Collagen, a protein found in bones and connective tissue, has been found in dinosaur fossils as old as 195 million years. That is much longer than the normal half-life of the peptide bonds that hold proteins together, which is about 500 years.
A new study from MIT offers an explanation for how collagen can survive so much longer than expected. The research team discovered that a special interaction at the atomic level defends collagen against attack by water molecules. This barricade prevents water from breaking the peptide bonds through a process called hydrolysis.
“We provide evidence that that interaction prevents water from attacking and cleaving the peptide bonds. That goes against what happens with a normal peptide bond, which has a half-life of only 500 years,” said Ron Raines, the Firmenich Professor of Chemistry at MIT.
Raines is the lead author of the new study, which will appear in ACS Central Science. MIT postdoc Jinyi Yang PhD ’24 is the lead author of the paper. MIT postdoc Volga Kojasoy and graduate student Gerard Porter are also authors of the study.
Water resistant
Collagen is the most abundant protein in animals and is found not only in the bones, but also in the skin, muscles and ligaments. It is made of long protein strands that intertwine to form a sturdy triple helix.
“Collagen is the scaffold that holds us together,” says Raines. “What makes the collagen protein so stable, and such a good choice for this platform, is that, unlike most proteins, it is fibrous.”
In the past decade, paleobiologists have found evidence that collagen is preserved in dinosaur fossils, including an 80-million-year-old dinosaur. Tyrannosaurus rex fossil, and a sauropodomorph fossil that is almost 200 million years old.
For the past 25 years, Raines’ lab has been studying collagen and how its structure enables its function. In the new study, they revealed why the peptide bonds that hold collagen together are so resistant to breakdown by water.
Peptide bonds are formed between a carbon atom of one amino acid and a nitrogen atom of the adjacent amino acid. The carbon atom also forms a double bond with an oxygen atom, forming a molecular structure called a carbonyl group. This carbonyl oxygen has a pair of electrons that do not form bonds with other atoms. Those electrons, the researchers discovered, can be shared with the carbonyl group of a neighboring peptide bond.
Because this pair of electrons is inserted into those peptide bonds, water molecules also cannot enter the structure to disrupt the bond.
To demonstrate this, Raines and his colleagues created two interconverting mimics of collagen: the one that usually forms a triple helix, known as trans, and another in which the corners of the peptide bonds are twisted into a different shape, known as cis . They discovered that the trans form of collagen does not allow water to attack the bond and hydrolyze it. In the cis form, water entered and the bonds were broken.
“A peptide bond is either cis or trans, and we can change the cis-trans ratio. By doing that, we can mimic the natural state of collagen or create an unprotected peptide bond. And we saw that when it was unprotected, it was. do not long for the world,” says Raines.
“Not a weak link”
This electron sharing has also been observed in protein structures known as alpha helices, which are found in many proteins. These helices may also be protected from water, but the helices are always connected by protein sequences that are more exposed, which are still susceptible to hydrolysis.
“Collagen is made up of triple helices, from one end to the other,” says Raines. “There is no weak link, which is why I think this one survived.”
Previously, some scientists have suggested other explanations for why collagen could be preserved for millions of years, including the possibility that the bones were so dehydrated that water could not reach the peptide bonds.
“I can’t discount the contributions of other factors, but 200 million years is a long time, and I think you need something at the molecular level, at the atomic level, to explain it,” says Raines.
The research was funded by the National Institutes of Health and the National Science Foundation.
