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Protein Science (2008), 17:899-907. Published by Cold Spring Harbor Laboratory Press. Copyright © 2008 The Protein Society
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RDC-assisted modeling of symmetric protein homo-oligomers

Xu Wang1,2, Sonal Bansal1,2, Mei Jiang3,4,5, and James H. Prestegard1,2

1 Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, USA
2 Northeast Structural Genomics Consortium, University of Georgia, Athens, Georgia 30602, USA
3 Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey 08854, USA
4 Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey 08854, USA
5 Northeast Structural Genomics Consortium, Rutgers University, Piscataway, New Jersey 08854, USA

(RECEIVED December 8, 2007; FINAL REVISION March 3, 2008; ACCEPTED March 4, 2008)

Protein oligomerization serves an important function in biological processes, yet solving structures of protein oligomers has always been a challenge. For solution NMR, the challenge arises both from the increased size of these systems and, in the case of homo-oligomers, from ambiguities in assignment of intra- as opposed to intersubunit NOEs. In this study, we present a residual dipolar coupling (RDC)-assisted method for constructing models of homo-oligomers with purely rotational symmetry. Utilizing the fact that one of the principal axes of the tensor describing the alignment needed for RDC measurement is always parallel to the oligomer symmetry axis, it is possible to greatly restrict possible models for the oligomer. Here, it is shown that, if the monomer structure is known, all allowed dimer models can be constructed using a grid search algorithm and evaluated based on RDC simulations and the quality of the interface between the subunits. Using the Bacillus subtilis protein YkuJ as an example, it is shown that the evaluation criteria based on just two sets of NH RDCs are very selective and can unambiguously produce a model in good agreement with an existing X-ray structure of YkuJ.

Keywords: NMR; residual dipolar coupling; homo-oligomer; YkuJ; computational modeling


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