maps are shown to be a central key for analyzing biologically relevant chemical influences such as complexation and confinement: the presence of a complexing macromolecule or a confining surface wall modulates the water mobility in the vicinity of the probe protein, hence revealing which residues of said protein are proximate to the foreign interface and which are chemically unaffected. This way, hydration phenomena can serve to indirectly map the precise influence (position) of other molecules or interfaces onto the protein surface. This proposed one-protein many-solvents approach may offer experimental benefits over classical one-protein other-protein pseudo-intermolecular transient NOEs. Furthermore, combined influences such as complexation and confinement may exert non-additive influences on the protein compared to a reference state. We offer a mathematical method to disentangle the influence of these two different chemical environments.
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Affiliation(s)
- Philipp Honegger
- University of Vienna, Faculty of Chemistry, Department of Computational Biological Chemistry, Währingerstr. 17, A-1090 Vienna, Austria.
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39
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More than a Confinement: “Soft” and “Hard” Enzyme Entrapment Modulates Biological Catalyst Function. Catalysts 2019. [DOI: 10.3390/catal9121024] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Catalysis makes chemical and biochemical reactions kinetically accessible. From a technological point of view, organic, inorganic, and biochemical catalysis is relevant for several applications, from industrial synthesis to biomedical, material, and food sciences. A heterogeneous catalyst, i.e., a catalyst confined in a different phase with respect to the reagents’ phase, requires either its physical confinement in an immobilization matrix or its physical adsorption on a surface. In this review, we will focus on the immobilization of biological catalysts, i.e., enzymes, by comparing hard and soft immobilization matrices and their effect on the modulation of the catalysts’ function. Indeed, unlike smaller molecules, the catalytic activity of protein catalysts depends on their structure, conformation, local environment, and dynamics, properties that can be strongly affected by the immobilization matrices, which, therefore, not only provide physical confinement, but also modulate catalysis.
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40
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Köster T, Henning P, Uhrmacher AM. Potential based, spatial simulation of dynamically nested particles. BMC Bioinformatics 2019; 20:607. [PMID: 31775608 PMCID: PMC6880518 DOI: 10.1186/s12859-019-3092-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 09/10/2019] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND To study cell biological phenomena which depend on diffusion, active transport processes, or the locations of species, modeling and simulation studies need to take space into account. To describe the system as a collection of discrete objects moving and interacting in continuous space, various particle-based reaction diffusion simulators for cell-biological system have been developed. So far the focus has been on particles as solid spheres or points. However, spatial dynamics might happen at different organizational levels, such as proteins, vesicles or cells with interrelated dynamics which requires spatial approaches that take this multi-levelness of cell biological systems into account. RESULTS Based on the perception of particles forming hollow spheres, ML-Force contributes to the family of particle-based simulation approaches: in addition to excluded volumes and forces, it also supports compartmental dynamics and relating dynamics between different organizational levels explicitly. Thereby, compartmental dynamics, e.g., particles entering and leaving other particles, and bimolecular reactions are modeled using pair-wise potentials (forces) and the Langevin equation. In addition, forces that act independently of other particles can be applied to direct the movement of particles. Attributes and the possibility to define arbitrary functions on particles, their attributes and content, to determine the results and kinetics of reactions add to the expressiveness of ML-Force. Its implementation comprises a rudimentary rule-based embedded domain-specific modeling language for specifying models and a simulator for executing models continuously. Applications inspired by cell biological models from literature, such as vesicle transport or yeast growth, show the value of the realized features. They facilitate capturing more complex spatial dynamics, such as the fission of compartments or the directed movement of particles, and enable the integration of non-spatial intra-compartmental dynamics as stochastic events. CONCLUSIONS By handling all dynamics based on potentials (forces) and the Langevin equation, compartmental dynamics, such as dynamic nesting, fusion and fission of compartmental structures are handled continuously and are seamlessly integrated with traditional particle-based reaction-diffusion dynamics within the cell. Thereby, attributes and arbitrary functions allow to flexibly describe diverse spatial phenomena, and relate dynamics across organizational levels. Also they prove crucial in modeling intra-cellular or intra-compartmental dynamics in a non-spatial manner, and, thus, to abstract from spatial dynamics, on demand which increases the range of multi-compartmental processes that can be captured.
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Affiliation(s)
- Till Köster
- Institute of Computer Science, University of Rostock, Albert-Einstein-Straße 22, Rostock, 18059 Germany
| | - Philipp Henning
- Institute of Computer Science, University of Rostock, Albert-Einstein-Straße 22, Rostock, 18059 Germany
| | - Adelinde M. Uhrmacher
- Institute of Computer Science, University of Rostock, Albert-Einstein-Straße 22, Rostock, 18059 Germany
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41
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Perez CP, Elmore DE, Radhakrishnan ML. Computationally Modeling Electrostatic Binding Energetics in a Crowded, Dynamic Environment: Physical Insights from a Peptide–DNA System. J Phys Chem B 2019; 123:10718-10734. [DOI: 10.1021/acs.jpcb.9b09478] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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42
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Hall D. On the nature of the optimal form of the holdase-type chaperone stress response. FEBS Lett 2019; 594:43-66. [PMID: 31432502 DOI: 10.1002/1873-3468.13580] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 08/12/2019] [Accepted: 08/14/2019] [Indexed: 11/08/2022]
Abstract
The holdase paradigm of chaperone action involves preferential binding by the chaperone to the unfolded protein state, thereby preventing it from either, associating with other unstable proteins (to form large dysfunctional aggregates), or being degraded by the proteolytic machinery of the cell/organism. In this paper, we examine the necessary physical constraints imposed upon the holdase chaperone response in a cell-like environment and use these limitations to comment on the likely nature of the optimal form of chaperone response in vivo.
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Affiliation(s)
- Damien Hall
- Laboratory of Biochemistry and Genetics, NIDDK, NIH, Bethesda, MD, USA.,Institute for Protein Research, Osaka University, Suita, Osaka, Japan
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43
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Carbohydrate-Based Macromolecular Crowding-Induced Stabilization of Proteins: Towards Understanding the Significance of the Size of the Crowder. Biomolecules 2019; 9:biom9090477. [PMID: 31547256 PMCID: PMC6769620 DOI: 10.3390/biom9090477] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 09/02/2019] [Accepted: 09/06/2019] [Indexed: 11/23/2022] Open
Abstract
There are a large number of biomolecules that are accountable for the extremely crowded intracellular environment, which is totally different from the dilute solutions, i.e., the idealized conditions. Such crowded environment due to the presence of macromolecules of different sizes, shapes, and composition governs the level of crowding inside a cell. Thus, we investigated the effect of different sizes and shapes of crowders (ficoll 70, dextran 70, and dextran 40), which are polysaccharide in nature, on the thermodynamic stability, structure, and functional activity of two model proteins using UV-Vis spectroscopy and circular dichroism techniques. We observed that (a) the extent of stabilization of α-lactalbumin and lysozyme increases with the increasing concentration of the crowding agents due to the excluded volume effect and the small-sized and rod-shaped crowder, i.e., dextran 40 resulted in greater stabilization of both proteins than dextran 70 and ficoll 70; (b) structure of both the proteins remains unperturbed; and (c) enzymatic activity of lysozyme decreases with the increasing concentration of the crowder.
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44
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Fan C, Lim LKP, Loh SQ, Ying Lim KY, Upton Z, Leavesley D. Application of “macromolecular crowding” in vitro to investigate the naphthoquinones shikonin, naphthazarin and related analogues for the treatment of dermal scars. Chem Biol Interact 2019; 310:108747. [DOI: 10.1016/j.cbi.2019.108747] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 06/14/2019] [Accepted: 07/10/2019] [Indexed: 01/05/2023]
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45
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Enzymatic activity of human immunodeficiency virus type 1 protease in crowded solutions. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2019; 48:685-689. [PMID: 31463540 PMCID: PMC6742607 DOI: 10.1007/s00249-019-01392-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 06/27/2019] [Accepted: 08/12/2019] [Indexed: 11/02/2022]
Abstract
Cells are crowded with various macromolecules and metabolites, which affect biochemical reactions in many ways, from the diffusion of substrates to catalytic activities of enzymes. We herein investigated the proteolytic activity of the human immunodeficiency virus type 1 protease (HIV-1 PR) under non-crowded and crowded conditions. The latter environment was mimicked with various (poly)ethylene glycol molecules as crowding agents. We found that these crowding agents affect the kinetic parameters of the HIV-1 PR catalyzed reaction by increasing the Michaelis-Menten constant and decreasing the maximum velocity. The influence of crowding was concentration dependent. We explain this effect by the dynamics of the HIV-1 PR flexible flaps that cover the peptide substrate binding site and are crucial for enzyme activity, and by a possibly slower substrate-enzyme association time in the crowded conditions.
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46
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Trajkovski M, Endoh T, Tateishi-Karimata H, Ohyama T, Tanaka S, Plavec J, Sugimoto N. Pursuing origins of (poly)ethylene glycol-induced G-quadruplex structural modulations. Nucleic Acids Res 2019; 46:4301-4315. [PMID: 29648656 PMCID: PMC5934638 DOI: 10.1093/nar/gky250] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 03/28/2018] [Indexed: 01/18/2023] Open
Abstract
Molecular crowding conditions provided by high concentration of cosolutes are utilized for characterization of biomolecules in cell-mimicking environment and development of drug-delivery systems. In this context, (poly)ethylene glycols are often used for studying non-canonical DNA structures termed G-quadruplexes, which came into focus by emerging structural biology findings and new therapeutic drug design approaches. Recently, several reports were made arguing against using (poly)ethylene glycols in role of molecular crowding agents due to their direct impact on DNA G-quadruplex stability and topology. However, the available data on structural details underlying DNA interaction is very scarce and thus limits in-depth comprehension. Herein, structural and thermodynamic analyses were strategically combined to assess G-quadruplex-cosolute interactions and address previously reported variances regarding the driving forces of G-rich DNA structural transformations under molecular crowding conditions. With the use of complementary (CD, NMR and UV) spectroscopic methods and model approach we characterized DNA G-quadruplex in the presence of the smallest and one of the largest typically used (poly)ethylene glycols. Dehydration effect is the key contributor to ethylene-glycol-induced increased stability of the G-quadruplex, which is in the case of the large cosolute mainly guided by the subtle direct interactions between PEG 8000 and the outer G-quartet regions.
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Affiliation(s)
- Marko Trajkovski
- Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, Ljubljana, SI-1000, Slovenia
| | - Tamaki Endoh
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Hisae Tateishi-Karimata
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Tatsuya Ohyama
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Shigenori Tanaka
- Department of Computational Science, Graduate School of System Informatics, Kobe University, 1-1, Rokkodai, Nada-ku, Kobe 657-8501, Japan
| | - Janez Plavec
- Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, Ljubljana, SI-1000, Slovenia.,EN→FIST Centre of Excellence, Trg OF 13, SI-1000 Ljubljana, Slovenia.,Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, p. p. 537, SI-1000 Ljubljana, Slovenia
| | - Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan.,Graduate School of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-Minamimachi, Kobe 650-0047, Japan
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47
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Guin D, Gruebele M. Weak Chemical Interactions That Drive Protein Evolution: Crowding, Sticking, and Quinary Structure in Folding and Function. Chem Rev 2019; 119:10691-10717. [PMID: 31356058 DOI: 10.1021/acs.chemrev.8b00753] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
In recent years, better instrumentation and greater computing power have enabled the imaging of elusive biomolecule dynamics in cells, driving many advances in understanding the chemical organization of biological systems. The focus of this Review is on interactions in the cell that affect both biomolecular stability and function and modulate them. The same protein or nucleic acid can behave differently depending on the time in the cell cycle, the location in a specific compartment, or the stresses acting on the cell. We describe in detail the crowding, sticking, and quinary structure in the cell and the current methods to quantify them both in vitro and in vivo. Finally, we discuss protein evolution in the cell in light of current biophysical evidence. We describe the factors that drive protein evolution and shape protein interaction networks. These interactions can significantly affect the free energy, ΔG, of marginally stable and low-population proteins and, due to epistasis, direct the evolutionary pathways in an organism. We finally conclude by providing an outlook on experiments to come and the possibility of collaborative evolutionary biology and biophysical efforts.
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Affiliation(s)
- Drishti Guin
- Department of Chemistry , University of Illinois , Urbana , Illinois 61801 , United States
| | - Martin Gruebele
- Department of Chemistry , University of Illinois , Urbana , Illinois 61801 , United States.,Department of Physics , University of Illinois , Urbana , Illinois 61801 , United States.,Center for Biophysics and Quantitative Biology , University of Illinois , Urbana , Illinois 61801 , United States
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48
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Nakamura Y, Arai S, Kinoshita M, Yoshimori A, Akiyama R. Reduced density profile of small particles near a large particle: Results of an integral equation theory with an accurate bridge function and a Monte Carlo simulation. J Chem Phys 2019; 151:044506. [PMID: 31370562 DOI: 10.1063/1.5100040] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Solute-solvent reduced density profiles of hard-sphere fluids were calculated by using several integral equation theories for liquids. The traditional closures, Percus-Yevick (PY) and the hypernetted-chain (HNC) closures, as well as the theories with bridge functions, Verlet, Duh-Henderson, and Kinoshita (named MHNC), were used for the calculation. In this paper, a one-solute hard-sphere was immersed in a one-component hard-sphere solvent and various size ratios were examined. The profiles between the solute and solvent particles were compared with those calculated by Monte Carlo simulations. The profiles given by the integral equations with the bridge functions were much more accurate than those calculated by conventional integral equation theories, such as the Ornstein-Zernike (OZ) equation with the PY closure. The accuracy of the MHNC-OZ theory was maintained even when the particle size ratio of solute to solvent was 50. For example, the contact values were 5.7 (Monte Carlo), 5.6 (MHNC), 7.8 (HNC), and 4.5 (PY), and the first minimum values were 0.48 (Monte Carlo), 0.46 (MHNC), 0.54 (HNC), and 0.40 (PY) when the packing fraction of the hard-sphere solvent was 0.38 and the size ratio was 50. The asymptotic decay and the oscillation period for MHNC-OZ were also very accurate, although those given by the HNC-OZ theory were somewhat faster than those obtained by Monte Carlo simulations.
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Affiliation(s)
- Yuka Nakamura
- Department of Engineering Science, The University of Electro-Communications, Tokyo 182-8585, Japan
| | - Shota Arai
- Department of Physics, Niigata University, Niigata 950-2181, Japan
| | | | - Akira Yoshimori
- Department of Physics, Niigata University, Niigata 950-2181, Japan
| | - Ryo Akiyama
- Department of Chemistry, Kyushu University, Fukuoka 819-0395, Japan
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49
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Junker NO, Vaghefikia F, Albarghash A, Höfig H, Kempe D, Walter J, Otten J, Pohl M, Katranidis A, Wiegand S, Fitter J. Impact of Molecular Crowding on Translational Mobility and Conformational Properties of Biological Macromolecules. J Phys Chem B 2019; 123:4477-4486. [PMID: 31059260 DOI: 10.1021/acs.jpcb.9b01239] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Effects of molecular crowding on structural and dynamical properties of biological macromolecules do depend on the concentration of crowding agents but also on the molecular mass and the structural compactness of the crowder molecules. By employing fluorescence correlation spectroscopy (FCS), we investigated the translational mobility of several biological macromolecules ranging from 17 kDa to 2.7 MDa. Polyethylene glycol and Ficoll polymers of different molecular masses were used in buffer solutions to mimic a crowded environment. The reduction in translational mobility of the biological tracer molecules was analyzed as a function of crowder volume fractions and was generally more pronounced in PEG as compared to Ficoll solutions. For several crowding conditions, we observed a molecular sieving effect, in which the diffusion coefficient of larger tracer molecules is reduced to a larger extent than predicted by the Stokes-Einstein relation. By employing a FRET-based biosensor, we also showed that a multiprotein complex is significantly compacted in the presence of macromolecular crowders. Importantly, with respect to sensor in vivo applications, ligand concentration determining sensors would need a crowding specific calibration in order to deliver correct cytosolic ligand concentration.
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Affiliation(s)
- Niklas O Junker
- I. Physikalisches Institut (IA) , RWTH Aachen University , 52074 Aachen , Germany
| | - Farzaneh Vaghefikia
- I. Physikalisches Institut (IA) , RWTH Aachen University , 52074 Aachen , Germany
| | - Alyazan Albarghash
- I. Physikalisches Institut (IA) , RWTH Aachen University , 52074 Aachen , Germany
| | - Henning Höfig
- I. Physikalisches Institut (IA) , RWTH Aachen University , 52074 Aachen , Germany
| | - Daryan Kempe
- I. Physikalisches Institut (IA) , RWTH Aachen University , 52074 Aachen , Germany
| | - Julia Walter
- I. Physikalisches Institut (IA) , RWTH Aachen University , 52074 Aachen , Germany
| | | | | | | | - Simone Wiegand
- Physikalische Chemie , Universität zu Köln , 50923 Köln , Germany
| | - Jörg Fitter
- I. Physikalisches Institut (IA) , RWTH Aachen University , 52074 Aachen , Germany
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Petersen CF, Franosch T. Anomalous transport in the soft-sphere Lorentz model. SOFT MATTER 2019; 15:3906-3913. [PMID: 30998231 DOI: 10.1039/c9sm00442d] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The sensitivity of anomalous transport in crowded media to the form of the inter-particle interactions is investigated through computer simulations. We extend the highly simplified Lorentz model towards realistic natural systems by modeling the interactions between the tracer and the obstacles with a smooth potential. We find that the anomalous transport at the critical point happens to be governed by the same universal exponent as for hard exclusion interactions, although the mechanism of how narrow channels are probed is rather different. The scaling behavior of simulations close to the critical point confirm this exponent. Our result indicates that the simple Lorentz model may be applicable to describing the fundamental properties of long-range transport in real crowded environments.
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Affiliation(s)
- Charlotte F Petersen
- Institut für Theoretische Physik, Leopold-Franzens-Universität Innsbruck, Technikerstraße 21A, A-6020 Innsbruck, Austria.
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