Ambiguous distance restraints were employed: each restraint was applied to the Cα atom of Lys(i) of the fixed subunit and to the Cα atom of Lys j) of any conformer of the moving subunit, in which i and j are the residue numbers of cross-linked lysine residues in Table 1.
A total of 199 NOE-based distance restraints were employed, which included 103 internucleotide restraints and 96 internucleotide restraints (Table 1).
Additional phosphodiester backbone restraints and deoxyribose pseudorotation restraints were employed, derived from B-DNA.
A total of 24 distance restraints, including seven intranucleotide, nine internucleotide, and eight internucleotide cross-strand distance restraints, were employed at nucleotide X, which allowed the position of X in the duplex to be determined with confidence.
In the ensemble refinement, ambiguous distance restraints are employed, and the back-calculated distance R is defined as R = left( {mathop sum limits_{k = 1}^{N} r_{k}^{ - 6} } right)^{ - 1/6}.
In addition, distance restraints were employed, based on the known structures of several other D-siteMAPK complexes [22], [30], [31], [32], [33].
Empirical Watson Crick base pair restraints were employed with the exception of the modified base pairs.
No restraints were employed in any step of any simulation to strictly assess the suitability of the parameters to discriminate between active/inactive analogs of Compstatin.
Based on NMR evidence for specific base pairing obtained from NOESY and HNN-COSY spectra, canonical distance restraints were employed to define the hydrogen bonds and planarity of standard W C and G U wobble base pairs.
