'Digging up' 4-billion-year-old fossil protein structures to reveal how they evolved

Aug 08, 2013

Modern proteins exhibit an impressive degree of structural diversity, which has been well characterized, but very little is known about how and when over the course of evolution 3D protein structures arose. In a study published by Cell Press August 8 in Structure, researchers resurrected 4-billion-year-old Precambrian proteins in the laboratory and gained novel insights into protein evolution by analyzing their X-ray crystal structures. This method has revealed a remarkable degree of structural similarity among proteins since life first evolved on this planet, and it represents a powerful and novel approach to explore the evolution of protein structures.

"So far, attempts to understand evolution have been based on the comparison between structures of modern proteins. This is equivalent to trying to understand the evolution of birds by comparing several living birds," says senior study author Jose Sanchez-Ruiz of the University of Granada. "But it is most useful to study fossils so that changes over are apparent. Our approach comes as close as possible to 'digging up' fossil protein structures."

In a recent study, Sanchez-Ruiz and his collaborators constructed a of by analyzing the amino acid sequences of thioredoxins—proteins found in organisms from the three domains of life, including bacteria, archaea and eukaryotes. Using this phylogenetic tree, they were able to resurrect Precambrian proteins in the laboratory and characterize their features.

In the new study, Sanchez-Ruiz teamed up with Jose Gavira of the Andalusian Institute of Earth Sciences (Spanish National Research Council – University of Granada) to analyze the X-ray crystal structures of the previously resurrected Precambrian proteins. They found that present-day thioredoxin structures are remarkably similar to those that existed at a time close to the origin of life, even though their are very different. This finding supports a punctuated-equilibrium model of evolution in which protein structures remain constant over long time periods, with new changes occurring intermittently over short periods.

"In addition to uncovering the basic principles of protein structure evolution, our approach will provide invaluable information regarding how the 3D structure of a protein is encoded by its amino acid sequence," Sanchez-Ruiz says. "It could also provide information about how to design proteins with novel structures—an important goal in protein engineering and biotechnology."

Explore further: Deciphering structure of NatA, an enzyme complex that modifies most human proteins

More information: Structure, Ingles-Prieto et al.: "Conservation of protein structure over four billion years." dx.doi.org/10.1016/j.str.2013.06.020

Related Stories

Protein origami: Quick folders are the best

Jan 31, 2013

The evolutionary history of proteins shows that protein folding is an important factor. Especially the speed of protein folding plays a key role. This was the result of a computer analysis carried out by ...

Untangling life's origins

Mar 11, 2013

Researchers in the Evolutionary Bioinformatics Laboratory at the University of Illinois in collaboration with German scientists have been using bioinformatics techniques to probe the world of proteins for answers to questions ...

Recommended for you

Molecular gate that could keep cancer cells locked up

16 hours ago

In a study published today in Genes & Development, Dr Christian Speck from the MRC Clinical Sciences Centre's DNA Replication group, in collaboration with Brookhaven National Laboratory (BNL), New York, ...

The 'memory' of starvation is in your genes

20 hours ago

During the winter of 1944, the Nazis blocked food supplies to the western Netherlands, creating a period of widespread famine and devastation. The impact of starvation on expectant mothers produced one of the first known ...

Sugar mimics guide stem cells toward neural fate

Jul 30, 2014

Embryonic stem cells can develop into a multitude of cells types. Researchers would like to understand how to channel that development into the specific types of mature cells that make up the organs and other structures of ...

User comments : 0