Pore helix

The polypeptide chain of the bacterial channel comprises 158 residues folded into two transmembrane helices, a pore helix and a cytoplasmic tail of 33 residues that was removed before crystallization. Four subunits... 

The C-terminal transmembrane helix, the inner helix, faces the central pore while the N-terminal helix, the outer helix, faces the lipid membrane. The four inner helices of the molecule are tilted and kinked so that the subunits open like petals of a flower towards the outside of the cell (Figure 12.10). The open petals house the region of the polypeptide chain between the two transmembrane helices. This segment of about 30 residues contains an additional helix, the pore helix, and loop regions which form the outer part of the ion channel. One of these loop regions with its counterparts from the three other subunits forms the narrow selectivity filter that is responsible for ion selectivity. The central and inner parts of the ion channel are lined by residues from the four inner helices. 

All K channels are tetrameric molecules. There are two closely related varieties of subunits for K channels, those containing two membrane-spanning helices and those containing six. However, residues that build up the ion channel. Including the pore helix and the inner helix, show a strong sequence similarity among all K+ channels. Consequently, the structural features and the mechanism for ion selectivity and conductance described for the bacterial K+ channel in all probability also apply for K+ channels in plant and animal cells. 

SI— S4 forms the voltage-sensing domain, while S5—S6 forms the pore domain of the channel. The majority of drugs that directly modify hERG function bind to the channel pore. Between S5 and S6 is a peptide loop that contains the pore helix and the selectivity filter. N- and C-terminal domains are on the cytoplasmic side of the... 

Figure 4.3 Sequence alignment of hERG and other representative l<+ channels alignments of the pore helix, selectivity filter and inner helices. The inner helix of KcsA corresponds with S6 of the other l<+ channels shown here, which are all voltage-gated channels. hERG residues close to the selectivity filter and on S6 implicated in drug...

Figure 18.1 Schematic depiction of the putative filter form the inner cavity and the ligand-binding interactions between a spiropiperidine site. For clarity, S6 and pore helix domainsofonly...

Figure 5.7 View of the K ion channel, the pore helix, and helices S1-S6, PDB lORQ. Visualized using CambridgeSoft ChemSD Ultra 10.0 with notations in ChemDraw Ultra 10.0. (Printed with permission of CambridgeSoft Corporation.) (See color plate)...

Figure 2. RYR1 structure at 9.5 A. The color ribbons represent a helices, the inner helix is labeled red, the pore helix green, and other helices are colored blue or purple (See Colour Plate 17)...

Figure 4. Schematic representation of the KcsA K+ channel structure. Two of the four subunits are shown the other two lie above and below the plain of the page. Each subunit is composed of the N- and C-terminated a-helices, the pore helix, and the loop containing the conserved G-Y-G sequence. The selectivity filter resides near the extracellular face of the membrane. Three positive ions are shown as they appear approximately in the crystal structure. Reproduced with author s permission from Dougherty, D. A. Lester, H. A. Angew. Chem., Int. ed. Engl. 1998, 37, 2330.

Figure 163 Schematic diagram of the transmembrane topology of a hERG subunit. The transmembrane portion of the hERG channel contains the voltage Sensor (comprising SI, S2, S3, and S4) and pore (comprising S5, turret helix, pore helix, selectivity filter, and S6) domains. A complete hERG channel consists of a tetramer of subunits, which fashions a membrane pore.

A total of four subunits are required to form a functional channel, with the pore domains associating with one another to form a symmetrical tetrameric construct, encasing a conduction pore. The highly conserved pore helix and selectivity filter are critical to the selective and rapid throughput of K+ ions [96], These features appear as if mounted on the S5 and S6 transmembrane helices and constitute the extracellular portion of the membrane pore [97], The intracellular portion of the pore is predominantly lined by the S6 helix to create an aqueous cavity below the selectivity filter [97], It is to this site that compounds bind to prevent K+ ion conduction [87,98],... 

In addition to the pore domain, it is possible to create homology models of the voltage-sensor and C-terminal domains of hERG. There are also two structures of hERG itself, a crystal structure of the Per-Arnt-Sim (PAS) domain, found within the N-terminus [112], and an NMR solution structure of the S5 to pore helix linker (Turret) [113]. A full list of crystal structures that can be used to create homology models of hERG is shown in Table 16.2. 

In cases such as KcsA, where there are many PDB entries for the same general structure, an example PDB ID is given. The Turret is not a domain per se, rather an extracellular loop between S5 and the pore helix of the pore domain. 

The three K-channels listed above are tetrameric assemblies with subunits sharing the same signature amino acid sequence TXGYGD of the selectivity filter. Also common is the topology of the ionic permeation channel, composed of two transmembrane helices (inner and outer helix) per subunit. The two transmembrane helices are joined by a pore sequence constructed with a shorter pore helix plus the selectivity filter segment. 

Camphor has been shown to act on two members of the TRP family, TRP vanilloid subtype 1 and subtype 3. That is the reason for the modulating sensation of warmth in humans by this substance [141]. Marsakova et al. [142] investigated the molecular mechanism of this action and the possible interaction site on TRPVl. The results showed that camphor acts on the channel by affecting the gating equilibrium of the outer pore helix domain of the channel. Camphor might also induce changes in the spatial distribution of phosphatidylinositol-4,5-bisphosphate on the iimer leaflet of the plasma membrane, since it is known that the substance can decrease fluidity of the plasma membrane. 

Marsakova L, Touska F, Krusek J, Vlachova V (2012) Pore helix domain is critical to camphor sensitivity of transient receptor potential vanilloid 1 channel. Anesthesiology 116(4) 903-917... 

FIGURE 7 The selectivity filter of the potassium channel based on the X-ray crystallographic structure determination by MacKinnon and colleagues. The potassium channel is tetrameric with a hole in the middle that forms the ion pore. Each subunit forms two transmembrane helices, the inner and the outer helix. The pore helix and loop regions build up the ion pore in combination with the inner helix. The black spheres in the middle of the channel represent potassium ions. (Reproduced with permission from Branden, C., and Tooze, J. (1999). Fig. 12.11, p. 233. /n Introduction to Protein Structure, 2nd edition. Garland Publishing, New York.)... 

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