Dynamics based alignment of proteins: an alternative approach to quantify dynamic similarity
<p>Abstract</p> <p>Background</p> <p>The dynamic motions of many proteins are central to their function. It therefore follows that the dynamic requirements of a protein are evolutionary constrained. In order to assess and quantify this, one needs to compare the dynamic...
| Prif Awduron: | , , , |
|---|---|
| Fformat: | Erthygl |
| Iaith: | English |
| Cyhoeddwyd: |
BMC
2010-04-01
|
| Cyfres: | BMC Bioinformatics |
| Mynediad Ar-lein: | http://www.biomedcentral.com/1471-2105/11/188 |
| _version_ | 1828420127878545408 |
|---|---|
| author | Lyngsø Rune Münz Márton Hein Jotun Biggin Philip C |
| author_facet | Lyngsø Rune Münz Márton Hein Jotun Biggin Philip C |
| author_sort | Lyngsø Rune |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>The dynamic motions of many proteins are central to their function. It therefore follows that the dynamic requirements of a protein are evolutionary constrained. In order to assess and quantify this, one needs to compare the dynamic motions of different proteins. Comparing the dynamics of distinct proteins may also provide insight into how protein motions are modified by variations in sequence and, consequently, by structure. The optimal way of comparing complex molecular motions is, however, far from trivial. The majority of comparative molecular dynamics studies performed to date relied upon prior sequence or structural alignment to define which residues were equivalent in 3-dimensional space.</p> <p>Results</p> <p>Here we discuss an alternative methodology for comparative molecular dynamics that does not require any prior alignment information. We show it is possible to align proteins based solely on their dynamics and that we can use these dynamics-based alignments to quantify the dynamic similarity of proteins. Our method was tested on 10 representative members of the PDZ domain family.</p> <p>Conclusions</p> <p>As a result of creating pair-wise dynamics-based alignments of PDZ domains, we have found evolutionarily conserved patterns in their backbone dynamics. The dynamic similarity of PDZ domains is highly correlated with their structural similarity as calculated with Dali. However, significant differences in their dynamics can be detected indicating that sequence has a more refined role to play in protein dynamics than just dictating the overall fold. We suggest that the method should be generally applicable.</p> |
| first_indexed | 2024-12-10T15:06:29Z |
| format | Article |
| id | doaj.art-3e22c1102acd442d9ca6aab9c380017f |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-12-10T15:06:29Z |
| publishDate | 2010-04-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-3e22c1102acd442d9ca6aab9c380017f2022-12-22T01:44:02ZengBMCBMC Bioinformatics1471-21052010-04-0111118810.1186/1471-2105-11-188Dynamics based alignment of proteins: an alternative approach to quantify dynamic similarityLyngsø RuneMünz MártonHein JotunBiggin Philip C<p>Abstract</p> <p>Background</p> <p>The dynamic motions of many proteins are central to their function. It therefore follows that the dynamic requirements of a protein are evolutionary constrained. In order to assess and quantify this, one needs to compare the dynamic motions of different proteins. Comparing the dynamics of distinct proteins may also provide insight into how protein motions are modified by variations in sequence and, consequently, by structure. The optimal way of comparing complex molecular motions is, however, far from trivial. The majority of comparative molecular dynamics studies performed to date relied upon prior sequence or structural alignment to define which residues were equivalent in 3-dimensional space.</p> <p>Results</p> <p>Here we discuss an alternative methodology for comparative molecular dynamics that does not require any prior alignment information. We show it is possible to align proteins based solely on their dynamics and that we can use these dynamics-based alignments to quantify the dynamic similarity of proteins. Our method was tested on 10 representative members of the PDZ domain family.</p> <p>Conclusions</p> <p>As a result of creating pair-wise dynamics-based alignments of PDZ domains, we have found evolutionarily conserved patterns in their backbone dynamics. The dynamic similarity of PDZ domains is highly correlated with their structural similarity as calculated with Dali. However, significant differences in their dynamics can be detected indicating that sequence has a more refined role to play in protein dynamics than just dictating the overall fold. We suggest that the method should be generally applicable.</p>http://www.biomedcentral.com/1471-2105/11/188 |
| spellingShingle | Lyngsø Rune Münz Márton Hein Jotun Biggin Philip C Dynamics based alignment of proteins: an alternative approach to quantify dynamic similarity BMC Bioinformatics |
| title | Dynamics based alignment of proteins: an alternative approach to quantify dynamic similarity |
| title_full | Dynamics based alignment of proteins: an alternative approach to quantify dynamic similarity |
| title_fullStr | Dynamics based alignment of proteins: an alternative approach to quantify dynamic similarity |
| title_full_unstemmed | Dynamics based alignment of proteins: an alternative approach to quantify dynamic similarity |
| title_short | Dynamics based alignment of proteins: an alternative approach to quantify dynamic similarity |
| title_sort | dynamics based alignment of proteins an alternative approach to quantify dynamic similarity |
| url | http://www.biomedcentral.com/1471-2105/11/188 |
| work_keys_str_mv | AT lyngsørune dynamicsbasedalignmentofproteinsanalternativeapproachtoquantifydynamicsimilarity AT munzmarton dynamicsbasedalignmentofproteinsanalternativeapproachtoquantifydynamicsimilarity AT heinjotun dynamicsbasedalignmentofproteinsanalternativeapproachtoquantifydynamicsimilarity AT bigginphilipc dynamicsbasedalignmentofproteinsanalternativeapproachtoquantifydynamicsimilarity |