Skip to Main Content

New technology for protein complex discovery holds promise for biotechnology and crop improvement

Living cells survive and adapt by forming stable protein complexes that allow them to modulate protein activity, do mechanical work and convert signals into predictable responses, but identifying the proteins in those complexes is technically challenging. Purdue University researchers have developed a method to predict the composition of thousands of proteins complexes at one time, a discovery that will speed discoveries about cell functions.

The method predicts the composition of naturally occurring protein complexes that are extracted from living cells. It is significantly faster and cheaper than traditional methods that use large-scale cloning, affinity labels or antibodies to identify protein complex components. The method has the potential to help scientists understand how thousands of protein complexes function together to enable plant cells to grow normally and respond to changing environments.

Daniel Szymanski, a professor in Purdue’s Department of Botany and Plant Pathology, and graduate students Zach McBride and Youngwoo Lee, separated thousands of proteins based on size and charge and used mass spectrometry to predict which proteins were likely to bind to one another and form a stable protein complex. In this guilt-by-association approach, proteins that form a stable complex should co-purify with each other using any separation strategy.

Szymanski’s team also validated the process. The team confirmed the presence of many known and novel protein complexes that were predicted from the profiling method.

“From one of these separations, we get elution profiles for thousands of proteins,” said Szymanski, whose findings were published in the journal Molecular and Cellular Proteomics. “We can combine all of the protein profile data from the columns, identify the elution profiles that are most similar to each other, and predict which proteins are physically associated with one another.”

Once protein complexes are identified, scientists can determine their function in cells, how cellular pathways are regulated, how those proteins affect cell signaling, and more. Szymanski said the method works in any organism that has a sequenced genome, including corn, soybeans, rice, and cotton.

“This method has been used to globally analyze protein complexes in plants of differing genotypes or those grown under different conditions. It’s like a new phenotyping tool to analyze systems-level changes in protein abundance, binding partners, and subcellular localization,” Szymanski said.

The method serves as a large-scale hypothesis-generating machine that will accelerate understanding of the complicated workings of plant cells and give researchers broad knowledge about how plants adapt to heat, water, and other stresses.

The research was supported by the National Science Foundation Plant Genome Research Program. 

Purdue University’s Daniel Szymanski developed a mass spectrometry method to identify the composition of protein complexes. Proteins that co-purify are predicted interactors. The profile data are generated from extracts isolated from developing Arabidopsis leaves. (Purdue Agricultural Communication photo) Purdue University’s Daniel Szymanski developed a mass spectrometry method to identify the composition of protein complexes. Proteins that co-purify are predicted interactors. The profile data are generated from extracts isolated from developing Arabidopsis leaves. (Purdue Agricultural Communication photo)

Featured Stories

Simerdeep Kaur sits at a lab bench wearing black gloves, a black lab coat, and safety glasses as she places a vial in a blue light up box
Purdue researchers show common bacterial assay is unreliable

As food recalls become more prevalent, more families toss more lettuce and deli meat into the...

Read More
A field of woody vegetation
Managing Conservation Plantings Series Provides Science-Based Recommendations for Landowners, Managers

The Managing Conservation Plantings series provides landowners and managers with science-based...

Read More
four women smiling
Purdue Animal Sciences deepens global reach through visiting scholars program

Visiting scholars contribute to cutting-edge livestock research and global collaboration at Purdue.

Read More
Shelby Sliger works in the lab with Arabidopsis plants.
Shelby Sliger: My Purdue View

My biggest draw to Purdue was getting into research early with a supportive mentor, but my...

Read More
Ag Barometer
Producer sentiment slips due to rising policy uncertainty

Farmer sentiment declined in March as concerns over agricultural trade and farm policy weighed on...

Read More
Michelle Lihon
Michelle Lihon - Graduate Ag Research Spotlight

Michelle Lihon is a third-generation scientist. Her father works in biotechnology, and her...

Read More
To Top