Four fundamentally novel, recent developments make a basis for the Theory of Early Molecular Evolution. The theory outlines the molecular events from the onset of the triplet code to the formation of the earliest sequence/structure/function modules of proteins. These developments are: (1) Reconstruction of the evolutionary chart of codons; (2) Discovery of omnipresent protein sequence motifs, apparently conserved since the last common ancestor; (3) Discovery of closed loops—standard structural modules of modern proteins; (4) Construction of protein sequence space of module size fragments, with far-reaching evolutionary implications. The theory generates numerous predictions, confirmed by massive nucleotide and protein sequence analyses, such as existence of two distinct classes of amino acids, and their periodical distribution along the sequences. The emerging picture of the earliest molecular evolutionary events is outlined: consecutive engagement of codons, formation of the earliest short peptides, and growth of the polypeptide chains to the size of loop closure, 25-30 residues.
Prediction of protein-ligand interactions from paired protein sequence motifs and ligand substructures
