Single-molecule lysozyme dynamics monitored by an electronic circuit

Plasma-enabled graded nanotube biosensing arrays on a Si nanodevice platform: catalyst-free integration and in situ detection of nucleation events

Low-temperature plasmas in direct contact with arbitrary, written linear features on a Si wafer enable catalyst-free integration of carbon nanotubes into a Si-based nanodevice platform and in situ resolution of individual nucleation events. The graded nanotube arrays show reliable, reproducible, and competitive performance in electron field emission and biosensing nanodevices.

Origins of charge noise in carbon nanotube field-effect transistor biosensors

Determining the major noise sources in nanoscale field-effect transistor (nanoFET) biosensors is critical for improving bioelectronic interfaces. We use the carbon nanotube (CNT) FET biosensor platform to examine the noise generated by substrate interactions and surface adsorbates, both of which are present in current nanoFET biosensors. The charge noise model is used as a quantitative framework to show that insulating substrates and surface adsorbates are both significant contributors to the noise floor of CNT FET biosensors. Removing substrate interactions and surface adsorbates reduces the power spectral density of background voltage fluctuations by 19-fold.

Not all protein-mediated single-wall carbon nanotube dispersions are equally bioactive

Single-wall carbon nanotubes (SWCNTs) have been dispersed with proteins to increase biocompatibility and specificity, but examinations of dispersion parameters on functional cellular uptake are required for utilization of SWCNTs in biological applications. Here we correlate conditions of SWCNT dispersion with various proteins to uptake these SWCNTs in NIH-3T3 fibroblasts and J774A.1 macrophage-like cells. We varied protein types (bovine serum albumin - BSA, lysozyme - LSZ, and γ-globulins - γG), protein : SWCNT ratio and sonication time. Each protein created stable, high yield (~25%) dispersions in water while preserving intrinsic SWCNT fluorescence, but SWCNT-LSZ flocculated in media and SWCNT-γG formed clusters in both water and media, drastically altering cellular internalization. Dispersion quality and yield improved with increased protein : SWCNT - without substantial effects from depletion attraction, even at 100 : 1 protein : SWCNT - and slightly increased internalized SWCNTs for both NIH-3T3 and J774A.1 cells. Longer sonication time (12 versus 2 h) improved the dispersion yield and quality but caused minor damage to SWCNTs and altered protein structure. Cell association of SWCNT-BSA was homogenous and unaltered by sonication time. Bulk assay showed that cell association of SWCNT-LSZ and SWCNT-γG was altered with 12 versus 2 h sonication, but imaging of individual cells showed that these differences are likely from precipitation of clusters of SWCNT-LSZ and SWCNT-γG in media onto cells. Hence, the quality of SWCNT-protein dispersions in water does not necessarily correlate with bulk cellular uptake, and quantification at the level of individual cells is required to determine delivery efficacy.

Graphene: an emerging electronic material

Graphene, a single layer of carbon atoms in a honeycomb lattice, offers a number of fundamentally superior qualities that make it a promising material for a wide range of applications, particularly in electronic devices. Its unique form factor and exceptional physical properties have the potential to enable an entirely new generation of technologies beyond the limits of conventional materials. The extraordinarily high carrier mobility and saturation velocity can enable a fast switching speed for radio-frequency analog circuits. Unadulterated graphene is a semi-metal, incapable of a true off-state, which typically precludes its applications in digital logic electronics without bandgap engineering. The versatility of graphene-based devices goes beyond conventional transistor circuits and includes flexible and transparent electronics, optoelectronics, sensors, electromechanical systems, and energy technologies. Many challenges remain before this relatively new material becomes commercially viable, but laboratory prototypes have already shown the numerous advantages and novel functionality that graphene provides.

Test of normality for integrated change point detection and mixture modeling

Single-molecule data often show step-like changes in the quantity measured between constant levels. Analysis of this data consists of detecting the steps, i.e., change point detection (CPD), and determining the levels, i.e., clustering. We describe a novel algorithm which integrates these two analyses, based on a statistical test of a normal distribution. The test of normality (TON) algorithm integrates statistical CPD with gaussian mixture model clustering. We used TON with both simulated data and ion channel patch-clamp recordings. It performed well with simulated data except at a high signal-to-noise ratio and when the frequency of steps was high compared to the sampling frequency. TON has advantages over separate CPD and mixture modeling algorithms, especially for complex single-molecule data. This was illustrated by its application to the maxichannel, an ion channel with multiple subconductance states.

Direct observation of T4 lysozyme hinge-bending motion by fluorescence correlation spectroscopy

Bacteriophage T4 Lysozyme (T4L) catalyzes the hydrolysis of the peptidoglycan layer of the bacterial cell wall late in the infection cycle. It has long been postulated that equilibrium dynamics enable substrate access to the active site located at the interface between the N- and C-terminal domains. Crystal structures of WT-T4L and point mutants captured a range of conformations that differ by the hinge-bending angle between the two domains. Evidence of equilibrium between open and closed conformations in solution was gleaned from distance measurements between the two domains but the nature of the equilibrium and the timescale of the underlying motion have not been investigated. Here, we used fluorescence fluctuation spectroscopy to directly detect T4L equilibrium conformational fluctuations in solution. For this purpose, Tetramethylrhodamine probes were introduced at pairs of cysteines in regions of the molecule that undergo relative displacement upon transition from open to closed conformations. Correlation analysis of Tetramethylrhodamine intensity fluctuations reveals hinge-bending motion that changes the relative distance and orientation of the N- and C-terminal domains with ≅ 15 μs relaxation time. That this motion involves interconversion between open and closed conformations was further confirmed by the dampening of its amplitude upon covalent substrate trapping. In contrast to the prevalent two-state model of T4L equilibrium, molecular brightness and number of particles obtained from cumulant analysis suggest that T4L populates multiple intermediate states, consistent with the wide range of hinge-bending angles trapped in the crystal structure of T4L mutants.

Possible origin of life between mica sheets: does life imitate mica?

The mica hypothesis for the origin of life proposes that life originated between the sheets of muscovite mica. This paper elaborates on two ways that life resembles what might have originated between mica sheets. First, enzymes: The configurations and dynamics of enzymes, with their substrates, cofactors, and sometimes transition metal ions, often resemble mica sheets, with their open-and-shut motions, acting on small molecules between them, sometimes assisted by transition metal ions. Second, organisms: Mica world had the potential to be a community or ecosystem of prebiotic organisms in a way unlike other models for the origin of life.

Quantitative nanoscale visualization of heterogeneous electron transfer rates in 2D carbon nanotube networks

Carbon nanotubes have attracted considerable interest for electrochemical, electrocatalytic, and sensing applications, yet there remains uncertainty concerning the intrinsic electrochemical (EC) activity. In this study, we use scanning electrochemical cell microscopy (SECCM) to determine local heterogeneous electron transfer (HET) kinetics in a random 2D network of single-walled carbon nanotubes (SWNTs) on an Si/SiO(2) substrate. The high spatial resolution of SECCM, which employs a mobile nanoscale EC cell as a probe for imaging, enables us to sample the responses of individual portions of a wide range of SWNTs within this complex arrangement. Using two redox processes, the oxidation of ferrocenylmethyl trimethylammonium and the reduction of ruthenium (III) hexaamine, we have obtained conclusive evidence for the high intrinsic EC activity of the sidewalls of the large majority of SWNTs in networks. Moreover, we show that the ends of SWNTs and the points where two SWNTs cross do not show appreciably different HET kinetics relative to the sidewall. Using finite element method modeling, we deduce standard rate constants for the two redox couples and demonstrate that HET based solely on characteristic defects in the SWNT side wall is highly unlikely. This is further confirmed by the analysis of individual line profiles taken as the SECCM probe scans over an SWNT. More generally, the studies herein demonstrate SECCM to be a powerful and versatile method for activity mapping of complex electrode materials under conditions of high mass transport, where kinetic assignments can be made with confidence.

Single enzyme studies reveal the existence of discrete functional states for monomeric enzymes and how they are "selected" upon allosteric regulation

Allosteric regulation of enzymatic activity forms the basis for controlling a plethora of vital cellular processes. While the mechanism underlying regulation of multimeric enzymes is generally well understood and proposed to primarily operate via conformational selection, the mechanism underlying allosteric regulation of monomeric enzymes is poorly understood. Here we monitored for the first time allosteric regulation of enzymatic activity at the single molecule level. We measured single stochastic catalytic turnovers of a monomeric metabolic enzyme (Thermomyces lanuginosus Lipase) while titrating its proximity to a lipid membrane that acts as an allosteric effector. The single molecule measurements revealed the existence of discrete binary functional states that could not be identified in macroscopic measurements due to ensemble averaging. The discrete functional states correlate with the enzyme's major conformational states and are redistributed in the presence of the regulatory effector. Thus, our data support allosteric regulation of monomeric enzymes to operate via selection of preexisting functional states and not via induction of new ones.

Single-molecule dynamics of lysozyme processing distinguishes linear and cross-linked peptidoglycan substrates

The dynamic processivity of individual T4 lysozyme molecules was monitored in the presence of either linear or cross-linked peptidoglycan substrates. Single-molecule monitoring was accomplished using a novel electronic technique in which lysozyme molecules were tethered to single-walled carbon nanotube field-effect transistors through pyrene linker molecules. The substrate-driven hinge-bending motions of lysozyme induced dynamic electronic signals in the underlying transistor, allowing long-term monitoring of the same molecule without the limitations of optical quenching or bleaching. For both substrates, lysozyme exhibited processive low turnover rates of 20-50 s(-1) and rapid (200-400 s(-1)) nonproductive motions. The latter nonproductive binding events occupied 43% of the enzyme's time in the presence of the cross-linked peptidoglycan but only 7% with the linear substrate. Furthermore, lysozyme catalyzed the hydrolysis of glycosidic bonds to the end of the linear substrate but appeared to sidestep the peptide cross-links to zigzag through the wild-type substrate.