PROBING THE OUTER MOUTH STRUCTURE OF THE hERG CHANNEL WITH PEPTIDE TOXIN FOOTPRINTING AND MOLECULAR MODELING

¹ Virginia Commonwealth University
² NIH

^* To whom correspondence should be addressed. E-mail: gtseng{at}hsc.vcu.edu.

Submitted on September 13, 2006
Revised on November 5, 2006
Accepted on 12 January 2007

	Abstract

Previous studies have shown that the unusually long S5-P linker lining hERG's outer vestibule is critical for its channel function: point mutations at high-impact positions here can interfere with the inactivation process and, in many cases, also reduce the pore's K⁺ selectivity. Since no data are available on the equivalent region in the available K channel crystal structures to allow for homology modeling, we used alternative approaches to model its 3-dimensional structure. The first part of this paper describes mutant cycle analysis used to identify residues on hERG's outer vestibule that interact with specific residues on the interaction surface of BeKm-1, a peptide toxin with known NMR structure and a high binding affinity to hERG. The second part describes molecular modeling of hERG's pore domain. The transmembrane region was modeled after the crystal structure of KvAP pore domain. The S5-P linker was docked to the transmembrane region based on data from previous NMR and mutagenesis experiments, as well as a set of modeling criteria. The models were further restrained by contact points between hERG's outer vestibule and the bound BeKm-1 toxin molecule deduced from the mutant cycle analysis. Based on these analyses, we propose a working model for the open conformation of the outer vestibule of the hERG channel, in which the S5-P linkers interact with the pore-loops to influence ion flux through the pore.

Key Words: BeKm-1, hERG, homology modeling, molecular dynamics, potassium channel

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