Why we are made of proteins and nucleic acids: Structural biology views on extraterrestrial life

Abstract

Is it a miracle that life exists on the Earth, or is it a common phenomenon in the universe? If extraterrestrial organisms exist, what are they like? To answer these questions, we must understand what kinds of molecules could evolve into life, or in other words, what properties are generally required to perform biological functions and store genetic information. This review summarizes recent findings on simple ancestral proteins, outlines the basic knowledge in textbooks, and discusses the generally required properties for biological molecules from structural biology viewpoints (e.g., restriction of shapes, and types of intra- and intermolecular interactions), leading to the conclusion that proteins and nucleic acids are at least one of the simplest (and perhaps very common) forms of catalytic and genetic biopolymers in the universe. This review article is an extended version of the Japanese article, On the Origin of Life: Coevolution between RNA and Peptide, published in SEIBUTSU BUTSURI Vol. 61, p. 232-235 (2021).

Keywords: astrobiology; origin of life.

Figure 1

Schematic structures of simple peptide assemblies with secondary structures. Hydrophilic and hydrophobic parts are colored blue and orange, respectively.

Figure 2

Structures of natural pseudo-symmetric proteins (A–D) and engineered symmetric proteins (E–H). Different monomers in oligomeric designs are colored with different colors. Multiple repeats in the monomer units are colored with different brightness.

Figure 3

Engineered proteins with simplified hydrophobic cores. Experimental or predicted structures of engineered proteins with simplified hydrophobic cores are shown with their amino acid compositions. Protein sequences are adopted from each reference or PDB. Structural models of Rop Ala2Leu2-8, SrcSH3 FP2, and 434 Cro M-5 were predicted by Alphafold2 [–53]. Structures of Rop Ala2Leu2-8 and mk2h_∆MILPYS are shown as homodimers. The C-terminal tag was removed from the model and amino acid composition of R2x2_VAL88. Hydrophobic side chains are shown as stick models. Alanine residues are colored yellow. Another enriched hydrophobic amino acid in each design is colored orange. Other hydrophobic residues and non-hydrophobic residues are colored black and light cyan, respectively.

Figure 4

Structures of ancient (poly-) nucleotide-binding motifs. (A) Structure of the P-loop NTPase domain from HPr kinase and the closeup view of the β-(P-loop)-α element. The β-(P-loop)-α element is colored cyan. (B) Structure of the pseudo-dimeric HhH motifs in a Holliday junction binding protein, RuvA. The two HhH motifs are colored cyan and yellow, respectively.

Figure 5

Molecular bonds and interactions. (A) Types of molecular bonds and interactions. (B) Properties of representative bonds and interactions in biomolecules.

Figure 6

Required conditions for ideal functional biopolymers.

Figure 7

Required conditions for ideal genetic biopolymers.