Binding potential

Besides yielding qualitative information, these biologically and pharmaceutically motivated applications of SMD can also yield quantitative information about the binding potential of the ligand-receptor complex. A first advance in the reconstruction of the thermodynamic potential from SMD data by discounting irreversible work was made by Balsera et al. (1997) as outlined in Sect. Reconstruction of the potential of mean force below. 

Unbinding processes can be viewed as taking place in several qualitatively different regimes (Izrailev et al., 1997 Marrink et al., 1998). These regimes can be illustrated by considering the simplest binding potential... 

In this regime the applied force completely overwhelms the binding potential and the ligand is subject to free diffusion. The mean free passage time in this regime is equal to Td and is on the order of 25 ns. 

Scaffolding. Because 14-3-3s can bind potentially bind more than one phosphoprotein at once due the presence of two phosphopeptide-binding sites in a... 

Receptor occupancy refers to the ratio of receptors occupied by a ligand at equilibrium and the total number of receptors available, usually expressed as a percentage of the total number of receptors. Since it is often not possible to quantify the total number of receptors or the number of receptors occupied by a ligand, another parameter called binding potential is often used to measure receptor occupancy. Binding potential (BP) refers to the ratio of the maximum number of receptors and the equilibrium dissociation constant of the drug, so that % receptor occupancy equals to... 

Here > = kBT, AUa is the binding potential energy of a molecule of type a to... 

The only potential deficiency in using D-biotin to modify directly a protein is the relatively short spacer arm afforded by the indigenous valeric acid group. Some applications may require longer spacers to maintain good binding potential toward avidin or streptavidin. 

NHS-iminobiotin can be used to label amine-containing molecules with an iminobiotin tag, providing reversible-binding potential with avidin or streptavidin. The NHS ester reacts with proteins and other amine-containing molecules to create stable amide bond derivatives (Figure 11.6). An iminobiotinylated molecule then can be used to target and purify other... 

The use of silica particles in bioapplications began with the publication by Stober et al. in 1968 on the preparation of monodisperse nanoparticles and microparticles from a silica alkoxide monomer (e.g., tetraethyl orthosilicate or TEOS). Subsequently, in the 1970s, silane modification techniques provided silica surface treatments that eliminated the nonspecific binding potential of raw silica for biomolecules (Regnier and Noel, 1976). Derivatization of silica with hydrophilic, hydroxylic silane compounds thoroughly passivated the surface and made possible the use of both porous and nonporous silica particles in all areas of bioapplications (Schiel et al., 2006). 

Removal of nonspecific binding potential in the B chain must be done before using an A-B intact toxin conjugate in vivo. See step 5 of the MBS conjugation protocol discussed previous to this section. 

In the high-field limit (F > 1 atomic unit meaning that it is greater than the binding potential) the smoothed Coulomb potential in Eq. (2) can be treated as a perturbation on the regular, classical motion of a free electron in an oscillating field. So, let us first consider the Hamiltonian for the one-dimensional motion of a free electron in the... 

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