Water wires

WATER WIRES, H+/OH CURRENTS, AND THE PERMEABILITY OF AMINO ACIDS 73... 

Gutknecht, J., Proton conductance through phospholipid bilayers Water wires or weak acids, J. Bioenerg. Biomem. 19, 427-442 (1987). 

Another property relevant to the current discussion is the distribution of water in the active site. Specifically, we characterize the population of various water wires connecting the zinc-bound water/hydroxide and His 64 found in the SCC-DFTB/MM simulations. These wires were identified following a definition of hydrogen-bond in terms of both distance (O—O < 3.5 A) and angle (O—H—O > 140°) and care... 

Conduction along water wires may as well be the dominant mechanism in the permeation of protons in channels an MD study of proton transport through a gramicidin channel can be found in, for example, [156]. 

Venable, R. M., and Pastor, R. W. (2002). Molecular dynamics simulations of water wires in a lipid bilayer and water/octane model systems, J. Chem. Phys., 116, 2663-2664. 

C. Manca, C. Tanner and S. Leutwyler, Excited-state hydrogen atom transfer in ammonia-wire and water-wire clusters, Ini. Rev. Phys. Chem., 24 (2005) 457-488. 

In contrast to the LS3 pore, the water molecules were frozen in the tetrameric LS2 pore, with diffusion coefficients of zero. They were found to be aligned antiparallel to the helix dipole caused by the orientation of the hydroxyl groups of the serine residues. This enabled formation of a water wire network important for the transport of protons by the proton wire or Grotthiis mechanism. 

It could be shown by IR spectrometry (8) that, in the dried state, about four to five HjO molecules per repeat unit remain embedded, as shown in Figure 10.1. They are aU anchored by H-bonds on C=0 groups of carboxylate COO groups and form water wires that otherwise hydrate neighbouring hydrophilic groups, establishing H-bonds with them. 

The results summarized above suggest important mechanistic differences in the long-range relay mechanism of protons by water wires embedded in non-polar (NP) and polar (GA) channels, respectively. Whereas GA constitutes an example of of fast proton equilibration by water-filled pores, NP channels may... 

Figure 4. Leakage vs, conduction models for the permeation of protons. Left transient water wires form very infrequently in the nonpolar environment provided by lipid bilayers, but when they do, they could translocate just one proton very rapidly before breaking up only the hop step ofGrotthuss takes place. Right in polar channels such as GA, water wires are much more long-lived, which is consistent with their rapid relay of proton via a complete Grotthuss mechanism involving both hop and turn steps (l(f s ).

FIGURE 4.15 Proton transfer QM system Proton water wire, proton donor Glu242, and proton acceptor Prop D. The boundary of the QM/MM system is at beta-carbons of Glu242 and Prop D, where the dangling bonds are snbstitnted with H-atoms. This system interacts with the medium via LJ (walls of the QM cavity) and Conlomb forces screened by the external solvent and the membrane. 

The obvious contradiction is resolved by taking into account that measuring electrophoretic ion mobility is a dynamic method, but protons and hydroxyls as such do not need to move in the aqueous phase under the action of an electric field. Instead, a rapid shift of electrons along a hydrogen-bonded water wire (the chain of hydrogen bonds between... 

Figure 18.1. Snapshot of the water arrangement from two different visual angles inside the CNT. (a) Structure of the hydrogen-bonded water network inside the CNT (b) Preferential alignment of encapsulated water wire was obtained from ab initio simulation. Figure 18.1(b) is reproduced from Phys. Rev. Lett., 90 (2003), 195503.

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