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1. High‐Affinity Host–Guest Recognition for Efficient Assembly and Enzymatic Responsiveness of DNA Nanostructures

   https://doi.org/10.1002/smll.202307585  

   Narayanan, Raghu Pradeep ; Prasad, Abhay ; Buchberger, Alex ; Zou, Lei ; Bernal‐Chanchavac, Julio ; MacCulloch, Tara ; Fahmi, Nour Eddine ; Yan, Hao ; Zhang, Fei ; Webber, Matthew J. ; et al ( October 2023 , Small)

   The combination of multiple orthogonal interactions enables hierarchical complexity in self‐assembled nanoscale materials. Here, efficient supramolecular polymerization of DNA origami nanostructures is demonstrated using a multivalent display of small molecule host–guest interactions. Modification of DNA strands with cucurbit[7]uril (CB[7]) and its adamantane guest, yielding a supramolecular complex with an affinity of order 10¹⁰m⁻¹, directs hierarchical assembly of origami monomers into 1D nanofibers. This affinity regime enables efficient polymerization; a lower‐affinity β‐cyclodextrin–adamantane complex does not promote extended structures at a similar valency. Finally, the utility of the high‐affinity CB[7]–adamantane interactions is exploited to enable responsive enzymatic actuation of origami nanofibers assembled using peptide linkers. This work demonstrates the power of high‐affinity CB[7]–guest recognition as an orthogonal axis to drive self‐assembly in DNA nanotechnology.

    

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2. One‐step affinity capture and precipitation for improved purification of an industrial monoclonal antibody using Z‐ELP functionalized nanocages

   https://doi.org/10.1002/bit.26467  

   Swartz, Andrew R. ; Xu, Xuankuo ; Traylor, Steven J. ; Li, Zheng J. ; Chen, Wilfred ( October 2017 , Biotechnology and Bioengineering)

   Protein A chromatography has been identified as a potential bottleneck in the monoclonal antibody production platform, leading to increased interest in non‐chromatographic capture technologies. Affinity precipitation using environmentally responsive, Z‐domain‐elastin‐like polypeptide (Z‐ELP) fusion proteins has been shown to be a promising alternative. However, elevated temperature and salt concentrations necessary for precipitation resulted in decreased antibody monomer content and reduced purification capacity. To improve upon the existing technology, we reported an enhanced affinity precipitation of antibodies by conjugating Z‐ELP to a 25 nm diameter, self‐assembled E2 protein nanocage (Z‐ELP‐E2). The enlarged scale of aggregate formation and IgG‐triggered crosslinking through multi‐valent binding significantly outperformed traditional Z‐ELP‐based methods. In the current work, we sought to develop an affinity precipitation process capable of purifying industrial monoclonal antibodies (mAbs) at ambient temperature with minimal added salt. We discovered that the mAb‐nanocage complex aggregated within 10 min at room temperature without the addition of salt due to the enhanced multi‐valent cross‐linking. After precipitating out of solution, the complex remained insoluble under all wash buffers tested, and only resolubilized after a low pH elution. Through optimization of key process steps, the affinity precipitation yield and impurity clearance met or exceeded protein A chromatography performance with 95% yield, 3.7 logs host cell protein reduction, and >5 logs of DNA reduction from mAb cell culture. Because of the operational flexibility afforded by this one‐step affinity capture and precipitation process, the Z‐ELP‐E2 based approach has the potential to be a viable alternative to platform mAb purification.

    

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3. Single‐step purification of a small non‐mAb biologic by peptide‐ELP‐based affinity precipitation

   https://doi.org/10.1002/bit.27539  

   Mullerpatan, Akshat ; Kane, Erin ; Ghosh, Ronit ; Nascimento, André ; Andersen, Henrik ; Cramer, Steven ; Karande, Pankaj ( August 2020 , Biotechnology and Bioengineering)

   Affinity precipitation using stimulus‐responsive biopolymers such as elastin‐like polypeptides (ELPs) have been successfully employed for the purification of monoclonal antibodies. In the current work, we extend these studies to the development of an ELP‐peptide fusion for the affinity precipitation of the therapeutically relevant small non‐mAb biologic, AdP. A 12‐mer affinity peptide ligand (P10) was identified by a primary phage biopanning followed by a secondary in‐solution fluorescence polarization screen. Peptide P10 and AdP interacted with aK_Dof 19.5 µM. A fusion of P10 with ELP was then shown to be successful in selectively capturing the biologic from a crude mixture. While pH shifts alone were not sufficient for product elution, the use of pH in concert with fluid‐phase modifiers such as NaCl, arginine, or ethylene glycol was effective. In particular, the use of pH 8.5 and an arginine concentration of 500 mM enabled >80% product recovery. The overall process performance evaluated by sodium dodecyl sulfate‐polyacrylamide gel electrophoresis and reversed‐phase ultra‐performance liquid chromatography analyses indicated successful single‐step purification of the biologic from anEscherichia colilysate resulting in ∼90% purity and >80% recovery. These results demonstrate that phage display can be readily employed to identify a peptide ligand capable of successfully carrying out the purification of a non‐antibody biological product using ELP‐based affinity precipitation.

    

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4. Peptide ligands targeting the vesicular stomatitis virus G (VSV‐G) protein for the affinity purification of lentivirus particles

   https://doi.org/10.1002/bit.28594  

   Barbieri, Eduardo ; Mollica, Gina N. ; Moore, Brandyn D. ; Sripada, Sobhana A. ; Shastry, Shriarjun ; Kilgore, Ryan E. ; Loudermilk, Casee M. ; Whitacre, Zachary H. ; Kilgour, Katie M. ; Wuestenhagen, Elena ; et al ( November 2023 , Biotechnology and Bioengineering)

   The recent uptick in the approval of ex vivo cell therapies highlights the relevance of lentivirus (LV) as an enabling viral vector of modern medicine. As labile biologics, however, LVs pose critical challenges to industrial biomanufacturing. In particular, LV purification—currently reliant on filtration and anion-exchange or size-exclusion chromatography—suffers from long process times and low yield of transducing particles, which translate into high waiting time and cost to patients. Seeking to improve LV downstream processing, this study introduces peptides targeting the enveloped protein Vesicular stomatitis virus G (VSV-G) to serve as affinity ligands for the chromatographic purification of LV particles. An ensemble of candidate ligands was initially discovered by implementing a dual-fluorescence screening technology and a targeted in silico approach designed to identify sequences with high selectivity and tunable affinity. The selected peptides were conjugated on Poros resin and their LV binding-and-release performance was optimized by adjusting the flow rate, composition, and pH of the chromatographic buffers. Ligands GKEAAFAA and SRAFVGDADRD were selected for their high product yield (50%–60% of viral genomes; 40%–50% of HT1080 cell-transducing particles) upon elution in PIPES buffer with 0.65 M NaCl at pH 7.4. The peptide-based adsorbents also presented remarkable values of binding capacity (up to 3·109 TU per mL of resin, or 5·1011 vp per mL of resin, at the residence time of 1 min) and clearance of host cell proteins (up to a 220-fold reduction of HEK293 HCPs). Additionally, GKEAAFAA demonstrated high resistance to caustic cleaning-in-place (0.5 M NaOH, 30 min) with no observable loss in product yield and quality. 

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5. Systematic evaluation of Copper(II)-loaded immobilized metal affinity chromatography for selective enrichment of copper-binding species in human serum and plasma

   https://doi.org/10.1093/mtomcs/mfac059  

   Janisse, Samuel E. ; Sharma, Vibha A. ; Caceres, Amanda ; Medici, Valentina ; Heffern, Marie C. ( August 2022 , Metallomics)

   Copper is essential in a host of biological processes, and disruption of its homeostasis is associated with diseases including neurodegeneration and metabolic disorders. Extracellular copper shifts in its speciation between healthy and disease states, and identifying molecular components involved in these perturbations could widen the panel of biomarkers for copper status. While there have been exciting advances in approaches for studying the extracellular proteome with mass spectrometry–based methods, the typical workflows disrupt metal–protein interactions due to the lability of these bonds either during sample preparation or in gas-phase environments. We sought to develop and apply a workflow to enrich for and identify protein populations with copper-binding propensities in extracellular fluids using an immobilized metal affinity chromatography (IMAC) resin. The strategy was optimized using human serum to allow for maximum quantity and diversity of protein enrichment. Protein populations could be differentiated based on protein load on the resin, likely on account of differences in abundance and affinity. The enrichment workflow was applied to plasma samples from patients with Wilson’s disease and protein IDs and differential abundancies relative to healthy subjects were compared to those yielded from a traditional proteomic workflow. While the IMAC workflow preserved differential abundance and protein ID information from the traditional workflow, it identified several additional proteins being differentially abundant including those involved in lipid metabolism, immune system, and antioxidant pathways. Our results suggest the potential for this IMAC workflow to identify new proteins as potential biomarkers in copper-associated disease states.

    

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