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Proton transport in biological systems can be probed by two-dimensional infrared spectroscopy
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10.1063/1.3522770
/content/aip/journal/jcp/134/4/10.1063/1.3522770
http://aip.metastore.ingenta.com/content/aip/journal/jcp/134/4/10.1063/1.3522770
View: Figures

Figures

Image of FIG. 1.
FIG. 1.

Schematic figure of (a) the PT in bulk water, (b) the PT in channel water, and (c) the channel water reorientation after PT.

Image of FIG. 2.
FIG. 2.

Schematic figure of the states of the water molecules in the PT model (top) and list of all rate constants that describe the different processes accounted for in our kinetic model. ⊕ represents the hydronium ion, relates to water rotation in the channel entrance, and relates to the proton entering the channel.

Image of FIG. 3.
FIG. 3.

The results of all-atom MD simulations of a channel without proton: (a) The standard deviation of the frequency fluctuation due to various contributions as a function of residue number. The insert shows the alternating arrangement of the C=O groups along the peptide backbone. (b) Illustration of the C=O groups close to the channel entrance (carbon: thick blue stick, oxygen: thick red stick) that are affected by lipid head groups (green spheres) and water molecules (oxygen: thin red stick, hydrogen: thin white stick). (c) The average projection of the water dipole along the channel axis as a function of time. The probability distribution of the projection is shown in the left part of the figure.

Image of FIG. 4.
FIG. 4.

The auto-correlation function of the frequency fluctuation for different values: (a) proton contribution, (b) water contribution, and (c) including all the contributions (proton+water+protein).

Image of FIG. 5.
FIG. 5.

The 2DIR spectra for the isotope labeled site within the PT model with = 1 ps (left column) and with = 0.2 ps (right column) at different waiting times. Each color contour represents 5% of the maximal amplitude.

Image of FIG. 6.
FIG. 6.

Antidiagonal linewidths of the isotope label 2DIR spectra as a function of: (a) the waiting time with two different (crosses: 1 ps and circles: 0.2 ps) and pure water (triangles), (b) the PT time scale ( ) with two different waiting times (crosses: 1 ps and circles: 5 ps). For comparison, the dashed lines represent the case of pure water.

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/content/aip/journal/jcp/134/4/10.1063/1.3522770
2011-01-24
2014-04-24
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Proton transport in biological systems can be probed by two-dimensional infrared spectroscopy
http://aip.metastore.ingenta.com/content/aip/journal/jcp/134/4/10.1063/1.3522770
10.1063/1.3522770
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