Designed by: Brian Ee   Group: iGEM18_UNSW_Australia   (2018-10-05)

His-Alpha Prefoldin

A HisTag and GSG linker was added to the N-terminus of the alpha subunit of the prefoldin protein.

Usage and Biology

Prefoldin is a molecular chaperone protein which assists in the correct folding of nascent proteins1. Alpha prefoldin (aPFD) and beta prefoldin (bPFD) are two subclasses of prefoldin which oligomerise to form a heterohexameric structure consisting of two alpha subunits and four beta subunits1(Figure 1). Alpha prefoldin (15.7 kDa) and beta prefoldin (13.8 kDa) derived from the thermophilic arcahea Methanobacterium thermoautotrophicum self assemble into an 87 kDa hexamer. The prefoldin hexamer is assembled through interactions between beta hairpins in each subunit, whereby the beta hairpins form two, eight-stranded up and down beta barrels1. Each subunit contains flexible alpha-helical coiled coils, 60 to 70 Å in length, which extend from the beta barrel platform1. The hexamer is stable at high temperatures, with a Tm ≥ 70°C1. This makes it suitable for use in an scaffold system.


Figure 1: aPFD (red) and bPFD (pink) form hexamers. Image created using PDB ID: 1FXK2

A 6x HisTag (six consecutive histidine residues, also known as a hexahistidine tag) was added to aPFD to enable purification, utilising the affinity of the HisTag for nickel ions for Immobilised Metal Affinity Chromatography purification2.

Sequence and Features

Assembly Compatibility:
  • 10
  • 12
  • 21
  • 23
  • 25
  • 1000


Protein Purification

BBa_K2710000 (encoding 6xHis aPFD) was subcloned into the multiple cloning site of pET19b for expression in E. coli T7 Express (NEB) and purified by Immobilised Metal Affinity Chromatography (IMAC). The purification was analysed by SDS-PAGE (Figure 2). The 6xHis aPFD was successfully purified as reflected by the clear bands seen at the expected molecular weight range (17 kDa) in the elution lanes.


Figure 2: SDS-PAGE analysis of IMAC purification of 6xHis aPFD (left) and 6xHis bPFD (right). SeeBlue Plus 2 Pre-stained Protein Standard (Invitrogen) was used as the molecular weight standard. Lanes are labelled as flow through (FT1 and FT2), wash (W) and elutions (E1, E2, E3). Successful purification of 6xHis aPFD confirmed (MW: 17 kDa).


Size Exclusion Chromatography (SEC) is an appropriate method for analysing the assembly of prefoldin hexamers as it retains the native structure of assemblies and can distinguish between molecules of varying size. SEC was used to demonstrate the formation of aPFD and bPFD hexamers, and to investigate of the monodispersity of the sample.

IMAC purified alpha prefoldin and beta prefoldin were mixed in a 1:2 molar ratio to a total volume of 1 mL at concentrations of 1 mg/mL in PBS pH 8 and incubated overnight at 4°C. Size Exclusion Chromatography was kindly performed by Ms Hélène Lebhar. Alpha prefoldin, beta prefoldin and the mixture were loaded onto a Superdex S200 Increase 10/300 GL column using an AKTA start, and separated by SEC. The chromatograms of the three runs were then overlayed for analysis, and compared to the molecular weight standards thyroglobulin (670 kDa), gamma-globulin (158 kDa), ovalbumin (44 kDa) and myoglobulin (17 kDa).


Figure 3:Overlayed SEC chromatograms of aPFD (pink), bPFD (brown) and a 1:2 molar ratio mixture of aPFD and bFPD (orange).

SEC chromatograms of aPFD, bPFD and a 1:2 molar mixture of aPFD and bPFD were overlayed, revealing the formation of larger molecular weight structures in the mixture of aPFD and bFPD. The peak was not of a Gaussian distribution, suggesting that the larger structures were not monodisperse, and that several oligomers exist. Four peaks were identified as potential oligomeric structures, with the largest peak eluting at 13.3 mL.


Figure 4: SEC calibration curve obtained using molecular weight standards thyroglobulin (670 kDa), gamma-globulin (158 kDa), ovalbumin (44 kDa) and myoglobulin (17 kDa).

The predicted molecular weight of the largest alpha beta peak is consistent with the size of a hexamer, but the peak does not appear to be monodispersed (Table 1). It appears that largest structures are present.

Table 1: Predicted molecular weights of peaks from SEC using the SEC calibration curve.



  1. Siegert, R., Leroux, M. R., Scheufler, C., Hartl, F. U. & Moarefi, I. Structure of the molecular chaperone prefoldin: unique interaction of multiple coiled coil tentacles with unfolded proteins. Cell 103, 621–32 (2000).
  2. Hochuli, E., Dobeli, H. & Schacher, A. New metal chelate adsorbent selective for proteins and peptides containing neighbouring histidine residues. J Chromatogr 411, 177-184 (1987).