Low Noise Hybrid Nanopore with Engineered OmpG and Bilayer MoS2.

Hybrid nanopores combine the durability of a solid-state nanopore with the precise structure of a biological nanopore. When a DNA strand is pulled electrophoretically through a solid-state nanopore it can be sensed using the ionic blockade current produced by each translocating molecule. However, owing to the lack of chemical specificity and pore size reproducibility, solid-state nanopore sensing suffers from poor repeatability. Biological nanopores which have a constant geometry ensure sensitive and repeatable sensing. In this study, hybrid nanopores were formed by insertion of a engineered outer membrane porin G (eOmpG) in a bilayer (BL) molybdenum disulfide (MoS2) solid-state nanopore. Engineered outer membrane porin G (eOmpG) is used as the biological counterpart of the hybrid nanopore due to its uniform cylindrical geometry and controlled gating useful for specific detection of label-free analytes. BL MoS2 is used as the solid-state support for the hybrid construct owing to its surface charge and 2D layered properties, which ensures a stable support with low capacitive noise, favorable for precise sensing. To realize the hybried nanopore a single eOmpG was electrophoretically pulled through a 3.4 nm BL MoS2 solid-state nanopore at neutral pH and +80 mV trans bias. A hybrid BL MoS2-eOmpG nanopore was found to demonstrate 32% lower noise levels with nearly 1.9 times improved in the signal-to-noise ratio (SNR) and 6.5 times longer dwell times for dA30 molecular sensing compared to the BL MoS2 solid-state nanopore. Thus, the low-noise biocompatible platform of the hybrid BL MoS2-eOmpG nanopore can be used for highly resolved biomolecular sensing.

Enhanced overexpression, purification of a channelrhodopsin and a fluorescent flux assay for its functional characterization.

Channelrhodopsins (ChRs) are a group of membrane proteins that allow cation flux across the cellular membrane when stimulated by light. They have been emerged as important tools in optogenetics where light is used to trigger a change in the membrane potential of live cells which induces downstream physiological cascades. There is also increased interest in their applications for generating light-responsive biomaterials. Here we have used a two-step screening protocol to develop a Pichia pastoris strain that produces superior yields of an enhance variant of CaChR2 (from Chlamydomonas reinhardtii), called ChIEF. We have also studied the effect of the co-factor, namely all-trans retinal (ATR), on the recombinant overexpression, folding, and function of the protein. We found that both ChIEF-mCitrine and CaChR2 can be overexpressed and properly trafficked to the plasma membrane in yeast regardless of the presence of the ATR. The purified protein was reconstituted into large unilamellar lipid vesicle using the detergent-assisted method. Using 9-amino-6-chloro-2-methoxyacridine (ACMA) as the fluorescent proton indicator, we have developed a flux assay to verify the light-activated proton flux in the ChIEF-mCitrine vesicles. Hence such vesicles are effectively light-responsive nano-compartments. The results presented in this work lays foundations for creating bio-mimetic materials with a light-responsive function using channelrhodopsins.

Immobilization of membrane proteins on solid supports using functionalized ß-sheet peptides and click chemistry.

We have developed two functionalized ß-sheet peptides (FBPs) and demonstrated that they can stabilize a variety of integral membrane proteins (IMPs), and most importantly allow covalent crosslinking of the IMPs onto solid supports via the highly selective click chemistry. The FBPs are promising tools for the preparation of IMP-based biomaterials or biosensors.

Biofunctionalized silicon nitride platform for sensing applications.

Silicon nitride (SiNx) based biosensors have the potential to converge on the technological achievements of semiconductor microfabrication and biotechnology. Development of biofunctionalized SiNx surface and its integration with other devices will allow us to integrate the biosensing capability with probe control, data acquisition and data processing. Here we use the hydrogen plasma generated by inductively coupled plasma-reactive ion etching (ICP-RIE) technique to produce amino-functionality on the surface of SiNx which can then be readily used for biomolecule immobilization. ICP-RIE produces high-density hydrogen ions/radicals at low energy, which produces high-density amino group on the SiNx surface within a short duration of time and with minimal surface damage. In this work, we have demonstrated selective amination of SiNx surface as compared to Si surface. The as-activated SiNx surface can be readily biofunctionalized with both protein and oligonucleotide through covalent immobilization. N-5-azido-2-nitrobenzoyloxysuccinimide, a photoactivable amino reactive bifunctional crosslinker, was used and greater than 90% surface coverage was achieved for protein immobilization. In addition, ssDNA immobilization and hybridization with its complemented strand was shown. Thus, we demonstrate a uniform, reliable, fast and economical technique for creating biofunctionalized SiNx surface that can be used for developing compact high-sensitivity biosensors.

Single-molecule study of full-length NaChBac by planar lipid bilayer recording.

Planar lipid bilayer device, alternatively known as BLM, is a powerful tool to study functional properties of conducting membrane proteins such as ion channels and porins. In this work, we used BLM to study the prokaryotic voltage-gated sodium channel (Nav) NaChBac in a well-defined membrane environment. Navs are an essential component for the generation and propagation of electric signals in excitable cells. The successes in the biochemical, biophysical and crystallographic studies on prokaryotic Navs in recent years has greatly promoted the understanding of the molecular mechanism that underlies these proteins and their eukaryotic counterparts. In this work, we investigated the single-molecule conductance and ionic selectivity behavior of NaChBac. Purified NaChBac protein was first reconstituted into lipid vesicles, which is subsequently incorporated into planar lipid bilayer by fusion. At single-molecule level, we were able to observe three distinct long-lived conductance sub-states of NaChBac. Change in the membrane potential switches on the channel mainly by increasing its opening probability. In addition, we found that individual NaChBac has similar permeability for Na+, K+, and Ca2+. The single-molecule behavior of the full-length protein is essentially highly stochastic. Our results show that planar lipid bilayer device can be used to study purified ion channels at single-molecule level in an artificial environment, and such studies can reveal new protein properties that are otherwise not observable in in vivo ensemble studies.

Optogenetic control with a photocleavable protein, PhoCl.

To expand the range of experiments that are accessible with optogenetics, we developed a photocleavable protein (PhoCl) that spontaneously dissociates into two fragments after violet-light-induced cleavage of a specific bond in the protein backbone. We demonstrated that PhoCl can be used to engineer light-activatable Cre recombinase, Gal4 transcription factor, and a viral protease that in turn was used to activate opening of the large-pore ion channel Pannexin-1.

Optimization of a genetically encoded biosensor for cyclin B1-cyclin dependent kinase 1.

Fluorescent protein (FP)-based biosensors have revolutionized the ability of researchers to monitor enzyme activities in live cells. While the basic design principles for FP-based biosensors are well established, first-generation biosensor constructs typically suffer from relatively low fluorescence responses that limit their general applicability. The protein engineering efforts required to substantially improve the biosensor responses are often both labour and time intensive. Here we report the application of a high throughput bacterial colony screen for improving the response of kinase biosensors. This effort led to the development of a second-generation cyclin B1-CDK1 biosensor with a 4.5-fold greater response than the first-generation biosensor.

An engineered monomeric Zoanthus sp. yellow fluorescent protein.

Protein engineering has created a palette of monomeric fluorescent proteins (FPs), but there remains an ~30 nm spectral gap between the most red-shifted useful Aequorea victoria green FP (GFP) variants and the most blue-shifted useful Discosoma sp. red FP (RFP) variants. To fill this gap, we have engineered a monomeric version of the yellow FP (YFP) from Zoanthus sp. coral. Our preferred variant, designated as mPapaya1, displays excellent fluorescent brightness, good photostability, and retains its monomeric character both in vitro and in living cells in the context of protein chimeras. We demonstrate that mPapaya1 can serve as a good Förster resonance energy transfer (FRET) acceptor when paired with an mTFP1 donor. mPapaya1 is a valuable addition to the palette of FP variants that are useful for multicolor imaging and FRET-based biosensing.

Highlightable Ca2+ indicators for live cell imaging.

Two of the most powerful implementations of fluorescent protein (FP) technology are "highlighters", which can be converted from nonfluorescent to fluorescent or from one color to another by illumination, and calcium ion (Ca(2+)) indicators. Combining the properties of both of these FP classes into a single construct would produce a highlightable Ca(2+) indicator that would enable researchers to mark a single cell spectrally in a transfected tissue and image its intracellular Ca(2+) dynamics. In an effort to create such a hybrid tool, we explored three different protein design strategies. The strategy that ultimately proved successful involved the creation of a circularly permuted version of a green-to-red photoconvertible FP and its introduction into a G-CaMP-type single-FP-based Ca(2+) indicator. Optimization by directed evolution led to the identification of two promising variants that exhibit excellent photoconversion properties and have an up to 4.6-fold increase in red fluorescence intensity upon binding of Ca(2+). We demonstrate the utility of these variants in HeLa cells and rat hippocampal neurons.

mMaple: a photoconvertible fluorescent protein for use in multiple imaging modalities.

Recent advances in fluorescence microscopy have extended the spatial resolution to the nanometer scale. Here, we report an engineered photoconvertible fluorescent protein (pcFP) variant, designated as mMaple, that is suited for use in multiple conventional and super-resolution imaging modalities, specifically, widefield and confocal microscopy, structured illumination microscopy (SIM), and single-molecule localization microscopy. We demonstrate the versatility of mMaple by obtaining super-resolution images of protein organization in Escherichia coli and conventional fluorescence images of mammalian cells. Beneficial features of mMaple include high photostability of the green state when expressed in mammalian cells and high steady state intracellular protein concentration of functional protein when expressed in E. coli. mMaple thus enables both fast live-cell ensemble imaging and high precision single molecule localization for a single pcFP-containing construct.

Förster resonance energy transfer-based biosensors for multiparameter ratiometric imaging of Ca2+ dynamics and caspase-3 activity in single cells.

As one of the principal cytoplasmic second messengers, the calcium ion (Ca(2+)) is central to a variety of intracellular signal transduction pathways. Accordingly, there is a sustained interest in methods for spatially- and temporally resolved imaging of the concentration of Ca(2+) in live cells using noninvasive methods such as genetically encoded biosensors based on Förster resonance energy transfer (FRET) between fluorescent proteins (FPs). In recent years, protein-engineering efforts have provided the research community with FRET-based Ca(2+) biosensors that are dramatically improved in terms of enhanced emission ratio change and optimized Ca(2+) affinity for various applications. We now report the development and systematic optimization of a pair of spectrally distinct FRET-based biosensors that enable the simultaneous imaging of Ca(2+) in two compartments of a single cell without substantial spectral crosstalk between emission channels. Furthermore, we demonstrate that these new biosensors can be used in conjunction with previously reported caspase-3 substrates based on the same set of FRET pairs.

A monomeric photoconvertible fluorescent protein for imaging of dynamic protein localization.

The use of green-to-red photoconvertible fluorescent proteins (FPs) enables researchers to highlight a subcellular population of a fusion protein of interest and to image its dynamics in live cells. In an effort to enrich the arsenal of photoconvertible FPs and to overcome the limitations imposed by the oligomeric structure of natural photoconvertible FPs, we designed and optimized a new monomeric photoconvertible FP. Using monomeric versions of Clavularia sp. cyan FP as template, we employed sequence-alignment-guided design to create a chromophore environment analogous to that shared by known photoconvertible FPs. The designed gene was synthesized and, when expressed in Escherichia coli, found to produce green fluorescent colonies that gradually switched to red after exposure to white light. We subjected this first-generation FP [named mClavGR1 (monomeric Clavularia-derived green-to-red photoconvertible 1)] to a combination of random and targeted mutageneses and screened libraries for efficient photoconversion using a custom-built system for illuminating a 10-cm Petri plate with 405-nm light. Following more than 15 rounds of library creation and screening, we settled on an optimized version, known as mClavGR2, that has eight mutations relative to mClavGR1. Key improvements of mClavGR2 relative to mClavGR1 include a 1.4-fold brighter red species, 1.8-fold higher photoconversion contrast, and dramatically improved chromophore maturation in E. coli. The monomeric status of mClavGR2 has been demonstrated by gel-filtration chromatography and the functional expression of a variety of mClavGR2 chimeras in mammalian cells. Furthermore, we have exploited mClavGR2 to determine the diffusion kinetics of the membrane protein intercellular adhesion molecule 1 both when the membrane is in contact with a T-lymphocyte expressing leukocyte-function-associated antigen 1 and when it is not. These experiments clearly establish that mClavGR2 is well suited for rapid photoconversion of protein subpopulations and subsequent tracking of dynamic changes in localization in living cells.