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Table 1 Comparison of Debye-Hückel fits vs. ionic strength between experiment and simulations

From: Numerical calculation of protein-ligand binding rates through solution of the Smoluchowski equation using smoothed particle hydrodynamics

Data

\({k_{\text {on}}^{0}}\)

\({k_{\text {on}}^{\mathrm {H}}}\)

Z E

RMSD exp

Experimental [4]

9.8±0.6

1.30

2.3±0.2

0.00

BD

9.1±0.3

2.66

1.7±0.2

1.52

SMOL FEM [7]

9.5±0.1

1.92

2.8±0.1

0.37

SPH (Dirichlet)

10.2±0.1

2.19

2.9±0.1

0.57

SPH (Robin, α=8×103)

9.6±0.1

1.88

3.0±0.1

0.33

Hexa-mutant (experiment)

1.8±0.1

0.57

1.2±0.2

0.00

Hexa-mutant (SPH, Robin)

2.23±0.00

1.77

2.37±0.02

0.88

  1. RMSD exp of simulation results to experimental k on is calculated over the range of ionic strengths between 0 and 0.67 M. The unit of \(\textit {k}_{\text {on}}^{\text {0}}\), \(\textit {k}_{\text {on}}^{\text {H}}\) and RMSD is 1011M-1 min -1. And the error is the standard deviation of parameter fits using nonlinear least squares.
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BMC Biophysics

ISSN: 2046-1682

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