NORINE: a database of nonribosomal peptides

Abstract

Norine is the first database entirely dedicated to nonribosomal peptides (NRPs). In bacteria and fungi, in addition to the traditional ribosomal proteic biosynthesis, an alternative ribosome-independent pathway called NRP synthesis allows peptide production. It is performed by huge protein complexes called nonribosomal peptide synthetases (NRPSs). The molecules synthesized by NRPS contain a high proportion of nonproteogenic amino acids. The primary structure of these peptides is not always linear but often more complex and may contain cycles and branchings. In recent years, NRPs attracted a lot of attention because of their biological activities and pharmacological properties (antibiotic, immunosuppressor, antitumor, etc.). However, few computational resources and tools dedicated to those peptides have been available so far. Norine is focused on NRPs and contains more than 700 entries. The database is freely accessible at http://bioinfo.lifl.fr/norine/. It provides a complete computational tool for systematic study of NRPs in numerous species, and as such, should permit to obtain a better knowledge of these metabolic products and underlying biological mechanisms, and ultimately to contribute to the redesigning of natural products in order to obtain new bioactive compounds for drug discovery.

Figure 1.

Description page of a peptide. The page is obtained when a peptide is selected after a search in the database. (a) Part ‘Peptide’ contains general information on the peptide. (b) Part ‘Structure’ compiles all the information on the peptide structure. A Java applet allows the peptide visualization in two-dimensions. (c) Part ‘Organisms’ concerns the organisms known to produce the peptide. Via a link, the user can access to NCBI taxonomy. (d) Part ‘References’ contains bibliographical references associated to the peptide. The user can access the corresponding entry of NCBI PubMed through a link. (e) Part ‘Links’ contains links to NCBI PubChem and UniProt.

Figure 2.

Representation of NRP structures in Norine. (a) Chemical representation of actinomycin D (16). (b) Linear representation of actinomycin D. Monomers are encoded and separated by an underscore. Cycles are represented by brackets. (c) Graph representation of actinomycin D. It starts with a list of monomers each of which is associated with its rank in the list (numbered from zero) and corresponds to a node of the graph. Then, the adjacency list represents the edges incident to each node.

Figure 3.

Example of structure-based search. Two search features are provided. The structure search looks up for a peptide having exactly the query structure. The structural pattern search looks up for the peptides containing the query pattern as a subgraph. The query pattern can contain joker or alternatively-labeled nodes (X and/). In both types of search, the query can be specified using either linear or graph representation. A link to the dedicated peptide structure editor (in green) allows the user to automatically obtain the graph representation. Alternatively, the user can specify the query through the linear representation. In the last row, examples of resulting peptides are given.