Permeation through nanochannels: revealing fast kinetics

Abstract

The permeation of water soluble molecules across cell membranes is controlled by channel-forming proteins and, in particular, the channel surface determines the selectivity. An adequate method to study the properties of these channels is electrophysiology and, in particular, analyzing the ion current fluctuation in the presence of permeating solutes. Ion current fluctuation analysis provides information on possible interactions of solutes with the channel surface. Due to the limited time resolution, fast permeation events are not visible using standard techniques. Here, we demonstrate that miniaturization of the lipid bilayer; varying the temperature or changing the solvent may enhance the resolution. Although electrophysiology is considered as a single molecule technique, it does not provide atomic resolution. Molecular details of solute permeation can be revealed by combining electrophysiology and all-atom computer modeling; these methods include ion conductance, selectivity, ion pair formation, and rate limiting interactions of the solute with the channel walls during permeation.

Structural Insights into Outer Membrane Permeability of Acinetobacter baumannii

“…The observation that OccAB1 shows liposome swelling uptake rates similar to those of the well-studied OmpF porin from E. coli is surprising, given that the OccAB1 pore is smaller and its channel conductance fluctuates strongly. By comparison, OmpF has a stable conductance of $4 nS for the trimer (Mahendran et al, 2010). Therefore, and on a more fundamental level, we have to ask whether the observed high uptake via OccAB1 is consistent with the low-permeability OM of A. baumannii.…”

Constant electric field simulations of the membrane potential illustrated with simple systems

“…However, non-equilibrium properties are more sensitive to the finite system size due to changes in the resistance and long-range dissipative effects. In part owing to its simplicity, the method has been applied in several simulation studies of membrane systems, including ion permeation in proteins and nanopores [20–26], electroporation [31–34], translocation of molecules through nanopores [33, 35–40], and conformational transitions in biological systems [41–43]. …”

“…The pioneering application of the constant electric field approach in Aksimentiev and Schulten (2005) [20] demonstrated its ability to quantitatively determine the conductance of a membrane channel from only its X-ray structure. This approach has also been successfully used in many other applications studying ion conduction [21–26], voltage-regulated water flux [27–29], insertion of peptides into membranes [30], electroporation [31–34], translocation of DNA, ions, and large biomolecules through nanopores [33, 35–40], and induced conformational changes of membrane proteins [41–43]. …”

Channel-Forming Bacterial Toxins in Biosensing and Macromolecule Delivery

“…Currently, one of the greatest problems hampering the study of polymer transport and nucleic acid pore-assisted sequencing is the high translocation rate of these molecules. Several approaches have been developed to slow down the single-molecule transport through a protein nanopore [ 192 , 350 , 351 , 352 ]. Thus, genetically optimized porin MspA of Myobacterium smegmatis is believed [ 19 ] to be a promising pore for biosensing and sequencing applications due to its conical shape providing a very narrow (~10-Å) sensing zone [ 194 ].…”