scholarly journals Gigavalent display of proteins on monodisperse polyacrylamide hydrogels as a versatile modular platform for functional assays and protein engineering

2021 ◽  
Author(s):  
Thomas Fryer ◽  
Joel David Rogers ◽  
Christopher Mellor ◽  
Ralph Minter ◽  
Florian Hollfelder
Keyword(s):  
Protein Purification ◽  
Protein Function ◽  
Large Scale ◽  
Solid Phase ◽  
3D Structure ◽  
Solid Support ◽  
Covalent Bonds ◽  
Functional Assays ◽  
Protein Molecules ◽  
Modular Platform

The robust modularity of biological components that are assembled into complex functional systems is central to synthetic biology. Here we apply modular 'plug and play' design principles to a microscale solid phase protein display system that enables protein purification and functional assays for biotherapeutics. Specifically, we capture protein molecules from cell lysates on polyacrylamide hydrogel display beads ('PHD beads'), made in microfluidic droplet generators. These monodisperse PHD beads are decorated with predefined amounts of anchors, methacrylate-PEG-benzylguanine (BG) and methacrylate-PEG-chloroalkane (CA). Anchors form covalent bonds with fusion proteins bearing cognate tag recognition (SNAP and Halo-tags) in specific, orthogonal and stable fashion. Given that these anchors are copolymerised throughout the 3D structure of the beads, proteins are also distributed across the entire bead sphere, allowing attachment of ~109 protein molecules per bead (∅ 20 μm). This mode of attachment reaches a higher density than possible on widely used surface-modified beads, and additionally mitigates surface effects that often complicate studies with proteins on beads. We showcase a diverse array of protein modules that enable the secondary capture of proteins, either non-covalently (IgG and SUMO-tag) or covalently (SpyCatcher, SpyTag, SnpCatcher and SnpTag). Proteins can be displayed in their monomeric forms, but also reformatted as a multivalent display (using secondary capture modules that create branches) to test the contributions of avidity and multivalency towards protein function. Finally, controlled release of modules by irradiation of light is achieved by incorporating the photocleavable protein PhoCl: irradiation severs the displayed protein from the solid support, so that functional assays can be carried out in solution. As a demonstration of the utility of valency engineering, an antibody drug screen is performed, in which an anti-TRAIL-R1 scFv protein is released into solution as monomers-hexamers, showing a ~50-fold enhanced potency in the pentavalent format. The ease of protein purification on solid support, quantitative control over presentation and release of proteins and choice of valency make this experimental format a versatile, modular platform for large scale functional analysis of proteins, in bioassays of protein-protein interactions, enzymatic catalysis and bacteriolysis.

Fully Automated Parallel Oligonucleotide Synthesizer

2001 ◽  
Vol 66 (8) ◽  
pp. 1299-1314 ◽  
Author(s):  
Michal Lebl ◽  
Christine Burger ◽  
Brett Ellman ◽  
David Heiner ◽  
Georges Ibrahim ◽  
...  
Keyword(s):  
Solid Phase ◽  
Building Blocks ◽  
Solid Support ◽  
Continuous Operation ◽  
Gear Pump ◽  
Oligonucleotide Synthesis ◽  
Center Of Rotation ◽  
Microtiter Plates ◽  
The Individual ◽  
Design And Construction

Design and construction of automated synthesizers using the tilted plate centrifugation technology is described. Wash solutions and reagents common to all synthesized species are delivered automatically through a 96-channel distributor connected to a gear pump through two four-port selector valves. Building blocks and other specific reagents are delivered automatically through banks of solenoid valves, positioned over the individual wells of the microtiterplate. These instruments have the following capabilities: Parallel solid-phase oligonucleotide synthesis in the wells of polypropylene microtiter plates, which are slightly tilted down towards the center of rotation, thus generating a pocket in each well, in which the solid support is collected during centrifugation, while the liquid is expelled from the wells. Eight microtiterplates are processed simultaneously, providing thus a synthesizer with a capacity of 768 parallel syntheses. The instruments are capable of unattended continuous operation, providing thus a capacity of over two millions 20-mer oligonucleotides in a year.

scholarly journals A simple and efficient automated microvolume radiosynthesis of [18F]Florbetaben

2020 ◽  
Vol 5 (1) ◽  
Author(s):  
Ksenia Lisova ◽  
Jia Wang ◽  
Philip H. Chao ◽  
R. Michael van Dam
Keyword(s):  
Large Scale ◽  
Solid Phase ◽  
Acetonitrile Solution ◽  
Synthesis Methods ◽  
Pet Tracers ◽  
Molar Activity ◽  
Alternative Approaches ◽  
High Yields ◽  
Sufficient Concentration

Abstract Background Current automated radiosynthesizers are generally optimized for producing large batches of PET tracers. Preclinical imaging studies, however, often require only a small portion of a regular batch, which cannot be economically produced on a conventional synthesizer. Alternative approaches are desired to produce small to moderate batches to reduce cost and the amount of reagents and radioisotope needed to produce PET tracers with high molar activity. In this work we describe the first reported microvolume method for production of [18F]Florbetaben for use in imaging of Alzheimer’s disease. Procedures The microscale synthesis of [18F]Florbetaben was adapted from conventional-scale synthesis methods. Aqueous [18F]fluoride was azeotropically dried with K2CO3/K222 (275/383 nmol) complex prior to radiofluorination of the Boc-protected precursor (80 nmol) in 10 μL DMSO at 130 °C for 5 min. The resulting intermediate was deprotected with HCl at 90 °C for 3 min and recovered from the chip in aqueous acetonitrile solution. The crude product was purified via analytical scale HPLC and the collected fraction reformulated via solid-phase extraction using a miniature C18 cartridge. Results Starting with 270 ± 100 MBq (n = 3) of [18F]Fluoride, the method affords formulated product with 49 ± 3% (decay-corrected) yield,> 98% radiochemical purity and a molar activity of 338 ± 55 GBq/μmol. The miniature C18 cartridge enables efficient elution with only 150 μL of ethanol which is diluted to a final volume of 1.0 mL, thus providing a sufficient concentration for in vivo imaging. The whole procedure can be completed in 55 min. Conclusions This work describes an efficient and reliable procedure to produce [18F]Florbetaben in quantities sufficient for large-scale preclinical applications. This method provides very high yields and molar activities compared to reported literature methods. This method can be applied to higher starting activities with special consideration given to automation and radiolysis prevention.

scholarly journals Characterization of Pharmaceutical Tablets Using UV Hyperspectral Imaging as a Rapid Line to Line Analysis Tool

Sensors ◽  
2021 ◽  
Vol 21 (13) ◽  
pp. 4436
Author(s):  
Mohammad Al Ktash ◽  
Mona Stefanakis ◽  
Barbara Boldrini ◽  
Edwin Ostertag ◽  
Marc Brecht
Keyword(s):  
Hyperspectral Imaging ◽  
Large Scale ◽  
Solid Phase ◽  
Ultra Violet ◽  
Principal Component ◽  
Ccd Camera ◽  
Conveyor Belt ◽  
Hyperspectral Data ◽  
Analysis Tool ◽  
Sample Set

A laboratory prototype for hyperspectral imaging in ultra-violet (UV) region from 225 to 400 nm was developed and used to rapidly characterize active pharmaceutical ingredients (API) in tablets. The APIs are ibuprofen (IBU), acetylsalicylic acid (ASA) and paracetamol (PAR). Two sample sets were used for a comparison purpose. Sample set one comprises tablets of 100% API and sample set two consists of commercially available painkiller tablets. Reference measurements were performed on the pure APIs in liquid solutions (transmission) and in solid phase (reflection) using a commercial UV spectrometer. The spectroscopic part of the prototype is based on a pushbroom imager that contains a spectrograph and charge-coupled device (CCD) camera. The tablets were scanned on a conveyor belt that is positioned inside a tunnel made of polytetrafluoroethylene (PTFE) in order to increase the homogeneity of illumination at the sample position. Principal component analysis (PCA) was used to differentiate the hyperspectral data of the drug samples. The first two PCs are sufficient to completely separate all samples. The rugged design of the prototype opens new possibilities for further development of this technique towards real large-scale application.

scholarly journals Novel Dominant KCNQ2 Exon 7 Partial In-Frame Duplication in a Complex Epileptic and Neurodevelopmental Delay Syndrome

2020 ◽  
Vol 21 (12) ◽  
pp. 4447
Author(s):  
Pedro A. Lazo ◽  
Juan L. García ◽  
Paulino Gómez-Puertas ◽  
Íñigo Marcos-Alcalde ◽  
Cesar Arjona ◽  
...  
Keyword(s):  
Protein Function ◽  
De Novo ◽  
3D Structure ◽  
Unknown Origin ◽  
Unknown Etiology ◽  
Neurodevelopmental Delay ◽  
Calmodulin Binding ◽  
Whole Exome ◽  
Dynamics Simulations ◽  
Frame Duplication

Complex neurodevelopmental syndromes frequently have an unknown etiology, in which genetic factors play a pathogenic role. This study utilizes whole-exome sequencing (WES) to examine four members of a family with a son presenting, since birth, with epileptic-like crises, combined with cerebral palsy, severe neuromotor and developmental delay, dystonic tetraparexia, axonal motor affectation, and hyper-excitability of unknown origin. The WES study detected within the patient a de novo heterozygous in-frame duplication of thirty-six nucleotides within exon 7 of the human KCNQ2 gene. This insertion duplicates the first twelve amino acids of the calmodulin binding site I. Molecular dynamics simulations of this KCNQ2 peptide duplication, modelled on the 3D structure of the KCNQ2 protein, suggest that the duplication may lead to the dysregulation of calcium inhibition of this protein function.

scholarly journals Insights into Hox Protein Function from a Large Scale Combinatorial Analysis of Protein Domains

PLoS Genetics ◽  
2011 ◽  
Vol 7 (10) ◽  
pp. e1002302 ◽  
Author(s):  
Samir Merabet ◽  
Isma Litim-Mecheri ◽  
Daniel Karlsson ◽  
Richa Dixit ◽  
Mehdi Saadaoui ◽  
...  
Keyword(s):  
Protein Function ◽  
Large Scale ◽  
Protein Domains ◽  
Combinatorial Analysis ◽  
Hox Protein

scholarly journals deepNF: Deep network fusion for protein function prediction

2017 ◽  
Author(s):  
Vladimir Gligorijević ◽  
Meet Barot ◽  
Richard Bonneau
Keyword(s):  
Protein Function ◽  
Large Scale ◽  
Protein Function Prediction ◽  
Predictive Performance ◽  
Substantial Improvement ◽  
Function Prediction ◽  
Interaction Networks ◽  
Highly Nonlinear ◽  
High Level ◽  
String Networks

AbstractThe prevalence of high-throughput experimental methods has resulted in an abundance of large-scale molecular and functional interaction networks. The connectivity of these networks provide a rich source of information for inferring functional annotations for genes and proteins. An important challenge has been to develop methods for combining these heterogeneous networks to extract useful protein feature representations for function prediction. Most of the existing approaches for network integration use shallow models that cannot capture complex and highly-nonlinear network structures. Thus, we propose deepNF, a network fusion method based on Multimodal Deep Autoencoders to extract high-level features of proteins from multiple heterogeneous interaction networks. We apply this method to combine STRING networks to construct a common low-dimensional representation containing high-level protein features. We use separate layers for different network types in the early stages of the multimodal autoencoder, later connecting all the layers into a single bottleneck layer from which we extract features to predict protein function. We compare the cross-validation and temporal holdout predictive performance of our method with state-of-the-art methods, including the recently proposed method Mashup. Our results show that our method outperforms previous methods for both human and yeast STRING networks. We also show substantial improvement in the performance of our method in predicting GO terms of varying type and specificity.AvailabilitydeepNF is freely available at: https://github.com/VGligorijevic/deepNF

scholarly journals The Breaking Beads Approach for Photocleavage from Solid Support

2020 ◽  
Author(s):  
yasmeen bakhatan ◽  
Israel Alshanski ◽  
Dana Grunhaus ◽  
Mattan Hurevich
Keyword(s):  
Continuous Flow ◽  
Solid Phase Synthesis ◽  
Solid Phase ◽  
High Energy ◽  
Solid Support ◽  
Phase Synthesis ◽  
Polystyrene Beads ◽  
Magnetic Stirring ◽  
Photolabile Linkers

Photocleavage from polystyrene beads is a pivotal reaction for solid phase synthesis that relies on photolabile linkers. The photocleavage, usually performed by batch irradiation, suffers from incomplete and slow cleavage. To overcome these issues, continuous flow and high-energy lamps are frequently used, but these setups are hazardous, technically challenging, and expensive. We developed a photocleavage approach that relies on a benchtop LED lamp and magnetic stirring. In this approach, we crush the beads instead of keeping their integrity to increase the yield of photocleavage. This approach proved very efficient for photocleavage of protected oligosaccharides.

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