Differential Enzyme Flexibility Probed Using Solid-State Nanopores.

Enzymes and motor proteins are dynamic macromolecules that coexist in a number of conformations of similar energies. Protein function is usually accompanied by a change in structure and flexibility, often induced upon binding to ligands. However, while measuring protein flexibility changes between active and resting states is of therapeutic significance, it remains a challenge. Recently, our group has demonstrated that breadth of signal amplitudes in measured electrical signatures as an ensemble of individual protein molecules is driven through solid-state nanopores and correlates with protein conformational dynamics. Here, we extend our study to resolve subtle flexibility variation in dihydrofolate reductase mutants from unlabeled single molecules in solution. We first demonstrate using a canonical protein system, adenylate kinase, that both size and flexibility changes can be observed upon binding to a substrate that locks the protein in a closed conformation. Next, we investigate the influence of voltage bias and pore geometry on the measured electrical pulse statistics during protein transport. Finally, using the optimal experimental conditions, we systematically study a series of wild-type and mutant dihydrofolate reductase proteins, finding a good correlation between nanopore-measured protein conformational dynamics and equilibrium bulk fluorescence probe measurements. Our results unequivocally demonstrate that nanopore-based measurements reliably probe conformational diversity in native protein ensembles.

Nanopore-Based Measurements of Protein Size, Fluctuations, and Conformational Changes.

Proteins are structurally dynamic macromolecules, and it is challenging to quantify the conformational properties of their native state in solution. Nanopores can be efficient tools to study proteins in a solution environment. In this method, an electric field induces electrophoretic and/or electro-osmotic transport of protein molecules through a nanopore slightly larger than the protein molecule. High-bandwidth ion current measurement is used to detect the transit of each protein molecule. First, our measurements reveal a correlation between the mean current blockade amplitude and the radius of gyration for each protein. Next, we find a correlation between the shape of the current signal amplitude distributions and the protein fluctuation as obtained from molecular dynamics simulations. Further, the magnitude of the structural fluctuations, as probed by experiments and simulations, correlates with the ratio of α-helix to ß-sheet content. We highlight the resolution of our measurements by resolving two states of calmodulin, a canonical protein that undergoes a conformational change in response to calcium binding.

Direct and Scalable Deposition of Atomically Thin Low-Noise MoS2 Membranes on Apertures.

Molybdenum disulfide (MoS2) flakes can grow beyond the edge of an underlying substrate into a planar freestanding crystal. When the substrate edge is in the form of an aperture, reagent-limited nucleation followed by edge growth facilitate direct and selective growth of freestanding MoS2 membranes. We have found conditions under which MoS2 grows preferentially across micrometer-scale prefabricated solid-state apertures in silicon nitride membranes, resulting in sealed membranes that are one to a few atomic layers thick. We have investigated the structure and purity of our membranes by a combination of atomic-resolution transmission electron microscopy, elemental analysis, Raman spectroscopy, photoluminescence spectroscopy, and low-noise ion-current recordings through nanopores fabricated in such membranes. Finally, we demonstrate the utility of fabricated ultrathin nanopores in such membranes for single-stranded DNA translocation detection.

Programmed synthesis of freestanding graphene nanomembrane arrays.

Freestanding graphene membranes are unique materials. The combination of atomically thin dimensions, remarkable mechanical robustness, and chemical stability make porous and non-porous graphene membranes attractive for water purification and various sensing applications. Nanopores in graphene and other 2D materials have been identified as promising devices for next-generation DNA sequencing based on readout of either transverse DNA base-gated current or through-pore ion current. While several ground breaking studies of graphene-based nanopores for DNA analysis have been reported, all methods to date require a physical transfer of the graphene from its source of production onto an aperture support. The transfer process is slow and often leads to tears in the graphene that render many devices useless for nanopore measurements. In this work, we report a novel scalable approach for site-directed fabrication of pinhole-free graphene nanomembranes. Our approach yields high quality few-layer graphene nanomembranes produced in less than a day using a few steps that do not involve transfer. We highlight the functionality of these graphene devices by measuring DNA translocation through electron-beam fabricated nanopores in such membranes.

Branched polymer models and the mechanism of multilayer film buildup.

The "in and out diffusion" hypothesis does not provide a conclusive explanation of the buildup displayed by some polyelectrolyte multilayer film systems. Here, we report initial tests of an alternative hypothesis, on which the completion of each adsorption cycle results in an increase in the number of polymer binding sites on the film surface. Polycationic dendrimeric peptides, which can potentially bind several oppositely-charged peptides each, have been designed, synthesized and utilized in comparative film buildup experiments. Material deposited, internal film structure and film surface morphology have been studied by ultraviolet spectroscopy (UVS), circular dichroism spectroscopy (CD), quartz crystal microbalance (QCM) and atomic force microscopy (AFM). Polycations tended to contribute more to film buildup than did polyanions on quartz but not on gold. Increasing the number of branches in the dendrimeric peptides from 4 to 8 reproducibly resulted in an increase in the film growth rate on quartz but not on gold. Peptide backbones tended to adopt a ß-strand conformation on incorporation into a film. Thicker films had a greater surface roughness than thin films. The data are consistent with film buildup models in which the average number of polymer binding sites will increase with each successive adsorption cycle in the range where exponential growth is displayed.

"In and out diffusion" hypothesis of exponential multilayer film buildup revisited.

A hypothesis concerning the exponential buildup of polyelectrolyte multilayer films prepared by layer-by-layer assembly has become widely accepted in the scientific community. This model was first introduced with experimental data in Langmuir. It was subsequently described in Proceedings of the National Academy of Sciences and extended and amended in papers in Langmuir and other journals. According to the "in and out diffusion" hypothesis, as it is called, or "common rule" of exponential multilayer film buildup, as it is widely regarded, "a diffusion-based buildup mechanism ... explains most of the exponential-like growth process of polyelectrolyte multilayers reported in the literature." The present work offers an alternative viewpoint to specific elements of the hypothesis and the model as a whole.