Noncontact Dipole Effects on Channel Permeation. IV. Kinetic Model of 5F-Trp13 Gramicidin A Currents

Abstract

Nonlinear least squares fitting was used to assign rate constants for the three-barrier, two-site, double-occupancy, single-filing kinetic model for previously reported current-voltage relations of (5F-Indole)Trp(13) gramicidin A and gramicidin A channels (, 75:2830-2844). By judicious coupling of parameters, it was possible to reduce the parameter space from 64 parameters to 24, and a reasonable fit consistent with other experimental data was obtained. The main features of the fit were that fluorination increased the rate constant for translocation by a factor of 2.33, consistent with a free energy change in the translocation barrier of -0.50 kcal/mol, and increased first-ion binding affinity by a factor of 1.13, primarily by decreasing the first-ion exit rate constant. The translocation rate constant was 5.62 times slower in diphytanoyl phosphatidylcholine (DPhPC) bilayers than in monoolein (GMO) bilayers (coupled for the four combinations of peptide and salt), suggesting a 44.2-mV difference in the projection of the interfacial dipole into the channel. Thus fluorination caused increased currents in DPhPC bilayers, where a high interfacial dipole potential makes translocation more rate limiting because the translocation barrier was reduced, and decreased currents in GMO bilayers, where ion exit or entry is rate limiting because these barriers were increased.

Gramicidin A Backbone and Side Chain Dynamics Evaluated by Molecular Dynamics Simulations and Nuclear Magnetic Resonance Experiments. I: Molecular Dynamics Simulations

“…The new Trp FF (P27+TRP), nevertheless, leads to predicted conductances that are in better agreement with experiments (cf. reference 47,57). Indeed, dCMAP and the new Trp parameterization have opposite effects on the gA channel K + and Na + PMFs.…”

Molecular dynamics simulations of Trp side‐chain conformational flexibility in the gramicidin A channel

“…When Trp11 started in o2 it remained in o2 67% of the time instead of changing to the i2 state. Interestingly, Trp9 did not vary from the pattern shown in Figure 5; the o1 state was very stable, whereas the o2 state was quite unstable.…”

“…The conformations of the Trp side chains in gA channels are interesting because the indole dipole appears to affect channel conductance 5–9. Recently, the importance of Trp side chains to the formation of low‐conductance channels by gramicidin A (gA) was demonstrated 10.…”

“…For Trp9 there is disagreement over whether the side chain is in the o1 state or in an alternative conformation, o2, which yields nearly equivalent chemical shifts in solid state NMR 12, 15–18. The o1 was the lowest energy conformation in a conformational search14 with a fixed backbone, but o2 and i1 have nearly the same conformational energy in the charmm force field.…”

Semimicroscopic Modeling of Permeation Energetics in Ion Channels

“…SMC studies using the electrical geometry of Fig. 2(c) treat the ion, channel waters, and carbonyls and amides of the backbone as mobile; the peptide's aryl residues and the membrane dipoles [53] impose a fixed background potential. A correction is used to compensate for Fig.…”