Macromolecular structures ensembles

Molecular modeling is an indispensable tool in the determination of macromolecular structures from NMR data and in the interpretation of the data. Thus, state-of-the-art molecular dynamics simulations can reproduce relaxation data well [9,96] and supply a model of the motion in atomic detail. Qualitative aspects of correlated backbone motions can be understood from NMR structure ensembles [63]. Additional data, in particular residual dipolar couplings, improve the precision and accuracy of NMR structures qualitatively [12]. 

The work of GAF and LAF shows that the strong distance dependence of the microscopic transfer rate will yield a collective or macroscopic rate of EET that is very sensitive to chromophore density, and to fluctuations in chromophore density. It is this feature of collective EET that has initiated the present investigation of EET as a probe of macromolecular structure. When chromophores are attached to polymer chains in a well defined manner, the EET dynamics will reflect ensemble averaged properties such as local chain segment density and flexibility, global configurational statistics, and intramolecular dimensions. 

Diffusion selectivity is based on the ability of the polymer matrix to transmit molecules of a certain shape and size. This ability is determined by the structure of the polymer and the rigidity of the macromolecular ensemble as well as by the properties of the penetrant, the size and shape of its molecules. 

It may not be obvious how we would locate the x, y, z coordinates of the heavy atom in the unit cell. Indeed it is sometimes not a simple matter to find those coordinates, but as for the heavy atom method described above, it can be achieved using Patterson methods (described in Chapter 9). As we will see later, Patterson maps were used for many years to deduce the positions of heavy atoms in small molecule crystals, and with only some modest modification they can be used to locate heavy atoms substituted into macromolecular crystals as well. Another point. It is not necessary to have only a single heavy atom in the unit cell. In fact, because of symmetry, there will almost always be several. This, however, is not a major concern. Because of the structure factor equation, even if there are many heavy atoms, we can still calculate Juki, the amplitude and phase of the ensemble. This provides just as good a reference wave as a single atom. The only complication may lie in finding the positions of multiple heavy atoms, as this becomes increasingly difficult as their number increases. 

---