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Protein Science (2007), 16:69-81. Published by Cold Spring Harbor Laboratory Press. Copyright © 2007 The Protein Society
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A complete algorithm to resolve ambiguity for intersubunit NOE assignment in structure determination of symmetric homo-oligomers

Shobha Potluri1, Anthony K. Yan2, Bruce R. Donald2,3, and Chris Bailey-Kellogg1

1 Department of Computer Science, Dartmouth College, Hanover, New Hampshire 03755, USA
2 Department of Computer Science, Duke University, Durham, North Carolina 27708, USA
3 Department of Biochemistry, School of Medicine, Duke University Medical Center, Durham, North Carolina 27708, USA

(RECEIVED July 5, 2006; FINAL REVISION September 25, 2006; ACCEPTED October 5, 2006)

Assignment of nuclear Overhauser effect (NOE) data is a key bottleneck in structure determination by NMR. NOE assignment resolves the ambiguity as to which pair of protons generated the observed NOE peaks, and thus should be restrained in structure determination. In the case of intersubunit NOEs in symmetric homo-oligomers, the ambiguity includes both the identities of the protons within a subunit, and the identities of the subunits to which they belong. This paper develops an algorithm for simultanous intersubunit NOE assignment and Cn symmetric homo-oligomeric structure determinations, given the subunit structure. By using a configuration space framework, our algorithm guarantees completeness, in that it identifies structures representing, to within a user-defined similarity level, every structure consistent with the available data (ambiguous or not). However, while our approach is complete in considering all conformations and assignments, it avoids explicit enumeration of the exponential number of combinations of possible assignments. Our algorithm can draw two types of conclusions not possible under previous methods: (1) that different assignments for an NOE would lead to different structural classes, or (2) that it is not necessary to uniquely assign an NOE, since it would have little impact on structural precision. We demonstrate on two test proteins that our method reduces the average number of possible assignments per NOE by a factor of 2.6 for MinE and 4.2 for CCMP. It results in high structural precision, reducing the average variance in atomic positions by factors of 1.5 and 3.6, respectively.

Keywords: nuclear Overhauser effect (NOE) assignment; nuclear magnetic resonance (NMR) spectroscopy; protein complex structure determination; homo-oligomer; symmetry; complete search; configuration space; ambiguity; hierarchical subdivision


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