NMR structure of the protein NP_247299.1: comparison with the crystal structure

Abstract

The NMR structure of the protein NP_247299.1 in solution at 313 K has been determined and is compared with the X-ray crystal structure, which was also solved in the Joint Center for Structural Genomics (JCSG) at 100 K and at 1.7 Å resolution. Both structures were obtained using the current largely automated crystallographic and solution NMR methods used by the JCSG. This paper assesses the accuracy and precision of the results from these recently established automated approaches, aiming for quantitative statements about the location of structure variations that may arise from either one of the methods used or from the different environments in solution and in the crystal. To evaluate the possible impact of the different software used for the crystallographic and the NMR structure determinations and analysis, the concept is introduced of reference structures, which are computed using the NMR software with input of upper-limit distance constraints derived from the molecular models representing the results of the two structure determinations. The use of this new approach is explored to quantify global differences that arise from the different methods of structure determination and analysis versus those that represent interesting local variations or dynamics. The near-identity of the protein core in the NMR and crystal structures thus provided a basis for the identification of complementary information from the two different methods. It was thus observed that locally increased crystallographic B values correlate with dynamic structural polymorphisms in solution, including that the solution state of the protein involves a slow dynamic equilibrium on a time scale of milliseconds or slower between two ensembles of rapidly interchanging conformers that contain, respectively, the cis or trans form of the C-terminal proline and represent about 25 and 75% of the total protein.

Analysis of Cytochrome P450 CYP119 Ligand-dependent Conformational Dynamics by Two-dimensional NMR and X-ray Crystallography

“…This could allow the FG and BC loops considerable flexibility in the binding of small ligands. The precise position of the FG loop in the imidazolebound CYP119 crystal structure therefore probably reflects the most thermodynamically stable conformation under the crystallization conditions and not the range of conformations accessible in solution (57,58). NMR methods have sometimes revealed additional states that are not adequately captured in crystal structures (19,20).…”

J-UNIO protocol used for NMR structure determination of the 206-residue protein NP_346487.1 from Streptococcus pneumoniae TIGR4

“…The J-UNIO protocol for automated structure determination (Serrano et al 2012) is used routinely in our laboratory for studies of proteins with up to about 150 amino acid residues (for example, Jaudzems et al 2010; Mohanty et al 2010; Serrano et al 2010, 2014; Wahab et al 2011). Here, the protein NP_346487.1 was selected from the list of JCSG targets to explore how J-UNIO, with the use of APSY-NMR and 3D heteronuclear-resolved [ 1 H, 1 H]-NOESY experiments, would cope with the complexities of the spectra of larger proteins.…”

“…For the core domain, the backbone and all-heavy-atom RMSD values between the mean atom coordinates of the bundle of 20 NMR conformers and the bundle of four molecules in the crystallographic unit cell are 1.2 and 1.8 Å, respectively, and the corresponding values for the cap domain are 1.3 and 2.3 Å, where the somewhat larger all-heavy-atom RMSD value for the cap domain can be rationalized by its smaller size and concomitantly larger percentage of solvent-exposed amino acid residues (Jaudzems et al 2010). Previously introduced additional criteria for comparison of crystal and NMR structures (Jaudzems et al 2010; Mohanty et al 2010; Serrano et al 2010) showed that the values of the backbone dihedral ϕ angles and ψ of the crystal structure are outside of the value ranges covered by the bundle of NMR conformers for less than 10 residues. Both the high-precision of the individual domain structures (Table 1) and the close fit with the crystal structure document the success of the use of J-UNIO with this larger protein.…”

NMR in a crystallography-based high-throughput protein structure-determination environment

“…These were computed using the NMR software with input of upper-limit distance constraints derived from the molecular models that represent the results of the structure determinations by NMR and by X-ray diffraction, respectively. Details of the determination of reference crystal structures and reference NMR structures are described in Jaudzems et al (2010), and applications have been made to all of the proteins in the three papers. From the combined observations with the different proteins, there is an indication that the concept of reference crystal structures computed with NMR structure-determination software could be an efficient and inexpensive alternative for deriving information on the solution behavior of proteins for which a crystal structure is available.…”

“…Whereas the paper by Jaudzems et al (2010) introduces the tools used for systematic structure comparisons, the paper by applies these tools to proteins that have multiple molecules in the crystal asymmetric unit. The results of this study seem to indicate that information on solution behavior might also be obtained from comparison of multiple molecular structures in the asymmetric crystal unit.…”