AUTOMATED EXTRACTING OF AMINO-ACID SPIN SYSTEMS IN PROTEINS USING 3D HCCH-COSY TOCSY SPECTROSCOPY AND CONSTRAINED PARTITIONING ALGORITHM (CPA)/

An automated approach has been developed to extract amino acid spin sy stems from proteins or peptides by analyzing 3D HCCH-COSY/TOCSY spectr a through a constrained,partitioning algorithm. The key step in this a pproach is that two cross peaks are merged to form a spin system not o nly by sharing one frequency but also by observing additional contrain ing cross peaks, such as from COSY and/or TOCSY data. The extracted am ino acid spin systems show the connectivity relationships between thes e spins as well as their chemical shifts. This feature differs from ot her automated spin system extraction programs making it easier to be a pplied to automatic amino acid recognition applications. The 90 amino acid protein N-domain of chicken skeletal troponin-C (1-90) was used t o test the implementation of the algorithm with both simulated and rea l experimental data. Limitations of the algorithm are discussed.