Guidelines to Reach High-Quality Purified Recombinant Proteins
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View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Universidade do Minho: RepositoriUM Appl Microbiol Biotechnol (2018) 102:81–92 https://doi.org/10.1007/s00253-017-8623-8 MINI-REVIEW Guidelines to reach high-quality purified recombinant proteins Carla Oliveira1 & Lucília Domingues1 Received: 6 September 2017 /Revised: 24 October 2017 /Accepted: 27 October 2017 /Published online: 18 November 2017 # Springer-Verlag GmbH Germany, part of Springer Nature 2017 Abstract The final goal in recombinant protein production is Keywords Recombinant protein . Fusion tags . Protein to obtain high-quality pure protein samples. Indeed, the suc- purification . Structural characterization . Quality control . cessful downstream application of a recombinant protein de- Protein quantification pends on its quality. Besides production, which is conditioned by the host, the quality of a recombinant protein product relies mainly on the purification procedure. Thus, the purification Introduction strategy must be carefully designed from the molecular level. On the other hand, the quality control of a protein sample must Recombinant protein production (RPP) has been increasingly be performed to ensure its purity, homogeneity and structural used in laboratorial research for obtaining recombinant pro- conformity, in order to validate the recombinant production teins for biophysical and structural studies (Vedadi et al. and purification process. Therefore, this review aims at pro- 2010), diagnostic and therapeutic purposes (Jozala et al. viding succinct information on the rational purification design 2016), as well as emerging applications, such as smart mate- of recombinant proteins produced in Escherichia coli,specif- rials (Hollingshead et al. 2017). The RPP field constitutes a ically the tagging purification, as well as on accessible tools multi-billion dollar market since a significant part of the main for evaluating and optimizing protein quality. The classical biotechnological market products are recombinant proteins. techniques for structural protein characterization—denaturing Namely, the total market sales from microbial recombinant protein gel electrophoresis (SDS-PAGE), size exclusion chro- products have reached approximately $50 billion in 2016, matography (SEC), dynamic light scattering (DLS) and circu- representing one third of the total sales of biopharmaceuticals lar dichroism (CD)—are revisited with focus on the protein (Jozala et al. 2016). Regardless the final protein application, and their main advantages and disadvantages. Furthermore, high-quality protein samples must be obtained upon the RPP methods for determining protein concentration and protein process, which could fulfil established purity and conforma- storage are also presented. The guidelines compiled herein tional requirements. Purification and characterization of re- will aid preparing pure, soluble and homogeneous functional combinant proteins can be demanding, expensive and time- recombinant proteins from the very beginning of the molecu- consuming, but can determine protein quality. That is, the lar cloning design. successful application of a recombinant protein depends, to a great extent, on its efficient downstream processing. This comprises protein purification, quality validation, quantifica- tion and storage. The design of a rational protein purification strategy should be the first step in the overall RPP strategy. A poor purification design may result in misfolded or heteroge- * Lucília Domingues neous protein samples due to the interference of sequence [email protected] additions, such as tags or extra amino acids resulting from the cloning procedure, and/or absence of refining steps in 1 CEB - Centre of Biological Engineering, University of Minho, the purification procedure. Thus, adequate structural studies 4710-057 Braga, Portugal must be conducted to access the quality of the purified 82 Appl Microbiol Biotechnol (2018) 102:81–92 recombinant proteins and/or to aid optimizing their purity, modifications (e.g. glycosylation), where low levels of native homogeneity and solubility. proteins are found. Thus, in this case, purification is quite The RPP field has attracted a raising interest as indicated by simple; a single purification step may be sufficient (Oliveira the number of new molecular tools and methods described in et al. 2008). In Escherichia coli, purification is more complex recent years (e.g. Costa et al. 2014; Oliveira et al. 2015). because recombinant proteins are mainly produced inside the Protein purification and structural characterization have al- cells, even though the expressed protein can comprise up to ready been the focus of some reviews (e.g. Manta et al. 50% of the total cellular protein (Francis and Page 2010). The 2011; Saraswat et al. 2013; Yadav et al. 2016). Moreover, purification strategy also depends on the purity level required. consensus RPP protocols (Gräslund et al. 2008)and Efficient purification of a target protein from a crude cell ex- workflows for quality control have been proposed (e.g. tract is not always straightforward, and sometimes, more than Lebendiker et al. 2014; Raynal et al. 2014) to instruct re- one purification step is necessary. As such, fusion tag technol- searchers in the production of soluble and reliable recombi- ogy has been employed to facilitate purification, by reducing nant products. However, the subjects of protein purification purification steps to a minimum, while increasing yield and and quality assessment are found separately, while both are purity. The main difficulty is to decide which and how many strictly linked. Furthermore, both subjects are essential for tags should be employed, where to attach them in the protein those who are working in the RPP field and thus would be and whether or not they should be removed from the protein. preferably found in a single document. Thus, this review in- The main guidelines to design a rational tagging purification tends to get relevant information altogether, by providing a strategy are discussed below. succinct updated summary on the purification and quality evaluation of recombinant proteins. For more detailed infor- Overall fusion strategy: molecular design mation on the different referenced techniques, the reader is of the purification procedure directed to specific reviews on the topic. Specifically, we will give key guidelines for designing a rational purification strat- The purification strategy should be designed together with egy and choosing accessible methods for characterizing re- the gene expression procedure (Saccardo et al. 2016). combinant proteins in order to obtain high-quality samples. Thereisnouniversalfusiontagtopurifyanyrecombinant The core of the review will be divided into three main sec- protein, and many times, it requires experimental identifi- tions, namely (i) protein purification strategies, (ii) protein cation (Lebendiker and Danieli 2014). However, the design quality assessment: structural characterization and (iii) optimi- of a rational purification strategy can increase the chances zation of protein stability, quantification and storage. of success. The choice of the fusion partner often relies on Important aspects in the molecular design of the purification costs and tools available at each lab. However, tag type, procedure will be highlighted, such as how to introduce re- size and location can be the most important criteria of movable protein tags in gene cloning and the use of bioinfor- selection. matics to predict protein properties and structure, to help choosing fusion partners and where to attach them in the pro- (i) Tag type. The most used purification tags for protein pu- tein. In sum, a concise review covering essential aspects of rification are the affinity tags (see BTag-dependent purification and refining of recombinant protein samples will purification^ section). Affinity tags can deliver different be provided for researchers starting in the area as well as purposes. The His-tag is the most popular affinity tag experienced researchers searching for compiled and updated either as single tag or as a handle in non-traditional tan- information. dem affinity purification (TAP) tags (i.e. two affinity tags fused in tandem) (Yadav et al. 2016). Its utility in protein detection and crystallization has also been well Protein purification strategies established (Costa et al. 2014). However, contrary to a general belief, it can interfere with protein structural The purification of recombinant proteins must be carefully and/or functional properties (e.g. Noirclerc-Savoye et al. designed not only because this is the most expensive step in 2015;Chenetal.2015). For solving problems of insolu- RPP but also due to its significant impact on protein function/ bility, affinity tags that also work as solubility enhancers application. There is no single or simple way to purify all are used (see BTag-dependent purification^ section) kinds of proteins because of their diversity and different prop- (Costa et al. 2014). New computational tools for erties (Costa et al. 2014). Furthermore, the purification proce- predicting protein solubility from the primary sequence dure depends on the expression system, and namely, if the have been recently described, such as ccSOL (Agostini protein is produced inside or outside de host cells. In yeast, et al. 2014), Protein-Sol (Hebditch et al. 2017) and PON- such as Pichia pastoris, production is typically directed into Sol (Yang et al. 2016)(Table1).