Influence of structural symmetry on protein dynamics.
Structural symmetry in homooligomeric proteins has intrigued many researchers over the past several decades. However, the implication of protein symmetry is still not well understood. In this study, we performed molecular dynamics (MD) simulations of two forms of trp RNA binding attenuation protein...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2012-01-01
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| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC3506605?pdf=render |
| _version_ | 1818962352401285120 |
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| author | Yasuhiro Matsunaga Ryotaro Koike Motonori Ota Jeremy R H Tame Akinori Kidera |
| author_facet | Yasuhiro Matsunaga Ryotaro Koike Motonori Ota Jeremy R H Tame Akinori Kidera |
| author_sort | Yasuhiro Matsunaga |
| collection | DOAJ |
| description | Structural symmetry in homooligomeric proteins has intrigued many researchers over the past several decades. However, the implication of protein symmetry is still not well understood. In this study, we performed molecular dynamics (MD) simulations of two forms of trp RNA binding attenuation protein (TRAP), the wild-type 11-mer and an engineered 12-mer, having two different levels of circular symmetry. The results of the simulations showed that the inter-subunit fluctuations in the 11-mer TRAP were significantly smaller than the fluctuations in the 12-mer TRAP while the internal fluctuations were larger in the 11-mer than in the 12-mer. These differences in thermal fluctuations were interpreted by normal mode analysis and group theory. For the 12-mer TRAP, the wave nodes of the normal modes existed at the flexible interface between the subunits, while the 11-mer TRAP had its nodes within the subunits. The principal components derived from the MD simulations showed similar mode structures. These results demonstrated that the structural symmetry was an important determinant of protein dynamics in circularly symmetric homooligomeric proteins. |
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| format | Article |
| id | doaj.art-d246b2ae729142dcb15ffc1429a6d6f7 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-20T12:27:57Z |
| publishDate | 2012-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-d246b2ae729142dcb15ffc1429a6d6f72022-12-21T19:40:48ZengPublic Library of Science (PLoS)PLoS ONE1932-62032012-01-01711e5001110.1371/journal.pone.0050011Influence of structural symmetry on protein dynamics.Yasuhiro MatsunagaRyotaro KoikeMotonori OtaJeremy R H TameAkinori KideraStructural symmetry in homooligomeric proteins has intrigued many researchers over the past several decades. However, the implication of protein symmetry is still not well understood. In this study, we performed molecular dynamics (MD) simulations of two forms of trp RNA binding attenuation protein (TRAP), the wild-type 11-mer and an engineered 12-mer, having two different levels of circular symmetry. The results of the simulations showed that the inter-subunit fluctuations in the 11-mer TRAP were significantly smaller than the fluctuations in the 12-mer TRAP while the internal fluctuations were larger in the 11-mer than in the 12-mer. These differences in thermal fluctuations were interpreted by normal mode analysis and group theory. For the 12-mer TRAP, the wave nodes of the normal modes existed at the flexible interface between the subunits, while the 11-mer TRAP had its nodes within the subunits. The principal components derived from the MD simulations showed similar mode structures. These results demonstrated that the structural symmetry was an important determinant of protein dynamics in circularly symmetric homooligomeric proteins.http://europepmc.org/articles/PMC3506605?pdf=render |
| spellingShingle | Yasuhiro Matsunaga Ryotaro Koike Motonori Ota Jeremy R H Tame Akinori Kidera Influence of structural symmetry on protein dynamics. PLoS ONE |
| title | Influence of structural symmetry on protein dynamics. |
| title_full | Influence of structural symmetry on protein dynamics. |
| title_fullStr | Influence of structural symmetry on protein dynamics. |
| title_full_unstemmed | Influence of structural symmetry on protein dynamics. |
| title_short | Influence of structural symmetry on protein dynamics. |
| title_sort | influence of structural symmetry on protein dynamics |
| url | http://europepmc.org/articles/PMC3506605?pdf=render |
| work_keys_str_mv | AT yasuhiromatsunaga influenceofstructuralsymmetryonproteindynamics AT ryotarokoike influenceofstructuralsymmetryonproteindynamics AT motonoriota influenceofstructuralsymmetryonproteindynamics AT jeremyrhtame influenceofstructuralsymmetryonproteindynamics AT akinorikidera influenceofstructuralsymmetryonproteindynamics |