Towards Genochemistry: Harnessing the Power of Biocatalysis for Research in the Life Sciences

Zizhang      Zhang; Atta-ur-Rahman

doi:10.2174/138527210792927573

Abstract

The annotation of the sequences that encode enzymes to their functions is a significant step towards better understanding of the worlds biological systems. This is precisely the body of knowledge that Biocatalysis has been building throughout the 20th century on a case-by-case basis. Candidate technologies and methodologies to accomplish this goal are largely available, yet they have not been brought into practice for this purpose. Combining the knowledge, technologies, and methodologies for this renewed purpose constitutes in fact, a new distinctive science which rests on the foundation of biocatalysis. We henceforth shall refer to it as Genomic Chemistry, or Genochemistry in short, the study of chemistry based on genomic information, resulting from numerous emerging disciplines in the ‘omics’ cascade. Genochemistry is expected to supply more detailed and descriptive information in order to reveal the relationships of enzymes and their catalytic function and annotation of the genomic sequences. Unlike other ‘omics’ investigations, Genochemistry cannot be conducted by any single technology platform. It requires the building of databases on the basis of experimental data and the use of computational methods as well as bioinformatics tools. In this article, we provide a discussion of a framework, a guideline, and the problems that Genochemistry can tackle from distilled information and amassed literatures, with emphasis on the potentially useful technologies.

Keywords: Genochemistry, biocatalysis, omics cascade, substrome, enzyome, bioinformatics, machine learning method, stereoselectivity, enan-tioselectivity, chemoselectivity, GenBank, Protein Data Bank, SNPs, Genochemis-try, Anfinsen's principle, Frankia sp, Epoxide Hydrolase, GWAS, convergence, divergence, mRNA, cytochrome P450, DE technology, E. coli, L-aminoacylase, D-enantiomer, E value, HTS method, Mass Spectrometry, Gene Databases, NMR, X-ray Crystallography, Circular Dichro-ism, Lipase, Biosym/MSI, CVL, EETs, HETEs, EpOMEs, RNA splicing