A calculation strategy for the structure determination of symmetric dimers by 1H NMR.
The structure determination of symmetric dimers by NMR is impeded by the ambiguity of inter- and intramonomer NOE crosspeaks. In this paper, a calculation strategy is presented that allows the calculation of dimer structures without resolving the ambiguity by additional experiments (like asymmetric labeling). The strategy employs a molecular dynamics-based simulated annealing approach to minimize a target function. The experimental part of the target function contains distance restraints that correctly describe the ambiguity of the NOE peaks, and a novel term that restrains the symmetry of the dimer without requiring the knowledge of the symmetry axis. The use of the method is illustrated by three examples, using experimentally obtained data and model data derived from a known structure. For the purpose of testing the method, it is assumed that every NOE crosspeak is ambiguous in all three cases. It is shown that the method is useful both in situations where the structure of a homologous protein is known and in ab initio structure determination. The method can be extended to higher order symmetric multimers.
Nilges
M
M
European Molecular Biology Laboratory, Heidelberg, Germany.
D001426:Bacterial Proteins / Q000737:chemistry*; D002118:Calcium / Q000378:metabolism; D016209:Interleukin-8 / Q000737:chemistry*; D009682:Magnetic Resonance Spectroscopy; D008432:Mathematical Computing; D008956:Models, Chemical; D008958:Models, Molecular; D011487:Protein Conformation; D011522:Protons; D012097:Repressor Proteins / Q000737:chemistry*; D014336:Troponin / Q000737:chemistry*; D019209:Troponin C; D014961:X-Ray Diffraction
D001426:Bacterial Proteins; D016209:Interleukin-8; D011522:Protons; D012097:Repressor Proteins; D014336:Troponin; D019209:Troponin C; C060486:methionine repressor protein, Bacteria; D002118:Calcium