Computational protocol: Molecular endpoints of Ca2+/calmodulin- and voltage-dependent inactivation of Cav1.3 channels

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Protocol publication

[…] For the closed-state molecular model of the CaV1.3 S5-S6 segments, the KcsA (Protein Data Bank accession no. 1BL8) crystal structure was used as template (). Modeller 9v4 () was used to generate 50 models, from which the structure with the lowest objective function was chosen. Modeller builds three-dimensional atomic structures by optimizing an objective function based on CHARMM energy terms and a set of distance and dihedral angle restraints from the alignment of target and template sequences. The four domains of CaV1.3 were arranged in a clockwise configuration as viewed from the extracellular surface by analogy to the orientation of voltage-gated sodium channels (). An analogous procedure was used for the open conformation, with the KvAP crystal structure as template (Protein Data Bank accession no. 1ORQ) (). […]

Pipeline specifications

Software tools MODELLER, CHARMM
Application Protein structure analysis
Diseases Diabetes Insipidus, Neurogenic