Technique speeds up analysis of proteins
9 May 2013
Method claims to reduce the time used to simulate how proteins take on their signature three-dimensional shape
A team of researchers of the International School for Advanced Studies (SISSA) of Trieste and of University of Cambridge have devised a method to speed up analysis of how proteins take on their shape.
Currently, the study of molecular dynamics of proteins is based on computer simulations in which the system is treated as a three-dimensional set of balls observed while it evolves through time.
This is a very accurate but rather slow technique. The research team have presented a new method which uses nuclear magnetic resonance to create restraints on experimental data.
Methods like ours optimise processing times and could give a big boost to research
“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,” explained Laio, who has coordinated the research.
“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.”
The technique employed by Granata and Laio, applied in this case to streptococcal protein G, has enabled the team to obtain results which are consistent with those obtained using the more common technique.
“Considering the slowness of standard computer molecular dynamics techniques, methods like ours optimise processing times and could give a big boost to research,” said Laio.
