PRESS-NEWS.org - Press Release Distribution
PRESS RELEASES DISTRIBUTION

A simple and robust experimental process for protein engineering

Easily interpretable technique can reduce the cost and increase the scale of protein optimization for applications in medicine, biofuels and more

2024-03-12
(Press-News.org) Image

A protein engineering method using simple, cost-effective experiments and machine learning models can predict which proteins will be effective for a given purpose, according to a new study by University of Michigan researchers.

The method has far-reaching potential to assemble proteins and peptides for applications from industry tools to therapeutics. For instance, this technique can help speed up the development of stabilized peptides for treating diseases in ways that current medicines can't, including improving how exclusively antibodies bind to their targets in immunotherapy.

"The rules that govern how proteins work, from sequence to structure to function, are so complicated. Contributing to the interpretability of protein engineering efforts is particularly exciting," said Marshall Case, a doctoral graduate of chemical engineering at U-M and first author of the study. 

Currently, most protein engineering experiments use complex, labor-intensive methods and expensive instruments to attain very precise data. The long process limits how much data can be acquired, and the complicated methods are challenging to learn and execute—a trade-off for precision.

"Our method has shown that for many applications, you can avoid these complicated methods," said Case, now a computational biologist at Manifold Biotechnologies.

The updated method starts by sorting cells into two groups, known as binary sorting, based on whether they express a desired trait—like binding to fluorescent molecules—or not. Then, the cells are sequenced to get the underlying DNA codes for the proteins of interest. Machine learning algorithms then reduce the noise in the sequencing data to identify the best possible protein. 

"Rather than selecting the 'best book' from the library, it's like reading many books, then piecing together different pages from different stories to come up with the best book possible, even if it wasn't  in your original library," said Greg Thurber, U-M associate professor of chemical engineering and corresponding author on the paper. "I was surprised to see the robustness of this technique using simple, binary sorting data."

Further enhancing its accessibility, the method uses linear machine learning models, which are easier to interpret compared to models with dozens of parameters.

"Because we can learn physical rules about how the proteins are actually working, we can use linear equations to model nonlinear protein behavior and make better drugs that way," Case said.

The research was conducted at the Advanced Genomics Core, Center for Structural Biology, Biological Mass Spectrometry Facility and Proteomics & Peptide Synthesis Core.  

Additional University of Michigan co-authors: Matthew Smith of the Peter Tessier Lab and Jordan Vinh.

Study: Machine learning to predict continuous protein properties from binary cell sorting data and map unseen sequence space (DOI: 10.1073/pnas.2311726121)

 

END


ELSE PRESS RELEASES FROM THIS DATE:

UTEP researchers to design movement-based training to support local health providers

UTEP researchers to design movement-based training to support local health providers
2024-03-12
EL PASO, Texas (Mar. 12, 2024) – Burnout among health care workers is a well-documented problem that can exacerbate health disparities and limit access to care. Now, researchers at The University of Texas at El Paso are taking a creative approach in their search for a solution – a training program for providers that combines elements of art and science. The project will examine the impact of a movement-based and somatics cross-training intervention on health care providers in the Paso del ...

Alaska dinosaur tracks reveal a lush, wet environment

2024-03-12
A large find of dinosaur tracks and fossilized plants and tree stumps in far northwestern Alaska provides new information about the climate and movement of animals near the time when they began traveling between the Asian and North American continents roughly 100 million years ago. The findings by an international team of scientists led by paleontologist Anthony Fiorillo were published Jan. 30 in the journal Geosciences. Fiorillo researched in Alaska while at Southern Methodist University. He is now executive director of the New Mexico Museum of Natural History and Science. University ...

Study: Best way to memorize stuff? It depends...

2024-03-12
Recent experiments by psychologists at Temple University and the University of Pittsburgh shed new light on how we learn and how we remember our real-world experiences. The research, described in the March 12 online edition of Proceedings of the National Academy of Sciences (PNAS), suggests that varying what we study and spacing out our learning over time can both be helpful for memory — it just depends on what we’re trying to remember. “Lots of prior research has shown that learning and ...

Exploring arctic plants and lichens: An important conservation baseline for Nunavut’s newest and largest territorial park

Exploring arctic plants and lichens: An important conservation baseline for Nunavut’s newest and largest territorial park
2024-03-12
Encompassing over 16 000 km2 of towering mountains, long fiords, lush valleys, and massive ice caps, Agguttinni Territorial Park is a protected area on northern Baffin Island, Nunavut, Canada. This park, and all of Nunavut, is Inuit Nunangat – Inuit homeland in Canada – and the park protects sites and biodiversity stewarded by Inuit since time immemorial. Agguttinni means “where the prevailing wind occurs” in the Inuktitut local dialect. The park includes important bird areas, key habitats for polar bears and caribou, and numerous important Inuit cultural sites. It is very remote: no roads lead to it, and access ...

Multiple organ attack and immune dysregulation: Study reveals how the chikungunya virus leads to death

2024-03-12
The chikungunya virus, transmitted by Aedes aegypti and Aedes albopictus mosquitoes and responsible for more than 900 deaths in Brazil since it arrived around ten years ago, is capable of spreading through the blood, reaching multiple organs and crossing the blood-brain barrier, which protects the central nervous system. The mechanisms of action observed for the first time in fatal cases by a group of Brazilian, American and British researchers were reported in an article published on March 12 in the journal Cell Host & Microbe. The findings reinforce the need ...

Setting realistic expectations for recovery after robotic lung surgery

2024-03-12
Are surgeons giving patients unrealistic expectations about recovery after robotic lung surgery? That’s what CU Department of Surgery faculty member Robert Meguid, M.D., MPH, and surgery resident Adam Dyas, M.D., set out to discover after realizing the guidance they were offering patients might be based on outdated or anecdotal information. “Traditionally, in surgery, we're taught to tell patients that they'll be back to normal from surgery within six weeks,” says Meguid, professor of cardiothoracic ...

UCF researchers lead $1.5 million project to improve efficiency of solar cells

2024-03-12
ORLANDO – A team of researchers from the University of Central Florida and the University of Delaware’s Institute of Energy Conversion has received a $1.5 million grant from the U.S. Department of Energy Solar Technologies Office to develop a novel metallization process that could improve the efficiency and lower the cost of solar cells, making solar energy more accessible to consumers. The metallization process produces the metal contacts that are placed on the surface of silicon solar cells to ...

AI analysis of historical satellite images show USSR collapse in 1990s increased methane emissions, despite lower oil and gas production

AI analysis of historical satellite images show USSR collapse in 1990s increased methane emissions, despite lower oil and gas production
2024-03-12
The collapse of the former Soviet Union in 1991 had social, political and economic effects worldwide. Among them was a suspected role in slowing human-generated methane emissions. Methane had been rising steadily in the atmosphere until about 1990. Atmospheric scientists theorized that economic collapse in the former USSR led to less oil and gas production, and thus a slowdown in the rise of global methane levels, which has since resumed. But new University of Washington research uses early satellite records to dispute that assumption. The study, published March 12 in the ...

Charging up the commute

Charging up the commute
2024-03-12
A team of researchers at Oak Ridge National Laboratory demonstrated that a light-duty passenger electric vehicle can be wirelessly charged at 100-kW with 96% efficiency using polyphase electromagnetic coupling coils with rotating magnetic fields. ORNL’s patented system transferred power to a Hyundai Kona EV across a five-inch airgap using electromagnetic fields, a process similar to the wireless charging of small consumer devices. “We’ve achieved the highest power density in the world for a wireless charging system for this class of vehicle,” ORNL’s Omer Onar said. “Our ...

$5 million grant bets on computational biology, AI to change the future of cancer

$5 million grant bets on computational biology, AI to change the future of cancer
2024-03-12
SAN FRANCISCO—A multidisciplinary research team at Gladstone Institutes, led by Senior Investigator Katie Pollard, PhD, has received $5 million in funding through a newly launched grant program designed to ignite a fresh wave of cancer discoveries using computational biology and artificial intelligence. The new Transformative Computational Biology Grant Program from the Biswas Family Foundation, in partnership with the nonpartisan think tank Milken Institute, is providing a total of nearly $14 million to five research groups. At Gladstone, the grant establishes ...

LAST 30 PRESS RELEASES:

Survey of 12 European countries reveals the best and worst for smoke-free homes

First new treatment for asthma attacks in 50 years

Certain HRT tablets linked to increased heart disease and blood clot risk

Talking therapy and rehabilitation probably improve long covid symptoms, but effects modest

Ban medical research with links to the fossil fuel industry, say experts

Different menopausal hormone treatments pose different risks

Novel CAR T cell therapy obe-cel demonstrates high response rates in adult patients with advanced B-cell ALL

Clinical trial at Emory University reveals twice-yearly injection to be 96% effective in HIV prevention

Discovering the traits of extinct birds

Are health care disparities tied to worse outcomes for kids with MS?

For those with CTE, family history of mental illness tied to aggression in middle age

The sound of traffic increases stress and anxiety

Global food yields have grown steadily during last six decades

Children who grow up with pets or on farms may develop allergies at lower rates because their gut microbiome develops with more anaerobic commensals, per fecal analysis in small cohort study

North American Early Paleoindians almost 13,000 years ago used the bones of canids, felids, and hares to create needles in modern-day Wyoming, potentially to make the tailored fur garments which enabl

Higher levels of democracy and lower levels of corruption are associated with more doctors, independent of healthcare spending, per cross-sectional study of 134 countries

In major materials breakthrough, UVA team solves a nearly 200-year-old challenge in polymers

Wyoming research shows early North Americans made needles from fur-bearers

Preclinical tests show mRNA-based treatments effective for blinding condition

Velcro DNA helps build nanorobotic Meccano

Oceans emit sulfur and cool the climate more than previously thought

Nanorobot hand made of DNA grabs viruses for diagnostics and blocks cell entry

Rare, mysterious brain malformations in children linked to protein misfolding, study finds

Newly designed nanomaterial shows promise as antimicrobial agent

Scientists glue two proteins together, driving cancer cells to self-destruct

Intervention improves the healthcare response to domestic violence in low- and middle-income countries

State-wide center for quantum science: Karlsruhe Institute of Technology joins IQST as a new partner

Cellular traffic congestion in chronic diseases suggests new therapeutic targets

Cervical cancer mortality among US women younger than age 25

Fossil dung reveals clues to dinosaur success story

[Press-News.org] A simple and robust experimental process for protein engineering
Easily interpretable technique can reduce the cost and increase the scale of protein optimization for applications in medicine, biofuels and more