Dataset Information

Cell-free synthesis of functional human epidermal growth factor receptor: Investigation of ligand-independent dimerization in Sf21 microsomal membranes using non-canonical amino acids.

ABSTRACT: Cell-free protein synthesis systems represent versatile tools for the synthesis and modification of human membrane proteins. In particular, eukaryotic cell-free systems provide a promising platform for their structural and functional characterization. Here, we present the cell-free synthesis of functional human epidermal growth factor receptor and its vIII deletion mutant in a microsome-containing system derived from cultured Sf21 cells. We provide evidence for embedment of cell-free synthesized receptors into microsomal membranes and asparagine-linked glycosylation. Using the cricket paralysis virus internal ribosome entry site and a repetitive synthesis approach enrichment of receptors inside the microsomal fractions was facilitated thereby providing analytical amounts of functional protein. Receptor tyrosine kinase activation was demonstrated by monitoring receptor phosphorylation. Furthermore, an orthogonal cell-free translation system that provides the site-directed incorporation of p-azido-L-phenylalanine is characterized and applied to investigate receptor dimerization in the absence of a ligand by photo-affinity cross-linking. Finally, incorporated azides are used to generate stable covalently linked receptor dimers by strain-promoted cycloaddition using a novel linker system.

SUBMITTER: Quast RB

PROVIDER: S-EPMC5037433 | biostudies-literature | 2016 Sep

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Cell-free synthesis of functional human epidermal growth factor receptor: Investigation of ligand-independent dimerization in Sf21 microsomal membranes using non-canonical amino acids.

Quast Robert B RB Ballion Biljana B Stech Marlitt M Sonnabend Andrei A Varga Balázs R BR Wüstenhagen Doreen A DA Kele Péter P Schiller Stefan M SM Kubick Stefan S

Scientific reports 20160927

Cell-free protein synthesis systems represent versatile tools for the synthesis and modification of human membrane proteins. In particular, eukaryotic cell-free systems provide a promising platform for their structural and functional characterization. Here, we present the cell-free synthesis of functional human epidermal growth factor receptor and its vIII deletion mutant in a microsome-containing system derived from cultured Sf21 cells. We provide evidence for embedment of cell-free synthesized ...[more]

PMID: 27670253

Similar Datasets

Project description:Machine learning (ML) models have become increasingly popular for predicting and designing structures and properties of peptides and proteins. These ML models typically use peptides and proteins containing only canonical amino acids as the training data. Consequently, these models struggle to make accurate predictions for peptides and proteins containing new amino acids that are absent in the training data set (e.g., noncanonical amino acids). One approach to improve the accuracy of the models is to collect more training data with the desired amino acids. However, this strategy is suboptimal as new data may not be easily attainable, and additional time is required to retrain the ML models. Alternatively, the extendibility of the ML models can be improved if the amino acid features used are representative and generalizable to the unseen amino acids. Herein, we develop amino acid features using molecular dynamics (MD) simulation results. Specifically, for a given amino acid, we perform MD simulation of its dipeptide to create features based on its backbone (ϕ, ψ) distributions and its electrostatic potentials. We demonstrate that these new features enable our ML models to more accurately predict the structural ensembles of cyclic peptides containing amino acids not present in the original training data set. For example, we build ML models to predict cyclic pentapeptide structures, with the training data set containing a library of 15 amino acids and the test data set containing the same 15-amino-acid library or an extended 50-amino-acid library. When using popular features such as Morgan fingerprints and MACCS keys to represent amino acids, the ML models achieve R2 = 0.963 for structural predictions of test cyclic pentapeptides containing the same 15-amino-acid library. However, these models' performances decrease significantly to R2 = 0.430 and R2 = 0.508, respectively, when tasked to predict the structures of cyclic pentapeptides containing a library of 50 amino acids. On the other hand, the model using our backbone (ϕ, ψ) features outperforms those using Morgan fingerprints and MACCS keys, with R2 = 0.700. Overall, instead of having to collect more training data, our new features enable predictions of peptide sequences containing amino acids not originally present in the training data set at the mere cost of performing new dipeptide simulations for the new amino acids.

Project description:Synthetic biology holds promise to revolutionize the life sciences and biomedicine via expansion of macromolecular diversity outside the natural chemical space. Use of non-canonical amino acids (ncAAs) via codon reassignment has found diverse applications in protein structure and interaction analysis, introduction of post-translational modifications, production of constrained peptides, antibody-drug conjugates, and novel enzymes. However, simultaneously encoding multiple ncAAs in vivo requires complex engineering and is sometimes restricted by the cell's poor uptake of ncAAs. In contrast the open nature of cell-free protein synthesis systems offers much greater freedom for manipulation and repurposing of the biosynthetic machinery by controlling the level and identity of translational components and reagents, and allows simultaneous incorporation of multiple ncAAs with non-canonical side chains and even backbones (N-methyl, D-, β-amino acids, α-hydroxy acids etc.). This review focuses on the two most used Escherichia coli-based cell-free protein synthesis systems; cell extract- and PURE-based systems. The former is a biological mixture with >500 proteins, while the latter consists of 38 individually purified biomolecules. We delineate compositions of these two systems and discuss their respective advantages and applications. Also, we dissect the translational components required for ncAA incorporation and compile lists of ncAAs that can be incorporated into polypeptides via different acylation approaches. We highlight the recent progress in using unnatural nucleobase pairs to increase the repertoire of orthogonal codons, as well as using tRNA-specific ribozymes for in situ acylation. We summarize advances in engineering of translational machinery such as tRNAs, aminoacyl-tRNA synthetases, elongation factors, and ribosomes to achieve efficient incorporation of structurally challenging ncAAs. We note that, many engineered components of biosynthetic machinery are developed for the use in vivo but are equally applicable to the in vitro systems. These are included in the review to provide a comprehensive overview for ncAA incorporation and offer new insights for the future development in cell-free systems. Finally, we highlight the exciting progress in the genomic engineering, resulting in E. coli strains free of amber and some redundant sense codons. These strains can be used for preparation of cell extracts offering multiple reassignment options.

Dataset Information

Cell-free synthesis of functional human epidermal growth factor receptor: Investigation of ligand-independent dimerization in Sf21 microsomal membranes using non-canonical amino acids.

Publications

Cell-free synthesis of functional human epidermal growth factor receptor: Investigation of ligand-independent dimerization in Sf21 microsomal membranes using non-canonical amino acids.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets