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      Early Onset Prion Disease from Octarepeat Expansion Correlates with Copper Binding Properties

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          Abstract

          Insertional mutations leading to expansion of the octarepeat domain of the prion protein (PrP) are directly linked to prion disease. While normal PrP has four PHGGGWGQ octapeptide segments in its flexible N-terminal domain, expanded forms may have up to nine additional octapeptide inserts. The type of prion disease segregates with the degree of expansion. With up to four extra octarepeats, the average onset age is above 60 years, whereas five to nine extra octarepeats results in an average onset age between 30 and 40 years, a difference of almost three decades. In wild-type PrP, the octarepeat domain takes up copper (Cu 2+) and is considered essential for in vivo function. Work from our lab demonstrates that the copper coordination mode depends on the precise ratio of Cu 2+ to protein. At low Cu 2+ levels, coordination involves histidine side chains from adjacent octarepeats, whereas at high levels each repeat takes up a single copper ion through interactions with the histidine side chain and neighboring backbone amides. Here we use both octarepeat constructs and recombinant PrP to examine how copper coordination modes are influenced by octarepeat expansion. We find that there is little change in affinity or coordination mode populations for octarepeat domains with up to seven segments (three inserts). However, domains with eight or nine total repeats (four or five inserts) become energetically arrested in the multi-histidine coordination mode, as dictated by higher copper uptake capacity and also by increased binding affinity. We next pooled all published cases of human prion disease resulting from octarepeat expansion and find remarkable agreement between the sudden length-dependent change in copper coordination and onset age. Together, these findings suggest that either loss of PrP copper-dependent function or loss of copper-mediated protection against PrP polymerization makes a significant contribution to early onset prion disease.

          Author Summary

          Prion diseases are neurodegenerative disorders involving the prion protein, a normal component of the central nervous system. An unusual class of inherited mutations giving rise to prion disease involves elongation of the so-called octarepeat domain, near the protein's N-terminus. Research from our lab and others shows that this domain binds the micronutrient copper, an essential element for proper neurological function. We investigated how octarepeat elongation influences copper binding by examining both the molecular features and the binding equilibrium. We find that elongation beyond a specific threshold, which confers profound early onset disease, gives rise to concomitant changes in copper uptake. The remarkable agreement between onset age and altered copper binding points to loss of copper protein function as significant in prion neurodegeneration.

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          Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA.

          Combined automated NOE assignment and structure determination module (CANDID) is a new software for efficient NMR structure determination of proteins by automated assignment of the NOESY spectra. CANDID uses an iterative approach with multiple cycles of NOE cross-peak assignment and protein structure calculation using the fast DYANA torsion angle dynamics algorithm, so that the result from each CANDID cycle consists of exhaustive, possibly ambiguous NOE cross-peak assignments in all available spectra and a three-dimensional protein structure represented by a bundle of conformers. The input for the first CANDID cycle consists of the amino acid sequence, the chemical shift list from the sequence-specific resonance assignment, and listings of the cross-peak positions and volumes in one or several two, three or four-dimensional NOESY spectra. The input for the second and subsequent CANDID cycles contains the three-dimensional protein structure from the previous cycle, in addition to the complete input used for the first cycle. CANDID includes two new elements that make it robust with respect to the presence of artifacts in the input data, i.e. network-anchoring and constraint-combination, which have a key role in de novo protein structure determinations for the successful generation of the correct polypeptide fold by the first CANDID cycle. Network-anchoring makes use of the fact that any network of correct NOE cross-peak assignments forms a self-consistent set; the initial, chemical shift-based assignments for each individual NOE cross-peak are therefore weighted by the extent to which they can be embedded into the network formed by all other NOE cross-peak assignments. Constraint-combination reduces the deleterious impact of artifact NOE upper distance constraints in the input for a protein structure calculation by combining the assignments for two or several peaks into a single upper limit distance constraint, which lowers the probability that the presence of an artifact peak will influence the outcome of the structure calculation. CANDID test calculations were performed with NMR data sets of four proteins for which high-quality structures had previously been solved by interactive protocols, and they yielded comparable results to these reference structure determinations with regard to both the residual constraint violations, and the precision and accuracy of the atomic coordinates. The CANDID approach has further been validated by de novo NMR structure determinations of four additional proteins. The experience gained in these calculations shows that once nearly complete sequence-specific resonance assignments are available, the automated CANDID approach results in greatly enhanced efficiency of the NOESY spectral analysis. The fact that the correct fold is obtained in cycle 1 of a de novo structure calculation is the single most important advance achieved with CANDID, when compared with previously proposed automated NOESY assignment methods that do not use network-anchoring and constraint-combination.
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            Practical statistics for medical researched

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              Shattuck lecture--neurodegenerative diseases and prions.

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                Author and article information

                Contributors
                Role: Editor
                Journal
                PLoS Pathog
                plos
                plospath
                PLoS Pathogens
                Public Library of Science (San Francisco, USA )
                1553-7366
                1553-7374
                April 2009
                April 2009
                17 April 2009
                : 5
                : 4
                : e1000390
                Affiliations
                [1 ]Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California, United States of America
                [2 ]Department of Applied Mathematics and Statistics, University of California Santa Cruz, Santa Cruz, California, United States of America
                [3 ]Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
                Istituto Superiore di Sanità, Italy
                Author notes

                Conceived and designed the experiments: DJS EW PD DRB GLM. Performed the experiments: DJS EW. Analyzed the data: DJS AR DD GLM. Contributed reagents/materials/analysis tools: PD DRB. Wrote the paper: DJS GLM.

                Article
                08-PLPA-RA-1417R2
                10.1371/journal.ppat.1000390
                2663819
                19381258
                74b54fac-1a69-47d2-9173-684b64c808de
                Stevens et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
                History
                : 12 November 2008
                : 20 March 2009
                Page count
                Pages: 11
                Categories
                Research Article
                Biophysics
                Biophysics/Protein Folding
                Infectious Diseases/Prion Diseases
                Neurological Disorders/Prion Diseases

                Infectious disease & Microbiology
                Infectious disease & Microbiology

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