Dynamics transitions at the outer vestibule of the KcsA potassium channel during gating

Abstract

Significance C-type inactivation gating in K + channels plays an important role in controlling the firing patterns of excitable cells and is fundamental in determining the length and frequency of the cardiac action potential. At a molecular level, toxins, blockers, and metal ions bind to the outer vestibule and modulate the functional behavior of K + channels. Using KcsA, we show that the shuttling between the inactivated and conductive states of K + channels is accompanied by changes in local outer vestibule dynamics, in the absence of large conformational changes. The altered structural and hydration dynamics of the outer vestibule appear to be likely and important modulators of selectivity filter gating transitions in K + channels.

Oxidative footprinting in the study of structure and function of membrane proteins: current state and perspectives

“…Using the comparison of water accessibility between the wild type and non-inactivatable mutant E71A of KcsA we were able not only to confirm the significant changes of the water accessibility of the Cterminal domain (Gupta, Chance, Tucker & Bavro in preparation) but also to demonstrate radical changes in the solvent profiles of residues behind the selectivity filter of the channel which harbours the E71A mutation. These findings are consistent with the recent suggestion of the important role played by structured/bound water in stabilizing the conductive selectivity filter conformation 83 and highlight the high potential of XF-MS for study of these systems. …”

Toward increased concentration sensitivity for continuous wave EPR investigations of spin-labeled biological macromolecules at high fields

“…Structure and structure-function relationships of macromolecules are areas of intense EPR effort [1][2][3][4][5][6][7][8][9][10][11][12][13][14][15][16]. Coupled with site-directed spin-labeling (SDSL), EPR is oftentimes used to characterize protein and nucleic acid structures and dynamics, conformational changes, molecule folding, macromolecule complexes, and oligomeric structures [1][2][3][4][5][6][7][8][9][10][11][12][13][14][15]17].…”

“…Coupled with site-directed spin-labeling (SDSL), EPR is oftentimes used to characterize protein and nucleic acid structures and dynamics, conformational changes, molecule folding, macromolecule complexes, and oligomeric structures [1][2][3][4][5][6][7][8][9][10][11][12][13][14][15]17]. The majority of biomolecules do not contain unpaired electrons from which one can obtain an EPR signal; therefore, spin-labeling approaches have been developed [15,[18][19][20][21][22][23][24][25] where site-specific persistent radicals or paramagnetic metal-probes are incorporated at specific locations within a biomolecule.…”

CHARMM-GUI PDB Manipulator for Advanced Modeling and Simulations of Proteins Containing Nonstandard Residues

“…D. Roberts, Lewis, Ballou, Olson, & Shafer, 1986; Chen, LiuChen, & Rudnick, 1997; Perozo, Cortes, & Cuello, 1998; Choi et al, 2000; Tombola, Pathak, & Isacoff, 2006; Hvorup et al, 2007; Forrest et al, 2008; J. A. Roberts et al, 2008; Jeschke, 2012; Kazmier et al, 2014; Raghuraman, Islam, Mukherjee, Roux, & Perozo, 2014). Since many biophysical experiments are routinely performed with these MTS reagents, it is often necessary to introduce them into proteins for the purpose of MD simulation.…”