Computational recognition of potassium channel sequences.
BACKGROUND
Potassium channels are mainly known for their role in regulating and maintaining the membrane potential. Since this is one of the key mechanisms of signal transduction, malfunction of these potassium channels leads to a wide variety of severe diseases. Thus potassium channels are priority targets of research for new drugs, despite the fact that this protein family is highly variable and closely related to other channels, which makes it very difficult to identify new types of potassium channel sequences.


RESULTS
Here we present a new method for identifying potassium channel sequences (PSM, Property Signature Method), which-in contrast to the known methods for protein classification-is directly based on physicochemical properties of amino acids rather than on the amino acids themselves. A signature for the pore region including the selectivity filter has been created, representing the most common physicochemical properties of known potassium channels. This string enables genome-wide screening for sequences with similar features despite a very low degree of amino acid similarity within a protein family.
Heil
Burkhard
B
Universität Bonn, IZMB Kirschallee 1, 53115 Bonn, Germany. Burkhard.Heil@gmail.com
Ludwig
Jost
J
Lichtenberg-Fraté
Hella
H
Lengauer
Thomas
T
D000465:Algorithms; D000595:Amino Acid Sequence; D000818:Animals; D019295:Computational Biology / Q000379:methods*; D016678:Genome; D016681:Genome, Fungal; D006801:Humans; D008969:Molecular Sequence Data; D015221:Potassium Channels / Q000737:chemistry*; D012441:Saccharomyces cerevisiae; D017386:Sequence Homology, Amino Acid; D015398:Signal Transduction; D012984:Software
D015221:Potassium Channels