Voltage sensor conformations in the open and closed states in rosetta structural models of K ⁺ channels

Abstract

Voltage-gated ion channels control generation and propagation of action potentials in excitable cells. Significant progress has been made in understanding structure and function of the voltage-gated ion channels, highlighted by the high-resolution open-state structure of the voltage-gated potassium channel, Kv1.2. However, because the structure of the closed state is unknown, the gating mechanism remains controversial. We adapted the ROSETTA membrane method to model the structures of the Kv1.2 and KvAP channels using homology, de novo, and domain assembly methods and selected the most plausible models using a limited number of experimental constraints. suggests gating movement that can be viewed as a sum of two previously suggested mechanisms: translation (2-4 Å) plus rotation (Ϸ180°) of the S4 segment as proposed in the original ''sliding helix'' or ''helical screw'' models coupled with a rolling motion of the S1-S3 segments around S4, similar to recent ''transporter'' models of gating. We propose a unified mechanism of voltagedependent gating for K v1.2 and KvAP in which this major conformational change moves the gating charge across the electric field in an analogous way for both channels.membrane protein ͉ ROSETTA method ͉ voltage-gated ion channel V oltage-gated potassium (Kv) channels are members of the voltage-gated ion channel superfamily (1, 2), which is important for initiation and propagation of action potentials in excitable cells. They are composed of four identical or homologous subunits, each containing six transmembrane segments: S1-S6. Segments S1-S4 form the voltage-sensing domain (VSD), and segments S5 and S6 connected by the P loop, which is involved in ion selectivity, comprise the pore-forming domain (PD). S4 has four gating-charge-carrying arginines (R1-R4) spaced at intervals of three amino acid residues, which are highly conserved and are thought to play a key role in coupling changes in membrane voltage to opening and closing of the pore (3-5). In the Kv channels Ϸ13 electronic charges cross the membrane electrical field per channel between the closed and open states (6-8).High-resolution structures of the bacterial potassium channel KvAP and the mammalian potassium channel K v 1.2 recently have been solved (9-11). Although the KvAP structures showed the VSD in a nonnative orientation with respect to the membrane and the PD, the K v 1.2 structure captured the VSD in a conformation that is thought to represent the open state of the channel. In addition, the structure reveals that the VSD from one subunit interacts closely with the PD of the adjacent subunit in a clockwise direction when the channel structure is viewed from the extracellular side of the membrane (9). However, the closedstate structure of these channels remains unknown, and the mechanism of action of the voltage sensor in translocating gating charge is a subject of controversy. The original ''sliding helix'' or ''helical screw'' models of gating posited that S4 moves outward along a clockwise spiral path through the protei...

Disulfide locking a sodium channel voltage sensor reveals ion pair formation during activation

“…We developed a structural model for activation of the voltage sensor of NaChBac by using the Rosetta-Membrane algorithm, and the approach we described for K V 1.2 channels (15). The model is based on the X-ray structure of the activated state of K v 1.2 (25), ab initio modeling of K v 1.2 in its resting and activated states (14,15), and extension of those methods to NaChBac. In the resting state, the first arginine gating charge (R1) of the S4 segment is predicted to interact with D60 in the S2 segment [ Fig.…”

“…The ''transporter'' model of gating posits that the transmembrane movement of the S4 segment is small, whereas the surrounding S1, S2, and S3 segment rearrange to change the accessibility of the gating charges from internal to external (38). The Rosetta-Membrane structural version of the sliding helix model also incorporates this feature in that the outward spiral movement of the S4 helical segment is accompanied by a counter-rotation of the S1 through S3 helical segments (14,15). Although the transporter model of gating does not include ion pair interactions between the R3 gating charge and the negatively charged residues in the S2 segment, the movement of the voltage sensor postulated in this model could also include formation of an ion pair interaction in an intermediate state or in the final open state.…”

“…The sliding helix model posits (12) that sequential formation of ion pairs with negatively charged amino acid residues in the S1, S2, and/or S3 segments serve to stabilize the S4 segments in the membrane and thereby catalyze their transmembrane movement. A detailed structural version of this gating model developed by using the Rosetta Membrane modeling method predicts sequential formation of specific ion pairs during gating (14,15), but the rapid, state-dependent formation of ion pairs predicted in this gating model has not been experimentally tested.…”

Hydrophobic plug functions as a gate in voltage-gated proton channels

“…We created models of the closed and open state of Hv1 channels, using the structures (20) and models (21,25,52,53) of the VSD of the Kv1.2 channel as templates and our experimental data as constraints for these homology models. The open state was modeled using Kv1.2-2.1 chimeric channel chain B (PDB ID code 2R9R) (20) as the template, and the closed state was modeled with several reported closed-state models (21).…”

Exploring Functional Roles of TRPV1 Intracellular Domains with Unstructured Peptide-Insertion Screening

“…Homology-membrane-symmetry-loop modeling of the pore-forming domain of TRPV1 channel was performed using the Rosetta method 31 . Coordinates of S1-S5, Pore helix, and S6, were taken from TRPV1 channel structures (PDB ID: 3J5P and 3J5R) and kept rigid during modeling.…”