The NKI Protein Facility is the well-known protein production, crystallisation and biophysical characterisation facility located at the Division of Biochemistry at The Netherlands Cancer Institute (NKI) in Amsterdam.
The NKI Protein Facility is part of the Instruct-NL national Instruct Centre of the Netherlands and provides services for production, purification, biophysical characterisation and crystallisation trials for proteins. For many years, its facility staff is participating in, sometimes leading, EC-funded projects, for instance in iNEXT-Discovery, ISIDORe, canSERV and Fragment-Screen. Beyond all experimental opportunities outlined below, participating NKI-groups also actively develop and offer computational structural biology tools, including the crystallographic structure refinement software package PDB-REDO and the algoprithm AlphaFill that positions ligands, cofactors and ions inAlphaFold predicted structural models.
Protein Facility services are available for internal (NKI) and external research groups, also national or from abroad, and for researchers from academia and industry alike. Also researchers without extensive experience or in-house facilities are of course very welcome to apply; they can receive assistance with the design, execution and analyses of their experiments.
A key strength of the facility is the characterisation of macromolecular interactions using integrative biophysical approaches. Experiments like high-throughput macromolecular crystallisation can be performed by facility staff. For most experimental access services, however, researchers can also visit us in Amsterdam to receive expert guidance with preparing experiments and analyses but for hands-on training.
To ensure a smooth process, we recommend researchers to contact our staff before preparing and submitting an application!
Proper expression of functional proteins depends on many different factors. NKI Protein Facility experts assist users with the design of proteins and protein domains using different (bio-informatics) tools. The facility houses large-scale expression platforms for protein expression in E. coli (not offered in Instruct!), in insect cells (baculovirus system) and in mammalian cells (e.g. HEK293, roller-bottle incubator for 90 bottles). For purification of expressed proteins, affinity, ion exchange and size exclusion chromatography can be done on different systems.
To characterise (bio)macromolecular properties, stability and interactions, the facility has a high-end equipment collection, including:
The NKI Protein Facility houses an automated high-throughput 96-well protein crystallisation platform to screen conditions using 100-200 nanoliter droplets. Plates are prepared by liquid handling robots, and being monitored over time by automated imaging systems (4 °C and 20 °C).
For more information on services and equipment, please visit the NKI Protein Facility website or contact facility staff directly.
For overall information on the availability of Instruct-ERIC technologies, visit the Technology Availability List or contact support@instruct-eric.org.
How to find us
The Netherlands Cancer Institute is conveniently located at the south-west of Amsterdam. From Schiphol airport it takes ~20 minutes to get to the institute by bus/car/taxi, and just ~15 minutes by train (to Amsterdam Lelylaan station) plus a 15 minute walk. The institute is also well-connected to Amsterdam's city centre. More details can be found at the NKI website.
The NKI Protein Facility is well-equipped for studying molecular biophysics and offers their users fluorescence-based fast kinetics and high-throughput experiments, ITC, MST, MALS, SPR and Thermal Shift Assays.
The facility also has a very strong record in sample preparation (X-ray, cryo-EM) and computational structure determination and refinement.
View All Molecular Biophysics at Instruct
The NKI Protein Facility has a strong record in sample preparation for structural biology, and offers their users access to macromolecular crystallisation:
- Robotics for preparation of nanoliter crystallisation drops in 96-well format.
- Storage of crystallisation plates (4°C or 20°C).
- Screening and ranking of crystallisation conditions in 96-well format (TOPAZ, AutoInspex station).
Solving experimental (crystal, crye-EM) structures of macromolecjules and their complexes is beyond the scope of the NKI Protein facility access services for Instruct-ERIC!
The NKI Protein Facility is highly experienced in protein production using insect and mammalian cells, and assists users with the design of expression constructs considering also solubility and domain boundaries. We collected a wide variety of expression vectors, including LIC vectors for Ligand Independent Cloning. For expression of intracellular and extracellular proteins in insect cells we have SF9 and SF21 systems. Our mammalian expression system is optimised for HEK-293T cells, but we have for instance also the glycosylation free, gnT1-deficient HEK293S variety.
Access to protein expression in bacteria (E. coli) is possible with the NKI Protein Facility, but not accessible via Instruct!
