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| Content Provider | World Health Organization (WHO)-Global Index Medicus |
|---|---|
| Author | Eisenberg, David Karanicolas, John Baker, David Sievers, Stuart A. Ivanova, Magdalena I. Thompson, Michael J. |
| Description | Author Affiliation: Thompson MJ ( Howard Hughes Medical Institute, University of California, Los Angeles, CA 90095, USA.); |
| Abstract | Based on the crystal structure of the cross-beta spine formed by the peptide NNQQNY, we have developed a computational approach for identifying those segments of amyloidogenic proteins that themselves can form amyloid-like fibrils. The approach builds on experiments showing that hexapeptides are sufficient for forming amyloid-like fibrils. Each six-residue peptide of a protein of interest is mapped onto an ensemble of templates, or 3D profile, generated from the crystal structure of the peptide NNQQNY by small displacements of one of the two intermeshed beta-sheets relative to the other. The energy of each mapping of a sequence to the profile is evaluated by using ROSETTADESIGN, and the lowest energy match for a given peptide to the template library is taken as the putative prediction. If the energy of the putative prediction is lower than a threshold value, a prediction of fibril formation is made. This method can reach an accuracy of approximately 80% with a P value of approximately 10(-12) when a conservative energy threshold is used to separate peptides that form fibrils from those that do not. We see enrichment for positive predictions in a set of fibril-forming segments of amyloid proteins, and we illustrate the method with applications to proteins of interest in amyloid research. |
| ISSN | 00278424 |
| e-ISSN | 10916490 |
| Journal | Proceedings of the National Academy of Sciences of the United States of America |
| Issue Number | 11 |
| Volume Number | 103 |
| Language | English |
| Publisher | National Academy of Sciences |
| Publisher Date | 2006-03-01 |
| Publisher Place | United States |
| Access Restriction | Open |
| Subject Keyword | Proteins Chemistry Amino Acid Sequence Amyloid Amyloid Beta-Peptides Animals Biophysical Phenomena Biophysics Computer Simulation In Vitro Techniques Models, Molecular Molecular Sequence Data Muramidase Myoglobin Oligopeptides Peptide Fragments Protein Structure, Secondary Thermodynamics Tau Proteins Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S. Multidisciplinary |
| Content Type | Text |
| Resource Type | Article |
| Subject | Multidisciplinary |
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