Exact restraint models

The second factor on the right-hand side of Eq. (5.1) is called the combinatorial factor. It is the partition sum of the equivalent ensemble of molecules that interact only through steric restraints. The combinatorial factor takes into account all size and shape effects of the molecules. There is no exact expression for Zc but, by fitting the simplified theoretical models to thermodynamic data of... 

A 3D model of the receptor binding site has been worked out with the aid of conformationally restrained analogues of acetylcholine. Acetylcholine itself has no conformational restraints. It is a straight-chain molecule in which bond rotation along the length of its chain can lead to numerous possible conformations (or shapes). Thus, it is impossible to know exactly the 3D shape of the receptor site from considering acetylcholine alone. In the past, it was assumed that a flexible neurotransmitter such as acetylcholine would interact with its receptor in its most stable conformation. In the case of acetylcholine, that would be the conformation represented by the sawhorse and Newman projections shown in Fig. 11.12. 

Models with exact secondary structure but no tertiary restraints... 

Aszodi et al. [165], employed distance geometry and a simplified polypeptide chain representation. Their model chain consisted of the Ca backbone and the CP positions of the side chains. They also assumed knowledge of secondary structure and a limited number of exact long-range restraints. These have been supplemented by a set of soft restraints, somewhat in a similar spirit as those used in the work of Mumenthaler and Braun [164], They found that in order to assemble low-resolution structures. 

It is usually necessary, and often desirable, to impose relations between the parameters of a model. The problem to be solved is then a minimization of Equation [6] while imposing subsidiary conditions. A constraint satisfies such a condition exactly. A restraint (soft constraint) is a condition accompanied by a measure of uncertainty or a weight, and accordingly satisfies the condition only approximately. 

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