Dynamics in aqueous solutions of the pentasaccharide corresponding to the binding site of heparin for antithrombin III studied by NMR relaxation measurements.

1H NMR and 13C NMR relaxation measurements at different magnetic field strengths were used to study the nature of overall and internal motions, in aqueous solution, of the synthetic pentasaccharide (A-G-A*-I-AM) corresponding to the binding site of heparin for antithrombin III. Two-dimensional double INEPT spectra were recorded at 11.7 T with and without suppression of cross-correlation effects between dipolar and chemical shift anisotropy relaxation mechanisms in measurements of spin-lattice and spin-spin relaxation times. Moreover, longitudinal relaxation times were collected at 7 T with the inversion recovery method. One dimensional NOESY spectra were recorded at 11.7 T and 9.4 T with various mixing times when spins of the A1* and A4* protons were inverted in the central residue of the pentasaccharide. Differences in the T1 relaxation times, as well as in the cross-relaxation rates between protons relaxing through fixed distances in the A* residue, indicated that the molecule tumbles anisotropically in solution. However, in order to achieve agreement between the spectral and the model data, the presence of internal motions had to be also considered, in addition to the assumption of a symmetric top model for the description of overall tumbling. The changes in the longitudinal and transversal relaxation times, collected with and without suppression of interference effects, supported the assumption that the cross-correlation between dipolar and chemical shift anisotropy relaxation mechanisms cannot be neglected in this medium-sized molecule. In fact, the influence of these effects was 10-15% in T1 and 20-25% in T2 relaxation times. The experimental data were analyzed using model free formalism and the computed order parameters indicate a decrease in spatial restriction from the central residue (S2 approximately 0.9) towards both ends of the pentasaccharide (S2 approximately 0.7). The anisotropy ratio found was approximately 3.3 with correlation times tau parallel = 450 ps and tau perpendicular = 1480 ps. The values of effective correlation time were within the range of tens of picoseconds. Thus, for a more precise interpretation of the experimental data for the pentasaccharide, in addition to internal motions and anisotropic tumbling, the effect of cross-correlation must be taken into account as well.