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Collective solvent flows around a protein investigated by molecular dynamics simulation
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View: Figures


Image of FIG. 1.
FIG. 1.

Diffusion constant as a function of water-protein distance . Equation was used to calculate . In this equation, the average is taken over water molecules whose positions are in the range of [, ] in each snapshot. The time average was then taken over snapshots.

Image of FIG. 2.
FIG. 2.

(Color) Panels (a) and (b) are coarse-grained flow vectors for and at , respectively. Panels in (c) and (d) are those for and at , respectively. Red arrows in (c) and (d) are added to highlight the vortex.

Image of FIG. 3.
FIG. 3.

Dependency of the averaged norm of the coarse-grained flow vectors, , on the coarse-grained range . See the text for the computation of .

Image of FIG. 4.
FIG. 4.

Flow-flow orientational correlation as a function of water-water distance in each of subregions , , , and .

Image of FIG. 5.
FIG. 5.

Time correlation function of flow orientations calculated in each subregion: , , , and (definition of subregions as shown in Fig. 4). The time correlations are similar among the four subregions.

Image of FIG. 6.
FIG. 6.

Distribution of flow orientations in a plane of water-protein distance and SP. SP [Eq. (7)] is defined as a scalar product between a displacement vector of a water molecule and the normal from the displacement vector to the protein surface. The density of the distribution is presented in the potential of mean force PMF (, SP) [Eq. (8)]. Each contour line represents an isodensity (or iso-free-energy) level, and values on the contour lines indicate the free energies.

Image of FIG. 7.
FIG. 7.

(Color) Coarse-grained flow vectors , with at . Flows indicated by red arrows a, b, and c dry up the circled region, although the flow indicated by the arrow d wets the region.

Image of Scheme 1.
Scheme 1.

Distant two solutes (a) and close two solutes (b). Solvent flows and wet the solute surfaces.

Image of FIG. 8.
FIG. 8.

Panels (a)–(c) assist in the explanation in the Appendix. Coordinate systems, vectors, and angles are defined in the text.


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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Collective solvent flows around a protein investigated by molecular dynamics simulation