PMC

Taken together the modified residues provide a picture of the dynamic motions involved in the transition between the open and closed state and support the proposed existence of three potential gates within the channel. Shown are schematic views of KirBac3.1 in the closed (left) and open (right) states. The regions that show the largest conformational changes during channel gating are circled in the closed state.

The color codes are the same as for . (A) A potential gating interface between the TM/pore domain and the cytoplasmic domain. Note the interaction between the modified residues and the G-loop/CD-loop and the slide-helix/N-terminal linker. (B) Location of modified residues in the intracellular domain. Most of the residues identified in this domain show only minor changes in accessibility (shown in blue 2-3 fold changes) and may reflect the fact that the cytoplasmic domains do not undergo as large allosteric changes during channel gating as other domains (e.g. the slide-helix and TM2).

The color codes are the same as for and residues with elemental color scheme (cpk) are not modified but involved in close packing interaction with the modified residues. (A) Conformational changes in TM2 and the pore-helix. For clarity only the TM section of two diagonally opposed monomers are shown. Note the proximity between M94 and G120 (the glycine gating hinge in TM2). (B) Dynamic gating near the selectivity filter. Top-down view of the pore domain. Note the clustering of these modified residues at an intersubunit interface. Residue K101 forms an inter-subunit salt bridge with modified residue E76 in the closed state conformation.

(A) Experimental Scheme: Dilute buffered solution of closed and open KirBac3.1 in tri-DM detergent were irradiated with a focused synchrotron X-ray beam for 0 - 20ms in a flow set-up for radiolytic labeling of the solvent accessible amino acid side chains. The exposed protein solution was rapidly quenched to stop secondary free radical reactions. The detergent was removed and controlled pepsin digestion was carried out to obtain peptide fragments of 4-10 amino acids. Reverse phase chromatography was used to separate the peptides and ESI-MS and MS/MS carried out to quantify the extent and identify site of modification. (B) Dose Response Plot: A representative dose response plot for peptide, 120-GML*GL*AVAASLI-131 (*indicates modification identified by MS/MS). The closed and open states of KirBac3.1 were prepared in buffer containing 50mM Mg²⁺ and 1mM EDTA respectively. EDTA is an •OH radical scavenger and reduces the X-ray dose by a factor of ^~ 2.5 (). The observed rate constant k_open is corrected and k_{open-corrected} is compared with that of k_closed (). The solvent accessibilities of L122 and L124 at the cavity of membrane pore are increased by a factor of ^~ 31 from close to open state of KirBac3.1. Rates were calculated for all the modified peptides and compared between the closed and open states to obtain information on conformation dynamics. (C) Mapping the solvent accessibility changes: Modified residues are represented by sticks on the X-ray crystal structure of KirBac3.1 in the closed state (PDB 1XL4). The color codes indicate the changes in rates of modification or solvent accessibilities upon transition from the closed to open state. Only the residues with >2 fold increase are highlighted.