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Toxin Binding Serves as an Initial Model for Studying the Effects of Anesthetics on Ion Channels
Stanford University.
Stanford University.ORCID iD: 0000-0002-2734-2794
Netherlands Cancer Institute.
Stanford University.
2007 (English)Conference paper, Published paper (Refereed)
Abstract [en]

Introduction: We have previously used molecular modeling techniques combined with experimental data to visualize a plausible model of an anesthetic binding site within a LGIC complex.We have also previously shown a computational mechanism by which these ion channels may open and close and postulated how this motion may be affected by the presence of anesthetics.2 The difficulties with these methods, however, lay in their inability to account for the modest effects of a separate anesthetic ligand or small mutation on ion channel motion. Here we show the successful application of an elastic network calculation on a homologue of the extracellular component of LGIC's, the acetycholine binding protein (AChBP), in the presence and absence of large cobratoxin ligands. These calculations demonstrate a clear alteration in the native symmetric motion of a protein due to the presence of multiple ligands, as may occur with anesthetics and muscle relaxants.

Methods: Coordinates of the AChBP with (1YI5)3 and without (1I9B)4 cobratoxin were obtained from the Research Collaboratory for Structural Biology (RCSB). Hydrogens were added using DSViewer 5.0 (Accelrys, San Diego, CA). Normal mode analysis was performed using an all atom elastic network model developed by Lindahl. Root-mean-square deviations (RMSD) of each residue were produced from the application of the RMSD analysis utility within the GROMACS software suite to the coordinate trajectory output files. The RMSD data was then imported into Microsoft Excel for plotting and further comparison of protein backbone motions between the two different normal mode trajectories.

Results: Normal mode analysis reveals that ligand binding to this protein alters its natural harmonic vibration. In this case, the axially symmetric motion of the AChBP, that may be associated with channel gating in the full nAChR, is highly dampened by the presence of bound cobratoxin. A large proportion of the kinetic energy within this mode seems to be absorbed by the cobratoxin, leaving the channel motion significantly decreased.

Conclusions: This is among the first descriptions of the effect of bound ligand on large scale protein dynamics, especially as it relates to ion channel gating. This analysis was possible using an elastic network approximation due to the large protein nature of the cobratoxin ligand. For nonpeptide drugs such as anesthetics which contain far fewer atoms, using the effects of bound ligand on protein motion as additional criteria for future drug design may require a more robust molecular mechanics treatment of the ligand-receptor complex.

Place, publisher, year, edition, pages
2007.
National Category
Biophysics Bioinformatics and Systems Biology Theoretical Chemistry
Identifiers
URN: urn:nbn:se:kth:diva-82718OAI: oai:DiVA.org:kth-82718DiVA: diva2:498540
Conference
Anesthesiology 2007
Note
QC 20120313Available from: 2012-02-12 Created: 2012-02-12 Last updated: 2012-03-13Bibliographically approved

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Lindahl, Erik

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