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Structural study of the Fox-1 RRM protein hydration reveal a role for key water molecules in RRM-RNA recognition

Blatter, Markus and Krepl, Miroslav and Cléry, Antoine and Allain, Frédéric H.T. and Sponer, Jiri (2017) Structural study of the Fox-1 RRM protein hydration reveal a role for key water molecules in RRM-RNA recognition. Nucleic Acids Research. ISSN 0305-10481362-4962

Abstract

The Fox-1 RNA recognition motif (RRM) domain is an important member of the RRM protein family. We report a 1.8 Å high-resolution X-ray structure of the free Fox-1 RRM, containing six crystallographically distinct monomers. We utilize this structure and our earlier NMR structure of Fox-1 protein/RNA complex for extended molecular dynamics (MD) analysis of the structured hydration. The individual monomers of the X-ray structure show diverse hydration patterns, however, MD excellently reproduces well the most occupied hydration sites found in the crystal structure. MD simulations of the protein/RNA complex show hydration patterns consistent with the isolated protein complemented by several hydration sites specific to the protein-RNA interface. We detected highly structured hydration sites with water binding times extending up to hundreds of nanoseconds. We then further study two of these sites using NMR spectroscopy, RNA binding with SwitchSENSE, and thermodynamics integration (TI) calculations of mutant proteins. These experiments confirm the presence of both hydration sites and their abolishment reduces the affinity of the complex. A prefect quantitative agreement between theory and experiment is achieved for the S155A substitution but less for S122A mutant. The S155 hydration site is evolutionarily conserved within the RRM domain motif. In conclusion, structured hydration sites, which are not easily detectable in NMR structures, may tune the affinity of protein/RNA complexes. MD is an effective tool for predicting and interpreting the hydration patterns of protein/RNA complexes, enhancing the structural experiments performed in solution.

Item Type: Article
Keywords: RNA Fox1 RRM Hydration NMR MD crystalization
Date Deposited: 10 Jun 2017 00:45
Last Modified: 10 Jun 2017 00:45
URI: https://oak.novartis.com/id/eprint/32032

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