Biological-to-electronic interface with pores of ATP synthase subunit C in silicon nitride barrier

Polymer amide as an early topology

Hydrophobic polymer amide (HPA) could have been one of the first normal density materials to accrete in space. We present ab initio calculations of the energetics of amino acid polymerization via gas phase collisions. The initial hydrogen-bonded di-peptide is sufficiently stable to proceed in many cases via a transition state into a di-peptide with an associated bound water molecule of condensation. The energetics of polymerization are only favorable when the water remains bound. Further polymerization leads to a hydrophobic surface that is phase-separated from, but hydrogen bonded to, a small bulk water complex. The kinetics of the collision and subsequent polymerization are discussed for the low-density conditions of a molecular cloud. This polymer in the gas phase has the properties to make a topology, viz. hydrophobicity allowing phase separation from bulk water, capability to withstand large temperature ranges, versatility of form and charge separation. Its flexible tetrahedral carbon atoms that alternate with more rigid amide groups allow it to deform and reform in hazardous conditions and its density of hydrogen bonds provides adhesion that would support accretion to it of silicon and metal elements to form a stellar dust material.

Pore-spanning lipid membrane under indentation by a probe tip: a molecular dynamics simulation study

We study the indentation of a free-standing lipid membrane suspended over a nanopore on a hydrophobic substrate by means of molecular dynamics simulations. We find that in the course of indentation the membrane bends at the point of contact and the fringes of the membrane glide downward intermittently along the pore edges and stop gliding when the fringes reach the edge bottoms. The bending continues afterward, and the large strain eventually induces a phase transition in the membrane, transformed from a bilayered structure to an interdigitated structure. The membrane is finally ruptured when the indentation goes deep enough. Several local physical quantities in the pore regions are calculated, which include the tilt angle of lipid molecules, the nematic order, the included angle, and the distance between neighboring lipids. The variations of these quantities reveal many detailed, not-yet-specified local structural transitions of lipid molecules under indentation. The force-indentation curve is also studied and discussed. The results make a connection between the microscopic structure and the macroscopic properties and provide deep insight into the understanding of the stability of a lipid membrane spanning over nanopore.

Entrapment of water by subunit c of ATP synthase

We consider an ancient protein, and water as a smooth surface, and show that the interaction of the two allows the protein to change its hydrogen bonding to encapsulate the water. This property could have made a three-dimensional microenvironment, 3-4 Gyr ago, for the evolution of subsequent complex water-based chemistry. Proteolipid, subunit c of ATP synthase, when presented with a water surface, changes its hydrogen bonding from an alpha-helix to beta-sheet-like configuration and moves away from its previous association with lipid to interact with water surface molecules. Protein sheets with an intra-sheet backbone spacing of 3.7A and inter-sheet spacing of 6.0 A hydrogen bond into long ribbons or continuous surfaces to completely encapsulate a water droplet. The resulting morphology is a spherical vesicle or a hexagonal crystal of water ice, encased by a skin of subunit c. Electron diffraction shows the crystals to be highly ordered and compressed and the protein skin to resemble beta-sheets. The protein skin can retain the entrapped water over a temperature rise from 123 to 223 K at 1 x 10(-4) Pa, whereas free water starts to sublime significantly at 153 K.

Integrated electrodes on a silicon based ion channel measurement platform

We demonstrate the microfabrication of a low-noise silicon based device with integrated silver/silver chloride electrodes used for the measurement of single ion channel proteins. An aperture of 150 microm diameter was etched in a silicon substrate using a deep silicon reactive ion etcher and passivated with 30 nm of polytetrafluoroethylene via chemical vapor deposition. The average recorded noise in measurements of lipid bilayers was reduced by a factor of four through patterning of a 75 microm thick SU-8 layer around the aperture. Integrated electrodes were fabricated on both sides of the device and used for repeatable, stable, giga-seal bilayer formations as well as characteristic measurements of the transmembrane protein OmpF porin.

Transport across artificial membranes–an analytical perspective

Biosensors that make use of transport processes across lipid membranes are very rare even though a stimulus, the binding of a single analyte molecule, can enhance the sensor response manifold if the analyte leads to the transport of more than one ion or molecule across the membrane. Prerequisite for a proper function of such membrane based biosensors is the formation of lipid bilayers attached to a support that allow for the insertion of membrane peptides and proteins in a functional manner. In this review, the current state of the art technologies to obtain lipid membranes on various supports are described. Solid supported membranes on transparent and electrically conducting surfaces, lipid bilayers on micromachined apertures and on porous materials are discussed. The focus lies on the applicability of such membranes for the investigation of transport phenomena across lipid bilayers facilitated by membrane embedded peptides, channel proteins and transporters. Carriers and channel forming peptides, which are easy to handle and rather robust, are used frequently to build up membrane based biosensors. However, channel forming proteins and transporters are more difficult to insert functionally and thus, there are yet only few examples that demonstrate the applicability of such systems as biosensor devices.

Microfabricated teflon membranes for low-noise recordings of ion channels in planar lipid bilayers

We present a straightforward, accessible method for the fabrication of micropores with diameters from 2 to 800 micro m in films of amorphous Teflon (Teflon AF). Pores with diameters </=40 micro m made it possible to record ion fluxes through ion channels in planar bilayers with excellent signal characteristics. These pores afforded: i), stable measurements at transmembrane voltages up to 460 mV; ii), recordings at low noise levels (0.4 pA rms at 4.3 kHz bandwidth); iii), recordings at high effective bandwidth (10.7 kHz); and iv), formation of multiple planar lipid bilayers in parallel. Microfabricated pores in films of Teflon AF made it possible to examine, experimentally and theoretically, the influence of the pore diameter on the current noise in planar bilayer recordings. Reducing the pore diameter below 40 micro m mainly increased the stability of the planar bilayers, but had only a small effect on the level of the current noise. The low-noise properties of bilayer recordings on micropores in Teflon AF films were exploited to record the smallest conductance state of alamethicin (24 pS) at an unprecedentedly high bandwidth of 10.7 kHz.

Stochastic sensors inspired by biology

Sensory systems use a variety of membrane-bound receptors, including responsive ion channels, to discriminate between a multitude of stimuli. Here we describe how engineered membrane pores can be used to make rapid and sensitive biosensors with potential applications that range from the detection of biological warfare agents to pharmaceutical screening. Notably, use of the engineered pores in stochastic sensing, a single-molecule detection technology, reveals the identity of an analyte as well as its concentration.