LUCA Archives

Three hypotheses of metabolic evolution, and where appropriate, a reference to iron sulfur cluster development is given. Top left: the retrograde hypothesis of metabolic evolution (A–D = molecules of a biosynthetic pathway, with A being the end product; E1–E3 = enzymes). Top right: Granick’s forward hypothesis of metabolic evolution (A–D = small molecules that are of a biosynthetic pathway, with A being the end product; E1–E3 = enzymes). Bottom: the patchwork hypothesis of metabolic evolution (A–C = precursor molecules; D–F = products of an enzymatic transformation; E1 represents the ancestral catalyst which endowed substrate promiscuity that was able to catalyze three different, but similar reactions; E2 represents the next generation of enzymes, in which the amino acid sequence has diverged slightly and substrate specificity and catalytic activity have been increased). -- LIFE

Biophysics, Genomics, Proteomics, Bioinformatics, Origin & Evolution of Life, Status Report

Evolution At The Origins Of Life?

by Keith CowingFebruary 26, 2024February 25, 2024

The role of evolutionary theory at the origin of life is an extensively debated topic. The origin and early development of life is usually separated into a prebiotic phase and […]

Xeno amino acids potentially change the biochemistry of protein folding (A) Combinations of peptide torsion angles (𝜙 & 𝛹: see Box 1) summarize peptide/protein secondary structure (adapted from Elsliger et al., 2012). Zones A & B are torsion-angle pairs disallowed by biophysics under strict steric considerations yet observed empirically upon careful investigation for specific combinations of side chains (discussed in Kalamankar et al., 2015). This provides one clue that the current, well-established map of secondary structure could shift or become unrecognizable if rebuilt for xeno amino acids (B) The dominant secondary structures of life on Earth, α-helices and ꞵ-sheets (first described by Linderstrøm-Lang, 1952), form and are stabilized by hydrogen bonds (blue dotted lines). These hydrogen bonds usually involve atoms in the amino acid backbone. The bonds and therefore protein structures would be obstructed or altered if peptides comprised a heterogeneous enantiomeric mixture, more than one sidechain per amino acid or longer backbones (i.e. β- γ- δ-) (C) Multiple secondary structures within a single polymerized amino acid sequence combine to form the larger, folded tertiary structure. It follows from A-C that protein structures could be unpredictably different if the fundamental building blocks (amino acids) were changed. Images were created using Mol* Viewer (Sehna et al., 2021) with PDB 4LV0 AmpC beta-lactamase in complex with m-aminophenyl boronic acid (London et al., 2014). -- q-bio.BM

Astrochemistry, Biochemistry & Organic Chemistry, Biosignatures & Paleobiology, Genomics, Proteomics, Bioinformatics, Status Report

Xeno Amino Acids: A Look Into Biochemistry As We Don’t Know It

by Keith CowingNovember 8, 2023November 8, 2023

Would Another Origin Of Life Resemble Earth’s Biochemical Use Of Amino Acids? Here we review current knowledge at three levels:

Secondary structure of the tt_A1P1 construct predicted by mfold (Zuker, 2003). With a ΔG of -64.30 Kcal/mol. Thermus thermophilus numbering system is used. According to this prediction base paring shift occur in H74, H89 and H90. The overall shape of H90 has grown by at least three base pairs at the beginning of the helix compared to the secondary structure of the extant ribosome. -- PNAS

Genomics, Proteomics, Bioinformatics, Origin & Evolution of Life, Status Report

How To Build A Protoribosome

by Keith CowingApril 1, 2023April 1, 2023

NASA-supported scientists have reexamined some previous assumptions about how the ribosome in living cells is constructed. The ribosome is a large molecule found in all living cells that catalyzes the […]