Protein model discrimination attempts using mutational sensitivity, predicted secondary structure, and model quality information

Khare, Shruti and Bhasin, Munmun and Sahoo, Anusmita and Varadarajan, Raghavan (2019) Protein model discrimination attempts using mutational sensitivity, predicted secondary structure, and model quality information. In: PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 87 (4). pp. 326-336.

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Abstract

Structure prediction methods often generate a large number of models for a target sequence. Even if the correct fold for the target sequence is sampled in this dataset, it is difficult to distinguish it from other decoy structures. An attempt to solve this problem using experimental mutational sensitivity data for the CcdB protein was described previously by exploiting the correlation of residue depth with mutational sensitivity (r similar to 0.6). We now show that such a correlation extends to four other proteins with localized active sites, and for which saturation mutagenesis datasets exist. We also examine whether incorporation of predicted secondary structure information and the DOPE model quality assessment score, in addition to mutational sensitivity, improves the accuracy of model discrimination using a decoy dataset of 163 targets from CASP. Although most CASP models would have been subjected to model quality assessment prior to submission, we find that the DOPE score makes a substantial contribution to the observed improvement. We therefore also applied the approach to CcdB and four other proteins for which reliable experimental mutational data exist and observe that inclusion of experimental mutational data results in a small qualitative improvement in model discrimination relative to that seen with just the DOPE score. This is largely because of our limited ability to quantitatively predict effects of point mutations on in vivo protein activity. Further improvements in the methodology are required to facilitate improved utilization of single mutant data.

Item Type:	Journal Article
Publication:	PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
Publisher:	WILEY
Additional Information:	Copyright of this article belongs to WILEY
Keywords:	CASP; deep sequencing; DOPE; model ranking; protein folding; saturation mutagenesis
Department/Centre:	Division of Biological Sciences > Molecular Biophysics Unit
Date Deposited:	17 May 2019 11:43
Last Modified:	17 May 2019 11:43
URI:	http://eprints.iisc.ac.in/id/eprint/62398

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