A warning message
If more than one model exists, as for NMR-derived structures, the 13Cα chemical shifts should be obtained for each conformation.
However, the ensemble should be validated as a "whole", i.e., after obtaining the prediction for each model from the CheShift server, the conformational-average rmsd (ca-rsmd) should be computed.1,2
You may get a predicted value of 999 ppm for a residue. If this occurs, it may happen that the residue is populating a high energy region in the Ramachandran map. For such cases the server does not contain a prediction and a, meaningless, value of 999 ppm is returned; it is also recommended that the whole conformation should be disregarded.1
CheShift provides 13Cα chemical shift predictions for the 20 naturally occurring amino acids. Other groups can be present in the uploaded file. For such a case the server does not contain predictions and a, meaningless, value of 0.00 ppm is returned.
References
1.- 1.- Vila J.A., Arnautova Y.A., Martin O.A. and Scheraga H.A. Quantum-Mechanics-Derived 13Cα Chemical Shift Server (CheShift) for Protein Structure Validation. Proc. Natl. Acad. Sci. USA 2009 (in press).
2.-Vila J.A. and Scheraga H.A. Assessing the Accuracy of Protein Structures by Quantum Mechanical Computations of 13Cα Chemical Shifts Accounts of Chemical Research (2009), in press.
3.- Villegas M.E.; Vila J.A.; Scheraga H.A. Effects of Side-Chain Orientation on the 13C Chemical Shifts of Antiparallel β-sheet Model Peptides. J Biomol. NMR 2007, 37, 137-146.
4.- Vila J.A.; Villegas M.E.; Baldoni H.A.; Scheraga H.A. Predicting 13Cα chemical shifts for validation of protein structures. J. Biomol. NMR 2007, 38, 221-235.
5.- Vila J.A.; Arnautova Y.A.; Scheraga H.A. Use of 13Cα chemical shifts for accurate determination of β-Sheet structures in solution. Proc. Natl. Acad. Sci. USA 2008, 105, 1891-1896.
6.- Vila, J. A.; Aramini J. M.; Rossi P.; Kuzin A.; Su M.; Seetharaman J.; Xiao R.; Tong L.; Montelione G. T.; H. A. Scheraga. Quantum Chemical 13C Chemical Shift Calculations for Protein NMR Structure Determination, Refinement, and Validation. Proc. Natl. Acad. Sci. USA. 2008, 38, 14389-14394.
7.- Vila J.A.; Scheraga H.A. Factors affecting the use of 13Cα chemical shifts to determine, refine, and validate protein structures. Proteins 2008, 71, 641-654.
8.- Arnautova Y.A., Vila J.A., Martin O.A. and Scheraga H.A. What can we learn by computing 13Cα chemical shifts for X-ray protein models? Acta Crystallographica D, 2009, D65, 697-703.
| |
