4.4 Theoretical Biology
191
Fig. 4.49 Illustrative expression of a satellite tobacco mosaic virus (STMV) particle in a box of
220 × 220 × 220 Å 3 with water as solvent molecules. The capsid is indicated by green color and
the RNA inside is shown by cutting out. Reprinted from Freddolino et al. (2006).Copyright 2006,
with permission from Elsevier
4.4.2.2 Poliovirus
More recently, all-atom MD calculation has been performed for empty poliovirus
capsid (Andoh et al. 2014). This system consists of very large numbers of molecules
(6.5 million) and the MD simulation has been achieved for sufficiently long time
(200 ns). The K-computer at RIKEN in Japan (Yonezawa et al. 2011) was employed
to perform the MD calculation. The CHARMM22 potential was applied for the
proteins and electrolytes, TIP3P for water. After achievement of the initial equilibration process, the calculation has been performed in the NPT ensemble at P =
0.1 MPa and T = 310.15 K. More details are to be referred to the original article.
The result of equilibrium state is shown in Fig. 4.51. The virus capsid has been
shown to exchange water molecules with high speed between the inside and the
outside thereof so as to result in achievement of equilibrium of hydrostatic pressure
(Fig. 4.52). This behavior assures prompt equilibrium of hydrostatic pressure with
exchanging water molecules under high pressure. However, within the time of the
simulation the capsid does not exchange ions present in the solution indicating the
behavior as semi-permeable membrane. Moreover, the solution inside the empty
capsid has negative pressure similarly to the xylem of trees which would come
191
Fig. 4.49 Illustrative expression of a satellite tobacco mosaic virus (STMV) particle in a box of
220 × 220 × 220 Å 3 with water as solvent molecules. The capsid is indicated by green color and
the RNA inside is shown by cutting out. Reprinted from Freddolino et al. (2006).Copyright 2006,
with permission from Elsevier
4.4.2.2 Poliovirus
More recently, all-atom MD calculation has been performed for empty poliovirus
capsid (Andoh et al. 2014). This system consists of very large numbers of molecules
(6.5 million) and the MD simulation has been achieved for sufficiently long time
(200 ns). The K-computer at RIKEN in Japan (Yonezawa et al. 2011) was employed
to perform the MD calculation. The CHARMM22 potential was applied for the
proteins and electrolytes, TIP3P for water. After achievement of the initial equilibration process, the calculation has been performed in the NPT ensemble at P =
0.1 MPa and T = 310.15 K. More details are to be referred to the original article.
The result of equilibrium state is shown in Fig. 4.51. The virus capsid has been
shown to exchange water molecules with high speed between the inside and the
outside thereof so as to result in achievement of equilibrium of hydrostatic pressure
(Fig. 4.52). This behavior assures prompt equilibrium of hydrostatic pressure with
exchanging water molecules under high pressure. However, within the time of the
simulation the capsid does not exchange ions present in the solution indicating the
behavior as semi-permeable membrane. Moreover, the solution inside the empty
capsid has negative pressure similarly to the xylem of trees which would come