Sequence-structure specificity--how does an inverse folding approach work? |
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Authors: | Hu WP; Godzik A; Skolnick J |
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Affiliation: | Scripps Research Institute, Department of Molecular Biology, La Jolla, CA 92037, USA. |
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Abstract: | The inverse folding approach is a powerful tool in protein structure
prediction when the native state of a sequence adopts one of the known
protein folds. This is because some proteins show strong sequence-
structure specificity in inverse folding experiments that allow gaps and
insertions in the sequence-structure alignment. In those cases when
structures similar to their native folds are included in the structure
database, the z-scores (which measure the sequence-structure specificity)
of these folds are well separated from those of other alternative
structures. In this paper, we seek to understand the origin of this
sequence-structure specificity and to identify how the specificity arises
on passing from a short peptide chain to the entire protein sequence. To
accomplish this objective, a simplified version of inverse folding, gapless
inverse folding, is performed using sequence fragments of different sizes
from 53 proteins. The results indicate that usually a significant portion
of the entire protein sequence is necessary to show sequence-structure
specificity, but there are regions in the sequence that begin to show this
specificity at relatively short fragment size (15-20 residues). An island
picture, in which the regions in the sequence that recognize their own
native structure grow from some seed fragments, is observed as the fragment
size increases. Usually, more similar structures to the native states are
found in the top-scoring structural fragments in these high-specificity
regions.
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