Deep Learning Algorithm reduces experimental burden to elevate protein engineering

Oct 20, 2021 | Shaoni Ghosh

Deep Learning Algorithm reduces experimental burden to elevate protein engineering title banner

Protein is a significant macronutrient that each and every cell in the body is in need of. Proteins are composed of building blocks which are known as amino acids. 


The body necessitates huge amounts of macronutrients in order to sustain life, and therefore the terminology 'macro', which is referred to by the University of Illinois McKinley Health Center. 


Proteins have been widely utilized in various applications ranging from therapeutics to being carriers as industrial catalysts.


 In order to minimize the various limitations that naturally occurring proteins pose, protein engineering is employed to enhance certain properties including that of capability and solidity.


The Research


In a new study published in the journal 'Nature Communications', the researchers have put forward a machine learning algorithm that may speed up the protein engineering procedures. 


The machine learning algorithms may direct protein engineering towards the minimization of experimental overload. By experimental overload, it suggests how the repeated rounds of mutagenesis and certain other methods are processed.


The algorithms work in parallel with each other, after being assisted on protein sequence databases, such that they simulate and detect the fitness of all possible arrangements of the target protein.


Even though machine learning algorithms are responsible for participating in the same, yet very few of them invoke the "evolutionary history of the target protein", as CS.Illinois.Edu suggests. And this is where the deep learning algorithm, ECNet (evolutionary context-integrated neural network) comes into play.


(Recommended Blog: Machine Learning vs Deep Learning: How are They Different?)


Through the help of ECNet, the researchers would be able to concentrate on the target protein, as the Director of the NSF-funded Molecule Maker Lab Institute, Zhao stated, and all its respective "homologs" to inspect "which residues are coupled together" and thus, prove significant for that one particular protein.


Zhao emphasized on the deep learning algorithm's focus on higher-order along with novel mutants during the process. 


(Must Check: Other Deep Learning-based Algorithms)


The researchers have laid their eyes on ECNet's applications on deep mutagenesis datasets. 


Consecutively, ECNet was employed to engineer TEM-1 β-lactamase. And it detected variants that had enhanced fitness and thus, in turn unaffected by ampicillin. 


And now that the researchers are equipped with a computational tool, it would help them to ensure that the former minimizes experimental burdens in return.


(Related Reading: The Methodology of Computational Science)


Zhao also stated that the researchers are currently focusing on how ECNet can be put to effect to generate enzyme catalysts with enhanced selectivities.Zhao explained that the amalgamation of all the proteins in the database and "the specific evolutionary history of the target protein" will increase the prediction efficiency. 


From the aforementioned beginning, the researchers will be able to make best use of the mutants to assist the model accordingly. Even though the improvement of the model is still ongoing, it has attracted substantial interest in the technological space. 

Tags #Deep Learning