KcsA channel

The QM/MM and ab initio methodologies have just begun to be applied to challenging problems involving ion channels [73] and proton motion through them [74]. Reference [73] utilizes Hartree-Fock and DFT calculations on the KcsA channel to illustrate that classical force fields can fail to include polarization effects properly due to the interaction of ions with the protein, and protein residues with each other. Reference [74] employs a QM/MM technique developed in conjunction with Car-Parrinello ab initio simulations [75] to model proton and hydroxide ion motion in aquaporins. Due to the large system size, the time scale for these simulations was relatively short (lOps), but the influences of key residues and macrodipoles on the short time motions of the ions could be examined. 

A careful study by McDermott and co-workers of the high-K+ and low-K+ states of the KcsA channel has focused exclusively on the selectivity filter.101 They discovered that low K+ also induces the "non-con-ductive" or "collapsed" structure of the selectivity filter at neutral pH, but only if the sample remains well hydrated this state is lost if the bulk buffer is removed from the NMR rotor after spinning. Comparison of the measured chemical shifts with predictions by the SHIFTX and SPARTA programs identified the crystal structures that are most consistent with the selectivity filter conformations in the high-K+ and low-K+ proteolipo-some samples. Titrations of the chemical shift changes were used to measure site-specific affinities for K+. Based on the slow exchange rate between these conformations (<500 s 1), the authors suggest that the low-K+ conformation is relevant to channel inactivation rather than to conduction.101... 

Fig. 4. A homology model of the channel domain of an NMDA receptor (Chohan et al, 2000) based on the structure of the KcsA channel (Doyle et al, 1998). (A) The side view of the channel is shown with only the Ml, M2, and M3 regions and each of the four subunits in a different color. Note that M2 is a reentrant pore loop that enters the pore from the cytoplasmic face of the membrane. (B) A view of the channel from the extracellular side of the membrane is shown. Both selectivity and gating is controlled at least partially by the M2 region. (See Color Insert.)...

Crouzy, S., Berneche, S., and Roux, B., Extracellular blockade of K+ channels by TEA results from molecular dynamics simulations of the KCSA channel. J. Gen. 

Shealy RT, Murphy AD, Ramarathnam R, Jakobsson E, Subramaniam S. Sequence-function analysis of the K+-selective family of ion channels using a comprehensive alignment and the KcsA channel structure. Biophys J 2003 84 2929 12. 

The KcsA channel has what is often referred to as an inverted tepee structural arrangement, nearly 45 A long, and made up of three distinct regions of variable width. On the cytoplasmic side (Figure 9.4), it starts with... 

In order to develop new ion channel targeted drugs, we must clearly understand ion channel struc-ture-to-function relationships. We now know the crystal protein structure of the bacterial KcsA channel, but soon we will have additional crystal ion-channel structures. In the past several decades, ion channel research has been one of the most rapidly developing... 

KcsA channel (Fig. 8-21). The structure of the Tl-P complex is from Gulbis et The drawing is modified from that of Zhou. (C) Ball-and-stick view of the selectivity filter showing positions of four bound K+ ions. Two of the four TVGYG peptide strands of the conduction pore are shown. Courtesy of Roderick MacKinnon. 

The KcsA channel, which is mostly closed at neutral pH, responds by opening at a low external pH. Using methods of spin labeling and EPR spectroscopy, Perozo et al. found small translational and rotational movements of the helices that form the pore (Fig. 30-... 

The KcsA channel, which is mostly closed at neutral pH, responds by opening at a low external pH. Using methods of spin labeling and EPR spectroscopy, Perozo et al. found small translational and rotational movements of the helices that form the pore (Fig. 30-18). These may alter the diameter of the pore, opening or closing it. How do the electrostatic sensors control the process The details are uncertain, but the sensor is thought to lie in a conserved sequence of arginine and lysine residues interspersed with hydro-phobic amino acids in transmembrane helix 4 of fhe channel protein (Fig. 30-18 see also Fig. 30-17). ... 

Liu YS, Sompompisut P, Perozo E (2001) Structure of the KcsA channel intracellular gate in the open state. Nat Struct Biol 8(10) 883-887... 

Dehydration, followed by addition of the organic phase, allows micelles to flip out into a reverse micelle configuration while maintaining the hydrophobic domain of the membrane protein in a membrane-mimetic environment. In this complex, each membrane protein is thought to be associated with two reverse micelles that converge around the hydrophobic domain of the protein (Fig. 3) [225, 227, 229]. In some cases co-surfactants (e.g., dihexadecyldimethylammonium bromide (DHAB)) and/or cosolvents (e.g., hexanol) are also required to stabilize this structure. This approach was shown to be successful using the tetrameric KcsA channel as a test system [228]. Reconstitution in reverse micelles was achieved by purification in CTAB, followed by lyophilization and addition of DHAB, hexanol, pentane, and water. The result was a well-resolved HSQC spectrum for KscA, with significantly enhanced trans-... 

Fig. 5 Inactivation of K channel, a) Crystal structure of KcsA channel with a hydrophobic cation, tetrabutylammonium TEA. b) Composite model of a voltage-dependent channel. The a-subunit is shown in blue and the P-subunit in red. The pore is represented by the KcsA K channel (5) and the Tl-P complex (15). The structures of the linker (Tl-Sl) connecting the voltage sensors to the TI domain are unknown. An N-terminal inactivation gate is shown entering a lateral opening to gain access to the pore. Fig. 5a was produced with a PDB file (lJ95.pdb from Ref. [14]) and Raswin Molecular Graphics (version 2.7.2. Glaxo Research and Development. U.K.).

Negoda A, Negoda E, Xian M, Reusch RN (2009) Role of polyph osphate in regulation of the Streptomyces lividans KcsA channel. Biochimica et Biophysica Acta (BBA) - Biomembranes 1788 608—614. 

The KcsA channel is characterized by this simple transmembrane architecture (see Ref. 40, and the left side of Fig. 2), and its activation has been attributed to pH-dependent translations and rotations of the two transmembrane helices.Because of its relative simplicity, KcsA has been simulated extensively with a variety of approaches, and, like gA, it too can be considered a benchmark system for simulation codes. 

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