Promiscuous protein droplets regulate immune gene activity

Biochemists at Emory are achieving insights into how an important regulator of the immune system switches its function, based on its orientation and local environment. New research demonstrates that the glucocorticoid receptor (or GR) forms droplets or “condensates” that change form, depending on its available partners.

The inside of a cell is like a crowded nightclub or party, with enzymes and other proteins searching out prospective partners. The GR is particularly well-connected and promiscuous, and has the potential to interact with many other proteins. It is a type of protein known as a transcription factor, which turns some genes on and others off, depending on how it is binding DNA.

These are fluorescent droplets of the glucocorticoid receptor (GR) in red, with a coregulator protein in green. When DNA is added, the co-regulator forms its own droplets on the surface of GR droplets. Image courtesy of Filipp Frank

“It is now thought that most transcription factors form or are recruited into condensates, and that condensation modulates their function,” says Filipp Frank, PhD, first author of the paper and a postdoctoral instructor in Eric Ortlund’s lab in the Department of Biochemistry. “What’s new is that we identified a DNA-dependent change in GR condensates, which has not been described for other transcription factors.”

The results are published in Proceedings of the National Academy of Sciences. Ortlund is a co-author of the paper, along with postdoctoral fellow Xu Liu, PhD.

Understanding how the GR works could help researchers find anti-inflammatory drugs with reduced side effects. The GR is the target for corticosteroid drugs such as dexamethasone, which is currently used to treat COVID-19 as well as allergies, asthma and autoimmune diseases.

Corticosteroids’ harmful side effects are thought to come from turning on genes involved in metabolism and bone growth, while their desired anti-inflammatory effects result from turning other inflammatory and immune system genes off. Researchers want to find alternatives that could separate those two functions.

Posted on July 21, 2021 by Quinn Eastman in Cancer, Immunology Leave a comment

Tweaks to corticosteroids may reduce side effects

Steroid anti-inflammatory drugs such as dexamethasone and prednisone are widely used to treat conditions such as allergies, asthma, autoimmune diseases, cancer – and now, COVID-19. Yet they can have harmful side effects on the skin, bones and metabolism.

The side effects are thought to come from a molecular mechanism that is separate from the anti-inflammatory one, and scientists have envisioned that it may be possible to divide the two. A new paper in PNAS from Emory biochemist Eric Ortlund’s lab sketches out how one potential alternative may work.

Synthetic corticosteroids mimic the action of the stress hormone cortisol; both bind the glucocorticoid receptor (GR) protein. Ortlund’s group obtained structural information on how vamorolone, an experimental drug, sticks to the part of GR that binds hormones.

The American company ReveraGen and Swiss partner Santhera are developing vamorolone for Duchenne muscular dystrophy, but it is possible to envision several other conditions such as ulcerative colitis for which vamorolone or a similar drug could be helpful. Vamorolone is NOT approved by the FDA for Duchenne muscular dystrophy or any other indication.

As far as its interaction with GR, what sets vamorolone apart from conventional corticosteroids is quite subtle: a missing hydrogen bond. This means that GR doesn’t interact as well with various partner proteins, which are needed to turn on genes involved in processes such as metabolism and bone growth. However, the anti-inflammatory effects result mainly from turning inflammatory and immune system genes off, and those interactions are maintained. More on that distinction here and here.

Posted on September 11, 2020 by Quinn Eastman in Uncategorized Leave a comment

Burning fat like a baby

Newborn humans and hibernating mammals have high levels of brown adipose tissue, which they use to generate heat. Adult humans generally don’t have abundant brown adipose tissue, even if they have lots of “white” fat. Increasing brown fat’s activity may be an approach to treat obesity and related metabolic disorders.

Recently researchers identified an enzyme called Them1 (thioesterase superfamily member 1) as a factor that limits heat generation in brown adipose tissue. Emory biochemist Eric Ortlund and his lab showed how part of the Them1 enzyme binds a certain type of lipid molecule, and also how that part of the enzyme anchors the enzyme close to lipid droplets in adipose cells. Former graduate student Matt Tillman, now a postdoc at Duke, was the first author of the new paper in Proceedings of the National Academy of Sciences.

“In this study, we show Them1 contains a lipid sensor module that detects specific lipids within the cell to regulate its activity,” says Tillman.

In brown adipose cells, the lipid-sensing domain of Them1 is needed for localization around lipid droplets

From Tillman et al PNAS (2020)

He and his colleagues showed that a lipid known for its role in cell signaling, lysophosphatidylcholine or LPC, inhibits Them1 activity, which in turn activates thermogenesis in brown adipose tissue. In contrast, other fatty acids that serve as fuel tend to activate Them1. This regulatory system within Them1 allows the cell to sense its metabolic state and decide when to burn or conserve fat.

Posted on August 21, 2020 by Quinn Eastman in Uncategorized Leave a comment

Triple play in science communication

Emory BCDB graduate student Emma D’Agostino

We are highlighting Emory BCDB graduate student Emma D’Agostino, who is a rare triple play in the realm of science communication.

Emma has her own blog, where she talks about what it’s like to have cystic fibrosis. Recent posts have discussed the science of the disease and how she makes complicated treatment decisions together with her doctors. She’s an advisor to the Cystic Fibrosis Foundation on patient safety, communicating research and including the CF community in the research process. She’s also working in biochemist Eric Ortlund’s lab on nuclear receptors in the liver:drug targets for the treatment of diabetes and intestinal diseases.

The triple play is this — on her blog, Emma has discussed how she has to deal with antibiotic resistance. Emory Antibiotic Resistance Center director David Weiss’ lab has published a lot on colistin: how it’s a last-resort drug because of side effects, and how difficult-to-detect resistance to it is spreading. Emma has some personal experience with colistin that for me, brought the issue closer. Read more

Posted on July 20, 2020 by Quinn Eastman in Uncategorized Leave a comment

Tracking how steroid hormone receptor proteins evolved

When thinking about the evolution of female and male, consider that the first steroid receptor proteins, which emerged about 550 million years ago, were responsive to estrogen. The ancestor of other steroid hormone receptors, responsive to hormones such as testosterone, progesterone and cortisol, emerged many millions of years later.

Blue = estrogen-responsive receptors, Orange = non-aromatized (progesterone, testosterone, cortisol) hormone-responsive

Biochemist Eric Ortlund and colleagues have a new paper in Structure that reconstructs how interactions of steroid receptor proteins evolved over time. This is a complex area to model, since the receptors change shape when they bind their respective hormones, allowing them to bring in other proteins and activate genes.

First author C. Denise Okafor, a FIRST postdoctoral fellow at Emory, will be starting a position as assistant professor at Penn State next month.

The scientists also show that a mutation in the mineralocorticoid receptor associated with severe hypertension (S810L), which makes the receptor more promiscuous, restores an ancestral interaction within the protein.

“Evolutionary substitutions rewired the networks, subsequently altering hormonal interactions and allowing steroid receptors to achieve ligand specificity over time,” the authors write.

Posted on December 9, 2019 by Quinn Eastman in Uncategorized Leave a comment

Biochemists grab slippery target: LRH-1

To fight fat, scientists had to figure out how to pin down a greasy, slippery target. Researchers at Emory University and Baylor College of Medicine have identified compounds that potently activate LRH-1, a liver protein that regulates the metabolism of fat and sugar. These compounds have potential for treating diabetes, fatty liver disease and inflammatory bowel disease.

Their findings were recently published online in Journal of Medicinal Chemistry.

LRH-1 is thought to sense metabolic state by binding a still-undetermined group of greasy molecules: lipids or phospholipids. It is a nuclear receptor, a type of protein that turns on genes in response to hormones or vitamins. The challenge scientists faced was in designing drugs that fit into the same slot occupied by the lipids.

“Phospholipids are typically big, greasy molecules that are hard to deliver as drugs, since they are quickly taken apart by the digestive system,” says Eric Ortlund, PhD, associate professor of biochemistry at Emory University School of Medicine. “We designed some substitutes that don’t fall apart, and they’re highly effective – 100 times more potent that what’s been found already.”

Previous attempts to design drugs that target LRH-1 ran into trouble because of the grease. Two very similar molecules might bind LRH-1 in opposite orientations. Ortlund’s lab worked with Emory chemist Nathan Jui, PhD and his colleagues to synthesize a large number of compounds, designing a “hook” that kept them in place. Based on previous structural studies, the hook could stop potential drugs from rotating around unpredictably. Read more

Posted on September 30, 2019 by Quinn Eastman in Uncategorized Leave a comment

Shaking up thermostable proteins

Imagine a shaker table, where kids can assemble a structure out of LEGO bricks and then subject it to a simulated earthquake. The objective is to design the most stable structure.

Biochemists face a similar task when they are attempting to design thermostable proteins, with heat analogous to shaking. Thermostable proteins, which do not become unfolded/denatured at high temperatures, are valuable for industrial processes.

Now imagine that these stable structures have to also perform a function. This is the two-part challenge of designing thermostable proteins. They have to maintain their physical structure, and continue to perform their function adequately, all at high temperatures.

Eric Ortlund and colleagues, working with Eric Gaucher at Georgia Tech*, have a new paper published in Structure, in which they examine different ways to achieve this goal in a component of the protein synthesis machinery, EF-Tu. This protein exists in both mesophilic bacteria, which live at around human body temperature, and thermophilic organisms (think: hot springs).

A previous analysis by Gaucher used the ASR technique (ancestral sequence reconstruction) to resurrect ancient, extinct EF-Tus and characterize them. It was shown that that ancestral EF-Tus were thermostable and functional. EF-Tu’s thermostability declined along with the environmental temperature; ancestral bacteria started off living in hot environments and those environments cooled off over millions of years.

In the new paper, Ortlund and first author Denise Okafor show that stable proteins generated by protein engineering methods do not always retain their functional capabilities. However, the ASR technique has a unique advantage, Ortlund says. By accounting for the evolutionary history of the protein, it preserves the natural motions required for normal protein function. Their results suggest that ASR could be used to engineer thermostability in other proteins besides EF-Tu.

*Gaucher recently moved to Georgia State.

Posted on January 5, 2018 by Quinn Eastman in Uncategorized Leave a comment

Unlocking a liver receptor puzzle

Imagine a key that opens a pin tumbler lock. A very similar key can also fit into the lock, but upside down in comparison to the first key.

Biochemist Eric Ortlund and colleagues have obtained analogous results in their study of how potential diabetes drugs interact with their target, the protein LRH-1. Their research, published in Journal of Biological Chemistry, shows that making small changes to LRH-1-targeted compounds makes a huge difference in how they fit into the protein’s binding pocket.

First author Suzanne Mays, a graduate student in Emory’s MSP program

This research was selected as “Paper of the Week” by JBC and is featured on the cover of the December 2 issue.

LRH-1 (liver receptor homolog-1) is a nuclear receptor, a type of protein that turns on genes in response to small molecules like hormones or vitamins. LRH-1 acts in the liver to regulate metabolism of fat and sugar.

Previous research has shown that activating LRH-1 decreases liver fat and improves insulin sensitivity in mice. Because of this, many research teams have been trying to design synthetic compounds that activate this protein, which could have potential to treat diabetes and nonalcoholic fatty liver disease. This has been a difficult task, because not much is known about how synthetic compounds interact with LRH-1 and switch it into the active state. Read more

Posted on December 6, 2016 by Quinn Eastman in Uncategorized Leave a comment

Ancient protein flexibility may drive ‘new’ functions

A mechanism by which stress hormones inhibit the immune system, which appeared to be relatively new in evolution, may actually be hundreds of millions of years old.

A protein called the glucocorticoid receptor or GR, which responds to the stress hormone cortisol, can take on two different forms to bind DNA: one for activating gene activity, and one for repressing it. In a paper published Dec. 28 in PNAS, scientists show how evolutionary fine-tuning has obscured the origin of GRâ€™s ability to adopt different shapes.

â€œWhat this highlights is how proteins that end up evolving new functions had those capacities, because of their flexibility, at the beginning of their evolutionary history,â€ says lead author Eric Ortlund, PhD, associate professor of biochemistry at Emory University School of Medicine.

GR is part of a family of steroid receptor proteins that control cellsâ€™ responses to hormones such as estrogen, testosterone and aldosterone. Our genomes contain separate genes encoding each one. Scientists think that this family evolved by gene duplication, branch by branch, from a single ancestor present in primitive vertebrates. Read more

Posted on January 7, 2016 by Quinn Eastman in Heart, Immunology Leave a comment

Unexpected mechanism for a longevity lipid

The idea that particular lipid components, such as omega-3 fatty acids, promote health is quite familiar, so the finding that the lipid oleoylethanolamide or OEA extends longevity in the worm C. elegans is perhaps not so surprising. However, a recent paper in Science is remarkable for what it reveals about how OEA exerts its effects.

Scientists at Baylor College of Medicine led by Meng Wang, with some help from biochemists Eric Ortlund and Eric Armstrong at Emory, discovered that OEA is a way one part of the cell, the lysosome, talks to another part, the nucleus. Lysosomes are sort of recycling centers/trash digestersÂ (important for autophagy) and the nucleus is the control tower for the cell. The authors show that starting in lysosomes, OEA travels to the nucleus and activates nuclear hormone receptors (the Ortlund labâ€™s specialty). Read more

Posted on January 9, 2015 by Quinn Eastman in Uncategorized Leave a comment

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