‘Molecular LEGO’ study analyzes the building blocks of a partially disordered protein

Bioengineering professor Victor Muñoz and his lab at the University of California, Merced, have created a new way to solve some of the mysteries of a growing class of proteins that don’t appear to have specific structures but perform very important functions, including the complex genetic processes that separate higher-order organisms from single-celled bacteria.

They call it “molecular Lego”, separating the proteins and reconstructing them, segment by segment.

This new method could significantly impact a relatively young and burgeoning field of biochemistry and biomolecular sciences for researchers around the world.

Courtesy of University of California, Merced

Professor Victor Muñoz, left, with his lab group, including paper co-authors Mourad Sadqi, right, and first author Thinh DN Luong, standing next to Sadqi.

Molecular LEGO is detailed in a new paper titled “A modular approach to mapping conformational landscapes of unrelated intrinsically disordered proteins” in the Proceedings of the National Academies of Sciences, now available.

For the past four decades, biochemists and biomolecular engineers have used techniques such as X-ray crystallography, nuclear magnetic resonance, and cryo-electron microscopy to study proteins that fold into defined structures that dictate how they function like tiny machines that they are.

Scientists have also traditionally used a method to help understand what makes these proteins behave the way they do. They create mutations in the protein, change single amino acids, and study how that change affects the protein’s structure, stability, and folding and unfolding rates.

“It’s the only experimental technique we have to study what makes a particular amino acid sequence special to fold into a particular structure and perform a particular function,” Muñoz said.

Intrinsically disordered proteins (IDPs), discovered in the past 20 years, have no apparent structures – at least none that current techniques can discern. They change shape depending on their environment and conditions and tend to fold into structures when they bind to specific partner molecules. They have the unique ability to morph in response to multiple partners and can process sophisticated inputs and outputs.

But it’s a mystery whether their response is passive – entirely determined by the partner – or controlled via an internal folding mechanism that has yet to be revealed.

That’s the question Muñoz and his group are trying to answer as they experiment and model a partially disordered protein called NCBD to uncover clues as to how it performs its sophisticated biological function. They take this messy protein and make it even messier by breaking the NCBD into pieces and studying each one separately.

“It’s the messiest thing you can have because you’ve removed all the connections,” Muñoz said. “But these are the LEGO building blocks. They give us a point of reference.

Then the researchers recombine the segments in order, one at a time, to see how each larger restored segment behaves.

“Is it just the sum of its parts or a cooperation between the connected parts?” he said.

Ordered proteins behave as if they have on/off switches, while IDPs appear to function more like rheostats, changing gradually.

It could turn out that the internally displaced only appear disorderly because scientists observe them using techniques that don’t give them the big picture. IDPs must have some structure because they are able to select specific partners, change form when bound to those partners, and carry out complicated actions in very specific ways, Muñoz explained.

Courtesy of University of California, Merced

Co-author of the article Suhani Nagpal

Muñoz authored the paper with graduate students Thinh DN Luong and Suhani Nagpal, as well as Mourad Sadqi, a project scientist from the National Science Foundation Center of Excellence in Scientific and Technological Research for Cellular and Biomolecular Machinery (CCBM), for which Muñoz serves as director.

More and more IDPs are being discovered and are rapidly becoming a very important class of proteins. They are found more frequently in higher-order organisms, such as humans.

“It seems that the emerging paradigm is that all of these proteins are essential for regulation and responsible for all the complexity that emerges in higher-order organisms without having to dramatically increase the number of genes,” Muñoz said.

For example, a E.coli a bacterium has about 5,000 genes, while a human has about 30,000.

“So you can see that we absolutely have to do something special with these 30,000 genes to make us, compared to a bacterium, a very simple thing,” Muñoz said. “The idea is that this is achieved through sophisticated regulation, networks and other complicated processes, and it seems that the key players in all of this are these IDPs. They are often found in the hubs of these networks.

The next steps in this work will be to apply the new technique to other proteins and recombine the proteins outside of the segment order defined by the gene sequence to see how this affects segments and function.

“It ties in with a lot of our engineering work where we try to build biosensors and new diagnostic methods,” Muñoz said. “We can use these proteins as scaffolds to create responsive systems at the molecular level.”

This article was republished with permission from the University of California, Merced. Read the original.

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