Study discovers protein structures that could be responsible for the origins of life

The question of how life first arose on our planet is one we haven’t yet fully answered, but science is getting closer all the time — and a new study identifies the structures of the proteins that may have caused this to happen.

First of all, the team behind the study decided to start from the premise that life as we know it depends on the collection and use of energy. In the primordial soup of the ancient Earth, this energy most likely came from the sky, in the form of radiation from the sun, or from the depths of the earth itself, where heat seeped through hydrothermal vents on the bottom of ancient seas.

At the molecular level, this energy use means the transfer of electrons, the basic chemical process that involves the transfer of an electron from one atom or molecule to another. Electron transfer is at the heart of oxidation-reduction reactions (also known as redox reactions) that are vital to some of the essential functions of life.

Since metals are the best elements to perform electron transfer, and complex molecules called proteins drive most biological processes, the researchers decided to combine the two and look for proteins that bind the metals.

A systematic and computational approach was used to compare metal-finding proteins, revealing some common features that are identical in all of these proteins – regardless of the protein’s function, the metal to which it binds, or the organism in question.

“We’ve seen that the metal-binding nuclei of the proteins present are actually similar even though the proteins themselves may not be,” says microbiologist Yana Bromberg, of Rutgers University in New Brunswick, NJ.

“We’ve also seen that these metal-binding nuclei often consist of repeating core structures, sort of like Lego blocks. Curiously, these blocks are also found in other regions of proteins, not just metal-binding nuclei, and in many other proteins that have not been taken into account in our study.”

The researchers suggest that these common features may have been present and operating in the first proteins, changing over time to become the proteins we see today — but while maintaining some common structures.

The idea is that soluble minerals in the ancient ocean that covered the Earth thousands of millions of years ago could have been used to power the electron mixing needed to transfer energy, and thus biological life.

“Our observation suggests that this rearrangement of these small building blocks may have had one or a small number of common ancestors, and gave rise to the full range of proteins and their functions currently available,” Bromberg says. “That is, in life as we know it.”

In particular, the team was able to identify developments in protein folds – the shapes that proteins adopted when they become biologically active – that may have produced the proteins we know today, almost like the Molecular Family Tree Project.

The study also concluded that biologically functional peptides, the smaller versions of proteins, may have predated the oldest proteins dating back 3.8 billion years. All of this adds to our understanding of how life first began.

As always, any analysis of the beginnings of life on Earth can be important in the search for life on other planets as well, as life may begin to develop (or may have already evolved) along similar biological pathways.

“We have very little information about how life originated on this planet, and our work contributes to an explanation that was not available before,” Bromberg says. “This explanation could also contribute to our search for life on planets and other planetary bodies.

“Our discovery of specific structural building blocks is also relevant to synthetic biology efforts, as scientists aim to build specifically active proteins anew.”

The search was published in science progress.

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