Structural changes of the KcsA potassium channel upon application of the electrode potential studied by surface-enhanced IR absorption spectroscopy

Specific interactions between alkali metal cations and the KcsA channel studied using ATR-FTIR spectroscopy

The X-ray structure of KcsA, a eubacterial potassium channel, displays a selectivity filter composed of four parallel peptide strands. The backbone carbonyl oxygen atoms of these strands solvate multiple K(+) ions. KcsA structures show different distributions of ions within the selectivity filter in solutions containing different cations. To assess the interactions of cations with the selectivity filter, we used attenuated total reflection Fourier-transform infrared (ATR-FTIR) spectroscopy. Ion-exchange-induced ATR-FTIR difference spectra were obtained by subtracting the spectrum of KcsA soaked in K(+) solution from that obtained in Li(+), Na(+), Rb(+), and Cs(+) solutions. Large spectral changes in the amide-I and -II regions were observed upon replacing K(+) with smaller-sized cations Li(+) and Na(+) but not with larger-sized cations Rb(+) and Cs(+). These results strongly suggest that the selectivity filter carbonyls coordinating Rb(+) or Cs(+) adopt a conformation similar to those coordinating K(+) (cage configuration), but those coordinating Li(+) or Na(+) adopt a conformation (plane configuration) considerably different from those coordinating K(+). We have identified a cation-type sensitive amide-I band at 1681 cm(-1) and an insensitive amide-I band at 1659 cm(-1). The bands at 1650, 1639, and 1627 cm(-1) observed for Na(+)-coordinating carbonyls were almost identical to those observed in Li(+) solution, suggesting that KcsA forms a similar filter structure in Li(+) and Na(+) solutions. Thus, we conclude that the filter structure adopts a collapsed conformation in Li(+) solution that is similar to that in Na(+) solution but is in clear contrast to the X-ray crystal structure of KcsA with Li(+).

Channel function reconstitution and re-animation: a single-channel strategy in the postcrystal age

The most essential properties of ion channels for their physiologically relevant functions are ion-selective permeation and gating. Among the channel species, the potassium channel is primordial and the most ubiquitous in the biological world, and knowledge of this channel underlies the understanding of features of other ion channels. The strategy applied to studying channels changed dramatically after the crystal structure of the potassium channel was resolved. Given the abundant structural information available, we exploited the bacterial KcsA potassium channel as a simple model channel. In the postcrystal age, there are two effective frameworks with which to decipher the functional codes present in the channel structure, namely reconstitution and re-animation. Complex channel proteins are decomposed into essential functional components, and well-examined parts are rebuilt for integrating channel function in the membrane (reconstitution). Permeation and gating are dynamic operations, and one imagines the active channel by breathing life into the 'frozen' crystal (re-animation). Capturing the motion of channels at the single-molecule level is necessary to characterize the behaviour of functioning channels. Advanced techniques, including diffracted X-ray tracking, lipid bilayer methods and high-speed atomic force microscopy, have been used. Here, I present dynamic pictures of the KcsA potassium channel from the submolecular conformational changes to the supramolecular collective behaviour of channels in the membrane. These results form an integrated picture of the active channel and offer insights into the processes underlying the physiological function of the channel in the cell membrane.

Surface-enhanced IR absorption spectroscopy of the KcsA potassium channel upon application of an electric field

Surface-enhanced IR absorption spectroscopy coupled with an electrochemical system enables the potassium-induced specific structural change of the potassium channel.

Probing “ambivalent” snug-fit sites in the KcsA potassium channel using three-dimensional reference interaction site model (3D-RISM) theory

The potassium channel is highly selective for K+ over Na+, and the mechanism underlying this selectivity remains unclear. We show the three-dimensional distribution functions (3D-DFs) of small cations (Li+, Na+, and K+) and the free energy profile of ions inside the open selectivity filter (SF) of the KcsA channel. Our previous results [S. Phongphanphanee, N. Yoshida, S. Oiki, F. Hirata. Abstract Book of 5th International Symposium on Molecular Science of Fluctuations toward Biological Functions, P062 (2012)] indicate that the 3D-DF for K+ exhibits distinct peaks at the sites formed by the eight carbonyl oxygen atoms belonging to the surrounding peptide-backbone and residues (the cage site). Li+ has sharp distributions in the 3D-DF at the center of a quadruplex composed of four carbonyl oxygen atoms (the plane site). Na+ has a rather diffuse distribution throughout the SF region with peaks both in the plane and in cage sites. The results provide microscopic evidence of the phenomenological findings that Li+ and Na+ are not excluded from the SF region and that the binding affinity alone does not cause the ion selectivity of KcsA. In the present study, with an ion placed explicitly along the pore axis, the free energy profiles of the ions inside the SF were calculated; from these profiles we suggest a new mechanism for selective K+ permeation. According to the model, a K+ ion must overcome a free energy barrier that is approximately half that of Na+ to exit from either of the SF mouths due to the existence of an intermediate local minimum along the route for climbing the barriers.