A method to identify protein sequences that fold into a known three-dimensional structure.
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.
Bowie
J U
JU
Molecular Biology Institute, University of California, Los Angeles 90024-1570.
Lüthy
R
R
Eisenberg
D
D
D000199:Actins / Q000737:chemistry / Q000648:ultrastructure; D000465:Algorithms; D000595:Amino Acid Sequence; D000818:Animals; D002352:Carrier Proteins / Q000737:chemistry; D029968:Escherichia coli Proteins; D015394:Molecular Structure; D009211:Myoglobin / Q000737:chemistry / Q000648:ultrastructure; D033902:Periplasmic Binding Proteins; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D011953:Receptors, Cyclic AMP / Q000737:chemistry / Q000648:ultrastructure; D013329:Structure-Activity Relationship
D000199:Actins; D002352:Carrier Proteins; D029968:Escherichia coli Proteins; D009211:Myoglobin; D033902:Periplasmic Binding Proteins; D011506:Proteins; C028003:RbsB protein, E coli; D011953:Receptors, Cyclic AMP