Abstract
Lipids are produced, transported, and recognized by the concerted actions of numerous enzymes, binding proteins, and receptors. A comprehensive analysis of lipid molecules, "lipidomics," in the context of genomics and proteomics is crucial to understanding cellular physiology and pathology; consequently, lipid biology has become a major research target of the postgenomic revolution and systems biology. To facilitate international communication about lipids, a comprehensive classification of lipids with a common platform that is compatible with informatics requirements has been developed to deal with the massive amounts of data that will be generated by our lipid community. As an initial step in this development, we divide lipids into eight categories (fatty acyls, glycerolipids, glycerophospholipids, sphingolipids, sterol lipids, prenol lipids, saccharolipids, and polyketides) containing distinct classes and subclasses of molecules, devise a common manner of representing the chemical structures of individual lipids and their derivatives, and provide a 12 digit identifier for each unique lipid molecule. The lipid classification scheme is chemically based and driven by the distinct hydrophobic and hydrophilic elements that compose the lipid. This structured vocabulary will facilitate the systematization of lipid biology and enable the cataloging of lipids and their properties in a way that is compatible with other macromolecular databases.
Highlights
Lipids are produced, transported, and recognized by the concerted actions of numerous enzymes, binding proteins, and receptors
The goal of collecting data on lipids using a “systems biology” approach to lipidomics requires the development of a comprehensive classification, nomenclature, and chemical representation system to accommodate the myriad lipids that exist in nature
Polyketides [PK] Polyketides are synthesized by classic enzymes as well as iterative and multimodular enzymes with semiautonomous active sites that share mechanistic features with the fatty acid synthases, including the involvement of specialized acyl carrier proteins [49, 50]; polyketide synthases generate a much greater diversity of natural product structures, many of which have the character of lipids
Summary
A naming scheme must unambiguously define a lipid structure in a manner that is amenable to chemists, biologists, and biomedical researchers. The issue of lipid nomenclature was last addressed in detail by the International Union of Pure and Applied Chemists and the International Union of Biochemistry and Molecular Biology (IUPAC-IUBMB) Commission on Biochemical Nomenclature in 1976, which subsequently published its recommendations [3]. A large number of novel lipid classes have been discovered during the last three decades that have not yet been systematically named. In conjunction with our proposed classification scheme, we provide examples of systematic (or semisystematic) names for the various classes and subclasses of lipids. The nomenclature proposal follows existing IUPAC-IUBMB rules closely and should not be viewed as a competing format. Key features of our lipid nomenclature scheme are as follows: a) The use of the stereospecific numbering (sn) method to describe glycerolipids and glycerophospholipids [3]. The glycerol group is typically acylated or alkylated at the sn-1 and/or sn-2 position, with the exception of some lipids
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