Nav: Home

Creating a global map of the protein shape universe

May 08, 2019

WEST LAFAYETTE, Ind. - Proteins can provide a detailed look inside the human body and how it protects itself from many diseases. Proteins, which make up about 15% of body mass, are the most abundant solid substances in the human body. They are important working molecules of the immune system, metabolism, brain function, body motion, and any physically and chemically functional parts in a body. Each protein has a specific function under the direction of its own gene.

Now, Purdue University researchers have come up with a novel way to classify proteins and their shapes, which lays the foundation of how we understand protein structures and functions. The shapes are important because they determine the role and effectiveness of the proteins. The research is published in the April edition of PLOS Computational Biology.

"We developed a new way to view and classify protein 3D shapes, which provides our basic understanding of protein shapes and will become a foundation of artificial protein design and other applications of proteins," said Daisuke Kihara, a professor of biological sciences and computer science in Purdue's College of Science, who leads the research team.

Kihara said proteins were conventionally classified by conformations of protein chains, a rather detailed level of structural features. They currently classify proteins by their overall surface shapes, which would be more directly relevant to how they interact with other proteins and compounds in a cell.

The Purdue team maps and classifies 3D surface shapes of proteins within a certain space inside the body. Surface shapes of proteins are represented with 3D Zernike descriptors, mathematical moment-based invariants, which have previously been demonstrated effective for biomolecular structure similarity search.

They also have analyzed the shape space occupied by protein complexes. The mapping provides data into the relationship between shapes, main-chain folds and complex formation.

"This work is in the area of bioinformatics," Kihara said. "Bioinformatics is not only useful for processing biological data or developing computational tools, but it is also helpful for providing a unique view and framework that can change the way people view and understand the biomolecular world."

Kihara has worked with the Purdue Research Foundation Office of Technology Commercialization on some of his research and technology.

His team's work aligns with Purdue's Giant Leaps celebration, celebrating the global advancements in health research and technology as part of Purdue's 150th anniversary. Health is one of the four themes of the yearlong celebration's Ideas Festival, designed to showcase Purdue as an intellectual center solving real-world issues.
-end-
About Purdue Research Foundation Office of Technology Commercialization

The Purdue Research Foundation Office of Technology Commercialization operates one of the most comprehensive technology transfer programs among leading research universities in the U.S. Services provided by this office support the economic development initiatives of Purdue University and benefit the university's academic activities. The office is managed by the Purdue Research Foundation, which received the 2016 Innovation and Economic Prosperity Universities Award for Innovation from the Association of Public and Land-grant Universities. For more information about funding and investment opportunities in startups based on a Purdue innovation, contact the Purdue Foundry at foundry@prf.org. For more information on licensing a Purdue innovation, contact the Office of Technology Commercialization at otcip@prf.org. The Purdue Research Foundation is a private, nonprofit foundation created to advance the mission of Purdue University.

Writer: Chris Adam, 765-588-3341, cladam@prf.org

Source: Daisuke Kihara, dkihara@purdue.edu

Purdue University

Related Proteins Articles:

New method to monitor Alzheimer's proteins
IBS-CINAP research team has reported a new method to identify the aggregation state of amyloid beta (Aβ) proteins in solution.
Composing new proteins with artificial intelligence
Scientists have long studied how to improve proteins or design new ones.
Hero proteins are here to save other proteins
Researchers at the University of Tokyo have discovered a new group of proteins, remarkable for their unusual shape and abilities to protect against protein clumps associated with neurodegenerative diseases in lab experiments.
Designer proteins
David Baker, Professor of Biochemistry at the University of Washington to speak at the AAAS 2020 session, 'Synthetic Biology: Digital Design of Living Systems.' Prof.
Gone fishin' -- for proteins
Casting lines into human cells to snag proteins, a team of Montreal researchers has solved a 20-year-old mystery of cell biology.
Coupled proteins
Researchers from Heidelberg University and Sendai University in Japan used new biotechnological methods to study how human cells react to and further process external signals.
Understanding the power of honey through its proteins
Honey is a culinary staple that can be found in kitchens around the world.
How proteins become embedded in a cell membrane
Many proteins with important biological functions are embedded in a biomembrane in the cells of humans and other living organisms.
Finding the proteins that unpack DNA
A new method allows researchers to systematically identify specialized proteins called 'nuclesome displacing factors' that unpack DNA inside the nucleus of a cell, making the usually dense DNA more accessible for gene expression and other functions.
A brewer's tale of proteins and beer
The transformation of barley grains into beer is an old story, typically starring water, yeast and hops.
More Proteins News and Proteins Current Events

Trending Science News

Current Coronavirus (COVID-19) News

Top Science Podcasts

We have hand picked the top science podcasts of 2020.
Now Playing: TED Radio Hour

Listen Again: Reinvention
Change is hard, but it's also an opportunity to discover and reimagine what you thought you knew. From our economy, to music, to even ourselves–this hour TED speakers explore the power of reinvention. Guests include OK Go lead singer Damian Kulash Jr., former college gymnastics coach Valorie Kondos Field, Stockton Mayor Michael Tubbs, and entrepreneur Nick Hanauer.
Now Playing: Science for the People

#562 Superbug to Bedside
By now we're all good and scared about antibiotic resistance, one of the many things coming to get us all. But there's good news, sort of. News antibiotics are coming out! How do they get tested? What does that kind of a trial look like and how does it happen? Host Bethany Brookeshire talks with Matt McCarthy, author of "Superbugs: The Race to Stop an Epidemic", about the ins and outs of testing a new antibiotic in the hospital.
Now Playing: Radiolab

Dispatch 6: Strange Times
Covid has disrupted the most basic routines of our days and nights. But in the middle of a conversation about how to fight the virus, we find a place impervious to the stalled plans and frenetic demands of the outside world. It's a very different kind of front line, where urgent work means moving slow, and time is marked out in tiny pre-planned steps. Then, on a walk through the woods, we consider how the tempo of our lives affects our minds and discover how the beats of biology shape our bodies. This episode was produced with help from Molly Webster and Tracie Hunte. Support Radiolab today at Radiolab.org/donate.