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Protein origami: Quick folders are the best
Date:1/31/2013

eins from the Protein Database (PDB) according to age. For this study, Minglei Wang in his laboratory identified protein sequences in the genomes, which had the same folding structure as the known proteins. He then applied an algorithm to compare them to each other on a time scale. In this way, it is possible to determine which proteins became part of which organism and when. After that, Cedric Debes, a member of Dr. Grter's group, applied a mathematical model to predict the folding rate of proteins. The individual folding steps differ in speed and can take from nanoseconds to minutes. No microscope or laser would be able to capture these different time scales for so many proteins. A computer simulation calculating all folding structures in all proteins would take centuries to run on a mainframe computer. This is why the researchers worked with a less data-intensive method. They calculated the folding speed of the single proteins using structures that have been previously determined in experiments: A protein always folds at the same points. If these points are far apart from each other, it takes longer to fold than if they lie close to each other. With the so-called Size-Modified Contact Order (SMCO), it is possible to predict how fast these points will meet and thus how fast the protein will fold, regardless of its length.

"Our results show that in the beginning there were proteins which could not fold very well," Dr. Grter summarizes. "Over time, nature improved protein folding so that eventually, more complex structures such as the many specialized proteins of humans were able to develop."

Shorter and faster for evolution

Amino acid chains, which make up proteins, also became shorter over the course of evolution. This was another factor contributing to the increase in folding speed, as has been shown in the study.

"Since eukaryotes, i.e. organisms with a cell nucleus, emerged, protein folding became somewhat less crucial," says Fr
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Contact: Peter Saueressig
peter.saueressig@hiits.org
49-622-153-3245
Heidelberg Institute for Theoretical Studies (HITS)
Source:Eurekalert  

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