Symmetric homodimers

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The calculation of multimeric structures is a growing domain of the NMR structure determination. Among the complexes, the symmetric homo-dimers occupy a special role in NMR studies, as the chemical shifts of the protons of both monomers are identical. Homodimer NOESY NMR spectra contain intra-monomer as well as inter-monmer NOEs, and it is not possible to discriminate between them on the spectrum:

M Nilges, Proteins 1993, in order to automatically sort between inter- and intra-monomer restraints, and was the starting point of the ARIA development. The principle of the calculation is to defined all restraints as ambiguous between inter- or intra- monomer:

For each peak observed in the spectrum between the chemical shifts corresponding to the spins Pi/Pi' and Pj/Pj', the following ambiguous inter- and intra-monomer restraints will be applied at the beginning of the protocol:

The homodimer symetry is enforced by using the non-crystallographic symetries during the CNS protocol. Furthermore, a packing restraint is applied between the center-of-mass of both monomers, to avoid the separation of monomers during the refinement.

ARIA 2.2 can be used, either to sort inter and intra-monomer restraints in the cas of a predetermined contact map, or to assign NOEs without any prior guess on the structure. In the last case, any additional information about the dimer interface can be essential to enforce the convergence of the calculation. This information can be entered using restraints into the unambiguous.tbl restraint file.

 http://aria.pasteur.fr/documentation/tutorials/symmetric-homodimers






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