Interaction between Sorbitol and Hen Egg White Lysozyme: From Dynamics to Structure
Background: The study of the molecular dynamics of proteins based on internal motions is crucial for understanding the mechanism of protein function. Internal movements of proteins play an important role in both protein folding processes and the mechanism of action of enzyme. Knowledge about these m...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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Bushehr University of Medical Sciences
2016-11-01
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| Series: | Iranian South Medical Journal |
| Subjects: | |
| Online Access: | http://ismj.bpums.ac.ir/browse.php?a_code=A-10-3-731&slc_lang=en&sid=1 |
| _version_ | 1811260395755667456 |
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| author | Mohammad Reza Ramezani Hosein Naderi Manesh Majid Erfani Moghadam |
| author_facet | Mohammad Reza Ramezani Hosein Naderi Manesh Majid Erfani Moghadam |
| author_sort | Mohammad Reza Ramezani |
| collection | DOAJ |
| description | Background: The study of the molecular dynamics of proteins based on internal motions is crucial for understanding the mechanism of protein function. Internal movements of proteins play an important role in both protein folding processes and the mechanism of action of enzyme. Knowledge about these movements will help us in understanding these processes correctly. Osmolites are small organic molecules which are utilized by the cells of all organisms, except hallobacteria. Osmolites are produced under extreme stressful conditions in order to help in stabilizing macro-molecules and retaining their biological function. They interact directly with macromolecules, but they exert their effect only when the characteristics or conditions of the solvent present around the cell change. Therefore, their presence affects the stability of the protein indirectly.
Materials and Methods: In this work we studied the effect(s) of the osmolite Sorbitol on the dynamics of Hen Egg White Lysozyme, and through our study we used NMR Hydrogen-Deuterium Exchange to characterize the effect(s). We performed spectrometery in two different conditions, in the absence and presence of sorbitol. The extent of peptide hydrogen exchange was assigned as a function time and in a decreasing manner in the intensity of the peak corresponding to amino acids. The resulting TOCSY spectra were assigned using SPARKY software, as well as we integrated the peaks using this software.
Results: The speed of hydrogen exchange, hydrogen atoms of the peptide bond, will give us information about the local structural oscillations where the exchange is taking place. The rate of hydrogen exchange varies from one amino acid to another, and the intensity of the peak of these hydrogen decreases as time passes by.
Conclusion: We found that the presence of sorbitol causes a decrease in proton exchange rate, and since there is no noticeable chemical shifts in the peaks of the spectra, in the presence or absence of sorbitol, we can conclude that sorbitol did not cause any change in the three dimensional structure. It seems that the decrease in the rate of exchange is a representative of a decrease in the accessible surface area or to strengthening of hydrogen bonds, and sorbitol caused one of these two possibilities. |
| first_indexed | 2024-04-12T18:46:48Z |
| format | Article |
| id | doaj.art-f92be9261bf047c6adc62f58b863adf0 |
| institution | Directory Open Access Journal |
| issn | 1735-4374 1735-6954 |
| language | English |
| last_indexed | 2024-04-12T18:46:48Z |
| publishDate | 2016-11-01 |
| publisher | Bushehr University of Medical Sciences |
| record_format | Article |
| series | Iranian South Medical Journal |
| spelling | doaj.art-f92be9261bf047c6adc62f58b863adf02022-12-22T03:20:35ZengBushehr University of Medical SciencesIranian South Medical Journal1735-43741735-69542016-11-01195832838Interaction between Sorbitol and Hen Egg White Lysozyme: From Dynamics to StructureMohammad Reza Ramezani0Hosein Naderi Manesh1Majid Erfani Moghadam2 Department of Biophysics, School of Sciences, Tarbiat Modares University, Tehran, Iran Department of Biophysics, School of Sciences, Tarbiat Modares University, Tehran, Iran Department of Biophysics, School of Sciences, Tarbiat Modares University, Tehran, Iran Background: The study of the molecular dynamics of proteins based on internal motions is crucial for understanding the mechanism of protein function. Internal movements of proteins play an important role in both protein folding processes and the mechanism of action of enzyme. Knowledge about these movements will help us in understanding these processes correctly. Osmolites are small organic molecules which are utilized by the cells of all organisms, except hallobacteria. Osmolites are produced under extreme stressful conditions in order to help in stabilizing macro-molecules and retaining their biological function. They interact directly with macromolecules, but they exert their effect only when the characteristics or conditions of the solvent present around the cell change. Therefore, their presence affects the stability of the protein indirectly. Materials and Methods: In this work we studied the effect(s) of the osmolite Sorbitol on the dynamics of Hen Egg White Lysozyme, and through our study we used NMR Hydrogen-Deuterium Exchange to characterize the effect(s). We performed spectrometery in two different conditions, in the absence and presence of sorbitol. The extent of peptide hydrogen exchange was assigned as a function time and in a decreasing manner in the intensity of the peak corresponding to amino acids. The resulting TOCSY spectra were assigned using SPARKY software, as well as we integrated the peaks using this software. Results: The speed of hydrogen exchange, hydrogen atoms of the peptide bond, will give us information about the local structural oscillations where the exchange is taking place. The rate of hydrogen exchange varies from one amino acid to another, and the intensity of the peak of these hydrogen decreases as time passes by. Conclusion: We found that the presence of sorbitol causes a decrease in proton exchange rate, and since there is no noticeable chemical shifts in the peaks of the spectra, in the presence or absence of sorbitol, we can conclude that sorbitol did not cause any change in the three dimensional structure. It seems that the decrease in the rate of exchange is a representative of a decrease in the accessible surface area or to strengthening of hydrogen bonds, and sorbitol caused one of these two possibilities.http://ismj.bpums.ac.ir/browse.php?a_code=A-10-3-731&slc_lang=en&sid=1Nuclear Magnetic Resonance (NMR) Hydrogen deuterium exchange Osmolyte (sorbitol) Hen egg white lysozyme |
| spellingShingle | Mohammad Reza Ramezani Hosein Naderi Manesh Majid Erfani Moghadam Interaction between Sorbitol and Hen Egg White Lysozyme: From Dynamics to Structure Iranian South Medical Journal Nuclear Magnetic Resonance (NMR) Hydrogen deuterium exchange Osmolyte (sorbitol) Hen egg white lysozyme |
| title | Interaction between Sorbitol and Hen Egg White Lysozyme: From Dynamics to Structure |
| title_full | Interaction between Sorbitol and Hen Egg White Lysozyme: From Dynamics to Structure |
| title_fullStr | Interaction between Sorbitol and Hen Egg White Lysozyme: From Dynamics to Structure |
| title_full_unstemmed | Interaction between Sorbitol and Hen Egg White Lysozyme: From Dynamics to Structure |
| title_short | Interaction between Sorbitol and Hen Egg White Lysozyme: From Dynamics to Structure |
| title_sort | interaction between sorbitol and hen egg white lysozyme from dynamics to structure |
| topic | Nuclear Magnetic Resonance (NMR) Hydrogen deuterium exchange Osmolyte (sorbitol) Hen egg white lysozyme |
| url | http://ismj.bpums.ac.ir/browse.php?a_code=A-10-3-731&slc_lang=en&sid=1 |
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