Predicting 13Cα chemical shifts for validation of protein structures

Abstract

The 13 C a chemical shifts for 16,299 residues from 213 conformations of four proteins (experimentally determined by X-ray crystallography and Nuclear Magnetic Resonance methods) were computed by using a combination of approaches that includes, but is not limited to, the use of density functional theory. Initially, a validation test of this methodology was carried out by a detailed examination of the correlation between computed and observed 13 C a chemical shifts of 10,564 (of the 16,299) residues from 139 conformations of the human protein ubiquitin. The results of this validation test on ubiquitin show agreement with conclusions derived from computation of the chemical shifts at the ab initio Hartree-Fock level. Further, application of this methodology to 5,735 residues from 74 conformations of the three remaining proteins that differ in their number of amino acid residues, sequence and three-dimensional structure, together with a new scoring function, namely the conformationally averaged root-mean-square-deviation, enables us to: (a) offer a criterion for an accurate assessment of the quality of NMRderived protein conformations; (b) examine whether X-ray or NMR-solved structures are better representations of the observed 13 C a chemical shifts in solution; (c) provide evidence indicating that the proposed methodology is more accurate than automated predictors for validation of protein structures; (d) shed light as to whether the agreement between computed and observed 13 C a chemical shifts is influenced by the identity of an amino acid residue or its location in the sequence; and (e) provide evidence confirming the presence of dynamics for proteins in solution, and hence showing that an ensemble of conformations is a better representation of the structure in solution than any single conformation.

Use of 13 C α chemical shifts for accurate determination of β-sheet structures in solution

“…An analysis in terms of violations of the torsional-angle constraints used during the last step of the structure-determination procedure was carried out for the , , and torsional angles (86 angles) of all of the residues of the Santiveri, Run 1, and Run 2 sets. The selected set of , , and torsional angles belongs to the minimal-rmsd model (2) in which the 13 C ␣ chemical shift of each residue individually best matched the experimental one. This analysis does not consider the torsional angles because the departure of the peptide unit from the planar trans conformation, except for proline, is Ͻ10° (19).…”

“…This methodology (2), validated on 139 conformations of the human protein ubiquitin, enabled us to offer a new criterion for an accurate assessment of the quality of NMR-derived protein conformations and to examine whether x-ray or NMR-solved structures are better representations of the observed 13 C ␣ chemical shifts in solution. A detailed analysis (2) of the disagreement between observed and density functional theory (DFT)-computed 13 C ␣ chemical shifts in these ubiquitin conformations illustrated the accuracy of the calculations and, more importantly, demonstrated that these disagreements reflect the dynamic nature of the protein rather than inaccuracies of the method. Our methodology has also been used (3) to show that neutral, rather than charged, basic and acidic groups are a better approximation of the observed 13 C ␣ chemical shifts of a protein in solution.…”

“…Furthermore, the results obtained (3) indicated that side-chain flexibility influences the computed 13 C ␣ chemical shifts in ubiquitin and, hence, revealed the importance of a proper consideration of side-chain conformations for an accurate refinement of protein structures. Because automated servers are widely used for prediction of backbone torsional angles using observed chemical shifts for a given protein sequence, we evaluated the performance of our method compared with that of automated servers (2). In particular, we considered a problem inverse to structure prediction-i.e., we tested the sensitivity of these methods to significant differences in protein conformation (in terms of DFT-computed and observed chemical shifts).…”

“…It should be noted that both of these applications require knowledge of high-quality conformations representing the native state. Until now, this approach has been confined mainly to x-ray-derived structures rather than to NMR-derived ones because it is often assumed that most of the NMR structures do not achieve the accuracy of high-quality x-ray structures (11,12), although NMR-derived structures for ubiquitin are better representations of the 13 C ␣ chemical shifts in solution than the x-ray structure (2).…”

Quantum-mechanics-derived 13 C α chemical shift server ( Che Shift) for protein structure validation

“…This arbitrary reference was chosen because this physics-based method is extremely sensitive to small conformational changes (10) and, hence, it represent a very accurate (9,36) method with which to computed the 13 C ␣ chemical shifts for a given protein structure model.…”