Probing Protein Structural Dynamics from Residual Dipolar Couplings

Residual dipolar couplings (RDCs) provide
explicit information of the molecular structure and
dynamics in solution at atomic level. Full utilization of
RDC datasets requires the acquisition under multiple
aligning conditions, which remains experimentally
challenging. We have illustrated in an application to
ubiquitin that molecular alignment can be modified by
varying the morphological characteristics of a composite
medium, composed of ordered bacteriophage Pf1 particles
embedded within stretched polyacrylamide gel matrix. The
molecular alignment in this composite media could be
adjusted by varying the angles between the directors of
ordering for the Pf1 and strained gel, or by varying the
concentrations of the components or magnesium. Since the
acquisition of five independent RDC datasets still remains
a difficulty, we develop a protocol that allows for the de
novo determination of bond vector orientations from RDC
measured in three independent alignment media assuming
rigidity. The method proceeds by least squares optimization
of both bond orientations and alignment tensors starting
from an appropriately chosen initial 'guess'.