“…The electronic structure of ChTX was obtained by total energy pseudopotential calculations (TEPC) . The geometry of the toxin was taken from recently reported NMR experiments. , In the TEPC methodology, the core electrons are substituted by a nonlocal atomic pseudopotential designed, in our case, by a procedure developed by Rappe et al , and tested in small molecules . The use of supercells to treat isolated molecules within the framework of TEPC has been tested for several groups; − in the present work, this supercell is 29.1 Å × 24.62 Å × 28.53 Å.…”
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.
“…The electronic structure of ChTX was obtained by total energy pseudopotential calculations (TEPC) . The geometry of the toxin was taken from recently reported NMR experiments. , In the TEPC methodology, the core electrons are substituted by a nonlocal atomic pseudopotential designed, in our case, by a procedure developed by Rappe et al , and tested in small molecules . The use of supercells to treat isolated molecules within the framework of TEPC has been tested for several groups; − in the present work, this supercell is 29.1 Å × 24.62 Å × 28.53 Å.…”
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.
“…As expected there is a loss of accuracy in the pseudopotential as the r c l values are increased. While the changes seem small (errors of this order have been accepted in other pseudopotential calculations ,, ), we will show in the next section that they can have a very significant effect on the predictions of structural properties of the isomers of larger systems. 3 Comparison of psp 0 pseudo-wave functions (solid lines) and the ab initio full-core atomic valence wave functions (dotted lines). The lower panels show the corresponding bare-ion psp 0 pseudopotentials.…”
Section: Carbon Pseudopotentials and Convergence Of A
Plane-wave Lda ...mentioning
The energies of isomers of C20 including neutral and
positively charged ring, fused ring, flake, and fullerene
structures have been calculated within the pseudopotential local
density approximation (LDA). The objective
is to predict the relative energies of the isomers as well as to
validate LDA calculations for the carbon system.
For C20, high-level coupled-cluster (CCSD(T))
calculations are just possible and are used for
comparison.
Our most accurate LDA calculations agree with prior calculations
quantitatively and remarkably well with
extrapolated CCSD(T) calculations. However, various
approximations can qualitatively affect the results.
For example softening the pseudopotential for carbon can cause the
ordering of the isomer stability to reverse
even though good agreement with smaller systems is retained.
Similar problems can occur if the plane-wave
basis is not sufficiently large.
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