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Analysis of protein chameleon sequence characteristics

Authors: Ghozlane, Amine; Joseph, Agnel; Bornot, Aurélie; de Brevern, Alexandre;

Analysis of protein chameleon sequence characteristics

Abstract

Conversion of local structural state of a protein from an alpha-helix to a beta-strand is usually associated with a major change in the tertiary structure. Similar changes were observed during the self assembly of amyloidogenic proteins to form fibrils, which are implicated in severe diseases conditions, e.g., Alzheimer disease. Studies have emphasized that certain protein sequence fragments known as chameleon sequences do not have a strong preference for either helical or the extended conformations. Surprisingly, the information on the local sequence neighborhood can be used to predict their secondary at a high accuracy level. Here we report a large scale-analysis of chameleon sequences to estimate their propensities to be associated with different local structural states such as alpha -helices, beta-strands and coils. With the help of the propensity information derived from the amino acid composition, we underline their complexity, as more than one quarter of them prefers coil state over to the regular secondary structures. About half of them show preference for both alpha-helix and beta-sheet conformations and either of these two states is favored by the rest.

Keywords

amyloid fibers., secondary structures, chameleon sequence, [SDV.BIBS] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], [INFO.INFO-BT] Computer Science [cs]/Biotechnology, protein structures, amyloid fibers, [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM], [SDV.BIO] Life Sciences [q-bio]/Biotechnology

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    This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
    26
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    This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
    Top 10%
    influence
    This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
    Top 10%
    impulse
    This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
    Average
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citations
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
26
Top 10%
Top 10%
Average
Green
gold