ArticlePloS one2012
Influence of structural symmetry on protein dynamics.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed, 17 citations in OpenAlex.
- GLMYsymm: inferring symmetry categories of protein complexes from single sequences using persistent GLMY homology.Briefings in bioinformatics · 2026Article
- Explicit description of viral capsid subunit shapes by unfolding dihedrons.Communications biology · 2024Article
- Quantifying the distribution of protein oligomerization degree reflects cellular information capacity.Scientific reports · 2020Article
- Modulation of Toroidal Proteins Dynamics in Favor of Functional Mechanisms upon Ligand Binding.Biophysical journal · 2020Article
- Dynamic properties of oligomers that characterize low-frequency normal modes.Biophysics and physicobiology · 2019Article
- Highly Coarse-Grained Representations of Transmembrane Proteins.Journal of chemical theory and computation · 2017Article
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Authors and funding
5 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
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.
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