Influence of Structural Symmetry on Protein Dynamics

Yasuhiro Matsunaga,Ryotaro Koike,Jeremy R H Tame,Akinori Kidera,Motonori Ota,Franca Fraternali

doi:10.1371/journal.pone.0050011

Yasuhiro Matsunaga, Ryotaro Koike + Show 4 more

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https://doi.org/10.1371/journal.pone.0050011

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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.

Highlights

Homooligomeric proteins have large interface areas between the subunits resulting in stable complexes [1,2,3,4]
In a statistical analysis of the Protein Data Bank (PDB) [9], we found that homooligomers composed of even numbers of subunits are dominant (Figure 1C) because of the abundance of the closepacked oligomers
Based on the results of the normal mode analysis, we looked into the details of the fluctuations observed in the trajectories of the molecular dynamics (MD) simulations

Summary

Introduction

Homooligomeric proteins have large interface areas between the subunits resulting in stable complexes [1,2,3,4]. The close-packed form has n/2-fold rotational symmetry around one rotational axis (designated as Dn where n is the number of subunits; axis 1 in Figure 1B) and 2-fold rotational symmetry around the other rotational axes (axes 2–4 in Figure 1B) perpendicular to the first rotational axis. In the close-packed form, the subunit interfaces are arranged in a face-to-face manner, and every structural feature or interaction is repeated twice. It was pointed out by Monod et al [10] that the effect of a single mutation in complexes with the close-packed form may be much greater than in complexes without dihedral symmetry. This effect may allow such complexes to evolve more readily by the efficient generation of favorable interactions, and this prediction has been supported by recent docking-simulation studies [11,12,13]

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