Chemically accurate protein structures: Validation of protein NMR structures by comparison of measured and predicted pK
a values |
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Authors: | N Powers Jan H Jensen |
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Institution: | (1) Department of Chemistry, University of Iowa, Iowa City, USA;(2) Department of Physics and Astronomy, University of Iowa, Iowa City, IA 52242, USA |
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Abstract: | 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 pK
a values of acidic residues, and protein structure. The accurate and fast empirical computational method employed by the PROPKA program () allows the user to test the ability of a given structure to reproduce known pK
a 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 pK
a 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. |
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Keywords: | pK a structure validation ubiquitin |
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