Exploring the universe of biochemical reactions

January 13, 2014
Exploring the universe of biochemical reactions
EC-BLAST lets researchers compare enzymes according to their function, rather than their sequence.

Scientists at EMBL-EBI have developed EC-BLAST: software that makes it easier to develop novel enzymes. Published in Nature Methods, the program makes it possible to quickly compare the functions of thousands of catalysts, facilitating research into anything from drug interactions to the efficient production of biofuels.

Washing machines and cookers might look much the same, but they do very different things. Similarly, while enzymes may look very much alike, a biologist who needs to speed up a specific reaction would want to compare them according function, rather than sequence.

Enzymes are proteins that are involved in countless reactions, from breaking down cellulose to synthesising DNA, and their functions depend on a very wide range of factors. Until now, comparing reactions was an arduous, manual process. The new EC-BLAST makes it possible to quickly compare a potentially useful enzyme against thousands of well-known reactions.

"If you are looking to swap one enzyme for another – say to make cheese differently or to break down sugar cane into ethanol – you would want to know exactly what reactions they are involved in, in which metabolic pathways," explains Professor Dame Janet Thornton. "EC-BLAST gives you a knowledge-based approach for this, because it combines everything we know about biological catalysis: where it is similar, where it is different, how enzymes have evolved and how they might continue to change. It really provides an overview of the world of ."

The computer scientists, chemists, biologist and physicist who developed EC-BLAST spent five years working through roadblocks to quantifying the comparison of enzymes already well described by the Enzyme Commission (EC). The interdisciplinary approach was vital to ensuring the final product was fit for purpose.

"EC-BLAST contains a series of algorithms that draw on a library that integrates our knowledge about structures, chemical transformations, bond changes, stereochemistry and other features," says Syed Asad Rahman, the computer scientist and programmer behind many of the algorithms. "We've basically created a binary fingerprint for these enzymes – a kind of reaction profile – that we hope will be very useful to people working in green biotech, drug discovery and many other areas."

You can try the new software and provide feedback at www.ebi.ac.uk/thornton-srv/software/rbl/

Explore further: Quantum biology and Ockham's razor

More information: Rahman, S.A., Martinez Cuesta, S., Furnham, N., Holliday, G.L. and Thornton, J.M. (2014) EC-BLAST: A Tool to Automatically Search and Compare Enzyme Reactions. Nat Methods (in press). Published online 12 January; DOI: 10.1038/nmeth.2803

Related Stories

Quantum biology and Ockham's razor

February 6, 2012

(PhysOrg.com) -- In a paper just published in Nature Chemistry, a team of University of Bristol scientists explores whether new models or concepts are needed to tackle one of the 'grand challenges' of chemical biology: understanding ...

New resource opens the door for enzyme research

February 27, 2012

The European Molecular Biology Laboratory's European Bioinformatics Institute has launched the Enzyme Portal, a freely available resource for people who are interested in the biology of enzymes and proteins with enzymatic ...

New small-molecule catalyst does the work of many enzymes

October 3, 2013

Researchers report that they have created a man-made catalyst that is an "enzyme mimic." Unlike most enzymes, which act on a single target, the new catalyst can alter the chemical profiles of numerous types of small molecules. ...

Enzyme catalysis unravelled in new research

October 7, 2013

(Phys.org) —New research by the School of Chemistry has significantly advanced our understanding of how enzymes (proteins) increase the rate of chemical reaction. Now potentially able to achieve greater control of enzyme ...

Recommended for you

Findings illuminate animal evolution in protein function

July 27, 2015

Virginia Commonwealth University and University of Richmond researchers recently teamed up to explore the inner workings of cells and shed light on the 400–600 million years of evolution between humans and early animals ...

New polymer able to store energy at higher temperatures

July 30, 2015

(Phys.org)—A team of researchers at the Pennsylvania State University has created a new polymer that is able to store energy at higher temperatures than conventional polymers without breaking down. In their paper published ...

How to look for a few good catalysts

July 30, 2015

Two key physical phenomena take place at the surfaces of materials: catalysis and wetting. A catalyst enhances the rate of chemical reactions; wetting refers to how liquids spread across a surface.

Yarn from slaughterhouse waste

July 29, 2015

ETH researchers have developed a yarn from ordinary gelatine that has good qualities similar to those of merino wool fibers. Now they are working on making the yarn even more water resistant.

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.