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Solvent reaction field potential inside an uncharged globular protein: A bridge between implicit and explicit solvent models?
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10.1063/1.2771171
/content/aip/journal/jcp/127/15/10.1063/1.2771171
http://aip.metastore.ingenta.com/content/aip/journal/jcp/127/15/10.1063/1.2771171

Figures

Image of FIG. 1.
FIG. 1.

(Color) Solvent reaction field potential due to SPC/E explicit solvent charge density around the uncharged protein. This particular slice cuts through the centroid of the protein. Potential values as low as are present, but the color scale has been adjusted for greater detail at more common values. As a guide, the protein’s solvent-accessible surface, measured with a probe, is shown as a black outline.

Image of FIG. 2.
FIG. 2.

(Color) Solvent reaction field potential due to SPC/E explicit solvent charge density around the charged protein. The charge density due to the protein, though present in simulations with SPC/E water, was omitted during the calculation of this potential grid. As in Fig. 1, the slice depicted cuts through the centroid of the protein. Potential values as low as and as high as are present, but the color scale has been adjusted for greater detail between these extremes. As a guide, the protein’s solvent-accessible surface, measured with a probe, and the outlines of charged side chain head groups and polypeptide chain termini are shown in a black outline.

Image of FIG. 3.
FIG. 3.

Properties of the solvent (denoted by text inset in each panel) as a function of distance from the uncharged protein van der Waals surface (VDWS, axis). Solid lines show mean values of each property, dashed lines show the standard deviation. In these plots, “” means that the center of a solvent atom is from the protein’s van der Waals surface; an oxygen that comes within of the VDWS of a protein nitrogen atom, for example, means that oxygen and nitrogen atoms are really apart.

Image of FIG. 4.
FIG. 4.

Properties of the solvent (denoted by text inset in each panel) as a function of the distance from the charged protein van der Waals surface (VDWS, axis). Solid lines show mean values of each property; dashed lines show the standard deviation. In the top two panels, a dotted line is a guide to show the mean value of the corresponding property from simulations of the uncharged protein (see Fig. 3 for an explanation of what it means for solvent atoms to be very close to the protein VDWS).

Image of FIG. 5.
FIG. 5.

(Color online) Average interaction energy of a water molecule located at (black, solid line), (red, dashed line), and (blue, dotted line) from the surface of the uncharged protein with nearby water molecules at other distances from the protein van der Waals surface as indicated by the axis. These graphs show the local interaction characteristics of the first and second solvation shells and deep solution, respectively.

Image of FIG. 6.
FIG. 6.

(Color online) Average interaction energy of a water molecule located (black, solid line), (red, dashed line), and (blue, dotted line) from the surface of the charged protein with nearby water molecules at other distances from the protein van der Waals surface as indicated by the axis. These graphs correspond to those in Fig. 5 describing water-water interaction energies around the uncharged protein.

Image of FIG. 7.
FIG. 7.

Comparison of protein atom electrostatic energies for the charged protein due to the solvent reaction field potential predicted by different implicit solvent models ( axis) plotted against those generated by an explicit solvent model ( axis). refers to per-atom energies in the explicit solvent reaction field, to per-atom energies in the implicit solvent reaction field, and to per-atom energies in an implicit solvent reaction field obtained from a solute volume definition optimized to fit the results of free-energy perturbation experiments. A ∼ denotes implicit energies adjusted by the energy , the energy of atomic charges in the solvent reaction field potential created by the uncharged protein. Dots and crosses represent positively and negatively charged atoms, respectively. The black lines show .

Tables

Generic image for table
Table I.

Maximum values of the statistical inefficiency (SI) for solvent observables around the protein in different charge states. denotes an average value of the function at all points at a distance from the protein surface. The SI was computed for all values of between 0.8 and , and the maximum value is reported. For , values of SI decreased for and but increased for .

Generic image for table
Table II.

Extrema of atom and charge density functions as seen in Figs. 3 and 4. Locations of the extrema are given Å from the protein surface, maxima are given in units of bulk density for hydrogen and oxygen densities, and in for charge densities. denotes an average of the density at a distance from the surface of the protein in charge state (e.g., ‘no ’ or ‘’).

Generic image for table
Table III.

Figure 7 shows three of these four sets of implicit solvent per-atom energies plotted against per-atom energies obtained with explicit SPC/E water.

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/content/aip/journal/jcp/127/15/10.1063/1.2771171
2007-10-15
2014-04-23
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Solvent reaction field potential inside an uncharged globular protein: A bridge between implicit and explicit solvent models?
http://aip.metastore.ingenta.com/content/aip/journal/jcp/127/15/10.1063/1.2771171
10.1063/1.2771171
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