NMR Structure Determination for Larger Proteins Using Backbone-Only Data

Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.
Science (Impact Factor: 33.61). 02/2010; 327(5968):1014-8. DOI: 10.1126/science.1183649
Source: PubMed


Conventional protein structure determination from nuclear magnetic resonance data relies heavily on side-chain proton-to-proton
distances. The necessary side-chain resonance assignment, however, is labor intensive and prone to error. Here we show that
structures can be accurately determined without nuclear magnetic resonance (NMR) information on the side chains for proteins
up to 25 kilodaltons by incorporating backbone chemical shifts, residual dipolar couplings, and amide proton distances into
the Rosetta protein structure modeling methodology. These data, which are too sparse for conventional methods, serve only
to guide conformational search toward the lowest-energy conformations in the folding landscape; the details of the computed
models are determined by the physical chemistry implicit in the Rosetta all-atom energy function. The new method is not hindered
by the deuteration required to suppress nuclear relaxation processes for proteins greater than 15 kilodaltons and should enable
routine NMR structure determination for larger proteins.

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Available from: James M Aramini, Mar 10, 2015
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    • "Recent advances in computational methods using the program Rosetta (Leaver-Fay et al., 2011) allow accurate modeling of protein structures from sparse NMR data sets containing chemical shifts (CSs), residual dipolar couplings (RDCs), and a minimal subset of the proton-proton distances used by conventional methods (Shen et al., 2008). By combining the use of CS-Rosetta with extensive deuteration of side-chain protons to improve 13 C relaxation and the use of transverse relaxation optimized spectroscopy (TROSY) at high magnetic fields to improve 15 N and amide 1 H relaxation (Pervushin et al., 1997), the structure of larger proteins and protein complexes can now be determined by solution NMR (Raman et al., 2010; Sgourakis et al., 2011). Methyl protons are reintroduced using site-specific labeling of Ile, Leu, and Val (ILV) residues (Tugarinov et al., 2006), a scheme that greatly simplifies the NMR spectra while still providing a sparse set of long-range methyl-methyl nuclear "
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