Local Reactivity of Charybdotoxin, a K⁺ Channel Blocker

Abstract

Charybdotoxin (ChTX) is a 37-residue polypeptide that has been extensively used in site-directed mutagenesis experiments as a template to deduce models for the external pore appearance of K+ channels. The microscopic details of the ChTX−channel interaction, however, remain as a challenge for experimental and theoretical approaches. In this work, regional charge-transfer abilities, measured by chemical softness, s(r), are used as companion properties of the electrostatic potential, V(r), in the search for a qualitative structure−function relationship in the ChTX−K+ channel interaction. Both quantities were obtained with an ab initio methodology in massively parallel computers. In the analysis of s(r) and V(r), regions of the size of amino acids were considered because this is the appropriate scale to correlate with site-directed mutagenesis experiments. The correspondence between experimentally identified crucial amino acids sites and regional softnesses indicates that charge transfer to ChTX could be one of the main stabilization effects in the ChTX−channel complex. Also, it provides an explanation for the strong dependence of the dissociation constant of the complex on mutations of crucial amino acids. In addition, it is shown to be feasible to find structure−function relationships by combining local reactivity parameters and experimental data involving site directed mutagenesis.

On the Existence of Electronic States Confined by Charged Groups in Proteins

“…The analysis of the density of states (DOS) of BgK toxin (top panel in Figure 1) reveals a similar pattern as the previously obtained for a scorpion toxin 19 and for nanotubes built from amino acids. 24 In systems such as solids, polymers, and surfaces, the frontier orbital concept, which is useful in a chemical reactivity analysis, is extended to that of the frontier bands; 25 this extension has shown to be useful in the analysis of the electronic structure of proteins.…”

“…19 Whether the existence of this extra electrophilic character of the toxin is relevant to the biological activity or not is an open question that our group is currently addressing by studying several mutant toxins. Besides, the existence of interstitial states could be of impact in other properties of proteins such as fotoconductivity and electron transport.…”

“…An isosurface of the accumulated orbital density for the LUMO band containing 30 states, as calculated with a plane wave expansion using a 6 Ry cutoff, is displayed in yellow; this isosurface was created using a value, in atomic units, of 0.1. a fragment of seven amino acids; in this calculation, frozen coordinates were used, and the corresponding dangling bonds were passivated to simulate complete amino acids (see Figure 3). This calculation used a plane wave expansion, truncated up to a 20 Ry cutoff, which is good enough to produce a reliable description of the inner and outer parts of the valence charge density; 19,20 for this fragment, a supercell of 15.9 × 12.4 × 16.7 Å was used. On the other hand, a different test was done using a localized basis set at the B3LYP/6-31G** 21,22 level of theory within the Gaussian 98 program.…”

The electronic structure and dipole moment of charybdotoxin, a scorpion venom peptide with K+ channel blocking activity

“…Using classical force fields Yu et al [15] showed that the dipole vector of ChTX and those of five other venomous peptides are oriented toward their -sheet regions in the corresponding molecular structures but the magnitude of each dipole moment was not given. On the other hand, Ireta et al [19] performed total energy pseudopotential calculations to investigate the electronic structure of ChTX using the experimental NMR structure of Bontems et al [11,12].…”

Toxins by first-principles: Electronic structure mapping structural changes

“…Indeed, theoretical works on toxins [1] have shown that the analysis of quantities related to the local reactivity, such as the chemical softness, makes it feasible to find structure-function relationships. Also important is the application of quantum mechanical tools to track the electronic structure features as the system evolves in time, as it has been recently done in the case of the ubiquitin protein [2].…”