What is a common challenge faced during the purification of GFP?

The common challenge faced during the purification of green fluorescent protein (GFP) is often related to the aggregation of GFP. This issue arises because, during the purification process, proteins can sometimes misfold or aggregate, leading to the formation of larger complexes that are not soluble. When proteins aggregate, they can become less active or lose their inherent properties, such as fluorescence.

Additionally, aggregation can complicate the purification process as aggregated proteins may not bind to affinity columns effectively, making it difficult to isolate pure GFP from other cellular components. This challenge is particularly prominent when the purification conditions, such as pH or salt concentration, are not optimized to maintain the protein in its soluble, monomeric form.

By addressing this challenge, such as by using gentle purification techniques or optimizing buffer conditions, one can significantly improve the yield and functionality of the purified GFP.