Distance restraints average structure calculation

Figure 5, "Average" structure calculated using all distance restraints for a one-to-one mixture of B- and A-forms. Restraints violated by more than 0.5 A are shown in dashed lines. The image was prepared with the NOESHOW delegate of the MIDASPlus program 42).

As it was mentioned in Section 9.4.1, 3D structures generated by DG have to be optimized. For this purpose, MD is a well-suited tool. In addition, MD structure calculations can also be performed if no coarse structural model exists. In both cases, pairwise atom distances obtained from NMR measurements are directly used in the MD computations in order to restrain the degrees of motional freedom of defined atoms (rMD Section 9.4.2.4). To make sure that a calculated molecular conformation is rehable, the time-averaged 3D structure must be stable in a free MD run (fMD Sechon 9.4.2.5J where the distance restraints are removed and the molecule is surrounded by expMcit solvent which was also used in the NMR measurement Before both procedures are described in detail the general preparation of an MD run (Section 9.4.2.1), simulations in vacuo (Section 9.4.2.2) and the handling of distance restraints in a MD calculation (Section 9.4.2.3) are treated. Finally, a short overview of the SA technique as a special M D method is given in Sechon 9.4.2.6. 

At this point it is essential to compare the calculated structure with both the experimental data and the results of the rMD run (6). On the one hand, the interatomic distances of the final model must match the NMR restraints additionally, the fMD-averaged structure should correspond with the refined conformation obtained by the rMD. Only if the rMD and the fMD simulations result in the same conformational model and no experimental restraints are severely violated the calculated structure can be presented as a 3D image (7). 

Another important component of the analysis phase, and which is especially germane to this chapter, involves assessing the structure of the ion distribution around DNA. > Ensemble averages of the cumulative fraction of the counterions as a function of distance from the global DNA helical axis allow one to estimate the fraction of condensed counterion. (Cumulative fraction is more convenient to compute than a concentration, which would necessitate calculation of the volume of a shell.) When the ions are restrained, this fraction and the concomitant structure will most likely be found to be a function of the restraint parameters. 

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