Model building of a protein-protein complexed structure using saturation transfer and residual dipolar coupling without paired intermolecular NOE.
For understanding the precise mechanisms of molecular recognition of proteins, three-dimensional structural analyses of the protein-protein complexes are essential. For this purpose, a new method to reveal complex structures was developed with the assistance of saturation transfer (SAT) and residual dipolar coupling (RDC) by heteronuclear NMR experiments, without any paired intermolecular NOE information. The SAT and RDC experiments provide the information of the interfacial residues and the relative orientations of the two protein molecules, respectively. Docking simulation was then made to reconstruct a complex conformation, which satisfies the SAT and RDC data. The method was applied to the CAD-ICAD complex structure, which was previously determined by the NOE-distance geometry method. The quality of the current model was evaluated.
Matsuda
Tomoki
T
Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan.
Ikegami
Takahisa
T
Nakajima
Nobuyuki
N
Yamazaki
Toshio
T
Nakamura
Haruki
H
D000818:Animals; D020169:Caspases / Q000737:chemistry; D003198:Computer Simulation; D003851:Deoxyribonucleases / Q000737:chemistry; D004791:Enzyme Inhibitors / Q000494:pharmacology; D009682:Magnetic Resonance Spectroscopy / Q000379:methods*; D051379:Mice; D008958:Models, Molecular; D015233:Models, Statistical; D011487:Protein Conformation; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*; D012984:Software
D004791:Enzyme Inhibitors; D011506:Proteins; D003851:Deoxyribonucleases; C109663:caspase-activated deoxyribonuclease; D020169:Caspases