Protein characterisation is an essential part of recombinant protein production, enabling quality control check on a purified or partially purified protein. Modern, sensitive techniques enable physical properties such as mass, size, concentration, amino acid sequence, stability and structure of a protein to be determined. Other methodologies, often protein-specific, can be used to elucidate biological functioning.

Some of the more commonly encountered characterisation techniques are described below.

Protein Quantification

The simplest method for protein quantification is measuring absorbance at 280 nm. This method does not require a dye-based kit or the preparation of a standard curve. However, the absorbance is sequence-dependent, so measurements of proteins with low tryptophan or tyrosine content may be inaccurate.

Two non-specific colorimetric assays are commonly used to obtain accurate protein concentration measurements. Both methods have different strengths and weaknesses, and the most appropriate assay will depend on the individual protein, buffer conditions and the intended application.

Bicinchoninic acid (BCA) – Proteins reduce copper ions in solution, resulting in the formation of a complex that absorbs strongly at 562 nm. Assay is linear over a broad range and is incompatible with reducing agents and chelating agents

Bradford assay – Proteins bind to Coomassie Brilliant Blue dye, resulting in a colour change in solution that can be measured at 595 nm. Assay has a relatively narrow linear range and is incompatible with detergents

Mass Spectrometry (MS)

MS is a powerful technique that can be used to determine various protein physical characteristics, including native molecular weight, sequencing information and post-translational modifications. Proteins are ionised, accelerated and separated according to their mass-to-charge ratio (m/z) under the influence of a magnetic field. As this technique is very sensitive it is possible to detect very small changes in mass e.g. a change in amino acid or chemical modification.

Analytical Size Exclusion Chromatography (SEC)

Analytical SEC can be used to elucidate protein quaternary structure. The solid phase consists of porous particles that retard the flow of smaller molecules, thereby enabling separation of proteins based on their size. The native protein molecular weight can be inferred by comparison to a reference protein, such as bovine serum albumin (BSA).

Circular dichroism (CD)

CD generates a unique spectrum based on protein secondary structure (alpha helices and beta sheets) that is used to verify correct protein folding. It is particularly useful for studying protein structure and thermodynamic stability under various environmental conditions.

Dynamic Light Scattering (DLS)

DLS is an analytical technique used to determine protein size distribution profile, and is amenable to high throughput applications. The Brownian motion of proteins in solution causes light to be scattered, with the resultant scattered intensity fluctuations dependent on particle size. Thus, average radius and the width of the distribution in terms of polydispersity can be determined. DLS can be used to quantify protein stability as a function of temperature, pH, concentration, and excipient profile.

Asymmetrical Flow Field-Flow Fractionation with Multi-angle Light Scattering (AF4-MALS)

The AF4-MALS technique offers high-resolution biophysical characterisation of large protein complexes and virus like-particles (VLPs). Complexes are separated based on their size, followed by MALS detection of each component’s dynamic properties. AF4-MALS is commonly applied to detect batch-to-batch variation, degradation or aggregation during VLP formulation and storage.

Transmission electron microscopy (TEM)

TEM is used for morphological characterisation of protein complexes or VLPs. A beam of electrons is transmitted through a fixed protein sample, enabling large-scale protein structures to be imaged. This technique is often used in conjunction with AF4-MALS for VLP characterisation.