Molecular dynamics simulation of the cytosolic mouth in Kcv-type potassium channels.
The functional effect of mutations near the intracellular mouth of the short viral Kcv potassium channel was studied by molecular dynamics simulations. As a model system we used the analogously mutated and truncated KirBac1.1, a channel with known crystal structure that shares genuine local sequence motifs with Kcv. By a novel simulated annealing methodology for structural averaging, information about the structure and dynamics of the intracellular mouth was extracted and complemented by Poisson-Boltzmann and 3D-RISM (reference interaction site model) integral equation theory for the determination of the K+ free energy surface. Besides the wild-type analogue of Kcv with its experimental reference activity (truncated KirBac1.1), two variants were studied: a deletion mutant where the N-terminus is further truncated by eight amino acids, showing inactivity in the Kcv reference system, and a point mutant where the kink-forming proline at position 13 is substituted by alanine, resulting in hyperactivity. The computations reveal that the change of activity is closely related to a hydrophilic intracellular constriction formed by the C-terminal residues of the monomers. Hyperactivity of the point mutant is correlated with both sterical and electrostatic factors, while inactivity of the deletion mutant is related to a loss of specific salt bridge patterns between the C- and N-terminus at the constriction and to the consequences for ion passage barriers, as revealed by integral equation theory. The cytosolic gate, however, is probably formed by the N-terminal segment up to the proline kink and not by the constriction. The results are compared with design principles found for other channels.
Tayefeh
Sascha
S
Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Petersenstrasse 20, 64287 Darmstadt, Germany.
Kloss
Thomas
T
Thiel
Gerhard
G
Hertel
Brigitte
B
Moroni
Anna
A
Kast
Stefan M
SM
D000595:Amino Acid Sequence; D003198:Computer Simulation; D008958:Models, Molecular; D008969:Molecular Sequence Data; D015221:Potassium Channels / Q000737:chemistry* / Q000235:genetics; D024661:Potassium Channels, Inwardly Rectifying / Q000737:chemistry*; D016415:Sequence Alignment; D013816:Thermodynamics; D014764:Viral Proteins / Q000737:chemistry* / Q000235:genetics
C405463:Kcv potassium channel, Chlorella virus; D015221:Potassium Channels; D024661:Potassium Channels, Inwardly Rectifying; D014764:Viral Proteins