An automated sequential assignment protocol for proteins is presented using heteronuclear 3D NMR. For the observed amino acid spin systems, the protocol includes an algorithm to determine their amino acid types. For the detected polypeptides, the protocol includes another algorithm to sequentially map them to the primary sequence. The former algorithm measures the similarity between the detected spin systems and the 20 standard amino acid patterns. Both chemical shift and topological likeness are considered. Knowing the amino acid types, the mapping algorithm assigns the detected polypeptides to proper positions within the protein primary sequence. The assignment protocol can be applied to spin systems generated from many different approaches. To demonstrate the assignment protocol, a few computer algorithms were designed to deduce the backbone and side-chain spin systems of proteins using heteronuclear 3D NMR. Magnetization transfer through peptide bonds can be observed in triple resonance 3D NMR. To automate the backbone assignment using the through-bond correlations, a generic algorithm is proposed. This algorithm searches and merges cross peaks among all available NMR spectra. Individual spin systems can be extracted and linked to create polypeptide chains based on the observed interresidue correlations. The algorithm is not restricted to any particular type of experiment. It is shown to be applicable to two sets of NMR spectra: the five experiment set of 3D HNCO, HNCA, HN(CO)CA, HCACO, $ sp{15}$N TOCSY-HMQC and the one-experiment set of 3D CBCANH. For the side chain assignment, an automated approach using a constrained partitioning algorithm has been developed to extract side chain spin systems of proteins by analyzing the 3D HCCH-COSY/TOCSY spectra. The extracted amino acid spin systems show the chemical shifts of the component nuclear spins as well as the connectivities between these spins. A 90-residue protein, the N-domain of chicken skeletal troponin-C
| Identifer | oai:union.ndltd.org:LACETR/oai:collectionscanada.gc.ca:QMM.40381 |
| Date | January 1996 |
| Creators | Li, Kuo-Bin. |
| Contributors | Sanctuary, B. C. (advisor) |
| Publisher | McGill University |
| Source Sets | Library and Archives Canada ETDs Repository / Centre d'archives des thèses électroniques de Bibliothèque et Archives Canada |
| Language | English |
| Detected Language | English |
| Type | Electronic Thesis or Dissertation |
| Format | application/pdf |
| Coverage | Doctor of Philosophy (Department of Chemistry.) |
| Rights | All items in eScholarship@McGill are protected by copyright with all rights reserved unless otherwise indicated. |
| Relation | alephsysno: 001537819, proquestno: NN19741, Theses scanned by UMI/ProQuest. |
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