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. 2002 Apr;11(4):852-61.
doi: 10.1110/ps.3180102.

Probability-based protein secondary structure identification using combined NMR chemical-shift data

Yunjun Wang  1 , Oleg Jardetzky
Affiliations

Probability-based protein secondary structure identification using combined NMR chemical-shift data

Yunjun Wang et al. Protein Sci. 2002 Apr.

Abstract

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.

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Figures

Fig. 1.
Fig. 1.
Simulated 13Cα chemical-shift distribution of (a) Ala and (b) Met. (•) Strand; (♦) coil; (▴) helix.
Fig. 2.
Fig. 2.
High-Low-Average charts displaying the distribution of (a) Rstand vs. coil and (b) Rhelix vs. coil among the 20 amino acids.
Fig. 3.
Fig. 3.
Normalized joint probabilities of the three secondary structure types for a fragment from Pathogenesis-related Protein P14a. The secondary structures derived from its 3D coordinates are marked at top. (▴) Strand; (▪) coil; (•) helix.
Fig. 4.
Fig. 4.
PSSI (top), and its graphic output (bottom) showing the secondary structure derived from NMR chemical-shift data.
See this image and copyright information in PMC

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