Structure determination of protein-protein complexes using NMR chemical shifts: case of an endonuclease colicin-immunity protein complex

Nuclear magnetic resonance (NMR) spectroscopy provides a range of powerful techniques for determining the structures and the dynamics of proteins. The high-resolution determination of the structures of protein-protein complexes, however, is still a challenging problem for this approach, since it can normally provide only a limited amount of structural information at protein-protein interfaces. We present here the determination using NMR chemical shifts of the structure (PDB code 2K5X) of the cytotoxic endonuclease domain from bacterial toxin colicin (E9) in complex with its cognate immunity protein (Im9). In order to achieve this result, we introduce the CamDock method, which combines a flexible docking procedure with a refinement that exploits the structural information provided by chemical shifts. The results that we report thus indicate that chemical shifts can be used as structural restraints for the determination of the conformations of protein complexes that are difficult to obtain by more standard NMR approaches.     

Reflection of plane waves from the boundary of a pre-stressed compressible elastic half-space

The effect of pre-stress on the propagation and reflection ofplane waves in an incompressible isotropic elastic half-spacehas been examined recently by the authors (Ogden & Sotiropoulos,1997). In the present paper the corresponding analysis for compressiblematerials is detailed. In the two-dimensional context consideredfor incompressible materials the (homogeneous) plane waves werenecessarily shear waves. By contrast, in the compressible contextpure shear waves can propagate only in specific directions inthe considered principal plane and, in a general direction,a quasi-shear wave may be accompanied by a quasi-longitudinalwave, as is the case in the anisotropic linear theory. The dependenceof the (in-plane) slowness section on the pre-stress (and finitedeformation) and on the choice of constitutive law is elucidated.This information is used to determine the reflection coefficientsfor reflection of either a (quasi-) shear wave or a (quasi-)longitudinal wave from the boundary of the half-space and tocharacterize the different cases which arise depending on thegeometry of the slowness section. The theoretical results are illustrated by numerical calculationsfor the range of possible types of behaviour with referenceforms of strain-energy function and different states of finitedeformation and to the question of stability of the half-space.     

Determination of Conformational Equilibria in Proteins Using Residual Dipolar Couplings

In order to carry out their functions, proteins often undergo significant conformational fluctuations that enable them to interact with their partners. The accurate characterization of these motions is key in order to understand the mechanisms by which macromolecular recognition events take place. Nuclear magnetic resonance spectroscopy offers a variety of powerful methods to achieve this result. We discuss a method of using residual dipolar couplings as replica-averaged restraints in molecular dynamics simulations to determine large amplitude motions of proteins, including those involved in the conformational equilibria that are established through interconversions between different states. By applying this method to ribonuclease A, we show that it enables one to characterize the ample fluctuations in interdomain orientations expected to play an important functional role.