A Gate in the Selectivity Filter of Potassium Channels (original) (raw)
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Conformational Changes and Gating at the Selectivity Filter of Potassium Channels
Journal of The American Chemical Society, 2008
The translocation of ions and water across cell membranes is a prerequisite for many of life's processes. K + channels are a diverse family of integral membrane proteins through which K + can pass selectively. There is an ongoing debate about the nature of conformational changes associated with the opening and closing and conductive and nonconductive states of potassium (K + ) channels. These changes depend on the membrane potential, the K + concentration gradient, and large scale motions of transmembrane helices and associated residues. Experiments also suggest that local structural changes in the selectivity filter may act as the dominant gate referred to as C-type inactivation. Herein we present an extensive computational study on KirBac, which supports the existence of a physical gate or constriction in the selectivity filter (SF) of K + channels. Our computations identify a new selectivity filter structure, which is likely associated with C-type inactivation. Specifically, the four peptide chains that comprise the filter adopt an unusual structure in which their dihedrals alternate between left-and right-handed Ramachandran angles, which also justifies the need for conservation of glycine in the K + selectivity filter, since it is the only residue able to play this bifunctional role.
K+ channel selectivity depends on kinetic as well as thermodynamic factors
Proceedings of the National Academy of Sciences, 2006
Potassium channels are necessary for a number of essential biological tasks such as the generation of action potentials and setting the resting membrane potential in cells, both of which require that these channels selectively permit the passage of potassium ions while suppressing the flow of other ions. Generally, this selectivity is attributed to a narrow stretch of the channel known as the selectivity filter. Over this stretch ions are dehydrated, and the backbone oxygen atoms of the protein mimic the ion's loss of coordination by water. However, channels are long pores with spatially distinct ion-binding sites that all must be traversed during ion permeation. We have shown that selectivity of mutant Kir3.2 (GIRK2) channels can be substantially amplified by introducing acidic residues into the cavity, a binding site below the selectivity filter. Here, we carry out electrostatic calculations on homology models to quantify the degree of stabilization that these mutations have on ions in the cavity. We then construct a multiion model of ion permeation to calculate the channel's permeability to potassium relative to sodium. This kinetic model uses rates derived from the electrostatic calculations and demonstrates that nonselective electrostatic stabilization of cations in the cavity can amplify channel selectivity independently of the selectivity filter. This nonintuitive result highlights the dependence of channel properties on the entire channel architecture and suggests that selectivity may not be fully understood by focusing solely on thermodynamic considerations of ion dehydration and the energetics of the selectivity filter.
A gate mechanism indicated in the selectivity filter of the potassium channel KscA
Theoretical Chemistry Accounts, 2007
Classical molecular dynamics (MD) and non-equilibrium steered molecular dynamics (SMD) simulations were performed on the molecular structure of the potassium channel KcsA using the GROMOS 87 force fields. Our simulations focused on mechanistic and dynamic properties of the permeation of potassium ions through the selectivity filter of the channel. According to the SMD simulations a concerted movement of ions inside the selectivity filter from the cavity to extracellular side depends on the conformation of the peptide linkage between Val76 and Gly77 residues in one subunit of the channel. In SMD simulations, if the carbonyl oxygen of Val76 is positioned toward the ion bound at the S3 site (gate-opened conformation) the net flux of ions through the filter is observed. When the carbonyl oxygen leaped out from the filter (gate-closed conformation), ions were blocked at the S3 site and no flux occurred. A reorientation of the Thr75-Val76 linkage indicated by the CHARMM-based MD simulations performed Berneche and Roux [(2005) Structure 13:591–600; (2000) Biophys J 78:2900–2917] as a concomitant process of the Val76-Gly77 conformational interconversion was not observed in our GROMOS-based MD simulations.
The Structure of the Potassium Channel: Molecular Basis of K + Conduction and Selectivity
Science, 1998
The potassium channel from Streptomyces lividans is an integral membrane protein with sequence similarity to all known K + channels, particularly in the pore region. X-ray analysis with data to 3.2 angstroms reveals that four identical subunits create an inverted teepee, or cone, cradling the selectivity filter of the pore in its outer end. The narrow selectivity filter is only 12 angstroms long, whereas the remainder of the pore is wider and lined with hydrophobic amino acids. A large water-filled cavity and helix dipoles are positioned so as to overcome electrostatic destabilization of an ion in the pore at the center of the bilayer. Main chain carbonyl oxygen atoms from the K + channel signature sequence line the selectivity filter, which is held open by structural constraints to coordinate K + ions but not smaller Na + ions. The selectivity filter contains two K + ions about 7.5 angstroms apart. This configuration promotes ion conduction by exploiting electrostatic repulsive for...
Ion selectivity in potassium channels
Potassium channels are tetrameric membrane-spanning proteins that provide a selective pore for the conduction of K + across the cell membranes. One of the main physiological functions of potassium channels is efficient and very selective transport of K + ions through the membrane to the cell. Classical views of ion selectivity are summarized within a historical perspective, and contrasted with the molecular dynamics (MD) simulations free energy perturbation (FEP) performed on the basis of the crystallographic structure of the KcsA phospholipid membrane. The results show that the KcsA channel does not select for K + ions by providing a binding site of an appropriate (fixed) cavity size. Rather, selectivity for K + arises directly from the intrinsic local physical properties of the ligands coordinating the cation in the binding site, and is a robust feature of a pore symmetrically lined by backbone carbonyl groups. Further analysis reveals that it is the interplay between the attractive ion-ligand (favoring smaller cation) and repulsive ligand-ligand interactions (favoring larger cations) that is the basic element governing Na + /K + selectivity in flexible protein binding sites. Because the number and the type of ligands coordinating an ion directly modulate such local interactions, this provides a potent molecular mechanism to achieve and maintain a high selectivity in protein binding sites despite a significant conformational flexibility.
Ion conduction and selectivity in K+ channels
Key Words molecular dynamic simulations, KcsA, free energy, potential of mean force, crystallographic B-factors, gating ■ Abstract Potassium (K + ) channels are tetrameric membrane-spanning proteins that provide a selective pore for the conductance of K + across the cell membranes. These channels are most remarkable in their ability to discriminate K + from Na + by more than a thousandfold and conduct at a throughput rate near diffusion limit. The recent progress in the structural characterization of K + channel provides us with a unique opportunity to understand their function at the atomic level. With their ability to go beyond static structures, molecular dynamics simulations based on atomic models can play an important role in shaping our view of how ion channels carry out their function. The purpose of this review is to summarize the most important findings from experiments and computations and to highlight a number of fundamental mechanistic questions about ion conduction and selectivity that will require further work.
Biophysical Journal, 2006
Potassium channels display a high conservation of sequence of the selectivity filter (SF), yet nature has designed a variety of channels that present a wide range of absolute rates of K 1 permeation. In KcsA, the structural archetype for K channels, under physiological concentrations, two K 1 ions reside in the SF in configurations 1,3 (up state) and 2,4 (down state) and ion conduction is believed to follow a throughput cycle involving a transition between these states. Using free-energy calculations of KcsA, Kv1.2, and mutant channels, we show that this transition is characterized by a channel-dependent energy barrier. This barrier is strongly influenced by the charges partitioned along the sequence of each channel. These results unveil therefore how, for similar structures of the SF, the rate of K 1 turnover may be fine-tuned within the family of potassium channels.
Exploring the origin of the ion selectivity of the KcsA potassium channel
Proteins-structure Function and Bioinformatics, 2003
The availability of structural information about biological ion channels provides an opportunity to gain a detailed understanding of the control of ion selectivity by biological systems. However, accomplishing this task by computer simulation approaches is very challenging. First, although the activation barriers for ion transport can be evaluated by microscopic simulations, it is hard to obtain accurate results by such approaches. Second, the selectivity is related to the actual ion current and not directly to the individual activation barriers. Thus, it is essential to simulate the ion currents and this cannot be accomplished at present by microscopic MD approaches. In order to address this challenge, we developed and refined an approach capable of evaluating ion current while still reflecting the realistic features of the given channel. Our method involves generation of semimacroscopic free energy surfaces for the channel/ions system and Brownian dynamics (BD) simulations of the corresponding ion current. In contrast to most alternative macroscopic models, our approach is able to reproduce the difference between the free energy surfaces of different ions and thus to address the selectivity problem. Our method is used in a study of the selectivity of the KcsA channel toward the K ؉ and Na ؉ ions. The BD simulations with the calculated free energy profiles produce an appreciable selectivity. To the best of our knowledge, this is the first time that the trend in the selectivity in the ion current is produced by a computer simulation approach. Nevertheless, the calculated selectivity is still smaller than its experimental estimate. Recognizing that the calculated profiles are not perfect, we examine how changes in these profiles can account for the observed selectivity. It is found that the origin of the selectivity is more complex than generally assumed. The observed selectivity can be reproduced by increasing the barrier at the exit and the entrance of the selectivity filter, but the necessary changes in the barrier approach the limit of the error in the PDLD/S-LRA calculations. Other options that can increase the selectivity are also considered, including the difference between the Na ؉ . . . Na ؉ and K ؉ . . . K ؉ interaction. However, this interesting effect does not appear to lead to a major difference in selectivity since the Na ؉ ions at the limit of strong interaction tend to move in a less concerted way than the K ؉ ions. Changes in the relative binding energies at the different binding sites are also not so effective in changing the selectivity. Finally, it is pointed out that using the calculated profiles as a starting point and forcing the model to satisfy different experimentally based constraints, should eventually provide more detailed understanding of the different complex factors involved in ion selectivity of biological channels. Proteins 2003;52:412-426.