New study shows how infrared lasers destroy harmful protein aggregates in Alzheimer's

August 4, 2020

Science Daily/Tokyo University of Science

The agglomeration of proteins into structures called amyloid plaques is a common feature of many neurodegenerative diseases, including Alzheimer's. Now, scientists reveal, through experiments and simulations, how resonance with an infrared laser, when it is tuned to a specific frequency, causes amyloid fibrils to disintegrate from the inside out. Their findings open doors to novel therapeutic possibilities for amyloid plaque-related neurodegenerative diseases that have thus far been incurable.

A notable characteristic of several neurodegenerative diseases, such as Alzheimer's and Parkinson's, is the formation of harmful plaques that contain aggregates -- also known as fibrils -- of amyloid proteins. Unfortunately, even after decades of research, getting rid of these plaques has remained a herculean challenge. Thus, the treatment options available to patients with these disorders are limited and not very effective.

In recent years, instead of going down the chemical route using drugs, some scientists have turned to alternative approaches, such as ultrasound, to destroy amyloid fibrils and halt the progression of Alzheimer's disease. Now, a research team led by Dr Takayasu Kawasaki (IR-FEL Research Center, Tokyo University of Science, Japan) and Dr Phuong H. Nguyen (Centre National de la Recherche Scientifique, France), including other researchers from the Aichi Synchrotron Radiation Center and the Synchrotron Radiation Research Center, Nagoya University, Japan, has used novel methods to show how infrared-laser irradiation can destroy amyloid fibrils.

In their study, published in Journal of Physical Chemistry B, the scientists present the results of laser experiments and molecular dynamics simulations. This two-pronged attack on the problem was necessary because of the inherent limitations of each approach, as Dr Kawasaki explains, "While laser experiments coupled with various microscopy methods can provide information about the morphology and structural evolution of amyloid fibrils after laser irradiation, these experiments have limited spatial and temporal resolutions, thus preventing a full understanding of the underlying molecular mechanisms. On the other hand, though this information can be obtained from molecular simulations, the laser intensity and irradiation time used in simulations are very different from those used in actual experiments. It is therefore important to determine whether the process of laser-induced fibril dissociation obtained through experiments and simulations is similar."

The scientists used a portion of a yeast protein that is known to form amyloid fibrils on its own. In their laser experiments, they tuned the frequency of an infrared laser beam to that of the "amide I band" of the fibril, creating resonance. Scanning electron microscopy images confirmed that the amyloid fibrils disassembled upon laser irradiation at the resonance frequency, and a combination of spectroscopy techniques revealed details about the final structure after fibril dissociation.

For the simulations, the researchers employed a technique that a few members of the current team had previously developed, called "nonequilibrium molecular dynamics (NEMD) simulations." Its results corroborated those of the experiment and additionally clarified the entire amyloid dissociation process down to very specific details. Through the simulations, the scientists observed that the process begins at the core of the fibril where the resonance breaks intermolecular hydrogen bonds and thus separates the proteins in the aggregate. The disruption to this structure then spreads outward to the extremities of the fibril.

Together, the experiment and simulation make a good case for a novel treatment possibility for neurodegenerative disorders. Dr Kawasaki remarks, "In view of the inability of existing drugs to slow or reverse the cognitive impairment in Alzheimer's disease, developing non-pharmaceutical approaches is very desirable. The ability to use infrared lasers to dissociate amyloid fibrils opens up a promising approach."

The team's long-term goal is to establish a framework combining laser experiments with NEMD simulations to study the process of fibril dissociation in even more detail, and new works are already underway. All these efforts will hopefully light a beacon of hope for those dealing with Alzheimer's or other neurodegenerative diseases.

https://www.sciencedaily.com/releases/2020/08/200804111501.htm

Biochemists discover new insights into what may go awry in brains of Alzheimer's patients

August 19, 2019

Science Daily/University of California - Los Angeles

More than three decades of research on Alzheimer's disease have not produced any major treatment advances for those with the disorder, according to a UCLA expert who has studied the biochemistry of the brain and Alzheimer's for nearly 30 years. "Nothing has worked," said Steven Clarke, a distinguished professor of chemistry and biochemistry. "We're ready for new ideas." Now, Clarke and UCLA colleagues have reported new insights that may lead to progress in fighting the devastating disease.

Scientists have known for years that amyloid fibrils -- harmful, elongated, water-tight rope-like structures -- form in the brains of people with Alzheimer's, and likely hold important clues to the disease. UCLA Professor David Eisenberg and an international team of chemists and molecular biologists reported in the journal Nature in 2005 that amyloid fibrils contain proteins that interlock like the teeth of a zipper. The researchers also reported their hypothesis that this dry molecular zipper is in the fibrils that form in Alzheimer's disease, as well as in Parkinson's disease and two dozen other degenerative diseases. Their hypothesis has been supported by recent studies.

Alzheimer's disease, the most common cause of dementia among older adults, is an irreversible, progressive brain disorder that kills brain cells, gradually destroys memory and eventually affects thinking, behavior and the ability to carry out the daily tasks of life. More than 5.5 million Americans, most of whom are over 65, are thought to have dementia caused by Alzheimer's.

The UCLA team reports in the journal Nature Communications that the small protein beta amyloid, also known as a peptide, that plays an important role in Alzheimer's has a normal version that may be less harmful than previously thought and an age-damaged version that is more harmful.

Rebeccah Warmack, who was a UCLA graduate student at the time of the study and is its lead author, discovered that a specific version of age-modified beta amyloid contains a second molecular zipper not previously known to exist. Proteins live in water, but all the water gets pushed out as the fibril is sealed and zipped up. Warmack worked closely with UCLA graduate students David Boyer, Chih-Te Zee and Logan Richards; as well as senior research scientists Michael Sawaya and Duilio Cascio.

What goes wrong with beta amyloid, whose most common forms have 40 or 42 amino acids that are connected like a string of beads on a necklace?

The researchers report that with age, the 23rd amino acid can spontaneously form a kink, similar to one in a garden hose. This kinked form is known as isoAsp23. The normal version does not create the stronger second molecular zipper, but the kinked form does.

"Now we know a second water-free zipper can form, and is extremely difficult to pry apart," Warmack said. "We don't know how to break the zipper."

The normal form of beta amyloid has six water molecules that prevent the formation of a tight zipper, but the kink ejects these water molecules, allowing the zipper to form.

"Rebeccah has shown this kink leads to faster growth of the fibrils that have been linked to Alzheimer's disease," said Clarke, who has conducted research on biochemistry of the brain and Alzheimer's disease since 1990. "This second molecular zipper is double trouble. Once it's zipped, it's zipped, and once the formation of fibrils starts, it looks like you can't stop it. The kinked form initiates a dangerous cascade of events that we believe can result in Alzheimer's disease."

Why does beta amyloid's 23rd amino acid sometimes form this dangerous kink?

Clarke thinks the kinks in this amino acid form throughout our lives, but we have a protein repair enzyme that fixes them.

"As we get older, maybe the repair enzyme misses the repair once or twice," he said. "The repair enzyme might be 99.9% effective, but over 60 years or more, the kinks eventually build up. If not repaired or if degraded in time, the kink can spread to virtually every neuron and can do tremendous damage."

"The good news is that knowing what the problem is, we can think about ways to solve it," he added. "This kinked amino acid is where we want to look."

The research offers clues to pharmaceutical companies, which could develop ways to prevent formation of the kink or get the repair enzyme to work better; or by designing a cap that would prevent fibrils from growing.

Clarke said beta amyloid and a much larger protein tau -- with more than 750 amino acids -- make a devastating one-two punch that forms fibrils and spreads them to many neurons throughout the brain. All humans have both beta amyloid and tau. Researchers say it appears that beta amyloid produces fibrils that can lead to tau aggregates, which can spread the toxicity to other brain cells. However, exactly how beta amyloid and tau work together to kill neurons is not yet known.

In this study, Warmack produced crystals, both the normal and kinked types, in 15 of beta amyloid's amino acids. She used a modified type of cryo-electron microscopy to analyze the crystals. Cryo-electron microscopy, whose development won its creators the 2017 Nobel Prize in chemistry, enables scientists to see large biomolecules in extraordinary detail. Professor Tamir Gonen pioneered the modified microscopy, called microcrystal electron diffraction, which enables scientists to study biomolecules of any size.

https://www.sciencedaily.com/releases/2019/08/190819164346.htm

Mapping the structure of protein aggregate that leads to Alzheimer's

August 12, 2019

Science Daily/Binghamton University

A research team including faculty at Binghamton University and University of Colorado Denver are the first to map the molecular structure of an aggressive protein aggregate that causes acceleration of Alzheimer's disease.

"Approximately 10 percent of Alzheimer's cases result from familial mutations," said Wei Qiang, assistant professor of biophysical chemistry at Binghamton University. "The other 90 percent cases are caused by misfolded wild-type amyloid proteins. We need to understand the molecular basis of the disease pathology. In doing so, we might one day create drugs that prevent the degenerative effects of the disease."

Alzheimer's disease starts developing when toxic protein fragments called beta amyloids form into chains known as fibrils, which build upon and kill brain cells. Qiang, along with researchers at the University of Colorado Denver, used high-resolution solid-state nuclear magnetic resonance spectroscopy to study these fibrils. Their work revealed that these fibrils may possess major variations in the molecular structure of amyloid depositions in the human brain. More importantly, the fibrils could serve as "seeds" for further fibril deposition, which is a potential risk factor in Alzheimer's pathology.

"This work describes a molecular structural model for a pathologically relevant beta-amyloid fibril variant," said Qiang. "We showed that this variant could lead to rapid seeding of new amyloid fibrils, which potentially contributes to the spreading and amplification of amyloid deposition in human brains."

Qiang and his team are looking at several other types of fibril variants and specifically, the correlation between the structural variations, their seeding abilities and the resulted cellular toxicity levels.

"We have already obtained exciting results and a new manuscript describing these further finding is in preparation," said Qiang.

https://www.sciencedaily.com/releases/2019/08/190812144924.htm