Structural models for the KCNQ1 voltage-gated potassium channel

Abstract

Mutations in the human voltage-gated potassium channel KCNQ1 are associated with predisposition to deafness and various cardiac arrhythmia syndromes including congenital long QT syndrome, familial atrial fibrillation, and sudden infant death syndrome. In this work 3-D structural models were developed for both the open and closed states of human KCNQ1 to facilitate structurally based hypotheses regarding mutation-phenotype relationships. The KCNQ1 open state was modeled using Rosetta in conjunction with Molecular Operating Environment software, and is based primarily on the recently determined open state structure of rat Kv1.2 (Long, S. B., et al. (2005) Science 309, 897-903). The closed state model for KCNQ1 was developed based on the crystal structures of bacterial potassium channels and the closed state model for Kv1.2 of Yarov-Yarovoy et al. ((2006) Proc. Natl. Acad. Sci. U.S.A. 103, 7292-7207). Using the new models for KCNQ1, we generated a database for the location and predicted residue-residue interactions for more than 85 disease-linked sites in both open and closed states. These data can be used to generate structure-based hypotheses for disease phenotypes associated with each mutation. The potential utility of these models and the database is exemplified by the surprising observation that four of the five known mutations in KCNQ1 that are associated with gain-of-function KCNQ1 defects are predicted to share a common interface in the open state structure between the S1 segment of the voltage sensor in one subunit and both the S5 segment and top of the pore helix from another subunit. This interface evidently plays an important role in channel gating.

Figure 1

Alignment of the human KCNQ1 channel domain sequence with that of the S1-S6 domain of the template, rat K_v1.2. K_v1.2 secondary structure elements are indicated in blue, highlighting the fact that segmental insertions and deletions in the aligned sequences occur in regions between experimentally well-defined structural elements of the template.

Figure 2

Ensembles of the 20 lowest energy models for open and closed state KCNQ1 monomers. This highlights the implicit flexibility and/or conformational uncertainty for the loop segments of the models. For the open state, blue regions were derived from the K_V1.2 crystal structure template (PDB entry 2A79). Green regions were derived from the crystal structure backbone coordinates for the S1 and S3 regions (that have no side chain electron density) using the side chain assignments worked out by Yarov-Yarovoy et al.(34) Orange regions were modeled de novo using Rosetta. For the closed state, blue regions were derived from the KcsA crystal structure (PDB entry 1K4C). Yellow regions were derived from the Yarov-Yaravoy et al. K_V1.2 closed state model. Orange regions were modeled de novo using Rosetta, with the ensemble of all 20 models shown for completeness. The views that were chosen to illustrate each ensemble are independent of each other in order to more clearly illustrate the conformational diversity of the calculated loops.

Figure 3

Open and closed state models for the S1-S6 domain of KCNQ1. (3A.) Left. Extracellular view. Right. View from membrane plane. (3B.) Intracellular stereo view, with the atoms of Ser349 being highlighted in Van der Waals representation.

Figure 3

Open and closed state models for the S1-S6 domain of KCNQ1. (3A.) Left. Extracellular view. Right. View from membrane plane. (3B.) Intracellular stereo view, with the atoms of Ser349 being highlighted in Van der Waals representation.

Figure 4

Primary sequence and membrane topology for the S1-S6 domain of KCNQ1, with disease-liked sites highlighted. The illustrated secondary structure is that of the lowest energy open state model. An annotated version of this figure is presented as the Supplementary Figure in the Supporting Information, which summarizes the differences between this KCNQ1 open state model and both the lowest energy KCNQ1 closed state model and the corresponding K_V1.2 structures.

Figure 5

Surface representations of the KCNQ1 models compared to the K_v1.2 models developed of Yarov-Yarovy et al. (34) In all cases the view is from the cytosol.

Figure 6

Locations of KCNQ1 gain-of-function mutation Ser140Gly, Val141Met, Ile274Val, and Ala300Thr in the open and closed state models. The side chains highlighted in Van der Waals format are for the wild type residues at those positions. (Top) Extracellular view. (Bottom) View from membrane plane.