Macromolecular Crowding Studies of Amino Acids Using NMR Diffusion Measurements and Molecular Dynamics Simulations
Molecular crowding occurs when the total concentration of macromolecular species in a solution is so high that a considerable proportion of the volume is physically occupied and therefore not accessible to other molecules. This results in significant changes in the solution properties of the molecul...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2015-02-01
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| Series: | Frontiers in Physics |
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| Online Access: | http://journal.frontiersin.org/Journal/10.3389/fphy.2015.00001/full |
| _version_ | 1819229488314056704 |
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| author | Amninder S Virk Timothy eStait-Gardner Scott A Willis Allan M Torres William S Price |
| author_facet | Amninder S Virk Timothy eStait-Gardner Scott A Willis Allan M Torres William S Price |
| author_sort | Amninder S Virk |
| collection | DOAJ |
| description | Molecular crowding occurs when the total concentration of macromolecular species in a solution is so high that a considerable proportion of the volume is physically occupied and therefore not accessible to other molecules. This results in significant changes in the solution properties of the molecules in such systems. Macromolecular crowding is ubiquitous in biological systems due to the generally high intracellular protein concentrations. The major hindrance to understanding crowding is the lack of direct comparison of experimental data with theoretical or simulated data. Self-diffusion is sensitive to changes in the molecular weight and shape of the diffusing species, and the available diffusion space (i.e., diffusive obstruction). Consequently, diffusion measurements are a direct means for probing crowded systems including the self-association of molecules. In this work, nuclear magnetic resonance measurements of the self-diffusion of four amino acids (glycine, alanine, valine and phenylalanine) up to their solubility limit in water were compared directly with molecular dynamics simulations. The experimental data were then analyzed using various models of aggregation and obstruction. Both experimental and simulated data revealed that the diffusion of both water and the amino acids were sensitive to the amino acid concentration. The direct comparison of the simulated and experimental data afforded greater insights into the aggregation and obstruction properties of each amino acid. |
| first_indexed | 2024-12-23T11:13:58Z |
| format | Article |
| id | doaj.art-17652c4bc4014fafbe82d83f4c6a2c8f |
| institution | Directory Open Access Journal |
| issn | 2296-424X |
| language | English |
| last_indexed | 2024-12-23T11:13:58Z |
| publishDate | 2015-02-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Physics |
| spelling | doaj.art-17652c4bc4014fafbe82d83f4c6a2c8f2022-12-21T17:49:16ZengFrontiers Media S.A.Frontiers in Physics2296-424X2015-02-01310.3389/fphy.2015.00001122044Macromolecular Crowding Studies of Amino Acids Using NMR Diffusion Measurements and Molecular Dynamics SimulationsAmninder S Virk0Timothy eStait-Gardner1Scott A Willis2Allan M Torres3William S Price4University of Western SydneyUniversity of Western SydneyUniversity of Western SydneyUniversity of Western SydneyUniversity of Western SydneyMolecular crowding occurs when the total concentration of macromolecular species in a solution is so high that a considerable proportion of the volume is physically occupied and therefore not accessible to other molecules. This results in significant changes in the solution properties of the molecules in such systems. Macromolecular crowding is ubiquitous in biological systems due to the generally high intracellular protein concentrations. The major hindrance to understanding crowding is the lack of direct comparison of experimental data with theoretical or simulated data. Self-diffusion is sensitive to changes in the molecular weight and shape of the diffusing species, and the available diffusion space (i.e., diffusive obstruction). Consequently, diffusion measurements are a direct means for probing crowded systems including the self-association of molecules. In this work, nuclear magnetic resonance measurements of the self-diffusion of four amino acids (glycine, alanine, valine and phenylalanine) up to their solubility limit in water were compared directly with molecular dynamics simulations. The experimental data were then analyzed using various models of aggregation and obstruction. Both experimental and simulated data revealed that the diffusion of both water and the amino acids were sensitive to the amino acid concentration. The direct comparison of the simulated and experimental data afforded greater insights into the aggregation and obstruction properties of each amino acid.http://journal.frontiersin.org/Journal/10.3389/fphy.2015.00001/fullAlanineAmino AcidsCrowdingDiffusionGlycinePhenylalanine |
| spellingShingle | Amninder S Virk Timothy eStait-Gardner Scott A Willis Allan M Torres William S Price Macromolecular Crowding Studies of Amino Acids Using NMR Diffusion Measurements and Molecular Dynamics Simulations Frontiers in Physics Alanine Amino Acids Crowding Diffusion Glycine Phenylalanine |
| title | Macromolecular Crowding Studies of Amino Acids Using NMR Diffusion Measurements and Molecular Dynamics Simulations |
| title_full | Macromolecular Crowding Studies of Amino Acids Using NMR Diffusion Measurements and Molecular Dynamics Simulations |
| title_fullStr | Macromolecular Crowding Studies of Amino Acids Using NMR Diffusion Measurements and Molecular Dynamics Simulations |
| title_full_unstemmed | Macromolecular Crowding Studies of Amino Acids Using NMR Diffusion Measurements and Molecular Dynamics Simulations |
| title_short | Macromolecular Crowding Studies of Amino Acids Using NMR Diffusion Measurements and Molecular Dynamics Simulations |
| title_sort | macromolecular crowding studies of amino acids using nmr diffusion measurements and molecular dynamics simulations |
| topic | Alanine Amino Acids Crowding Diffusion Glycine Phenylalanine |
| url | http://journal.frontiersin.org/Journal/10.3389/fphy.2015.00001/full |
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