Using this method, a similar surface area of 17 nm2 is obtained for each aptamer in extended conformation, three times more than that of the antibody. with either energy profiles lead to comparable estimates, however slightly smaller 0, x? and G? are found for the linear-cubic profile in the cases of peptide aptamer adhesion. Table 2 Kinetic and energetic parameters for aptamer-surface unbinding, from fits to the model Phloroglucinol of Evans-Ritchie,21 Hummer-Szabo22 and Dudko et al.23 assuming a cusp shaped (=1/2) or a linear-cubic (=2/3) energy barrier.
Phloroglucinol
Glass/aptamer96.90.747457.11.5867.47422.91.5687.38333.51.3406.48Polystyrene/aptamer109.50.6523366.71.76310.602945.21.73210.48725.11.2188.61CNTs/aptamer20.70.40446.40.8075.2846.40.8135.2437.40.6784.71 Open in a separate window aUnits are s bUnits are nm cG? is in kBT units. Table 3 Kinetic and energetic parameters for anti-fluorescein 4-4-20 unbinding from fluorescein, from fits to the model of Evans-Ritchie,21 Hummer-Szabo22 and Dudko et al.23 assuming a cusp shaped (=1/2) or a linear-cubic (=2/3) energy barrier.
6.1 pNs?19.340.17110.90.2633.6510.80.2623.6310.80.2482.9911.8 pNs?17.130.17610.50.3184.1410.10.3114.0910.80.3083.5424.7 pNs?17.840.14412.80.2594.6512.70.2574.6614.40.2604.01 Open in a separate window aUnits are s bUnits are nm cG? is in kBT units. Energy landscapes of peptide aptamers and antibody/fluorescein interactions are shown in Figures 5 with energy wells represented as harmonic potentials. The transition state distance x?, along the pulling direction is extended for the glass and polystyrene binders (~1.6 nm) compared to that of the CNT binding peptides (0.8 nm). The lengths are consistent with the shorter range of hydrophobic interactions compared to electrostatic. In addition, comparisons of 0 and G? indicate that adhesion is the weakest for the CNT binding aptamers and the strongest for the polystyrene binding aptamers with G? varying from 5.2 kBT for CNT, up to 10.5 kBT for polystyrene assuming a cusp shaped barrier. Values for 0 follow the same trend with 46 s for CNT, 423 s for glass and 2945 s for polystyrene. Open in a separate window Figure 5 Energy landscape from parameters fitted using the model of Dudko et al.23 assuming a cusp shaped (=1/2) barrier, with energy wells represented as harmonic potentials. For the antibody-fluorescein interaction, fitted parameters for the three loading rates are in close agreement and have a relative standard deviation of only ~10%, highlighting the remarkable consistency of our method. Furthermore, Boder.