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Protein Engineering, Vol. 15, No. 2, 109-122, February 2002
© 2002 Oxford University Press

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

Gabriela Barreiro, Cristiano Ruch Werneck Guimarães and Ricardo Bicca de Alencastro,1

Physical Organic Chemistry Group, Departamento de Química Orgânica, Instituto de Química, UFRJ, Bloco A, sala 609, Cidade Universitária,Ilha do Fundão, CT, RJ 21949-900, Rio de Janeiro, Brazil

In this work, we propose a molecular model of the L-type calcium channel pore from the human cardiac {alpha}1 subunit. Four glutamic acid residues, the EEEE locus, located at highly conserved P loops (also called SS1–SS2 segments) of the {alpha}1 subunit, molecularly express the calcium channel selectivity. The proposed {alpha}-helix structure for the SS1 segment, analyzed through molecular dynamics simulations in aqueous-phase, was validated by the plotting of Ramachandran diagrams for the averaged structures and by the analysis of i and i + 4 helical hydrogen bonding between the amino acid residues. The results of the simulation of the calcium channel model with one and two Ca2+ ions at the binding site are in accordance with mutation studies which suggest that the EEEE locus in the L-type calcium channel must form a single high-affinity binding site. These results suggest that the Ca2+ permeation through the channel would be derived from competition between two ions for the only high-affinity binding site. Furthermore, the experimentally observed blocking of the Na+ flux at micromolar Ca2+ concentrations, probably due to the occupancy of the single high-affinity binding site for one Ca2+, was also reproduced by our model.


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