ChromoBlog

Co-immunoprecipitation (Co-IP) describes the isolation of a protein and its binding partners from a cell extract using a Nanobody or antibody that is bound to beads. The protein, that directly interacts with the Nanobody, or antibody beads is called “bait”. The binding partner that is indirectly precipitated is called “prey”.

Co-IP describes the immunoprecipitation of a protein of interest and its interacting partners.

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Protein abundance is crucial for immunoprecipitation

During an immunoprecipitation (IP), the protein of interest (POI) is pulled down with a specific antibody or Nanobody conjugated to beads such as agarose or magnetic agarose. Unbound sample content, for example, other proteins, cell debris, and lipids, is removed by washing, while the precipitated protein is enriched on the beads.

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ChromoTek's Nano-Traps are optimized for the immunoprecipitation (IP) of proteins and their interacting factors. Nano-Traps comprise of a Nanobody/ V_HH conjugated to beads. For 3 Nano-Traps, e.g. GFP-Trap^®,  RFP-Trap^®, and Spot-Trap^®, we offer different types of beads:

• Agarose beads
• Magnetic Agarose beads
• Magnetic Particles M-270

Immunoprecipitation with GFP-Trap.
I: Input, FT: Flow-Through, B: Bound

Based on the properties of the different beads (see table), we recommend:

• Agarose beads for very low background and high binding capacity IP
• Magnetic Agarose beads for magnetic separation and high binding capacity IP
• Magnetic Particles M-270 for IP of very large proteins/complexes
  

Introduction

A high background from unspecific binding of proteins is a common problem in immunoprecipitation (IP). In this blog, the origin of background and different optimization strategies are discussed. Furthermore, it is shown how you can achieve a low background when using the ChromoTek GFP-Trap^®, a ready to use reagent for IP of a GFP-tagged proteins.

ChromoTek GFP-Trap^® is optimized for the immunoprecipitation of GFP-tagged proteins and their interacting factors.

The GFP-Trap consists of the ChromoTek anti-GFP Nanobody/ V_HH that is coupled to 3 different types of beads or is immobilized in a 96 multiwell plate:

• Agarose beads
• Magnetic Agarose beads
• Magnetic Particles M-270
• 96 Multiwell Plate

Immunoprecipitation with GFP-Trap.
I: Input, FT: Flow-Through, B: Bound

Based on the properties of the different matrices (see table), we recommend:

• GFP-Trap Agarose for very low background and high binding capacity IP
• GFP-Trap Magnetic Agarose for magnetic separation and high binding capacity IP
• GFP-Trap Magnetic Particles M-270 for IP of very large proteins/complexes
• GFP-Trap Multiwell Plates for high throughput analysis

What makes on-bead digestion favorable?

Just pull down your protein of interest with immobilized nanobodies, also termed V_HHs or single domain antibodies. Then follow the on-bead digestion protocol (see below) and submit the digest to your core facility for effective mass spectrometer analysis of (co-) precipitated proteins.