Probability-based protein secondary structure identification using combined NMR chemical-shift data
Autor: | Oleg Jardetzky, Yunjun Wang |
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Rok vydání: | 2002 |
Předmět: |
Magnetic Resonance Spectroscopy
Chemical Phenomena Molecular Structure Basis (linear algebra) Chemistry Physical Protein Conformation Chemistry Chemical shift Analytical chemistry Hydrogen Bonding Hydrogen-Ion Concentration Biochemistry Protein Structure Secondary Article Random coil Structure-Activity Relationship Identification (information) Fully automated Joint probability distribution Amino Acids Mathematical Computing Molecular Biology Algorithm Protein secondary structure Reliability (statistics) |
Zdroj: | Protein Science. 11:852-861 |
ISSN: | 1469-896X 0961-8368 |
Popis: | For a long time, NMR chemical shifts have been used to identify protein secondary structures. Currently, this is accomplished through comparing the observed (1)H(alpha), (13)C(alpha), (13)C(beta), or (13)C' chemical shifts with the random coil values. Here, we present a new protocol, which is based on the joint probability of each of the three secondary structural types (beta-strand, alpha-helix, and random coil) derived from chemical-shift data, to identify the secondary structure. In combination with empirical smooth filters/functions, this protocol shows significant improvements in the accuracy and the confidence of identification. Updated chemical-shift statistics are reported, on the basis of which the reliability of using chemical shift to identify protein secondary structure is evaluated for each nucleus. The reliability varies greatly among the 20 amino acids, but, on average, is in the order of: (13)C(alpha)(13)C'(1)H(alpha)(13)C(beta)(15)N(1)H(N) to distinguish an alpha-helix from a random coil; and (1)H(alpha)(13)C(beta)(1)H(N) approximately (13)C(alpha) approximately (13)C' approximately (15)N for a beta-strand from a random coil. Amide (15)N and (1)H(N) chemical shifts, which are generally excluded from the application, in fact, were found to be helpful in distinguishing a beta-strand from a random coil. In addition, the chemical-shift statistical data are compared with those reported previously, and the results are discussed. A JAVA User Interface program has been developed to make the entire procedure fully automated and is available via http://ccsr3150-p3.stanford.edu. |
Databáze: | OpenAIRE |
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