N the symmetric structure of TRAP. Figure 4 also suggests positional correlation

N the symmetric structure of TRAP. Figure 4 also suggests positional correlation between the wave nodes and the positions of the subunit interfaces. To quantify this correlation, we defined the following correlation function after Nishikawa and Go [27] and Yu and Leitner [28,29]: P P Ck a?iResults Vibrational Modes of TRAP with Perfect Rotational Symmetry: Normal Mode AnalysisTo characterize the vibrational fluctuations of the 11-mer and 12-mer TRAPs, we first present the group theoretical descriptionji ???? h nki : R Da kj d a r0 d Da{a r0 i j i , ??P P ??0 h 0 d Da{a rj i j d a riInfluence of Symmetry on Protein DynamicsFigure 2. Crystal structures of the 12926553 11-mer and 12-mer TRAP. (A) Crystal structure of 11-mer TRAP (PDB code: 1C9S). Subunits and bound tryptophans are shown in ribbon and sphere, respectively. (B) Crystal structure of 12-mer TRAP (PDB code: 2EXS). (C) Superimposed structures of subunits A and B of the 11-mer and the 12-mer, shown by main-chain trace and the stick model for some ZK 36374 manufacturer side-chains. Hydrogen bonds between tryptophan and the subunit are indicated with the yellow dashed lines. (D) Hydrophobic pockets of subunit B for the 11-mer (left) and 12-mer TRAP (right). Surfaces are colored according to the hydrophobic contribution calculated by VASCo [48]. All the figures were prepared using PyMOL. doi:10.1371/journal.pone.0050011.gvector through {Da around the z-axis, and a r0 is the angular jwhere nki eki =Deki D with eki being the eigenvector of the normal mode k for the Ca atom i, R Da?is a matrix which rotates aFigure 3. Normal modes of a ring-shaped object. Normal modes of a circularly symmetric object are viewed along the symmetry axis in the form of stationary waves on the ring. The individual mode of T’p has 2 {1?wave nodes on the ring. The red curves describe the displacements along the modes. The T’7 mode is found only in the 12mer. doi:10.1371/journal.pone.0050011.gposition of atom j around the z-axis with the center of mass of subunit A chosen as a 0. In this formula, the d function has the allowance of 64u, or d 1 for DxD40 and d 0 for DxDw40 . This function describes the motional correlation between the Ca atoms close to the center of mass of subunit A and those located at a^Da in the ring. Figure 5A and B show the values of Ck ?for the seven lowest-frequency normal modes of the 11-mer and the 12-mer, respectively. It was found in the 12-mer (Figure 5B) that the angles of Ck ?0; in 1516647 other words, the wave nodes almost perfectly matched the position of the subunit interfaces (indicated by the broken lines) in modes 1 (T’ ), 3 (T’ ), 6 (T’ ), and 7 (T’ ). This 3 3 4 4 is because the Met-Enkephalin number of nodes in T’3 and T’4 , 4 and 6, respectively, are the divisors of the composite number, 12. This matching was not found in the modes 2 and 4 (the degenerated pairs of modes 1 and 2, respectively) due to the phase shift. Mode 5 is the uniform breathing T’1 mode with no wave node. The observation that the wave nodes occur at the subunit interface mayInfluence of Symmetry on Protein DynamicsTable 1. Character table of 11-mer TRAP.R1 v v2 vET1 T2 T3 T4 … T10 T11 1 1 1 1 … 1R1 v2 v4 vR1 v3 v6 vR1 v4 v8 vR1 v5 v10 vR1 v6 v12 vR1 v7 v14 vR1 v8 v16 vR1 v9 v18 vR1 v10 v20 v30 … v90 v… v9 v… v18 v… v27 v… v36 v… v45 v… v54 v… v63 v… v72 v… v81 vCharacter table in the complex irreducible representation for the C11 group. R represents the rotation of 2p=11 around the symmetry axis, and v exp?pi=11 ?.N the symmetric structure of TRAP. Figure 4 also suggests positional correlation between the wave nodes and the positions of the subunit interfaces. To quantify this correlation, we defined the following correlation function after Nishikawa and Go [27] and Yu and Leitner [28,29]: P P Ck a?iResults Vibrational Modes of TRAP with Perfect Rotational Symmetry: Normal Mode AnalysisTo characterize the vibrational fluctuations of the 11-mer and 12-mer TRAPs, we first present the group theoretical descriptionji ???? h nki : R Da kj d a r0 d Da{a r0 i j i , ??P P ??0 h 0 d Da{a rj i j d a riInfluence of Symmetry on Protein DynamicsFigure 2. Crystal structures of the 12926553 11-mer and 12-mer TRAP. (A) Crystal structure of 11-mer TRAP (PDB code: 1C9S). Subunits and bound tryptophans are shown in ribbon and sphere, respectively. (B) Crystal structure of 12-mer TRAP (PDB code: 2EXS). (C) Superimposed structures of subunits A and B of the 11-mer and the 12-mer, shown by main-chain trace and the stick model for some side-chains. Hydrogen bonds between tryptophan and the subunit are indicated with the yellow dashed lines. (D) Hydrophobic pockets of subunit B for the 11-mer (left) and 12-mer TRAP (right). Surfaces are colored according to the hydrophobic contribution calculated by VASCo [48]. All the figures were prepared using PyMOL. doi:10.1371/journal.pone.0050011.gvector through {Da around the z-axis, and a r0 is the angular jwhere nki eki =Deki D with eki being the eigenvector of the normal mode k for the Ca atom i, R Da?is a matrix which rotates aFigure 3. Normal modes of a ring-shaped object. Normal modes of a circularly symmetric object are viewed along the symmetry axis in the form of stationary waves on the ring. The individual mode of T’p has 2 {1?wave nodes on the ring. The red curves describe the displacements along the modes. The T’7 mode is found only in the 12mer. doi:10.1371/journal.pone.0050011.gposition of atom j around the z-axis with the center of mass of subunit A chosen as a 0. In this formula, the d function has the allowance of 64u, or d 1 for DxD40 and d 0 for DxDw40 . This function describes the motional correlation between the Ca atoms close to the center of mass of subunit A and those located at a^Da in the ring. Figure 5A and B show the values of Ck ?for the seven lowest-frequency normal modes of the 11-mer and the 12-mer, respectively. It was found in the 12-mer (Figure 5B) that the angles of Ck ?0; in 1516647 other words, the wave nodes almost perfectly matched the position of the subunit interfaces (indicated by the broken lines) in modes 1 (T’ ), 3 (T’ ), 6 (T’ ), and 7 (T’ ). This 3 3 4 4 is because the number of nodes in T’3 and T’4 , 4 and 6, respectively, are the divisors of the composite number, 12. This matching was not found in the modes 2 and 4 (the degenerated pairs of modes 1 and 2, respectively) due to the phase shift. Mode 5 is the uniform breathing T’1 mode with no wave node. The observation that the wave nodes occur at the subunit interface mayInfluence of Symmetry on Protein DynamicsTable 1. Character table of 11-mer TRAP.R1 v v2 vET1 T2 T3 T4 … T10 T11 1 1 1 1 … 1R1 v2 v4 vR1 v3 v6 vR1 v4 v8 vR1 v5 v10 vR1 v6 v12 vR1 v7 v14 vR1 v8 v16 vR1 v9 v18 vR1 v10 v20 v30 … v90 v… v9 v… v18 v… v27 v… v36 v… v45 v… v54 v… v63 v… v72 v… v81 vCharacter table in the complex irreducible representation for the C11 group. R represents the rotation of 2p=11 around the symmetry axis, and v exp?pi=11 ?.