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Protein Science (2007), 16:1515-1521. Published by Cold Spring Harbor Laboratory Press. Copyright © 2007 The Protein Society
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ACCELERATED COMMUNICATION

Building native protein conformation from NMR backbone chemical shifts using Monte Carlo fragment assembly

Haipeng Gong1, Yang Shen2, and George D. Rose1

1 T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, USA
2 Laboratory of Chemical Physics, NIDDK, National Institutes of Health, Bethesda, Maryland 20892, USA

(RECEIVED May 6, 2007; FINAL REVISION May 14, 2007; ACCEPTED May 15, 2007)

We have been analyzing the extent to which protein secondary structure determines protein tertiary structure in simple protein folds. An earlier paper demonstrated that three-dimensional structure can be obtained successfully using only highly approximate backbone torsion angles for every residue. Here, the initial information is further diluted by introducing a realistic degree of experimental uncertainty into this process. In particular, we tackle the practical problem of determining three-dimensional structure solely from backbone chemical shifts, which can be measured directly by NMR and are known to be correlated with a protein's backbone torsion angles. Extending our previous algorithm to incorporate these experimentally determined data, clusters of structures compatible with the experimentally determined chemical shifts were generated by fragment assembly Monte Carlo. The cluster that corresponds to the native conformation was then identified based on four energy terms: steric clash, solvent-squeezing, hydrogen-bonding, and hydrophobic contact. Currently, the method has been applied successfully to five small proteins with simple topology. Although still under development, this approach offers promise for high-throughput NMR structure determination.

Keywords: protein structure/folding; NMR spectroscopy; computational analysis


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