Journal for Biophysical Chemistry
Table 2 Adsorption free energies based on MD with umbrella sampling for TGTG-X-GTGT peptides on a quartz (100) surface using available CHARMM parameters
-X- | Adsorption free energy (kcal/mol) | |
|---|---|---|
Exp.a | Sim.b | |
Asn (N) | −1.3 (0.9) | −7.2 |
Asp (D) | −0.5 (0.9) | −7.5 |
Gly (G) | −1.0 (0.9) | −7.7 |
Lys (K) | −1.5 (0.9) | −6.6 |
Phe (F) | −0.7 (0.9) | −9.1 |
Thr (T) | −0.2 (0.9) | −6.0 |
Trp (W) | −0.6 (0.9) | −13.0 |
Val (V) | −0.3 (0.9) | −6.1 |
- Experimental values are given as: Mean (95 % confidence interval)
- a95 % confidence interval for experimental data obtained from confidence intervals about linear regression line used for the correlation between F
des
measured by AFM and
determined by SPR - bAdsorption free energy values for (100) quartz were calculated from a single 3 ns umbrella simulation using default CHARMM parameters. Multiple independent simulations were not performed due to a decision to not proceed with tuning IFF parameters for this surface at this time. Confidence intervals are expected to be approximately √3 larger than those obtained for the silica glass surface using 3 independent simulations, shown in Table 3
determined by SPR