The cysteine accessibility method was used to explore calcium channel pore topology. Cysteine mutations were introduced into the SS1-SS2 segments of Motifs I-IV of the human cardiac L-type calcium channel, expressed in Xenopus oocytes and the current block by methanethiosulfonate compounds was measured. Our studies revealed that several consecutive mutants of motifs II and III are accessible to methanethiosulfonates, suggesting that these segments exist as random coils. Motif I cysteine mutants exhibited an intermittent sensitivity to these compounds, providing evidence for a -sheet secondary structure. Motif IV showed a periodic sensitivity, suggesting the presence of an ␣-helix. These studies reveal that the SS1-SS2 segment repeat in each motif have non-uniform secondary structures. Thus, the channel architecture evolves as a highly distorted 4-fold pore symmetry.Calcium entry via voltage-dependent calcium channels is a key chemical signal responsible for biological events such as E-C coupling, neurotransmitter release, and regulation of gene expression. Although the extracellular space contains high concentrations of sodium, potassium, and calcium ions, the voltagedependent calcium channel provides a selective means for a high throughput of calcium ions. Despite the large pore size of the calcium channel, the narrowest point being 6 Å (10 Ϫ10 m) in diameter (1), the channel is specifically permeable to calcium at concentrations as low as 1 M (2). For all calcium channels, the selectivity filter consists of four glutamate residues (3-9), one residing in each of the four motifs, with the exception of the newly cloned T-type channel family (10 -12), which contains two glutamates (motifs I and II) and two aspartates (motifs III and IV).There are different models describing calcium movement through the channel at an approximate rate of 1 ϫ 10 6 ions per second. The one-binding site model, first proposed by Almers and McCleskey (8,13,14) and recently reevaluated by Dang and McCleskey (15) utilizes the concept of charge repulsion to facilitate the movement of calcium ions through the channel. The multiple-binding site model (16 -20), however, suggests the presence of two calcium-binding sites of differing affinity, although it is unclear which, if any, of the four glutamates form the high affinity site(s) and which form the low affinity site(s).There is general agreement that the four glutamates do not equally contribute to the binding and subsequent movement of the calcium ion into the cell (6, 21), however, voltage-dependent calcium channel topology has not been experimentally determined.The experimental procedure known as scanning cysteine accessibility method (SCAM) 1 has been extensively applied to study short regions of the secondary structure of membrane bound proteins to elucidate secondary structure (22). SCAM is based on the fact that known protein secondary structures, such as an ␣-helix or -sheet, contain amino acids that are exposed to the extracellular space. The periodicity of these exposed amino a...