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β-Sheet Containment by Flanking Prolines: Molecular Dynamic Simulations of the Inhibition of β-Sheet Elongation by Proline Residues in Human Prion Protein

Previous molecular dynamic simulations have reported elongation of the existing β-sheet in prion proteins. Detailed examination has shown that these elongations do not extend beyond the proline residues flanking these β-sheets. In addition, proline has also been suggested to possess a possible str...

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Main Authors: Shamsir, Mohd. S., Dalby, Andrew
Format: Article
Published: Elsevier 2007
Subjects:
Q Science (General)
Online Access:http://eprints.utm.my/id/eprint/9258/
https://doi.org/10.1529/biophysj.106.092320
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spelling my.utm.92582018-10-21T04:29:34Z http://eprints.utm.my/id/eprint/9258/ β-Sheet Containment by Flanking Prolines: Molecular Dynamic Simulations of the Inhibition of β-Sheet Elongation by Proline Residues in Human Prion Protein Shamsir, Mohd. S. Dalby, Andrew Q Science (General) Previous molecular dynamic simulations have reported elongation of the existing β-sheet in prion proteins. Detailed examination has shown that these elongations do not extend beyond the proline residues flanking these β-sheets. In addition, proline has also been suggested to possess a possible structural role in preserving protein interaction sites by preventing invasion of neighbouring secondary structures. In this paper, we have studied the possible structural role of the flanling proline residues by simulating mutant structures with alternate substitution of the proline residues with valine. Simulations showed a directional inhibition of elongation with the elongation progressing in the direction of valine including evident inhibition of elongation by existing proline residues. This suggests that the flanking proline residues in prion proteins may have a containment role and would confine the β-sheet within a specific length. Elsevier 2007-03 Article PeerReviewed Shamsir, Mohd. S. and Dalby, Andrew (2007) β-Sheet Containment by Flanking Prolines: Molecular Dynamic Simulations of the Inhibition of β-Sheet Elongation by Proline Residues in Human Prion Protein. Biophysical Journal, 92 (6). pp. 2080-2089. (Submitted) https://doi.org/10.1529/biophysj.106.092320 DOI:10.1529/biophysj.106.092320
institution Universiti Teknologi Malaysia
building UTM Library
collection Institutional Repository
continent Asia
country Malaysia
content_provider Universiti Teknologi Malaysia
content_source UTM Institutional Repository
url_provider http://eprints.utm.my/
topic Q Science (General)
spellingShingle Q Science (General)
Shamsir, Mohd. S.
Dalby, Andrew
β-Sheet Containment by Flanking Prolines: Molecular Dynamic Simulations of the Inhibition of β-Sheet Elongation by Proline Residues in Human Prion Protein
description Previous molecular dynamic simulations have reported elongation of the existing β-sheet in prion proteins. Detailed examination has shown that these elongations do not extend beyond the proline residues flanking these β-sheets. In addition, proline has also been suggested to possess a possible structural role in preserving protein interaction sites by preventing invasion of neighbouring secondary structures. In this paper, we have studied the possible structural role of the flanling proline residues by simulating mutant structures with alternate substitution of the proline residues with valine. Simulations showed a directional inhibition of elongation with the elongation progressing in the direction of valine including evident inhibition of elongation by existing proline residues. This suggests that the flanking proline residues in prion proteins may have a containment role and would confine the β-sheet within a specific length.
format Article
author Shamsir, Mohd. S.
Dalby, Andrew
author_facet Shamsir, Mohd. S.
Dalby, Andrew
author_sort Shamsir, Mohd. S.
title β-Sheet Containment by Flanking Prolines: Molecular Dynamic Simulations of the Inhibition of β-Sheet Elongation by Proline Residues in Human Prion Protein
title_short β-Sheet Containment by Flanking Prolines: Molecular Dynamic Simulations of the Inhibition of β-Sheet Elongation by Proline Residues in Human Prion Protein
title_full β-Sheet Containment by Flanking Prolines: Molecular Dynamic Simulations of the Inhibition of β-Sheet Elongation by Proline Residues in Human Prion Protein
title_fullStr β-Sheet Containment by Flanking Prolines: Molecular Dynamic Simulations of the Inhibition of β-Sheet Elongation by Proline Residues in Human Prion Protein
title_full_unstemmed β-Sheet Containment by Flanking Prolines: Molecular Dynamic Simulations of the Inhibition of β-Sheet Elongation by Proline Residues in Human Prion Protein
title_sort β-sheet containment by flanking prolines: molecular dynamic simulations of the inhibition of β-sheet elongation by proline residues in human prion protein
publisher Elsevier
publishDate 2007
url http://eprints.utm.my/id/eprint/9258/
https://doi.org/10.1529/biophysj.106.092320
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score 13.211869

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