Articles you may be interested inAn image-based reaction field method for electrostatic interactions in molecular dynamics simulations of aqueous solutions

A multitude of biological processes requires the participation of specific cations, such as H + , Na + , K + , Ca 2+ , and Mg 2+ . Many of these processes can take place only when proteins have the ability to discriminate between different ions with a very high fidelity. How this is possible is a fundamental question that has fascinated scientists for a long time. At the most fundamental level, it is anticipated that ion selectivity must result from a delicate balance of strong interactions. Yet, identifying and quantifying the key microscopic factors is difficult, as many of these cannot be directly measured by experiments. Theory and computations can contribute by providing a virtual route to complement the missing information. Because ion selectivity is often dominated by thermodynamic factors, detailed molecular dynamics (MD) free energy simulations become important tools. This was vividly illustrated early on with studies of ion solvation (Straatsma and Berendsen, 1988;Åqvist, 1990) and ion-selective systems (Lybrand et al., 1986;Grootenhuis and Kollman, 1989;Åqvist, 1992). These pioneering studies inspired our own efforts.In this Perspective, we aim to present our understanding of ion selectivity as it has evolved over approximately 15 years from studies based on various specific structures: gramicidin A channels (e.g.

Potassium (K+) channels are specialized membrane proteins able to facilitate and regulate the conduction of K+ ions through cell membranes. Comprising five specific cation binding sites (S0 to S4) formed by the backbone carbonyl groups of conserved residues common to all K+ channels, the narrow selectivity filter allows fast conduction of K+ while being highly selective for K+ ions over sodium (Na+) ions. To extend our knowledge of the microscopic mechanism underlying selectivity in K+ channels, we characterize the free energy landscapes governing the entry and translocation of a Na+ or a K+ ion from the extracellular side into the selectivity filter of KcsA. The entry process of an extracellular ion is examined in the presence of two additional K+ ions in the pore and the 3-ion potential of mean force (PMF) is computed using extensive all-atom umbrella sampling molecular dynamics simulations. A comparison of the PMFs yields a number of important results. First, the free energy minima corresponding to configurations with the extracellular K+ or Na+ ion in the binding site S0 or S1 are similar in depth, suggesting that the thermodynamic selectivity governed by the free energy minima for those two binding sites is insignificant. Second, the free energy barriers between the stable multi-ion configurations are generally higher for the Na+ ion than for the K+ ion, implying that the kinetics of ion conduction is slower when a Na+ enters the pore. Third, the region corresponding to the binding site S2 near the center of the narrow pore emerges as being the most selective for K+ over Na+. In particular, while there is a stable minimum for K+ in the site S2, the Na+ ion faces a steep free energy increase with no local free energy well in this region. Lastly, analysis shows that selectivity is not correlated with the overall coordination number of the ion entering the pore, but is predominantly affected by changes in the type of coordinating ligands (carbonyls versus water molecules). These results further highlight the importance of the central region near the binding site S2 in the selectivity filter of K+ channels.

Brownian dynamics (BD) in a suitably constructed potential of mean force is an efficient and accurate method for simulating ion transport through wide ion channels. Here, a web-based graphical user interface (GUI) is presented for grand canonical Monte Carlo (GCMC) BD simulations of channel proteins: http://www.charmm-gui.org/input/gcmcbd. The webserver is designed to help users avoid most of the technical difficulties and issues encountered in setting up and simulating complex pore systems. GCMC/BD simulation results for three proteins, the voltage dependent anion channel (VDAC), α-Hemolysin, and the protective antigen pore of the anthrax toxin (PA), are presented to illustrate system setup, input preparation, and typical output (conductance, ion density profile, ion selectivity, and ion asymmetry). Two models for the input diffusion constants for potassium and chloride ions in the pore are compared: scaling of the bulk diffusion constants by 0.5, as deduced from previous all-atom molecular dynamics simulations of VDAC; and a hydrodynamics based model (HD) of diffusion through a tube. The HD model yields excellent agreement with experimental conductances for VDAC and α-Hemolysin, while scaling bulk diffusion constants by 0.5 leads to underestimates of 10–20%. For PA, simulated ion conduction values overestimate experimental values by a factor of 1.5 to 7 (depending on His protonation state and the transmembrane potential), implying that the currently available computational model of this protein requires further structural refinement.

In a previous study of ion selectivity of α-hemolysin (αHL) in complex with β-cyclodextrin (βCD) adapter we calculated the potential of mean force (PMF) and characterized the self-diffusion coefficients of isolated K + and Cl − ions using molecular dynamics simulations [Y. Luo et al. Ion Selectivity of α-Hemolysin with β-Cyclodextrin Adapter: I. Single Ion Potential of Mean Force and Diffusion Coefficient]. In the present effort, these results pertaining to single isolated ions in the wide aqueous pore are extended to take into account multi-ion effects. The grand canonical Monte Carlo/ Brownian dynamics (GCMC/BD) algorithm is used to simulate ion currents through the wild type αHL ion channel, as well as two engineered αHL mutants, with and without the cyclic oligosaccaride βCD lodged in the lumen of the pore. The GCMC/BD current-voltage curves agree well with experimental results and show that βCD increases the anion selectivity of αHL. Comparisons between multi-ion PMFs from GCMC/BD simulations and single ion PMFs demonstrate that multi-ion effects and pore shape are crucial for explaining this behavior. It is concluded that the narrow βCD adapter increases the anion selectivity of αHL because it reduces the pore radius locally, which decreases the ionic screening and the dielectric shielding of the strong electrostatic field induced by a nearby ring of positively charged αHL side chains.