Protein Quality Guidelines for Biophysical and Biochemical Studies

ARBRE-P4EU Consensus Protein Quality Guidelines - January 2016

P4EU: Protein Production Partnership for Europe
ARBRE: The Association of Resources for Biophysical Research in Europe

Minimal information to provide

• Protein name and full primary structure, by providing a NCBI (or UniProt) accession number and cloning pathway, i.e. the source of the DNA (species), expression vector and host strain, including the tags and cleavage sites used, accompanied by the full amino acid sequence of the final protein, or sufficient details to derive the full amino acid sequence of the final protein.
• Protein concentration (specifying the method used for quantification and the molar extinction coefficient at 280nm, if applicable).
• Storage conditions, i.e. final buffer composition (pH, buffers, salts and additives), storage temperature and, where applicable, freezing or lyophilization conditions.

Minimal quality control parameters

• Purity: checked by SDS-PAGE, Capillary Electrophoresis (CE) or Reversed-Phase-HPLC (RP-HPLC).
• Homogeneity (aggregation state): checked preferably by Size Exclusion Chromatography (SEC) and/or Dynamic Light Scattering (DLS) or by Size Exclusion Chromatography in combination with Multi Angle Light Scattering (SEC-MALS), Field Flow Fractionation (FFF) or Field Flow Fractionation in combination with Multi Angle Light Scattering (FFF-MALS) or Analytical Ultracentrifugation (AUC).
• Identity: checked preferably by intact protein mass or by peptide mass fingerprint or Edman sequencing.  

Extended quality control parameters
Depending on the intended use and in addition to the methods listed above:

• Nucleic acid content, checked by UV-Vis spectroscopy. Mandatory if protein is to be used to study protein-nucleic acid binding.
• Conformational stability/folding state: Circular Dichroism (CD), Differential Scanning Calorimetry (DSC) or NMR.
• Homogeneity: analytical Ion Exchange Chromatography (IEX), analytical Hydrophobic Interaction Chromatography (HIC) or Isoelectric Focusing (IEF).
• Protein competent fraction, i.e. the relative amount of functionally active protein, measured as specific activity, by active site titration or other suitable methods
• Optimization of storage conditions: long term stability, activity assay, thermal shift assay
• Batch-to-batch consistency: use some of the methods listed above. Mandatory if more than one batch is used

Guidelines Background

Protein Quality Guideline elaborated by a working group (WG) established in the P4EU-ARBRE joint meeting in Dresden, July 2015.

Members:
Bertrand Raynal  - Pasteur institute, Paris, France (ARBRE)
Stefan Knauer - Bayreuth University, Germany (ARBRE)
Stephan Uebel  - Max-Plank Institute for Biochemistry, Munich (ARBRE)
Rob Meijers - EMBL Hamburg, Germany (ARBRE)
Nick Berrow - Institute for research in Medicine, Barcelona, Spain (P4EU)
Annabel Parret  - EMBL Hamburg, Germany (P4EU)
Ario de Marco - University of Nova Gorica, Slovenia (P4EU)
Mario Lebendiker (coordinator) - Hebrew University of Jerusalem, Israel (P4EU)

Although many guidelines for the production of recombinant proteins for biophysical and biochemical studies can be found in the literature, in this project we aim to condense the expertise accumulated during many years of practical work by the members of two European groups of protein specialists into a working guide for protein quality requirements. The two groups are: P4EU (Protein Production Partnership for Europe), a network of near 100 members specializing in recombinant protein production, and ARBRE (The Association of Resources for Biophysical Research in Europe) that gathers more than 70 specialists in the biophysical characterization of biomolecules.

High quality, intact protein is often a pre-requisite for many research projects. Poor production practices or protein quality will undermine the robustness and reproducibility of these often complex, multidisciplinary research efforts. Protein production at the laboratory scale is rarely a straight-forward procedure and frequently relies on (re)iterative processes to evolve a definitive expression and purification protocol for each protein. Each step of this process involves decision-making, providing the necessary controls, and dealing with the obvious as well as the less well known/unappreciated pitfalls of the technology, such as changes in protein expression, physical and chemical factors that influence the protein structure, aggregation, and proteolysis.

The proposed guidelines are intended to lay the groundwork for the standardization and reproducibility of data. The goals of this document are to disseminate operative guidelines in our laboratories (through the existing networks), to raise awareness amongst colleagues and collaborators, and to support the highly professional work of people employed in facilities in their not always easy relationship with “customers”.

Our ultimate goal is to encourage the whole scientific community to implement these guidelines in research papers (for instance as part of the supplementary information). We believe that the inclusion of protein production and QC data will allow greater transparency to readers and enable efficient reproducibility in other laboratories. Currently this data is sadly lacking in many publications and often leads to confusion as laboratories using different protocols obtain conflicting results with the same proteins.

Lebendiker M., Danieli T. and de Marco A. (2014)                                                      
The Trip Adviser guide to the protein science world: a proposal to improve the awareness concerning the quality of
recombinant proteins.                                     
BMC Research Notes (2014) 7:585  doi:10.1186/1756-0500-7-58  (pdf)../PDF/Publications/Lebendiker2014B.pdf  (pdf-figure) ../PDF/Publications/Lebendiker2014B2.pdf

Raynal B., Lenormand P., Baron B., Hoos S. and England P.(2014). Quality assessment and optimization of purified protein samples: why and how? Microbial Cell Factories 2014, 13:180 (pdf)../PDF/Literature/Raynal2015.pdf