Biology subjects

Payne, G. F.

Publications and source records attributed to Payne, G. F..

5 recordsLinked to original sources

bioRxiv2023

Detecting Features of Protein Structure through their Mediator-Accessible Redox Activities

Protein function relies on sequence, folding, and post-translational modification, and molecular measurements are commonly used to reveal these structural features. Here, we report an alternative approach that represents these molecular features as readily measurable electronic patterns and validate this experimental approach by detecting structural perturbations commonly encountered during protein biomanufacturing. Specifically, we studied a monoclonal antibody standard (NISTmAb) and focused on the electronic detection of variants that have undergone interchain-disulfide bond reduction and methionine oxidation. Electronic detection of these structural perturbations is based on mediated electrochemical probing (MEP) that discerns patterns associated with the antibodys mediator-accessible redox activity. We demonstrate that MEP can rapidly (within minutes) and quantitatively transduce the proteins structural features into robust electronic signals that can enable bioprocess monitoring and control. More broadly, the ability to transduce information of a proteins molecular structure into a more convenient electronic domain offers fundamentally new opportunities to apply the power of microelectronics and real-time data analytics to chemical and biological analysis.

bioengineering↗

bioRxiv2023

Redox Active Plant Phenolic, Acetosyringone, for Electrogenetic Signaling

Redox is a unique, programmable modality capable of bridging communication between biology and electronics. Previous studies have shown that the E. coli redox-responsive OxyRS regulon can be re-wired to accept electrochemically generated hydrogen peroxide (H2O2) as an inducer of gene expression. Here we report that the redox-active phenolic plant signaling molecule acetosyringone (AS) can also induce gene expression from the OxyRS regulon. AS must be oxidized, however, as the reduced state present under normal conditions cannot induce gene expression. Thus, AS serves as a "pro-signaling molecule" that can be activated by its oxidation - in our case by application of oxidizing potential to an electrode. We show that the OxyRS regulon is not induced electrochemically if the imposed electrode potential is in the mid-physiological range. Electronically sliding the applied potential to either oxidative or reductive extremes induces this regulon but through different mechanisms: reduction of O2 to form H2O2 or oxidation of AS. Fundamentally, this work reinforces the emerging concept that redox signaling depends more on molecular activities than molecular structure. From an applications perspective, the creation of an electronically programmed "pro-signal" dramatically expands the toolbox for electronic control of biological responses in microbes, including in complex environments, cell-based materials, and biomanufacturing.

bioengineering↗

bioRxiv2023

Redox-enabled Electronic Interrogation and Feedback Control of Hierarchical and Networked Biological Systems

We enable microelectronic devices to interrogate biologys molecular communication, perform computations, and in real time control biological systems, including at several hierarchical levels: proteins, cells, and cell consortia. A key driver is establishing electronic access to and from biologys native redox networks. First, redox-mediated electro-biofabrication facilitates facile assembly of biological components onto microelectronic systems, then electrode-actuated redox allows digital programming of enzyme activity, and further, redox-mediated electrogenetics facilitates closed-loop electronic control of cellular function. Specifically, we show algorithm-based feedback control of enzyme activity, cellular genetic circuits (via eCRISPR) and cell consortia behavior, all enabled by electronic data transfer. We further demonstrate electronic switching of cell-cell quorum sensing communication from one autoinducer network to another, creating an electronically controlled "bilingual" cell. We suggest these methodologies will not only help us to better understand biological systems, but design and control those currently unimagined.

synthetic biology↗

bioRxiv2023

Mechanism of the Temperature-Dependent Self-Assembly and Polymorphism of Chitin

Chitin is the second most abundant natural biopolymer; its crystalline structures have been extensively studied; however, the mechanism of chitins self-assembly is unknown. Here we applied all-atom molecular dynamics to study chitins self-assembly process at different temperatures. Strikingly, at 278 K, an amorphous aggregate was formed, whereas at 300 K single-sheet and at 323 K both single- and multi-sheet nanofibril regions were formed. The nanofibrils contain antiparallel, parallel or mixed orientation chains, with antiparallel being slightly preferred, recapitulating chitins polymorphism observed in nature. The inverse temperature dependence is consistent with the recent experiment. The analysis suggested that the multi-sheet nanofibrils are assembled by stacking the single nanofibril sheets, which are formed through two types of pathways in which hydrophobic collapse either precedes or is concomitant with increasing number of interchain hydrogen bonds and solvent expulsion. Furthermore, the antiparallel and parallel chains are mediated by different interchain hydrogen bonds. The analysis also suggested that the inverse temperature dependence may be attributed to the hydrophobic effect reminiscent of the low critical solution temperature phase behavior. The present study provides a rich, atomic-level view of chitins polymorphic self-assembly process, paving the way for the rational design of chitin-derived novel materials.

bioengineering↗

bioRxiv2022

Electrogenetic signaling and information propagation for controlling microbial consortia via programmed lysis

To probe signal propagation and genetic actuation in microbial consortia, we have coopted the components of both redox and quorum sensing (QS) signaling into a communication network for guiding composition by "programming" cell lysis. Here, we use an electrode to generate hydrogen peroxide as a redox cue that determines consortia composition. The oxidative stress regulon of Escherichia coli, OxyR, is employed to receive and transform this signal into a QS signal that coordinates the lysis of a subpopulation of cells. We examine a suite of information transfer modalities including "monoculture" and "transmitter-receiver" models, as well as a series of genetic circuits that introduce time-delays for altering information relay, thereby expanding design space. A simple mathematical model aids in developing communication schemes that accommodate the transient nature of redox signals and the "collective" attributes of QS signals. We suggest this platform methodology will be useful in understanding and controlling synthetic microbial consortia for a variety of applications, including biomanufacturing and biocontainment.

synthetic biology↗