Name
Title | ||
|---|---|---|
Refinement of under-determined loops of Human Prion Protein by database-derived distance constraints. |
Abstract | ||
|---|---|---|
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. |
Year | DOI | Venue |
|---|---|---|
2009 | 10.1109/BIBMW.2007.4425395 | International Journal of Data Mining and Bioinformatics |
Keywords | Field | DocType |
secondary structural element,high resolution protein structure database,database-derived distance constraint,cellular biophysics,structural ensemble,diseases,increased accuracy,biologically critical loop region,protein x,refined structure,spongiform encephalopathy,binding site,cellular prion structures,proteins,computational simulations,ramachandran diagram,normal-scrapie cellular prion conversion,protein structure determination,distance constraints,human prion protein e200k variant,molecular biophysics,molecular configurations,favourable region,under-determined loop,sup align,human prion protein loop,cellular prion residues,human prion protein,protein structure,secondary structure,high resolution,computer simulation | Scrapie,Gene isoform,Cellular biophysics,Binding site,Computer science,Ramachandran plot,Molecular biophysics,Bioinformatics,Spongiform encephalopathy,Database,Protein structure | Journal |
Volume | Issue | ISSN |
3 | 4 | 1748-5673 |
ISBN | Citations | PageRank |
978-1-4244-1604-2 | 1 | 0.44 |
References | Authors | |
2 | 5 | |
Name | Order | Citations | PageRank |
|---|---|---|---|
| Feng Cui | 1 | 1 | 0.44 |
| Kriti Mukhopadhyay | 2 | 1 | 0.44 |
| Won-Bin Young | 3 | 1 | 0.44 |
| Robert L Jernigan | 4 | 224 | 25.36 |
| Zhijun Wu | 5 | 66 | 12.32 |