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

J U Bowie; R Lüthy; D Eisenberg

doi:10.1126/science.1853201

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PubMed · 1853201

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

J U Bowie·R Lüthy·D Eisenberg

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Abstract

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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Actins Algorithms Amino Acid Sequence Animals Carrier Proteins Escherichia coli Proteins Molecular Structure Myoglobin Periplasmic Binding Proteins Protein Conformation Proteins Receptors, Cyclic AMP Structure-Activity Relationship Comparative Study Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.Research Support, U.S. Gov't, P.H.S.

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J U Bowie, R Lüthy, D Eisenberg. 1991-07-12. A method to identify protein sequences that fold into a known three-dimensional structure.. https://doi.org/10.1126/science.1853201

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