Nav: Home

AI reveals nature of RNA-protein interactions

October 30, 2019

A new computational tool developed by KAUST scientists uses artificial intelligence (AI) to infer the RNA-binding properties of proteins.

The software, called NucleicNet, outperforms other algorithmic models of its kind and provides additional biological insights that could aid in drug design and development.

"RNA binding is a fundamental feature of many proteins," says Jordy Homing Lam, a former research associate at KAUST and co-first author of the study. "Our structure-based computational framework can reveal the detailed RNA-binding properties of these proteins, which is important for characterizing the pathology of many diseases."

Proteins routinely interface with RNA molecules as a way to control the processing and transporting of gene transcripts--and when these interactions go awry, information flow inside the cell is disrupted and disorders can arise, including cancer and neurodegenerative disease.

To better understand which parts of an RNA molecule tend to bind on different surface points of a protein, Lam and his colleagues turned to deep learning, a type of AI. Working in the laboratory of KAUST Professor Xin Gao in the Computational Bioscience Research Center, Lam and Ph.D. student Yu Li, taught NucleicNet to automatically learn the structural features that underpin interactions between proteins and RNA.

They trained the algorithm using three-dimensional structural data from 158 different protein-RNA complexes available on a public database. Pitting NucleicNet against other predictive models--all of which rely on sequence inputs rather than structural information--the KAUST team showed that the tool could most accurately detect which sites on a protein surface bound to RNA molecules or not.

What's more, unlike any other model, NucleicNet could predict which aspects of the RNA molecule were doing the binding, be it part of the sugar-phosphate backbone or one of the four letters of the genetic alphabet.

In collaboration with researchers in China and the United States, Lam, Li and Gao validated their algorithm on a diverse set of RNA-binding proteins, including proteins implicated in gum cancer and amyotrophic lateral sclerosis, to show that the interactions deduced by NucleicNet closely matched those revealed by experimental techniques. They reported the findings in Nature Communications.

"Structure-based features were little considered by other computational frameworks," says Lam. "We have harnessed the power of deep learning to infer those subtle interactions."

NucleicNet is openly available for researchers who want to predict RNA-binding sites and binding preference for any protein of interest. The software can be accessed at http://www.cbrc.kaust.edu.sa/NucleicNet/.
-end-


King Abdullah University of Science & Technology (KAUST)

Related Proteins Articles:

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.
New tool for the crystallization of proteins
ETH researchers have developed a new method of crystallizing large membrane proteins in order to determine their structure.
New interaction mechanism of proteins discovered
UZH researchers have discovered a previously unknown way in which proteins interact with one another and cells organize themselves.
When proteins shake hands
Protein nanofibres often have outstanding properties such as a high stability, biodegradability, or antibacterial effect.
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

Uncharted
There's so much we've yet to explore–from outer space to the deep ocean to our own brains. This hour, Manoush goes on a journey through those uncharted places, led by TED Science Curator David Biello.
Now Playing: Science for the People

#556 The Power of Friendship
It's 2020 and times are tough. Maybe some of us are learning about social distancing the hard way. Maybe we just are all a little anxious. No matter what, we could probably use a friend. But what is a friend, exactly? And why do we need them so much? This week host Bethany Brookshire speaks with Lydia Denworth, author of the new book "Friendship: The Evolution, Biology, and Extraordinary Power of Life's Fundamental Bond". This episode is hosted by Bethany Brookshire, science writer from Science News.
Now Playing: Radiolab

Dispatch 2: Every Day is Ignaz Semmelweis Day
It began with a tweet: "EVERY DAY IS IGNAZ SEMMELWEIS DAY." Carl Zimmer – tweet author, acclaimed science writer and friend of the show – tells the story of a mysterious, deadly illness that struck 19th century Vienna, and the ill-fated hero who uncovered its cure ... and gave us our best weapon (so far) against the current global pandemic. This episode was reported and produced with help from Bethel Habte and Latif Nasser. Support Radiolab today at Radiolab.org/donate.