Nuclear magnetic resonance solution structure of the Arc repressor using relaxation matrix calculations

Alexandre M.J.J. Bonvin, Hans Vis, Jan N. Breg, Maurits J.M. Burgering, Rolf Boelens, Robert Kaptein*

*Corresponding author for this work

    Research output: Contribution to journalArticleAcademicpeer-review


    The Arc repressor of Salmonella bacteriophage P22 is a dimeric sequence-specific DNA-binding protein. The solution structure of Arc has been determined from 2D NMR data using an ’ensemble’ iterative relaxation matrix approach (IRMA) followed by direct NOE refinement with DINOSAUR. A set of 51 structures was generated with distance geometry and further refined with a combination of restrained energy minimization and restrained molecular dynamics in a parallel refinement protocol. Distance constraints were obtained from an extensive set of NOE build-ups in H2O and 2H2O via relaxation matrix calculations from the ensemble of structures. Methyl group rotation, aromatic ring flips and internal mobility effects (via order parameters obtained from a free molecular dynamics run in water) were included in these calculations. The best structures were finally refined with direct NOE constraints following a slow-cooling simulated annealing protocol. In this final refinement stage, theoretical NOE intensities were directly compared with the experimental data and forces were derived using a simple two-spin approximation for the gradient of the NOE function. Dynamic assignment was applied to the peaks involving unassigned diastereotopic groups. The structure is determined to a precision (r.m.s.d. from the average excluding the ill defined C and N-terminal region) of 0.55 and 1.10 Å for backbone and all atoms, respectively. The final structures, with R factor values around 0.35, have good stereochemical qualities, contain an extensive network of hydrogen bonds consistent with the secondary structure elements and structural features in concordance with genetic data. The overall folding of the solution and crystal structures is the same.

    Original languageEnglish
    Pages (from-to)328-341
    Number of pages14
    JournalJournal of Molecular Biology
    Issue number1
    Publication statusPublished - 10 Feb 1994


    • Arc repressor
    • Ensemble IRMA
    • Internal motions
    • Relaxation matrix refinement


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