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Hydropathic Analysis and Comparison of KcsA and Shaker Potassium Channels
Author(s) -
Peng Yong,
Scarsdale J. Neel,
Kellogg Glen E.
Publication year - 2007
Publication title -
chemistry and biodiversity
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.427
H-Index - 70
eISSN - 1612-1880
pISSN - 1612-1872
DOI - 10.1002/cbdv.200790211
Subject(s) - kcsa potassium channel , shaker , chemistry , potassium channel , transmembrane domain , alamethicin , molecular dynamics , biophysics , gating , crystallography , ion channel , biochemistry , membrane , biology , computational chemistry , physics , receptor , quantum mechanics , vibration
The similarity in structure of potassium (K + ) channels from different families has been revealed by only recently available crystallographic 3D structural data. The hydropathic analysis presented in this work illuminates whether homologous residues perform the same functions in channels that use different gating mechanisms. We calculated and compared the hydropathic profiles of two K + channels, KcsA and Kv1.2 (the latter a member of the Shaker family), at their pore‐forming domain. Quantitative information describing important interactions stabilizing the protein beyond obvious secondary‐structure elements was extracted from the analysis and applied as a template for subsequent molecular‐dynamics (MD) analyses. For example, two key groups of interactions, defining the turns that connect the transmembrane helices and responsible for the orientation of the pore helix, were identified. Our results also indicate that Asp 80 and Asp 379 play a similar role in stabilizing the P‐loop of KcsA and Kv1.2, respectively, but to significantly different extents.