title: Visualizing KcsA conformational changes upon ion binding by infrared spectroscopy and atomistic modeling.
abstract: The effect of ion binding in the selectivity filter of the potassium channel KcsA is investigated by combining amide I Fourier-transform infrared spectroscopy with structure-based spectral modeling. Experimental difference IR spectra between K(+)-bound KcsA and Na(+)-bound KcsA are in good qualitative agreement with spectra modeled from structural ensembles generated from molecular dynamics simulations. The molecular origins of the vibrational modes contributing to differences in these spectra are determined not only from structural differences in the selectivity filter but also from the pore helices surrounding this region. Furthermore, the coordination of K(+) or Na(+) to carbonyls in the selectivity filter effectively decouples the vibrations of those carbonyls from the rest of the protein, creating local probes of the electrostatic environment. The results suggest that it is necessary to include the influence of the surrounding helices in discussing selectivity and transport in KcsA and, on a more general level, that IR spectroscopy offers a nonperturbative route to studying the structure and dynamics of ion channels.
authors: †Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, Massachusetts 02139, United States.|‡Department of Chemistry, James Frank Institute, and The Institute for Biophysical Dynamics, The University of Chicago, 929 E 57th Street, Chicago, Illinois 60637, United States.
authors: Paul
authors: P
authors: Stevenson
authors: §Research Institute of Molecular Pathology (IMP), Dr Bohr-Gasse 7, A-1030 Wien, Austria.
authors: Christoph
authors: C
authors: Götz
authors: ‡Department of Chemistry, James Frank Institute, and The Institute for Biophysical Dynamics, The University of Chicago, 929 E 57th Street, Chicago, Illinois 60637, United States.
authors: Carlos R
authors: CR
authors: Baiz
authors: Jasper
authors: J
authors: Akerboom
authors: ‡Department of Chemistry, James Frank Institute, and The Institute for Biophysical Dynamics, The University of Chicago, 929 E 57th Street, Chicago, Illinois 60637, United States.
authors: Andrei
authors: A
authors: Tokmakoff
authors: §Research Institute of Molecular Pathology (IMP), Dr Bohr-Gasse 7, A-1030 Wien, Austria.
authors: Alipasha
authors: A
authors: Vaziri
mesh_terms: D004926:Escherichia coli; D007477:Ions / Q000737:chemistry*; D062105:Molecular Docking Simulation; D011188:Potassium / Q000737:chemistry; D024642:Potassium Channels, Voltage-Gated / Q000737:chemistry* / Q000235:genetics; D011189:Potassium Chloride / Q000737:chemistry; D011487:Protein Conformation; D012964:Sodium / Q000737:chemistry; D012965:Sodium Chloride / Q000737:chemistry; D017550:Spectroscopy, Fourier Transform Infrared; D055672:Static Electricity; D014732:Vibration
chemical_list: D007477:Ions; D024642:Potassium Channels, Voltage-Gated; D012965:Sodium Chloride; D011189:Potassium Chloride; D012964:Sodium; D011188:Potassium