Topology fingerprint approach to the inverse protein folding problem.
We describe the most general solution to date of the problem of matching globular protein sequences to the appropriate three-dimensional structures. The screening template, against which sequences are tested, is provided by a protein "structural fingerprint" library based on the contact map and the buried/exposed pattern of residues. Then, a lattice Monte Carlo algorithm validates or dismisses the stability of the proposed fold. Examples of known structural similarities between proteins having weakly or unrelated sequences such as the globins and phycocyanins, the eight-member alpha/beta fold of triose phosphate isomerase and even a close structural equivalence between azurin and immunoglobulins are found.
Godzik
A
A
Department of Molecular Biology, Scripps Research Institute, La Jolla, CA 92037.
Kolinski
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A
Skolnick
J
J
D000465:Algorithms; D001400:Azurin / Q000737:chemistry; D001425:Bacterial Outer Membrane Proteins / Q000737:chemistry; D001426:Bacterial Proteins / Q000737:chemistry; D016208:Databases, Factual; D005914:Globins / Q000737:chemistry; D007146:Immunoglobulin lambda-Chains / Q000235:genetics; D008958:Models, Molecular; D010798:Phycocyanin / Q000737:chemistry; D010940:Plant Proteins / Q000737:chemistry*; D010970:Plastocyanin / Q000737:chemistry*; D011487:Protein Conformation; D016415:Sequence Alignment; D013329:Structure-Activity Relationship; D013816:Thermodynamics
D001425:Bacterial Outer Membrane Proteins; D001426:Bacterial Proteins; D007146:Immunoglobulin lambda-Chains; D010940:Plant Proteins; C017079:mauC protein, Methylobacterium extorquens; D010798:Phycocyanin; D001400:Azurin; D005914:Globins; D010970:Plastocyanin