Chemically accurate protein structures: Validation of protein NMR structures by comparison of measured and predicted pKa values
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A new method is presented for evaluating the quality of protein structures obtained by NMR. This method exploits the dependence between measurable chemical properties of a protein, namely pKa values of acidic residues, and protein structure. The accurate and fast empirical computational method employed by the PROPKA program (http://www.propka.chem.uiowa.edu) allows the user to test the ability of a given structure to reproduce known pKa values, which in turn can be used as a criterion for the selection of more accurate structures. We demonstrate the feasibility of this novel idea for a series of proteins for which both␣NMR and X-ray structures, as well as pKa values of all ionizable residues, have been determined. For the 17 NMR ensembles used in this study, this criterion is shown effective in the elimination of a large number of NMR structure ensemble members.
Key wordspKa structure validation ubiquitin
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This work was supported by a grant from the National Science Foundation (MCB 209941). We thank Prof. Lawrence McIntosh for helpful suggestions on the manuscript.
- Bode W., Wei A.Z., Huber R., Meyer E., Travis J., Neumann S. (1986). EMBO J. 5(10):2453–2458Google Scholar
- Fujiwara M., Kato T., Yamazaki T., Yamasaki K., Nagayam K. (2000). Biol. Pharm. Bull. 23(10):1147–1152Google Scholar
- Li, H., Robertson, A.D. and Jensen, J.H. (2005). Struct. Funct. Bioinform. 61(4), 704-21Google Scholar
- Linge, J. P., Williams, M. A., Spronk, C. A. E. M., Bonvin, A.␣M. J. J. and Nilges M. (2003). Proteins Struct. Funct. Genet. 50(3): 496-06.Google Scholar
- Rico, M., Santoro, J., Gonzalez, C., Bruix, M. and Neira, J. L. (1990). Structure, Mechanism and Function of Ribonucleases Proceedings of the 2nd International Meeting.Google Scholar