Classification of voltage-gated K(+) ion channels from 3D pseudo-folding graph representation of protein sequences using genetic algorithm-optimized support vector machines.
Voltage-gated K(+) ion channels (VKCs) are membrane proteins that regulate the passage of potassium ions through membranes. This work reports a classification scheme of VKCs according to the signs of three electrophysiological variables: activation threshold voltage (V(t)), half-activation voltage (V(a50)) and half-inactivation voltage (V(h50)). A novel 3D pseudo-folding graph representation of protein sequences encoded the VKC sequences. Amino acid pseudo-folding 3D distances count (AAp3DC) descriptors, calculated from the Euclidean distances matrices (EDMs) were tested for building the classifiers. Genetic algorithm (GA)-optimized support vector machines (SVMs) with a radial basis function (RBF) kernel well discriminated between VKCs having negative and positive/zero V(t), V(a50) and V(h50) values with overall accuracies about 80, 90 and 86%, respectively, in crossvalidation test. We found contributions of the "pseudo-core" and "pseudo-surface" of the 3D pseudo-folded proteins to the discrimination between VKCs according to the three electrophysiological variables.
Fernández
Michael
M
Molecular Modeling Group, Center for Biotechnological Studies, Faculty of Agronomy, University of Matanzas, 44740 Matanzas, Cuba. michael.fernandez@umcc.cu
Fernández
Leyden
L
Abreu
Jose Ignacio
JI
Garriga
Miguel
M
D000465:Algorithms; D000595:Amino Acid Sequence; D001185:Artificial Intelligence; D008969:Molecular Sequence Data; D024642:Potassium Channels, Voltage-Gated / Q000737:chemistry* / Q000145:classification* / Q000235:genetics; D017510:Protein Folding; D015203:Reproducibility of Results
D024642:Potassium Channels, Voltage-Gated