Consistent blind protein structure generation from NMR chemical shift data

Abstract

Protein NMR chemical shifts are highly sensitive to local structure. A robust protocol is described that exploits this relation for de novo protein structure generation, using as input experimental parameters the 13 C ␣ , 13 C ␤ , 13 C , 15 N, 1 H ␣ and 1 H N NMR chemical shifts. These shifts are generally available at the early stage of the traditional NMR structure determination process, before the collection and analysis of structural restraints. The chemical shift based structure determination protocol uses an empirically optimized procedure to select protein fragments from the Protein Data Bank, in conjunction with the standard ROSETTA Monte Carlo assembly and relaxation methods. Evaluation of 16 proteins, varying in size from 56 to 129 residues, yielded full-atom models that have 0.7-1.8 Å root mean square deviations for the backbone atoms relative to the experimentally determined x-ray or NMR structures. The strategy also has been successfully applied in a blind manner to nine protein targets with molecular masses up to 15.4 kDa, whose conventional NMR structure determination was conducted in parallel by the Northeast Structural Genomics Consortium. This protocol potentially provides a new direction for high-throughput NMR structure determination. molecular fragment replacement ͉ protein structure prediction ͉ ROSETTA ͉ structural genomics

Structure, Dynamics, Lipid Binding, and Physiological Relevance of the Putative GTPase-binding Domain of Dictyostelium Formin C

“…deviation with respect to one of the nine lowest CS-Rosetta energy models (see supplemental Fig. S2, B and C) (12,25). In addition, r.m.s.…”

“…Structure Prediction Based on Chemical Shifts Using CSRosetta-CS-Rosetta calculations were performed as described in the literature (12,25). Two sets of structures were predicted: the first based on N, H N , CЈ, C ␣ , H ␣ , and C ␤ chemical shifts and the second omitting the CЈ chemical shift information.…”

“…As many other GTPase-binding proteins, the ForC GBD adopts a ubiquitin-like ␣-/␤-roll fold, which, however, contains an exceptionally long loop between ␤-strands 1 and 2. The obtained high resolution data for the ForC GBD further allowed prediction of its structure based on chemical shift data only using the program CS-Rosetta (12). Because the large positively charged surface area of the ForC GBD may mediate interactions with membrane regions enriched with negatively charged lipids, its interaction with neutral dodecylphosphocholine micelles and such containing small amounts of negatively charged lipids (PS, PG, PIP345, and PIP45) was additionally analyzed by NMR and CD spectroscopy.…”

Cross-Validation of the Structure of a Transiently Formed and Low Populated FF Domain Folding Intermediate Determined by Relaxation Dispersion NMR and CS-Rosetta

“…as RDCs can be incorporated to improve structure quality [48][49][50][51]. Typically a protocol is used whereby small fragments are selected from a database of structures based on agreement with experimental data, with models derived subsequently from fragment assembly.…”

“…Typically a protocol is used whereby small fragments are selected from a database of structures based on agreement with experimental data, with models derived subsequently from fragment assembly. The approach has been cross-validated for the native states of a large number of small to medium sized proteins (approximately 150 residues or less) for which high resolution structural information is available from either NMR or X-ray studies, and in the majority of cases the structures produced by the database approach are within 2Å of those generated using traditional methods [48,49].…”