A Method to Identify Protein Sequences That Fold into a Known Three-Dimensional Structure

James U. Bowie, Roland Lüthy, David Eisenberg

doi:10.1126/science.1853201

A Method to Identify Protein Sequences That Fold into a Known Three-Dimensional Structure

DOI Web Site 被引用文献43件

James U. Bowie

Molecular Biology Institute and the Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90024-1570.
Roland Lüthy

Molecular Biology Institute and the Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90024-1570.
David Eisenberg

Molecular Biology Institute and the Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90024-1570.

抄録

<jats:p>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.</jats:p>