Addition of missing loops and domains to protein models by x-ray solution scattering.
Inherent flexibility and conformational heterogeneity in proteins can often result in the absence of loops and even entire domains in structures determined by x-ray crystallographic or NMR methods. X-ray solution scattering offers the possibility of obtaining complementary information regarding the structures of these disordered protein regions. Methods are presented for adding missing loops or domains by fixing a known structure and building the unknown regions to fit the experimental scattering data obtained from the entire particle. Simulated annealing was used to minimize a scoring function containing the discrepancy between the experimental and calculated patterns and the relevant penalty terms. In low-resolution models where interface location between known and unknown parts is not available, a gas of dummy residues represents the missing domain. In high-resolution models where the interface is known, loops or domains are represented as interconnected chains (or ensembles of residues with spring forces between the C(alpha) atoms), attached to known position(s) in the available structure. Native-like folds of missing fragments can be obtained by imposing residue-specific constraints. After validation in simulated examples, the methods have been applied to add missing loops or domains to several proteins where partial structures were available.
Petoukhov
Maxim V
MV
European Molecular Biology Laboratory, Hamburg Outstation, D-22603 Hamburg, Germany.
Eady
Nigel A J
NA
Brown
Katherine A
KA
Svergun
Dmitri I
DI
D000465:Algorithms; D000818:Animals; D003198:Computer Simulation; D018360:Crystallography, X-Ray / Q000379:methods; D004330:Drosophila / Q000737:chemistry; D004548:Elasticity; D004926:Escherichia coli / Q000737:chemistry; D005982:Glutathione Transferase / Q000737:chemistry; D046911:Macromolecular Substances; D008954:Models, Biological; D008956:Models, Chemical; D008958:Models, Molecular; D020409:Molecular Motor Proteins / Q000737:chemistry; D010446:Peptide Fragments / Q000737:chemistry; D011487:Protein Conformation; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*; D011786:Quality Control; D012264:Ribonucleotide Reductases / Q000737:chemistry; D012542:Scattering, Radiation; D012996:Solutions / Q000737:chemistry; D013314:Stress, Mechanical; D013762:Tetrahydrofolate Dehydrogenase / Q000737:chemistry; D014961:X-Ray Diffraction / Q000379:methods*
D046911:Macromolecular Substances; D020409:Molecular Motor Proteins; D010446:Peptide Fragments; D011506:Proteins; D012996:Solutions; D012264:Ribonucleotide Reductases; C108427:ribonucleotide reductase R2 subunit; D013762:Tetrahydrofolate Dehydrogenase; D005982:Glutathione Transferase