Studies of drug binding to plasma proteins using a variant of equilibrium dialysis.

The plasma protein binding of three model compounds was investigated using a variant of equilibrium dialysis, denoted comparative equilibrium dialysis (CED), and the results were compared with those obtained with ultrafiltration (UF). In CED, the buffer that the plasma is dialysed against in traditional equilibrium dialysis is replaced by, for example, plasma from other species. The CED method has the advantage that the unbound concentration (C(u)) does not need to be measured, which can be difficult for drugs with extremely small unbound fractions. Instead, the ratio of the total drug concentration (C(tot)) on either side of the dialysis membrane at equilibrium is a direct measure of the relative binding properties of the two plasma types. For the first model compound, having an unbound fraction (f(u)) of about 0.05% in human plasma, the time to reach equilibrium was too long (> or =40 h) to make the CED technique feasible in practice. For the second model compound, the more weakly bound drug NAD-299 (with an unbound fraction of about 2% in human plasma), the CED equilibration times were considerably shortened (< or =16 h), and the technique was applied to plasma from three different species. Large discrepancies between the CED and UF results were seen, CED always giving rise to much lower C(tot) differences than expected from the UF results. It is suspected that this discrepancy was due to equilibration between the dialysis chambers of all plasma components with a molecular weight less than the cut-off of the membrane. This equilibration causes altered binding properties compared to the initial plasma. When performing ultrafiltration on plasma where drug was added to untreated plasma or added to blank plasma that was equilibrated against plasma from the same or from another species, the change of binding properties was confirmed. To ensure that the results were not specific for NAD-299, a third model compound, tolterodine, was also included. The same trends as for NAD-299 were seen. Because of the long equilibration times for compounds with high protein binding and, in particular, the suspected partial mixture of low molecular weight compounds from the two plasma types and the subsequent change of binding properties, we cannot recommend the CED method as a tool for studying relative protein binding.

A variable residue in the pore of Kv1 channels is critical for the high affinity of blockers from sea anemones and scorpions.

Animal toxins are associated with well defined selectivity profiles; however the molecular basis for this property is not understood. To address this issue we refined our previous three-dimensional models of the complex between the sea anemone toxin BgK and the S5-S6 region of Kv1.1 (Gilquin, B., Racape, J., Wrisch, A., Visan, V., Lecoq, A., Grissmer, S., Ménez, A., and Gasparini, S. (2002) J. Biol. Chem. 277, 37406-37413) using a docking procedure that scores and ranks the structures by comparing experimental and back-calculated values of coupling free energies DeltaDeltaGint obtained from double-mutant cycles. These models further highlight the interaction between residue 379 of Kv1.1 and the conserved dyad tyrosine residue of BgK. Because the nature of the residue at position 379 varies from one channel subtype to another, we explored how these natural mutations influence the sensitivity of Kv1 channel subtypes to BgK using binding and electrophysiology experiments. We demonstrated that mutations at this single position indeed suffice to abolish or enhance the sensitivity of Kv1 channels for BgK and other sea anemone and scorpion toxins. Altogether, our data suggest that the residue at position 379 of Kv1 channels controls the affinity of a number of blocking toxins.

Modeling the structure of agitoxin in complex with the Shaker K+ channel: a computational approach based on experimental distance restraints extracted from thermodynamic mutant cycles.

Computational methods are used to determine the three-dimensional structure of the Agitoxin (AgTx2)-Shaker complex. In a first stage, a large number of models of the complex are generated using high temperature molecular dynamics, accounting for side chain flexibility with distance restraints deduced from thermodynamic analysis of double mutant cycles. Four plausible binding mode candidates are found using this procedure. In a second stage, the quality and validity of the resulting complexes is assessed by examining the stability of the binding modes during molecular dynamics simulations with explicit water molecules and by calculating the binding free energies of mutant proteins using a continuum solvent representation and comparing with experimental data. The docking protocol and the continuum solvent model are validated using the Barstar-Barnase and the lysozyme-antibody D1.2 complexes, for which there are high-resolution structures as well as double mutant data. This combination of computational methods permits the identification of two possible structural models of AgTx2 in complex with the Shaker K+ channel, additional structural analysis providing further evidence in favor of a single model. In this final complex, the toxin is bound to the extracellular entrance of the channel along the pore axis via a combination of hydrophobic, hydrogen bonding, and electrostatic interactions. The magnitude of the buried solvent accessible area corresponding to the protein-protein contact is on the order of 1000 A with roughly similar contributions from each of the four subunits. Some side chains of the toxin adopt different conformation than in the experimental solution structure, indicating the importance of an induced-fit upon the formation of the complex. In particular, the side chain of Lys-27, a residue highly conserved among scorpion toxins, points deep into the pore with its positively charge amino group positioned at the outer binding site for K+. Specific site-directed mutagenesis experiments are suggested to verify and confirm the structure of the toxin-channel complex.