X-ray laser study identifies crystalline intermediate in our 'pathway to breathing'

February 11, 2019

Scientists from Arizona State University’s School of Molecular Sciences, in collaboration with colleagues from Albert Einstein College of Medicine in New York City, have captured for the first time snapshots of crystal structures of intermediates in the biochemical pathway that enables us to breathe.

Their results, published today in the Proceedings of the National Academy of Sciences in the article "Snapshot of an Oxygen Intermediate in the Catalytic Reaction of Cytochrome c Oxidase," provide key insights into the final step of aerobic respiration. Austin Echelmeier et al (From left) Austin Echelmeier, Alexandra Ros, Petra Fromme and Raimund Fromme, all from ASU’s School of Molecular Sciences and the Biodesign Institute’s Center for Applied Structural Discovery. Download Full Image

“It takes a team to conduct such a sophisticated experiment,” said Associate Professor Alexandra Ros who, together with her graduate student Austin Echelmeier and former intern Gerrit Brehm, developed the hydrodynamic focusing mixer that made these experiments possible.

The mixer is a microfluidic device, which is high-resolution, 3D-printed and enables two streams of oxygen-saturated buffer to mix perfectly with a central stream containing bovine cytochrome c oxidase (bCcO) microcrystals. This initiates a catalytic reaction between the oxygen and the microcrystals.

In the beginning

This research was instigated by a conversation between Professor Petra Fromme, director of the Biodesign Institute’s Center for Applied Structural Discovery (CASD); Raimund Fromme, School of Molecular Sciences associate research professor; and Professor Denis Rousseau from the Albert Einstein College of Medicine in New York City who works on the structure of cytochrome c oxidase, a key enzyme involved with aerobic respiration.

Cytochrome c oxidase (CcO) is the last enzyme in the respiratory electron transport chain of cells located in the mitochondrial membrane. It receives an electron from each of four cytochrome c molecules, and transfers them to one oxygen molecule (two atoms), converting the molecular oxygen to two molecules of water.

cytochrome c oxidase intermediate

Researchers at CASD, including ASU’s Richard Snell Professor of Physics John Spence, helped to pioneer a new technique called time-resolved serial femtosecondA femtosecond is a millionth of a billionth of a second. crystallography (TR-SFX). This technique takes advantage of an X-ray Free Electron Laser (XFEL) at the Department of Energy's SLAC National Accelerator Laboratory at Stanford University. 

TR-SFX is a promising technique for protein structure determination, where a liquid stream containing protein crystals is intersected with a high-intensity XFEL beam that is a billion times brighter than traditional synchrotron X-ray sources.

While the crystals diffract and immediately are destroyed by the intense XFEL beam, the resulting diffraction patterns can be recorded with state-of-the-art detectors. Powerful new data analysis methods have been developed, allowing a team to analyze these diffraction patterns and obtain electron density maps and detailed structural information of proteins.

The method is specifically appealing for hard-to-crystallize proteins, such as membrane proteins, as it yields high-resolution structural information from small micro- or nanocrystals, thus reducing the contribution of crystal defects and avoiding tedious (if not impossible) growth of large crystals as is required in traditional synchrotron-based crystallography.

This new “diffraction before destruction” method has opened up new avenues for structural determination of fragile biomolecules under physiologically relevant conditions (at room temperature and in the absence of cryoprotectants) and without radiation damage.

CcO reduces oxygen to water and harnesses the chemical energy to drive proton (positively charged hydrogen atom) relocation across the inner mitochondrial membrane by a previously unresolved mechanism.

In summary, the TR-SFX studies have allowed the structural determination of a key oxygen intermediate of bCcO. The results of the team’s experiments provide new insights into the mechanism of proton relocation in the cow enzyme as compared to that in bacterial CcOs, and paves the way for the determination of the structures of other CcO intermediates, as well as transient species formed in other enzyme reactions.

Other coauthors on this paper, not previously mentioned, include Izumi Ishigami, Ariel Lewis-Ballester and Syun-Ru Yeh, all from the Albert Einstein College of Medicine; Nadia Zatsepin and Stella Lisova of the ASU Department of Physics; Jesse Coe, Zachary Dobson, Garrett Nelson and Shangji Zhang all from the School of Molecular Sciences and CASD; Thomas Grant from University at Buffalo, State University of New York; and Sébastien Boutet, Raymond Sierra and Alexander Batyuk all from SLAC.

This research was also supported by an NIH R01 (Petra Fromme) and the NSF BioXFEL STC.

Jenny Green

Clinical associate professor, School of Molecular Sciences


Book provides a new framework for making sense of mental illness

February 11, 2019

Fear. Anxiety. Hope. Desire. Love. Anger. Guilt. Grief. These are just a few of the emotions universal to our human experience.

But why some people can become vulnerable to extreme bad feelings and other mental disorders remains a mystery that has affected and divided families, and cost lost years or, worse, lives for millions of sufferers of disorders like depression, addiction, bipolar disorder, autism and schizophrenia. In Randy Nesse’s new book, he brings the well-established principles of evolutionary biology to bear on the urgent problem of better understanding mental illness. Download Full Image

What has happened in our brains to shape these disorders? Is it nature or nurture? Or both? Or would asking a different question help to get psychiatry around current roadblocks?

Despite evidence of mental illness tending to run in families, and billions of dollars fueling the DNA research efforts of many smart scientists, not a single specific brain cause has been found for any of the major mental disorders. And there is not a single lab test or scan that can help psychiatrists in their diagnoses.

“This is as astounding as it is disappointing,” writes Arizona State University School of Life Sciences Professor Randy Nesse in the introduction to his new book, “Good Reasons for Bad Feelings: Insights from the Frontier of Evolutionary Psychiatry.”

A leading psychiatrist compares the current state of diagnosis in psychiatry to “astronomy before Copernicus and biology before Darwin.” For example, the gold-standard DSM-V diagnostic manual in psychiatry was painstakingly revised in 2016 after more than a decade of often rancorous debate. It now includes more than 300 different classifications of mental disorders. And yet, despite this, the U.S. National Institute of Mental Health ended up abandoning the official DSM-V diagnoses for mental health.

“So much for a common diagnostic system creating consensus!” writes Nesse, who directs the Center for Evolution and Medicine at ASU. “The field of psychiatry is deeply confused.”

MORE: Study finds a lack of mental health interventions for ethnic minority youth in the U.S.

With confusing diagnoses and the hope for diagnosis based on genetics for now collapsed, what’s a psychiatrist or mental illness sufferer to do?

“Many books attack the field of psychiatry,” Nesse writes. “This is not one of them. Most of us (psychiatrists) lie awake some nights worrying about a patient in a crisis and wondering how to help. However, most patients get better, and the challenge of helping them makes the practice of psychiatry deeply satisfying.”

“The challenge of understanding mental disorders is, by contrast, deeply unsatisfying.”

Taking case studies from his own practice, Nesse offers a view of mental illness as seen through the lens of evolution. As famous geneticist Theodosius Dobzhansky once said, “Nothing in biology makes sense except in the light of evolution.”

randy nesse

Randy Nesse

That and dealing with decades of uncertainty in the field of psychiatry motivated Nesse to take a different point of view.   

“I was frustrated as well as confused,” writes Nesse. “To see the whole landscape of mental illness requires a view from a mile high using special glasses that show changes across evolutionary as well as historical time.”

An important point is that Charles Darwin’s natural selection shapes organisms to behave in ways that maximize their reproductive success — not their health. This ensures that their genes are passed down to the next generation.

It’s a perspective that first drove him to understand disease in general, and to now extend it to find the future of psychiatry in the evolutionary past of humans. The key insights to provide an evolutionary framework came from his first attempt to connect in his seminal book “Why People Get Sick.”

“Diseases are not adaptations,” writes Nesse. “They do not have evolutionary explanations. They were not shaped by natural selection. However, aspects of the body that make us vulnerable to disease do have evolutionary explanations.”

For Nesse, shifting the focus from diseases to traits that make bodies vulnerable to diseases was the crucial insight that became a cornerstone for evolutionary medicine.

The same goes for our brains.

“Our brains were shaped to benefit our genes, not us,” said Nesse. “And evolutionary psychiatry is the part of evolutionary medicine that asks why natural selection left us vulnerable to mental disorders.”

One of the reasons Nesse believes we are vulnerable is because so many of the environments we face today are vastly different from those that shaped our evolution. Another is what Nesse calls “the smoke-detector principle”, or how our minds evolved to respond with useful alarms to threats, like the sound of breaking branches that prevented us from being eaten by lions 200,000 years ago on the African savannas.

Now, in our modern attempts to stay constantly connected, every time our cellphones bleep or buzz with a new notification, we are triggering these same smoke detectors, leading to constant anxiety or insomnia. We are hijacking our threat response.

Genes for schizophrenia and autism may persist because natural selection pushes our brains to the point that maximizes genetic fitness. If that point is near a cliff edge, a few people may be left “off the edge” and very vulnerable to disease.             

Far from radical, Nesse’s approach simply brings the well-established principles of evolutionary biology to bear on the urgent problem of better understanding mental illness. He shows how this approach provides psychiatry with the same kind of foundation in biology that physiology provides for the rest of medicine and why it requires understanding individuals as individuals.

The book is available from Penguin Books or Amazon on Feb. 12, which is coincidentally Charles Darwin’s 210th birthday. In celebration of the new publication, Nesse will give a talk about the book at ASU on April 2 at 5:30 p.m.  

Joe Caspermeyer

Manager (natural sciences), Media Relations & Strategic Communications