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Implications of a high dielectric constant in proteins
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10.1063/1.2741543
/content/aip/journal/jcp/126/22/10.1063/1.2741543
http://aip.metastore.ingenta.com/content/aip/journal/jcp/126/22/10.1063/1.2741543

Figures

Image of FIG. 1.
FIG. 1.

Distances (Å) to the center of charge of titratable sites (circles) and the protein surface closest to that site (line). Plotted for calbindin (left) and ribonuclease (right) using an all atom description based on the crystal structures.

Image of FIG. 2.
FIG. 2.

Illustration of a protein model, where all charges (salt and protein) are located in a high-dielectric region and the nonpolar interior is described by a spherical, charge-less low dielectric cavity of radius .

Image of FIG. 3.
FIG. 3.

MC simulation of the decay of the excess chemical potential of a univalent ion outside a low dielectric, neutral sphere of different radii, . The energy offsets are arbitrary.

Image of FIG. 4.
FIG. 4.

Top: effect of the nonpolar protein interior on the electrostatic pair interaction between two positive charges situated in a polar region a few angstroms away from the dielectric interface. Calculated using Eq. (4) with and . Bottom: plotted as the difference with various values of .

Image of FIG. 5.
FIG. 5.

Measured (Ref. 46) and calculated titration curve for ribonuclease A at salt. The MC results are based on the crystal structure 1AFU (Ref. 47).

Image of FIG. 6.
FIG. 6.

Titration curve for calbindin obtained from intrinsic values (ideal), measurements (Ref. 24 and 40), and MC simulations using both the HDM and assuming the protein core to be a low dielectric spherical cavity of radius and dielectric constant, . The simulations were performed using the full atomic structure [PDB entry 3ICB (Ref. 48)] and with an ionic strength of matching the experimental conditions.

Tables

Generic image for table
Table I.

Measured ( salt) and calculated values for BPTI. The MC ( salt) and PB ( salt) results are based on the crystal structure (Ref. 41) (4PTI). The MC calculation was performed using an all atom description and a uniform dielectric response .

Generic image for table
Table II.

Measured and calculated values for turkey ovomucoid third domain at 1:1 salt concentrations. The MC and MTK calculations are both based on the crystal structure (Ref. 44) (1PPF). In the simulations, the amino acid model was applied.

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/content/aip/journal/jcp/126/22/10.1063/1.2741543
2007-06-14
2014-04-19
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Implications of a high dielectric constant in proteins
http://aip.metastore.ingenta.com/content/aip/journal/jcp/126/22/10.1063/1.2741543
10.1063/1.2741543
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