Computerstudien zur Physik von Ionenkanälen
Zusammenfassung der Projektergebnisse
Permeation of physiological ions such as K+, Na+, Cl- and Ca2+ across porins play an important physiological role. Here, using a step-by-step multi-scale approach based on coarse grain simulations, free energy umbrella sampling calculations, and hybrid Car-Parrinello QM/MM simulations, we have characterized the selectivity mechanisms and energetics associated with the permeation of physiological ions through the bacterial porin NanC. An understanding of these mechanisms may stimulate engineering of protein mutants with different selectivity. We first used coarse grain Charge-Space Competition (CSC) Monte Carlo-simulations to provide the more likely ion pathways along the pore. To achieve this goal we have successfully modified the traditional CSC Monte Carlo simulation code to include limited atomistic detail of ion channel proteins, namely the position and mobility of atoms, relative to the centre of mass of the protein. The modified program was able to demonstrate enhanced Na+ versus Ca2+ selectivity for a topological model of the mammalian Na+ (DEKA) channel. With this approach, we calculated the maximum probability pathways for these ions. Then, based on atomistic force field-based umbrella sampling calculations, we derived the free energy profiles for Cl- and K+ permeation through the pore of NanC. The reaction coordinate was guessed according to the maximum probability pathways calculated by CSC simulations. This approach allowed the identification of distinct pathways for both ions, depending on the distribution of charged residues along the pore. Both the Cl- and K+ ion densities were distributed across the region along the tracks of electropositive residues in the porin (facing each other on opposite sides of the pore), where the two tracks exist together, rather than localizing on one positive track or the other. Several local and small free energy barriers for the permeation were observed. They range between 1 and 3 kJ/mol for Cl- and between 1 and 7 kJ/mol for K+. They could all essentially be described by transitions between binding sites. The calculations suggested that the free energy barrier for Cl- is slightly lower than for K+, in agreement with the experimentally observed weak Cl- over K+ selectivity. Finally, we used selected configurations corresponding to minima of ion's permeation free energy to carry out the first DFT-based QM/MM study on ion permeation in the porin NanC. Preliminary results show that polarization effects of protein groups interacting with K+ ions are sizeable and that water molecules can replace some protein residues in the ion's coordination shell. These calculations address key issues regarding the force field accuracy of the ions since polarization effects and hydration might play a role for selectivity mechanisms. Based on our theoretical and computational findings Prof. Eisenberg's lab plans to engineer K+ selective ion channels via site-directed mutagenesis. Recently, we have further improved the CSC approach by including a model of ion hydration state, which extends the existing Eisenman's model of ion selectivity. This scheme has been used to predict the selectivity for three cation selective channel sub-types (K+, Na+ and Ca2+) with known X-ray structures. The model presented is very general and may greatly simplify future computational prediction of selectivity in cation channels.
Projektbezogene Publikationen (Auswahl)
- Ion permeation in the NanC Porin from Escherichia coli: free energy calculations along pathways identified by coarsegrain simulations, J. Phys. Chem. B 2013. 117: p. 13534–13542
Dreyer J., P. Strodel, E. Ippoliti, J. Finnerty, R. Eisenberg, P. Carloni
(Siehe online unter https://doi.org/10.1021/jp4081838) - Localizing the Charged Side Chains of Ion Channels within the Crowded Charge Models. Journal of Chemical Theory and Computation 2013. 9(1): p 766-773
Finnerty J. J., R. Eisenberg, P. Carloni
(Siehe online unter https://doi.org/10.1021/ct300768j) - Cation Selectivity in Biological Cation Channels Using Experimental Structural Information and Statistical Mechanical Simulation. PLoS ONE 10(10): e0138679, 2015
Finnerty J., Peyser A., and Carloni P.
(Siehe online unter https://doi.org/10.1371/journal.pone.0138679)
