A Proposal of the Ur-proteome.

Area of Science:

• Origin of Life Studies
• Biochemistry
• Computational Biology

Background:

• The earliest forms of life utilized a limited genetic code.
• Understanding the primordial proteome is key to deciphering early biological functions.

Purpose of the Study:

• To reconstruct a plausible ancestral proteome based on the RNY genetic code.
• To investigate the initial functions of proteins in early life forms.

Main Methods:

• Utilized the RNY (Red-Yellow-Green) genetic code to infer ancestral RNA sequences.
• Analyzed inferred protein fragments to identify conserved structural motifs and functional sites.
• Reconstructed potential protein module structures and associated cofactors.

Main Results:

• Identified an ancestral proteome primarily composed of 8 amino acids encoded by RNY triplets.
• Discovered that these early protein fragments were located in cofactor binding sites, not catalytic sites.
• Proposed that molecular stabilization preceded catalytic activity in the evolution of proteins.

Conclusions:

• The earliest proteome, termed the 'primitive bindome,' likely consisted of protein modules for Cofactor Stabilizing Binding Sites (CSBSs).
• This suggests a functional shift from stabilization to catalysis during early protein evolution.
• The findings provide insights into the structure and function of the first protein modules in progenotes.