Intrinsic flexibility and gating mechanism of the potassium channel KcsA

Abstract

The gating mechanism of the potassium channel KcsA was studied by normal mode analysis. The results provided an atomic description of the locations of the pivot points and the motional features of key structural elements in the gating process. Two pivot points were found in the motions of the inner TM2 helical bundle that directly modulate the size of the central channel pore. One point is an intrasubunit hinge point that sharply divides the structural flexibility between the more rigid selectivity filter and the more mobile peripheral transmembrane helices. Such a division is vital for KcsA because it permits the large-scale motions of transmembrane helices required for the gating and, in the meantime, maintains the rigidity of the filter region essential for the selectivity. The other pivot point is an intersubunit one at which all four TM2 helices are bundled together. During the gating process, each TM2 helix undergoes a lever-like swinging motion pivoting on the intrasubunit hinge, and the entire TM2 bundle undergoes a concerted rotational motion around the central channel axis constrained around the intersubunit bundle point. This series of motions leads to a dramatic enlargement of the intracellular gate without loosening up the structural integrity.normal mode analysis ͉ structural flexibility ͉ ion channel K csA is an ion channel that is capable of selecting K ϩ over Na ϩ by a factor of 10 4 and permits the near diffusion-limited throughput rate of 10 8 ions per second (1). KcsA is a tetrameric integral membrane channel protein gated by pH (ref. 2; Fig. 1). Each monomer has two transmembrane helices, TM1 and TM2. The overall shape of the inner core of the channel, formed mainly by the four inner helices TM2, resembles an inverted teepee. There is a selectivity filter located near the extracellular side of the structure, which is highly selective for K ϩ ion. Inside the selectivity filter, main-chain carbonyl oxygen atoms from the filter signature sequence TVGYG are arranged in such a way that the filter energetically favors the transmission of K ϩ or similar cations such as Rb ϩ and Cs ϩ , but not the smaller alkali cations like Na ϩ and Li ϩ (3, 4). Behind the TVGYG sequence is a small-pore helix that supports the selectivity filter. Just before the selectivity filter, roughly in the middle of the membrane, there is a cavity with a diameter of 10 Å, which has been suggested to play a role in stabilizing water molecules and cations in the middle of the phospholipid membrane (5, 6). This cavity is connected to the cytoplasm by a relatively long hydrophobic pore, which is also the location of the intracellular gate of KcsA. Electron paramagnetic resonance (EPR) measurements showed that the diameter of this hydrophobic pore increases when the pH is lowered (7-9). Minimal change in intersubunit distance near residues Thr-107 to Ala-108 also was observed (9), which led to the speculation that this region serves as a pivot point for the overall motions of the helices.The wealth of experimental data provides a...

Coupling between the voltage-sensing and pore domains in a voltage-gated potassium channel

“…Although both features are present in the sequence of most potassium ion channels, they have been considered as leading to a mutually exclusive mechanism of gating [11, 12]. In contrast, our results suggest that these two features may complement each other, as suggested previously [7, 60, 61]. The bend at G229 clearly plays the main role in the formation of the S6 helical bundle that constitutes the activation gate, but the associated conformational change starts at G220, allowing the formation of a hydrated inner vestibule while keeping the extracellular region of the pore relatively rigid.…”

Cooperative Transition between Open and Closed Conformations in Potassium Channels

“…This hinge contributes to the plasticity of the coupling between the two ends of the channel. This phenomenon was not observed in calculations of the individual subunits (data not shown), and previous normal mode analysis attributed it to the intersubunit contacts within the tetrameric structure [41]. The motion of the intracellular termini of the inner helices away from the pore at Ala108 was observed as part of the gate-opening process in recent atomistic normal-mode and Monte Carlo simulations [32].…”

“…The hinge was observed both in the isolated subunit (second mode; Figure 3A) and the tetramer (fifth mode; Figure 3B), which indicates that it is also an intrinsic property of the subunit. The presence of a hinge in this region has emerged in EPR studies [5] and in previous normal-mode calculations [41]. Interestingly, a recent normal-mode/Monte Carlo study showed that pore opening was initiated by the motion of the preceding residue, i.e., Ala108 [32].…”

Conformational sampling on acid-sensing ion channel 1 (ASIC1): implication for a symmetric conformation

“…Similar to other ion channels such as the potassium channel and nicotinic acetylcholine receptor, ASIC1 should undergo large-scale (occasionally global) conformational deformations when eliciting cellular functions, such as gating [5,6]. Simulating global conformational changes of proteins is beyond the scope of the conventional molecular dynamics and Monte Carlo simulation methods [6].…”