title: Influence of structural symmetry on protein dynamics.
abstract: 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.
authors.affiliation: Special Postdoctoral Researchers Program, RIKEN Advanced Institute for Computational Science, Kobe, Japan. ymatsunaga@riken.jp
authors.forename: Yasuhiro
authors.initials: Y
authors.lastname: Matsunaga
authors.forename: Ryotaro
authors.initials: R
authors.lastname: Koike
authors.forename: Motonori
authors.initials: M
authors.lastname: Ota
authors.forename: Jeremy R H
authors.initials: JR
authors.lastname: Tame
authors.forename: Akinori
authors.initials: A
authors.lastname: Kidera
mesh_terms: D000465:Algorithms; D001426:Bacterial Proteins / Q000737:chemistry*; D018360:Crystallography, X-Ray; D030562:Databases, Protein; D056004:Molecular Dynamics Simulation; D011485:Protein Binding; D011487:Protein Conformation; D021122:Protein Subunits / Q000737:chemistry; D016601:RNA-Binding Proteins / Q000737:chemistry*; D014157:Transcription Factors / Q000737:chemistry*
chemical_list: D001426:Bacterial Proteins; C079092:MtrB protein, Bacteria; D021122:Protein Subunits; D016601:RNA-Binding Proteins; D014157:Transcription Factors