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Science 12 July 1991:
Vol. 253. no. 5016, pp. 164 - 170
DOI: 10.1126/science.1853201
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Articles

Science, Vol 253, Issue 5016, 164-170
Copyright © 1991 by American Association for the Advancement of Science

articles

A method to identify protein sequences that fold into a known three-dimensional structure

JU Bowie, R Luthy, and D Eisenberg

Molecular Biology Institute, University of California, Los Angeles 90024-1570.

The inverse protein folding problem, the problem of finding which amino acid sequences fold into a known three-dimensional (3D) structure, can be effectively attacked by finding sequences that are most compatible with the environments of the residues in the 3D structure. The environments are described by: (i) the area of the residue buried in the protein and inaccessible to solvent; (ii) the fraction of side-chain area that is covered by polar atoms (O and N); and (iii) the local secondary structure. Examples of this 3D profile method are presented for four families of proteins: the globins, cyclic AMP (adenosine 3',5'-monophosphate) receptor-like proteins, the periplasmic binding proteins, and the actins. This method is able to detect the structural similarity of the actins and 70- kilodalton heat shock proteins, even though these protein families share no detectable sequence similarity.


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