computer modeling in molecular biology.pdf

6 Theory of Transport in Ion Channels 149waters, consistent with the dimer symmetry. Such differences may be due to severalfactors: Firstly, it has been observed that the structure and dynamics of the internalwater is very sensitive to the flexibility of the channel [32]; secondly, it may be thatthe dynamics and structure of the internal waters depends on detailed aspects of thepotential function, in particular those representing the hydrogen bonding interaction.6.3.2.4 Rare Events : Ethanolamine Tail IsomerizationObservation of rare events in a simulation, even though they are not statisticallysignificant, can give useful information. During the 100 ps trajectory, the ethanolaminetail of one of the monomers changed its conformation (the ethanol is locatedat x = + 1.4 nm and is labeled residue + 16). As can be seen in Figure 6-4, the transitionsof the three dihedral angles take place in a concerted fashion. The changes inthe successive dihedral angles are anticorrelated along the ethanolamine tail. Thiscan be observed clearly for the major transition at 25 ps and, to a lesser degree,around 50 ps for the second transition of the angle ty. The anticorrelation is relatedto the fact that the transition takes place without large and sudden displacements ofthe 0 - H group at the end of the tail [78]. The hydrogen bond with the entrancewater is lost in the time interval from 20 to 25 ps (see water 2 in Figure 6-3). Thelatter shows an increase in fluctuations compared to the water at the other entrance(water 11) which does not lose its ethanolamine hydrogen bond. From 25 to 50 psthe ethanolamine hydrogen bonds alternately to the three mouth waters and the twor 360 300 180r---12040030050 -P'CI 0 -.-L".ran -120 .-"-10 10 30 50 70 SO 110 -10 10 30 50 70 SO 110t in pat in paE *0°8:u 100c-r.x o-1 00-200 ..-10 10 30 50 70 SO 110t in psFigure 6-4. Dihedral angle transitions of the ethanolamine of monomer 1, ( -CNC,CBOH).The angles are defined as CN%,CB, NC,%BO and C,CDYOH.