Biology subjects

Coleman, M. A.

Publications and source records attributed to Coleman, M. A..

9 recordsLinked to original sources

bioRxiv2026

Incorporation of active cell-free expression lysates in chitosan coated alginate microcapsules

Oral routes of delivery are logistically simple and enables easy administration of therapeutics. However, oral delivery of proteins is still challenging due to the proteolytic environment within the gastrointestinal (GI) tract. To protect protein cargo from degradation, polymer encapsulation is commonly used, and when it is combined with cell-free gene expression (CFE) approaches that enable the rapid and flexible production of proteins, it potentially allows for on-demand production of protein therapeutics. Here, we investigated the suitability of chitosan coated alginate (Alg/Cht) microcapsules for encapsulation of proteins and CFE lysates for oral delivery. We show that CFE lysates can produce functional mCherry, a model fluorescent protein, in the presence of alginate polymers, although direct contact with chitosan did inhibit protein synthesis. We encapsulated CFE lysates or purified mCherry protein into alginate cores before crosslinking them using internal gelation techniques and coating with chitosan to test their protective capacity for oral delivery. Alg/Cht microcapsules protected mCherry protein cargo from degradation in simulated human gastric fluids and mouse gastric extracts and facilitated controlled cargo release upon exposure to conditions that simulate the intestinal environment. None of the individual CFE or encapsulation components induced inflammation in mouse GI tracts when administered via oral gavage. We also observed a delayed release of fluorescent bead cargo from Alg/Cht microcapsules in mouse intestines following oral gavage. Together, our data suggest that CFE lysate-loaded Alg/Cht formulations can be flexibly used to produce proteins and safely deliver them to the GI tract for potential therapeutic applications. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=40 SRC="FIGDIR/small/730178v1_ufig1.gif" ALT="Figure 1"> View larger version (12K): org.highwire.dtl.DTLVardef@d3e4c3org.highwire.dtl.DTLVardef@14fbea1org.highwire.dtl.DTLVardef@6c68cforg.highwire.dtl.DTLVardef@15508ec_HPS_FORMAT_FIGEXP M_FIG Graphical Abstract C_FIG HighlightsO_LICell-free gene expression lysates are active in chitosan coated alginate (Alg/Cht) microcapsules. C_LIO_LIAlg/Cht microcapsules exhibit controlled release in vitro in simulated intestinal-like conditions. C_LIO_LICell-free and encapsulation components do not induce inflammation in the gastrointestinal tracts of male or female mice. C_LIO_LIAlg/Cht microcapsules show controlled delayed cargo release in vivo when orally gavaged in mice. C_LI

bioengineering↗

bioRxiv2025

Rapid Antibody Fragment Production and Binding Analysis Using Cell-Free Protein Synthesis Combined with Fluorescence Correlation Spectroscopy

This study investigates the efficient development and production of single-chain variable fragments (scFvs) and antibody fragments (Fabs) using an E. coli-based cell-free protein synthesis system. Validation of the methodology was performed using a fluorescence correlation spectroscopy (FCS)-based assay to determine binding equilibrium constants (KD) between antibodies and the receptor binding domain (RBD) of SARS-CoV-2 Spike protein. An initial assessment employed two conventionally cell-produced anti-RBD antibodies. To optimize cell-free production, folding strategies were developed to enhance the solubility and yields of scFvs, including a two-stage refolding protocol that successfully recovered active proteins from misfolded precipitates. Fab fragments were also produced and characterized, with their binding properties analyzed to assess functionality. This study highlights the potential of cell-free systems for the rapid and efficient production of functional antibody fragments. The integration of advanced techniques, such as FCS-based kinetic measurements, underscores the versatility and applicability of cell-free platforms for antibody development and high-throughput screening. These findings offer a promising avenue for accelerating therapeutic antibody research and production. SIGNIFICANCE of WORKThis study highlights the transformative potential of integrating cell-free protein synthesis (CFPS) with fluorescence correlation spectroscopy (FCS) for the rapid and scalable production and characterization of functional antibody fragments. By leveraging an E. coli-based CFPS platform, we successfully designed and optimized the production of single-chain variable fragments (scFvs) compared to Fab fragments, addressing some common challenges of low solubility and yield. The development of a cost-efficient two-stage refolding strategy further enhanced the scalability and functionality of scFvs, enabling higher recovery of active proteins from the unfolded state. Additionally, FCS provided a sensitive, rapid method for accurately quantifying antigen-antibody binding kinetics across a range of affinities. This work establishes CFPS and FCS as versatile and complementary tools, offering a robust framework for accelerating antibody fragment development, particularly in time-sensitive scenarios like infectious disease outbreaks.

biophysics↗

bioRxiv2025

Apolipoprotein interaction induces shape remodeling and lipid phase separation in giant unilamellar vesicles

Apolipoprotein A-I (ApoA-I) - a 243-residue amphipathic protein containing an N-terminal globular domain and a primarily helical C-terminal lipid binding domain - is a principal protein component of high-density lipoprotein (HDL) or "good" cholesterol, which is an essential component of lipid homeostasis in humans. Synthesized in the liver and intestine and excreted in the blood, ApoA-I undergoes complex, cooperative, and dynamic self-assembly with membrane lipids, producing unlipi-dated (or weakly lipidated), nascent discoidal, and mature HDL states. In vitro studies demonstrate that the reconstitution of purified protein and lipids restores this cooperative self-assembly. However, the kinetic pathways by which these mesoscopic, proteolipidic assemblies form remain incompletely understood. Here, we monitor the dynamics of ApoA-I-membrane interactions through real-time monitoring of morphological changes, which ensue when ApoA-I is incubated with minimal giant unilamellar vesicles (GUVs) composed of single phospholipids or phase-separating phospholipid-cholesterol mixtures. Our fluorescence microscopy measurements reveal that the interaction initiates a gross, morphological remodeling of the parent vesicle proceeding through discrete stages involving membrane poration, solute leakage, vesiculation, and lipid-lipid phase separation. Our atomic force microscopy measurements confirm that the outcome includes discoidal nanoparticles. This qualitative phenomenology is robust and fully reproducible for different protein mutants and alleles (WT APOA-1, {Delta}49ApoA-I, ApoE-3, and ApoE-4) and other lipid mixtures (including mixtures containing phosphoserine lipids). Our molecular simulations recapitulate the essential shape changes and further reveal the composition dependence of the interactions. Together, these findings outline key steps in protein-lipid interactions that facilitate the assembly of mesoscopic reconstituted lipoproteins and nanodiscs.

biophysics↗

bioRxiv2025

Developing a model system to sustain ex vivo chloroplast function

Chloroplasts are critical organelles in plants and algae responsible for accumulating biomass through photosynthetic carbon fixation and cellular maintenance through metabolism in the cell. Chloroplasts are increasingly appreciated for their role in biomanufacturing, as they can produce many useful molecules, and a deeper understanding of chloroplast regulation and function would provide more insight for the biotechnological applications of these organelles. However, traditional genetic approaches to manipulate chloroplasts are slow, and generation of transgenic organisms to study their function can take weeks to months, significantly delaying the pace of research. To develop chloroplasts themselves as a quicker and more defined platform, we isolated chloroplasts from the green algae, Chlamydomonas reinhardtii, and examined their photosynthetic function after extraction. Combined with a metabolic modeling approach using flux-balance analysis, we identified key metabolic reactions essential to chloroplast function and leveraged this information into reagents that can be used in a "chloroplast media" capable of maintaining chloroplast photosynthetic function over time ex vivo compared to buffer alone. We envision this could serve as a model platform to enable more rapid design-build-test-learn cycles to study and improve chloroplast function and potentially as a foundation for the bottom-up design of a synthetic organelle-containing cell.

bioengineering↗

bioRxiv2024

Real-time affinity measurements of proteins synthesized in cell-free lysate using fluorescence correlation spectroscopy

Rapid, high throughput measurements of biomolecular interactions are essential across medicine and bioscience. Traditional methods for affinity-screening proteins require a long and costly process involving cell-based expression, purification, and titration of multiple concentrations to arrive at a binding curve. In contrast, we have developed a fast and simple approach that yields a wealth of information about the expression of the protein and its binding characteristics, all in a "one-pot reaction" and done in under several hours without the need for protein purification. The method uses cell-free protein synthesis to produce the protein of interest in the presence of its binding partner, while simultaneously using fluorescence correlation spectroscopy (FCS) to measure the increasing concentration of the protein and its binding to the binding partner. We characterize the sensitivity limits of this method by measuring the binding between the green fluorescent protein (GFP) and a low picomolar-affinity anti-GFP antibody and found that we can quantify KDs down to the high picomolar to low-nanomolar range. We further demonstrate the method in a potentially ultrahigh-throughput sample format, in which FCS measurements are collected inside microcapsules. This work lays the foundation for a platform aimed at production and in situ affinity screening of thousands of different proteins.

biophysics↗

bioRxiv2024

Cell-free screening, production and animal testing of a STI-related chlamydial major outer membrane protein supported in nanolipoproteins.

Vaccine development against Chlamydia, a prevalent sexually transmitted infection (STI), is imperative due to its global public health impact. However, significant challenges arise in the production of effective subunit vaccine based on recombinant protein antigens, particularly with membrane proteins like the Major Outer Membrane Protein (MOMP). Cell-free protein synthesis (CFPS) technology is an attractive method to address these challenges as a method of high-throughput membrane protein and protein complex production coupled with nanolipoprotein particles (NLPs). NLPs provides a supporting scaffold while allowing easy adjuvant addition during formulation. Over the last decade we have been working toward production and characterization of MOMP-NLP complexes for vaccine testing. The work presented here highlights the expression and biophysical analyses, including transmission electron microscopy (TEM) and dynamic light scattering (DLS), confirm formation and functionality of MOMP-NLP complexes for use in animal studies. Moreover, immunization studies in preclinical models compare the past and present protective efficacy of MOMP-NLP formulations, particularly when co-adjuvanted with CpG and FSL1. Ex vivo assessments further highlight the immunomodulatory effects of MOMP-NLP vaccinations, emphasizing their potential in eliciting robust immune responses. However, further research is warranted to further optimize vaccine formulations, validate efficacy against Chlamydia trachomatis, and better understand underlying mechanisms of immune response.

immunology↗

bioRxiv2024

Evaluation in mice of cell-free produced CT584 as a Chlamydia vaccine antigen

Chlamydia trachomatis is the most prevalent bacterial sexually transmitted pathogen worldwide. Since chlamydial infection is largely asymptomatic with the potential for serious complications, a preventative vaccine is likely the most viable long-term answer to this public health threat. Cell-free protein synthesis (CFPS) utilizes the cellular protein manufacturing machinery decoupled from the requirement for maintaining cellular viability, offering the potential for flexible, rapid, and de-centralized production of recombinant protein vaccine antigens. Here, we use CFPS to produce the putative chlamydial type three secretion system (T3SS) needle-tip protein, CT584, for use as a vaccine antigen in mouse models. High-speed atomic force microscopy (HS-AFM) imaging and computer simulations confirm that CFPS-produced CT584 retains a native-like structure prior to immunization. Female mice were primed with CT584 adjuvanted with CpG-1826 intranasally (i.n.) or CpG-1826 + Montanide ISA 720 intramuscularly (i.m.), followed four-weeks later by an i.m. boost before respiratory challenge with 104 inclusion forming units (IFU) of Chlamydia muridarum. Immunization with CT584 generated robust antibody responses but weak cell mediated immunity and failed to protect against i.n. challenge as demonstrated by body weight loss, increased lungs weights and the presence of high numbers of IFUs in the lungs. While CT584 alone may not be the ideal vaccine candidate, the speed and flexibility with which CFPS can be used to produce other potential chlamydial antigens makes it an attractive technique for antigen production.

immunology↗

bioRxiv2022

Sequence, Structure, and Epitope Analysis of the Polymorphic Membrane Protein Family in Chlamydia trachomatis

The polymorphic membrane proteins are a family of autotransporters that play an important role in infection, adhesion and immunity in Chlamydia trachomatis. Here we show that the characteristic GGA(I,L,V) and FxxN tetrapeptide repeats fit into a larger repeat sequence, and that these repeats correspond to the coils of a large beta-helical domain in high quality structure predictions. While the tetranucleotide motifs themselves are predicted to play a structural role in folding and close stacking of the beta-helical backbone of the passenger domain, we found many of the interesting features of Pmps are localized to the side loops jutting out from the beta helix - including protease cleavage, host cell adhesion, and B-cell epitopes; while T-cell epitopes are predominantly found in the beta-helix itself.

bioinformatics↗

bioRxiv2021

Ligand-induced transmembrane conformational coupling in monomeric EGFR

Single pass cell surface receptors regulate cellular processes by transmitting ligand-encoded signals across the plasma membrane via changes to their extracellular and intracellular conformations. While receptor-receptor interactions are established as key aspects of transmembrane signaling, the contribution from the single helix of a monomeric receptor has been challenging to isolate due to the complexity and ligand-dependence of the receptor-receptor interactions. By combining membrane nanodiscs produced wtih cell-free expression, single-molecule Forster Resonance Energy Transfer measurements, and molecular dynamics simulations, we report that ligand binding induces intracellular conformational changes within monomeric, full-length epidermal growth factor receptor (EGFR). Our observations establish the existence of extracellular/intracellular conformational coupling within a single receptor molecule. We implicate a series of electrostatic interactions in the conformational coupling and find the coupling is inhibited by targeted therapeutics and mutations that also inhibit phosphorylation in cells. Collectively, these results introduce a facile mechanism to link the extracellular and intracellular regions through the single transmembrane helix of monomeric EGFR, and raise the possibility that intramolecular transmembrane conformational changes are common to single-pass membrane proteins.

biophysics↗