NDLI: Refinement of under-determined loops of human prion protein by database-derived distance constraints

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Refinement of under-determined loops of human prion protein by database-derived distance constraints

Content Provider	IEEE Xplore Digital Library
Author	Feng Cui Mukhopadhyay, K. Won-Bin Young Jernigan, R.L. Zhijun Wu
Copyright Year	2007
Description	Author affiliation: Program on Bioinf. & Comput. Biol., Ames, IA (Feng Cui)
Abstract	Computational simulations of the conversion from the normal cellular prion $(PrP^{c})$ to the scrapie prion $(PrP^{Sc})$ are usually based on the structures determined by NMR because of the difficulties in crystallizing prion protein. Due to insufficient experimental restraints, a biologically critical loop region in $PrP^{c}$ (residues 167-171), which is a potential binding site for Protein X, is under-determined in most mammalian species. Here, we show that by adding information about distance constraints derived from a database of high-resolution protein structures, this under-determined loop as well as other secondary structural elements of the E200K variant of human prion protein $(hPrP^{c}),$ a disease-related isoform, can be refined into more realistic structures in the structural ensemble with improved quality and increased accuracy. In particular, the ensemble becomes more compact after the refinement and the percentage of residues in the most favourable region of the Ramachandran diagram is increased to about 90% in the refined structures from the 80 to 85% range in the previously reported structures. Our results not only provide significantly improved structures of the prion protein and hence would facilitate insights into its conversion in the spongiform encephalopathies, but also demonstrate the strong potential for using databases of known protein structures for structure determination and refinement.
Starting Page	14
Ending Page	23
File Size	820274
Page Count	10
File Format	PDF
ISBN	9781424416042
DOI	10.1109/BIBMW.2007.4425395
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2007-11-02
Publisher Place	USA
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Proteins Brain Pathogens Databases Genetic mutations Humans Amino acids Nuclear magnetic resonance Diseases Computational biology
Content Type	Text
Resource Type	Article

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