Rapid determination of protein folds using residual dipolar couplings

• Published in: Journal of molecular biology Vol. 304; no. 3; pp. 447 - 460
• Main Authors: Fowler, C.Andrew, Tian, Fang, Al-Hashimi, Hashim M., Prestegard, James H.
• Format: Journal Article
• Language: English
• Published: England Elsevier Ltd 01.12.2000
• Subjects: ACP; acyl carrier protein; Acyl Carrier Protein - chemistry; Acyl Carrier Protein - metabolism; Bacterial Proteins - chemistry; Bacterial Proteins - metabolism; Carbon Isotopes - metabolism; Deuterium - metabolism; Escherichia coli; Escherichia coli - chemistry; Magnetic Resonance Spectroscopy; Models, Molecular; Nitrogen Isotopes - metabolism; NMR; NodF; NodF protein; Protein Folding; protein structure; Protein Structure, Secondary; Rhizobium leguminosarum; Rhizobium leguminosarum - chemistry; Software; structural genomics; structural genomics; protein structure; SDS-PAGE; NMR; POSE; NOE; NodF; LB; IPTG; FFFs; ACP; HPLC
• ISSN: 0022-2836; 1089-8638
• DOI: 10.1006/jmbi.2000.4199

Over the next few years, various genome projects will sequence many new genes and yield many new gene products. Many of these products will have no known function and little, if any, sequence homology to existing proteins. There is reason to believe that a rapid determination of a protein fold, even at low resolution, can aid in the identification of function and expedite the determination of structure at higher resolution. Recently devised NMR methods of measuring residual dipolar couplings provide one route to the determination of a fold. They do this by allowing the alignment of previously identified secondary structural elements with respect to each other. When combined with constraints involving loops connecting elements or other short-range experimental distance information, a fold is produced. We illustrate this approach to protein fold determination on 15N-labeled Eschericia coli acyl carrier protein using a limited set of 15N- 1H and 1H- 1H dipolar couplings. We also illustrate an approach using a more extended set of heteronuclear couplings on a related protein, 13C, 15N-labeled NodF protein from Rhizobium leguminosarum.