2D Ir as an Experimental Probe of Ion-Induced Structural Changes in KCSA

Abstract

Ion channels are notoriously difficult to study at a structural level in situ. Studying the potassium channel KcsA is further complicated by the phenomenally high ion flux (>108 ions/sec), which demands a technique with high temporal resolution as well as structural sensitivity. Two-dimensional infrared spectroscopy (2D IR) is an ultrafast vibrational spectroscopy, which allows the correlation between vibrational modes in a molecule to be determined, providing picosecond-resolution structural snapshots of the system.Combining spectral calculations based on molecular dynamics (MD) simulations with experimental 2D IR spectra allows the features in the experimental data to be interpreted in terms of residue specific conformational changes upon binding either K+ or Na+. We find that when occupied by K+, the S2 and S3 binding sites have distinct vibrational modes. These assignments are able to explain the observations of previous salt-dependent FTIR experiments by Furutani et al and are consistent with the results of MD studies, demonstrating the utility of 2DIR as an ultrafast experimental probe of ion channels. Furthermore, we believe that ion-induced structural changes extend beyond the canonical TVGYG selectivity filter to the surrounding alpha-helices, in the form of increased deviation from an ideal helix when K+ is bound.