A molecular dynamics study of an L-type calcium channel model

Probing ion binding in the selectivity filter of the Cav1.1 channel with molecular dynamics

Cav1.1 is the voltage-gated calcium channel essential for the contraction of skeletal muscles upon membrane potential changes. Structural determination of the Cav1.1 channel opens the avenue toward understanding of the structure-function relationship of voltage-gated calcium channels. Here, we show that there exist two Ca2+-binding sites, termed S1 and S2, within the selectivity filter of Cav1.1 through extensive molecular dynamics simulations on various initial ion arrangement configurations. The formation of both binding sites is associated with the four Glu residues (Glu292/614/1014/1323) that constitute the so-called EEEE locus. At the S1 site near the extracellular side, the Ca2+ ion is coordinated with the negatively charged carboxylic groups of these Glu residues and of the Asp615 residue either in a direct way or via an intermediate water molecule. At the S2 site, Ca2+ binding shows two distinct states: an upper state involving two out of the four Glu residues in the EEEE locus and a lower state involving only one Glu residue. In addition, there exist two recruitment sites for Ca2+ above the entrance of the filter. These findings promote the understanding of mechanism for ion permeation and selectivity in calcium channels.

A New Computer Model for Evaluating the Selective Binding Affinity of Phenylalkylamines to T-Type Ca2+ Channels

To establish a computer model for evaluating the binding affinity of phenylalkylamines (PAAs) to T-type Ca²⁺ channels (TCCs), we created new homology models for both TCCs and a L-type calcium channel (LCC). We found that PAAs have a high affinity for domains I and IV of TCCs and a low affinity for domains III and IV of the LCC. Therefore, they should be considered as favorable candidates for TCC blockers. The new homology models were validated with some commonly recognized TCC blockers that are well characterized. Additionally, examples of the TCC blockers created were also evaluated using these models.

Protein structure and ionic selectivity in calcium channels: selectivity filter size, not shape, matters

Calcium channels have highly charged selectivity filters (4 COO(-) groups) that attract cations in to balance this charge and minimize free energy, forcing the cations (Na(+) and Ca(2+)) to compete for space in the filter. A reduced model was developed to better understand the mechanism of ion selectivity in calcium channels. The charge/space competition (CSC) mechanism implies that Ca(2+) is more efficient in balancing the charge of the filter because it provides twice the charge as Na(+) while occupying the same space. The CSC mechanism further implies that the main determinant of Ca(2+) versus Na(+) selectivity is the density of charged particles in the selectivity filter, i.e., the volume of the filter (after fixing the number of charged groups in the filter). In this paper we test this hypothesis by changing filter length and/or radius (shape) of the cylindrical selectivity filter of our reduced model. We show that varying volume and shape together has substantially stronger effects than varying shape alone with volume fixed. Our simulations show the importance of depletion zones of ions in determining channel conductance calculated with the integrated Nernst-Planck equation. We show that confining the protein side chains with soft or hard walls does not influence selectivity.

Understanding ion channel selectivity and gating and their role in cellular signalling

Ion channels play an essential role in the communication between and within cells. Here some of the different ion channel proteins and the roles they perform are introduced, before a discussion of the mechanisms by which they discriminate between different ion types and open and close to allow the passage of ions at the appropriate times.

Cellular mechanisms in sympatho-modulation of the heart

Cardiovascular function relies on complex servo-controlled regulation mechanisms that involve both fast-acting feedback responses and long-lasting adaptations affecting the gene expression. The adrenergic system, with its specific receptor subtypes and intracellular signalling cascades provides the major regulatory system, while the parasympathetic system plays a minor role. At the molecular level, Ca(2+) acts as the general signal trigger for the majority of cell activities including contraction, metabolism and growth. During recent years, important new results have emerged allowing an integrated view of how the multifarious Ca(2+)-signalling mechanisms transmit adrenergic impulses to intracellular target sites. These insights into cellular and molecular mechanisms are pivotal in improving pharmacological control of the sympathetic responses to surgical trauma and perioperative stress. They are examined in detail in this review, with particular emphasis being given to the differences in intracellular signalling between cardiomyocytes and vascular smooth muscle cells.

Permeation and selectivity in calcium channels

Recent advances-both experimental and theoretical-provide a tentative image of the structures in Ca channels that make them exceptionally selective. The image is very different from K channels, which obtain high selectivity with a rigid pore that tightly fits K(+) ions and is lined by carbonyl oxygens of the polypeptide backbone. Ca channels rely on four glutamate residues (the EEEE locus), whose carboxyl side chains likely reach into the pore lumen to interact with passing Ca(2+) ions. The structure is thought to be flexible, tightly binding a single Ca(2+) ion in order to block Na(+) flux but rearranging to interact with multiple Ca(2+) ions to allow Ca(2+) flux. The four glutamates are not equivalent, a fact that seems important for Ca(2+) permeation. This review describes the experimental evidence that leads to these conclusions and the attempts by theorists to explain the combination of high selectivity and high flux that characterizes Ca channels.

Potential of mean force calculations on an L-type calcium channel model

To understand the mechanisms of Na(+)/Li(+) permeation at submicromolar Ca(2+) concentrations, Na(+)/Li(+) blocking at higher Ca(2+) concentrations (10(-6)-10(-4) M) and Ca(2+) permeation at millimolar Ca(2+) concentrations, we used our recently described L-type calcium channel model. For this purpose, we obtained potential of mean force (pmf) curves for the position change of one Na(+) and one Ca(2+) ion inside the channel and for the position change of a second Ca(2+) ion when the EEEE locus is coordinated to Ca(2+). The pmf curves suggest that (i) at submicromolar Ca(2+) concentrations, because of the low velocity of Ca(2+) entry in the channel, monovalent ion flux occurs; (ii) at Ca(2+) concentrations between 10(-6) and 10(-4) M, thermodynamic equilibrium between the channel and Ca(2+) is achieved; as the coordination of Ca(2+) with the locus is more favorable than the coordination of Na(+), the monovalent ion flux is blocked; and (iii) to put a second Ca(2+) ion inside the channel at an appropriate rate, the Ca(2+) concentration should reach millimolar levels. Nevertheless, the entry of a second Ca(2+) is thermodynamically unfavorable, indicating that the competition of two Ca(2+) ions for the locus leads to Ca(2+) permeation.