Machine-learning model provides detailed insight on proteins

March 12, 2019, eLife

A novel machine-learning 'toolbox' that can read and analyse the sequences of proteins has been described today in the open-access journal eLife.

The study demonstrates that, when trained to read sequence data, called Restricted Boltzmann Machines (RBM) can provide a wealth of information on , function and evolutionary features. It is believed to be the first method that can extract this level of detail from alone.

Proteins are formed of sequences of molecules called amino acids, which determine a given 's structural and functional properties. But understanding which parts of the sequences are responsible for which properties is challenging. "Answering this question could have significant implications for pharmaceutical development," explains co-author Jérôme Tubiana, former Ph.D. student in the Physics Laboratory at l'École Normale Supérieure (ENS), Paris, France. "For example, it could help with the design of new proteins that have desired functions, or with predicting the future sequence evolution of proteins in living organisms, such as pathogens, and identifying appropriate drug targets."

To explore this question, Tubiana and his collaborators applied RBM to 20 protein 'families' - a group of proteins that share a common evolutionary origin. The researchers presented detailed results for four protein families, including two short protein domains called Kunitz and WW, one long chaperone protein called Hsp70, and synthetic lattice proteins for benchmarking.

They discovered that, after learning, the connections between the artificial neuronsin the RBM are interpretable and relate to the protein's structure, function (such asactivity) or phylogeny—the evolutionary relationships between protein sequences. Additionally, the team found that they could use RBM to design new protein sequences by composing and turning up or down the different artificial neural units at will.

"Our RBM model shows how machine-learning techniques can solve complex data recognition and draw conclusions from data in an interpretable way," says co-author Simona Cocco, CNRS Director of Research at the ENS Physics Laboratory. "This runs counter to the more complex, black-box models that are traditionally used in data science, as statistical analyses provided by these tools are largely uninterpretable. The interpretability of our method is a major benefit to scientists—it bears the promise of allowing them to generate proteins with desired functions in a controlled way."

"It will now be interesting to apply our model to proteins in pathogens," adds senior author Rémi Monasson, also CNRS Director of Research at the ENS Physics Laboratory, and Deputy Director of the Henri Poincaré Institute (CNRS/Sorbonne University), France. "Pathogens, particularly viruses, can often escape drugs through mutations that make treatments ineffective. Our method could be used to predict the mutational escape paths that are accessible to the functional protein from its current sequence, and help identify which combination of protein sites should be targeted by drugs to block all paths."

Explore further: New antibiotics are desperately needed—machine learning could help

More information: Jérôme Tubiana et al, Learning protein constitutive motifs from sequence data, eLife (2019). DOI: 10.7554/eLife.39397

Related Stories

Predicting sequence from structure

February 18, 2019

One way to probe intricate biological systems is to block their components from interacting and see what happens. This method allows researchers to better understand cellular processes and functions, augmenting everyday laboratory ...

Details of protein evolution investigated

October 25, 2018

Proteins govern the biology of the cell. Through random mutation the sequences of our proteins slowly change over time, usually without affecting function. But sometimes new functions will be invented in this process. Scientists ...

A new algorithm to predict the dynamic language of proteins

October 23, 2015

Researchers from the Structural Biology Computational Group of the Spanish National Cancer Research Centre (CNIO), led by Alfonso Valencia, in collaboration with a group headed by Francesco Gervasio at the University College ...

Recommended for you

Semimetals are high conductors

March 18, 2019

Researchers in China and at UC Davis have measured high conductivity in very thin layers of niobium arsenide, a type of material called a Weyl semimetal. The material has about three times the conductivity of copper at room ...

0 comments

Please sign in to add a comment. Registration is free, and takes less than a minute. Read more

Click here to reset your password.
Sign in to get notified via email when new comments are made.