COMPUTER-ASSISTED ASSIGNMENT OF PEPTIDES WITH NONSTANDARD AMINO-ACIDS

A comprehensive peptide assignment program and its application to a cy clic peptide, cyclosporin A, are presented in this paper. A group of g raph theoretical algorithms using fuzzy logic are discussed with the a id of examples from cyclosporin A. The algorithms deal with heavily ov erlapped peaks, recover disjointed and distorted spin coupling network s, and include strategies for sequence-specific assignment. A procedur e to extend the Protein Knowledge Base for automatically assigning non -standard amino acid residues is also presented. The program is capabl e of completely automated assignment for small peptides (similar to 20 residues). For such molecules, it is insensitive to whether the pepti de chain is cyclic or acyclic, and to whether amide protons are presen t or absent. For larger peptides/proteins, more user interaction is re quired and the sequence-specific assignment step usually must proceed through fragments smaller than the full length to avoid problems due t o occurrence of a combinatorial explosion. The program can be applied as a rigorous tool to check manual assignments. The fuzzy graph theore tical concepts built in the program are illustrated with 2D proton spe ctra of a peptide, but may be extended to higher-dimensional spectra, other biopolymers, natural products and other organic structures.