Bioinformatic Research On Structures And Functions Of Primitive Proteins

The origin of life is one of the three most important basical science questions. Since Miller's experiments depended on reducing gases that may be present on the primordial Earth in 1953, the research of the life origin had entered a new era.The origin of amino acid and genetic code has studied better in the past decades, but we know little about the primitive protein, because it is very difficult to explore the structures and functions of the very ancient proteins. However, fast development of the genomics and struct-genomics and so on have supply us much informations on protein structures and functions, which can be taken to study the evolution of the protein structures. Some elements of proteins,such as architectures (folds), catalytic site of enzymes, coenzymes, cofactors, and short sequences and so on, is very conserved during evolution that can serve as molecular fossils to help infer the characters of primitive proteins on structures and functions. The preliminary success of this strategy has been witnessed in the past few years.We propose a new strategy that we use new data set and new defined molecularfossil——the amino acid composition of catalytic sites of enzymes——to infer thecharacters of very ancient protein. We use the oldest age group of yeast proteins, and search for relating bioinformatics databases, such as SGD, SCOP, PDB and so on. We find that various molecular fossils and different protein datasets lead to similar conclusions on the features of very ancient proteins: i) the architectures of very ancient proteins belong to the following folds: P-loop containing nucleoside triphosphate hydrolases (c.37), TIM beta/alpha-barrel (c.l), NAD(P)-binding Rossmann-fold domains (c.2), Ferredoxin-like (d.58), Flavodoxin-like (c.23) and Ribonuclease H-like motif (c.55); ii) the functions of very ancient proteins are related to the metabolisms of purine, pyrimidine, porphyrin, chlorophyll and carbohydrates; iii) a certain part of very ancient proteins need cofactors (such as ATP, NADH or NADPH) to work normally.Moreover, we compared the time order of enzymes' appearance and analyzed the evolution patterns of the primary metabolic pathway by searching MANET Database, and found that the distribution of the oldest enzymes in the metabolic pathways can shed light on the rationality of the Horowitz-Retrograde evolution model.