Protein backbone structure determination using only residual dipolar couplings from one ordering medium.
Residual dipolar couplings provide significant structural information for proteins in the solution state, which makes them attractive for the rapid determination of protein folds. Unfortunately, dipolar couplings contain inherent structural ambiguities which make them difficult to use in the absence of additional information. In this paper, we describe an approach to the construction of protein backbone folds using experimental dipolar couplings based on a bounded tree search through a structural database. We filter out false positives via an overlap similarity measure that insists that protein fragments assigned to overlapping regions of the sequence must have self-consistent structures. This allows us to determine a backbone fold (including the correct Calpha-Cbeta bond orientations) using only residual dipolar coupling data obtained from one ordering medium. We demonstrate the applicability of the method using experimental data for ubiquitin.
Andrec
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Department of Chemistry, Wright-Rieman Laboratories, Rutgers, The State University of New Jersey, Piscataway 08854-8087, USA.
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Levy
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D000465:Algorithms; D030562:Databases, Protein; D008958:Models, Molecular; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods*; D010455:Peptides / Q000737:chemistry; D011487:Protein Conformation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*; D014452:Ubiquitins / Q000737:chemistry
D010455:Peptides; D011506:Proteins; D014452:Ubiquitins