A trick to fold proteins more quickly

May 8, 2013
A protein. Credits: Sissa Medialab

A team of researchers of the International School for Advanced Studies (SISSA) of Trieste and of University of Cambridge have devised a method to reduce the time used to simulate how proteins take on their signature three-dimensional shape. Such important information to comprehend their function is usually obtained using often very costly experimental techniques.

To understand how proteins work it is important to know their three-dimensional shape, but also the way it is produced. We need to know, in other words, how the amino acid which makes up the proteins is capable of folding over itself to take on a specific shape.

Today the study of molecular dynamics of proteins is based on in which the system is treated as a three-dimensional set of balls (1 ball = 1 atom) observed while it evolves through time. This is a very accurate but rather slow technique, therefore a group of researchers, including Daniele Granata and Alessandro Laio at SISSA of Trieste, have devised a trick to reduce simulation times.

"We exploit the experimental data obtained observing the proteins through , and use them to create restraints to be applied to the model", explained Laio, who has coordinated the research published in Proceedings of the National Academy of Sciences (PNAS).

"Basically, we used a 'trick'. Imagine I pulled your arm and directed you towards a certain place, let's say, to have a reference, from Trieste to Rimini. The trick enables to reach a destination in a period of time even a thousand times inferior to what usually required for that itinerary. Thanks to mathematical  rules– gathered from previous observations carried out on 'trips to Rimini' – I can calculate, starting from the fixed travel time, how long it would have taken the same individual to spontaneously reach the same destination without being pulled. The same assumption may be applied to a protein that must fold in order to take on a certain shape."

"There is a law that connects the time a protein takes to fold using the 'trick' and the time used to do it spontaneously," explains Laio.

The technique employed by Granata and Laio, applied in this case to streptococcal G, has enabled to obtain results which are perfectly consistent with those obtained using the more common technique, with the advantage it remarkably reduces calculation times. "Considering the slowness of standard computer techniques, methods like ours optimize processing times and could give a big boost to research."

Explore further: Protein pulling -- Learning how proteins fold by pulling them apart

More information: Granata, D. et al. Characterization of the free-energy landscapes of proteins by NMR-guided metadynamics, PNAS, April 23, 2013, vol. 110, no. 17, 6817–6822. www.pnas.org/cgi/doi/10.1073/pnas.1218350110

Related Stories

Researchers shed light on how proteins find their shapes

February 23, 2009

(PhysOrg.com) -- Researchers from the California Institute of Technology (Caltech) and the University of California at San Diego (UCSD) have brought together UCSD theoretical modeling and Caltech experimental data to show ...

Protein folding made easy

June 7, 2011

Protein folding has nothing to do with laundry. It is, in fact, one of the central questions in biochemistry. Protein folding is the continual and universal process whereby the long, coiled strings of amino acids that make ...

The movement of proteins

March 5, 2013

Cristian Micheletti, a scientist of the International School for Advanced Studies of Trieste (SISSA), has published in Physics of Life Reviews a review on an innovative instrument for protein analysis, a method for which ...

DNA: How to unravel the tangle

March 29, 2013

A research coordinated by the scientists at SISSA of Trieste has now developed and studied a numeric model of the chromosome that supports the experimental data and provides a hypothesis on the bundle's function.

Recommended for you

The universe's most miraculous molecule

October 9, 2015

It's the second most abundant substance in the universe. It dissolves more materials than any other solvent. It stores incredible amounts of energy. Life as we know it would not be possible without it. And although it covers ...

New method facilitates research on fuel cell catalysts

October 8, 2015

While the cleaning of car exhausts is among the best known applications of catalytic processes, it is only the tip of the iceberg. Practically the entire chemical industry relies on catalytic reactions. Therefore, catalyst ...

Trio wins Nobel Prize for mapping how cells fix DNA damage

October 7, 2015

Tomas Lindahl was eating his breakfast in England on Wednesday when the call came—ostensibly, from the Royal Swedish Academy of Sciences. It occurred to him that this might be a hoax, but then the caller started speaking ...


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.