Analysis of six protein structures predicted by comparative modeling techniques.
The protein structures of six comparative modeling targets were predicted in a procedure that relied on improved energy minimization, without empirical rules, to position all new atoms. The structures of human nucleoside diphosphate kinase NM23-H2, HPr from Mycoplasma capricolum, 2Fe-2S ferredoxin from Haloarcula marismortui, eosinophil-derived neurotoxin (EDN), mouse cellular retinoic acid protein I (CRABP1), and P450eryf were predicted with root mean square deviations on C alpha atoms of 0.69, 0.73, 1.11, 1.48, 1.69, and 1.73 A, respectively, compared to the target crystal structures. These differences increased as the sequence similarity between the target and parent proteins decreased from about 60 to 20% identity. More residues were predicted than form the common region shared by the two crystal structures. In most cases insertions or deletions between the target and the related protein of known structure were not correctly positioned. One two residue insertion in CRABP1 was predicted in the correct conformation, while a nine residue insertion in EDN was predicted in the correct spatial region, although not in the correct conformation. The positions of common cofactors and their binding sites were predicted correctly, even when overall sequence similarity was low.
Harrison
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RW
Department of Pharmacology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, USA.
Chatterjee
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D
Weber
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IT
D000595:Amino Acid Sequence; D000818:Animals; D001426:Bacterial Proteins; D018360:Crystallography, X-Ray; D003577:Cytochrome P-450 Enzyme System / Q000737:chemistry; D005288:Ferredoxins / Q000737:chemistry; D006801:Humans; D051379:Mice; D006899:Mixed Function Oxygenases / Q000737:chemistry; D008958:Models, Molecular; D008969:Molecular Sequence Data; D016296:Mutagenesis; D016254:Mutagenesis, Insertional; D009701:Nucleoside-Diphosphate Kinase / Q000737:chemistry; D010731:Phosphoenolpyruvate Sugar Phosphotransferase System / Q000737:chemistry; D011237:Predictive Value of Tests; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D018168:Receptors, Retinoic Acid / Q000737:chemistry; D011994:Recombinant Proteins / Q000737:chemistry; D017384:Sequence Deletion; D017386:Sequence Homology, Amino Acid
D001426:Bacterial Proteins; D005288:Ferredoxins; D011506:Proteins; D018168:Receptors, Retinoic Acid; D011994:Recombinant Proteins; C082927:retinoic acid binding protein I, cellular; D003577:Cytochrome P-450 Enzyme System; D006899:Mixed Function Oxygenases; C054444:eryF protein, Saccharopolyspora erythraea; D010731:Phosphoenolpyruvate Sugar Phosphotransferase System; C030182:phosphocarrier protein HPr; D009701:Nucleoside-Diphosphate Kinase