Final answer:
Proteinase K is used in protein extraction protocols to degrade unwanted proteins, improving the quality of the extracted proteins and facilitating effective separation on 2-DE gels, particularly in the presence of interfering substances found in soybean seeds.
Step-by-step explanation:
The enzyme Proteinase K serves a crucial role in protein extraction protocols. Its primary function is to degrade other proteins that might be present in a sample, thereby preventing degradation of the target proteins via proteolytic breakdown, and eliminating proteins that can interfere with downstream applications like electrophoresis. This step is necessary to ensure the quality and integrity of the extracted proteins, as it allows for the creation of reproducible protein spots on two-dimensional polyacrylamide gel electrophoresis (2-DE) gels and prevents issues such as streaking and smearing.
In the context of soybean seed protein extraction, Proteinase K would be particularly helpful in degrading the large amounts of storage proteins like ß-conglycinin and glycinin, which would otherwise hinder the isolation and characterization of less abundant seed proteins. In addition, this enzymatic treatment can help reduce the complexities introduced by secondary metabolites and other substances. Thus, Proteinase K facilitates the extraction of a more pure and representative sample of the proteins of interest.