Structure calculations were done using the CYANA 3.97 package in two steps. First, the NOESY cross peaks were converted into upper distance restraints (fig. S7) following an automated process in CYANA. These distance restraints, together with φ/ψ dihedral angles determined from Cα chemical shifts and 3JHNHA (fig. S8), were used as input for the initial structure calculations. The structures were calculated with 200,000 torsion angle dynamics steps for 100 conformers, starting from random torsion angles by simulated annealing. Initially, the structures of the CID and NCBD domains were determined separately without the intermolecular NOEs. In a second step, the calculations were repeated using the intermolecular NOE-derived distance restraints (table S1) and a linker with a weak harmonic well potential with a bottom width of 1.2 Å that kept the two domains together (39). The separate structures calculated in step 1 were used as the starting structures. For refinement and cross-validation, calculations were repeated with 1DHN RDCs (fig. S8, F to K). The axially symmetric and rhombic components of the alignment tensor were optimized by an iterative process in CYANA in three steps. For representation and analysis, the 20 conformers with the lowest target function values were selected. The structural statistics, together with all input data for the structure calculations, are presented in Table 1 and figs. S8 and S9. The total SASA was determined using the program PyMol from the domains in the complex.

Note: The content above has been extracted from a research article, so it may not display correctly.



Q&A
Please log in to submit your questions online.
Your question will be posted on the Bio-101 website. We will send your questions to the authors of this protocol and Bio-protocol community members who are experienced with this method. you will be informed using the email address associated with your Bio-protocol account.



We use cookies on this site to enhance your user experience. By using our website, you are agreeing to allow the storage of cookies on your computer.