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Sigridur Agustsdottir builds smooth structures of hand-coiled clay, which she coaxes into elegant organic forms.
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However, the final structures of coiled-coil fusion proteins have received relatively little attention.
Sitting in her living room, Ms. Dashee described how she shaped and rubbed the pots smooth, working not with a wheel but from hand-coiled lengths of clay.
Tests of this profile against a sequence database of proteins with the known 3D structures showed that (1) the scores above 3.0 corresponded exclusively to coiled coil structures; (2) some coiled coil structures may have scores above 2.1.
However, some proteins are highly elongated, either as a string of small globular domains or stabilized by specialized structures such as coiled coils or the collagen triple helix.
We included in the tables all sequences that seemed to have the correct domain structure, in particular coiled coils of approximately the right length and position.
The characteristic structure of the α-helical coiled coil allows randomizing the interaction partners of this dimeric system.
The coiled-coil structures of those proteins were predicted by COILS algorithm (Lupas et al. 1991) (http://www.ch.embnet.org/software/COILS_form.html).html
The binding strength values correlate well with the structure and stability of coiled coils.
Overall, low concentrations of tannins increased the coiled structures of the enzymes boosting their catalytic activity.
Results: We present CCBuilder, a web-based application that tackles the problem for a defined but large class of protein structure, the α-helical coiled coils.
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