Imaging alpha-hemolysin with molecular dynamics: ionic conductance, osmotic permeability, and the electrostatic potential map

Aleksei Aksimentiev, and Klaus Schulten
Biophys J 88(6) 3745-61 (2005)
DOI:10.1529/biophysj.104.058727  PMID:15764651  BibTex


In a biological cell, membrane channels act like miniature valves regulating the flow of ions and other solutes between intracellular compartments and across the cell's boundary. Assembled in complex circuits, they generate, transmit, and amplify signals orchestrating cell function. To investigate how membrane channels work, a tiny patch of a cell membrane is isolated using an extremely fine pipette, and, in so-called patch clamp measurements, electric currents in response to applied electric potentials are determined. Dramatic increase in computational power and its efficient utilization by a massively parallel molecular dynamics code allows one today to reproduce such studies computationally, calculating the permeability of a membrane channel to ions, water, and solutes directly from its atomic structure. In what was one of the largest molecular dynamics simulations in 2005, one copy of the membrane channel α-hemolysin, submerged in a lipid membrane and water, was subject to an external electric field that drove ions, water, and DNA through the channel. Repeating simulations at several voltage biases yielded the current-voltage curve of α-hemolysin and a set of electrostatic potential maps. We observed sensitivity of the channel conductance to the solution pH, computed osmotic permeability of water through the transmembrane pore, and estimated water and ion fluxes through the side channels. The results of the simulations were found in excellent agreement with available experimental data. This study demonstrated for the first time the ability of molecular dynamics simulations to predict ionic conductance of a membrane channel starting from its X-ray structure. This study appeared in Biophysical Journal and has been cited more than 200 times.


alpha-Hemolysin of Staphylococcus aureus is a self-assembling toxin that forms a water-filled transmembrane channel upon oligomerization in a lipid membrane. Apart from being one of the best-studied toxins of bacterial origin, alpha-hemolysin is the principal component in several biotechnological applications, including systems for controlled delivery of small solutes across lipid membranes, stochastic sensors for small solutes, and an alternative to conventional technology for DNA sequencing. Through large-scale molecular dynamics simulations, we studied the permeability of the alpha-hemolysin/lipid bilayer complex for water and ions. The studied system, composed of approximately 300,000 atoms, included one copy of the protein, a patch of a DPPC lipid bilayer, and a 1 M water solution of KCl. Monitoring the fluctuations of the pore structure revealed an asymmetric, on average, cross section of the alpha-hemolysin stem. Applying external electrostatic fields produced a transmembrane ionic current; repeating simulations at several voltage biases yielded a current/voltage curve of alpha-hemolysin and a set of electrostatic potential maps. The selectivity of alpha-hemolysin to Cl(-) was found to depend on the direction and the magnitude of the applied voltage bias. The results of our simulations are in excellent quantitative agreement with available experimental data. Analyzing trajectories of all water molecule, we computed the alpha-hemolysin's osmotic permeability for water as well as its electroosmotic effect, and characterized the permeability of its seven side channels. The side channels were found to connect seven His-144 residues surrounding the stem of the protein to the bulk solution; the protonation of these residues was observed to affect the ion conductance, suggesting the seven His-144 to comprise the pH sensor that gates conductance of the alpha-hemolysin channel.