Bioinformatic Analysis On Structure And Function For Primitive Enzymes And Chemical Basis

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 enzymes, because it is very difficult to explore the structures and functions of the very ancient protein enzymes. The reasons are as follows: first, there are no fossils of primitive protein enzymes to consult; second, the biosynthesis of pre-protien enzymes need too long time to simulate in the labotatory. However, fast development of the genomics and struct-genomics and so on have supplied us much informations on protein structures and functions, which can be taken to study the evolution of the protein enzymes structures.As is well known, some elements of protein enzymes, such as architectures (folds), catalytic site of enzymes, 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 protein enzymes on structures and functions. The preliminary success of this strategy has been witnessed in the past few years. However, it is very different for us to approve the structrures and functions of primitive protein enzymes by experiments. We need different methods,standard,experiment data to validate the previous results.Objectives: Make a theoretics analysis on structures and functions of primitive protein enzymes in order to explore the character of primitive protein enzymes. Furthermore,we made a preliminary research for the chemical baisis of primitive enzymes. Methods: Firstly,we analysed use the oldest age group of yeast enzymes and manet putative primitive enzymes by searching for relating bioinformatics databases, such as Saccharomyces Genome Database——SGD,Structural Classification of Proteins——SCOP,Protein Data Bank——PDB and so on. We found the distribution character of the fold; a certain part of very ancient enzymes need cofactors to work normally. Secondly, we calculated the topological indicators of yeast enzymes that located at different evolultion stages. We made the elucidation of redox cofactor preference in primitive enzymes by analyzing cofactor-binding residues in primitive enzymes. Thirdly, we explored the cofactors usage bias of primitive enzymes in order to research the function of primitive enzymes by bioinformatics method. Fourthly, we calculated the chemical characters of small molecules participating in the primitive enzymes reactions in order to explore the primitive enzymes based on the small molecules.Results: Firstly,the distribution of folds that primitive enzymes used follows power-law rule. Therefore, we infer that the architectures of very ancient proteins belong to the following folds: P-loop containing nucleoside triphosphate hydrolases (c.37), TIM beta/alpha-barrel (c.1), NAD(P)-binding Rossmann-fold domains (c.2). Secondly, the structure complexity of yeast primitive enymes is increasing with the evolution by calculating the topological indicators of yeast enzymes that located at different evolultion stages. Thirdly, the primitive enzymes are convenient to use young amino acid to bind cofactors by analyzing cofactor-binding residues in primitive enzymes. Fourthly, we found the distribution zone of the small molecule descriptor by calculating the chemical characters of small molecules participating in the primitive enzymes reactions. This will offer the theory assistance ande the foundation for the further research. Significance: This paper made a research on the function and structure of primitive enzymes by combining the bioinformatic metheod and chemoinformatic method, the small molecule (such as cofactors) research and the big molecule (such as enzymes) research. This offers a new notion for the further life research.