Template backbone

Abbreviations used in table (see also caption to Table 5.2) HB -hydrogen bonding potential energy term self-bb - prediction of side-chain conformation on to template backbone of modeled sequence non-self - prediction of side-chain conformation onto backbone borrowed from a homologous protein structure. 

For the construction of a four-helix bundle, the spatial orientation of template amino acids is considered. The conformational characteristics of the side chains of lysine predict a direction perpendicular to the plane of the template, and all attachment sites for peptide modules may be oriented cis relative to the plane of the template backbone. 

Two distinct but related strategies that rely on templates to control the number of monomers incorporated into an oligomeric product can be envisioned. One of these approaches, shown in Scheme 8-2, relies on templated radical macrocyclization reactions to control telomer size [14, 15]. This strategy requires attachment of all of the monomer units to the template backbone and uses macrocyclization, which faces competition from intermolecular chain transfer, to control the telomer length. The chain transfer agent T-I (i.e., telomerization terminator) is not attached to the template. 

Given a set of aligned structures from a fold family, we can generate a statistical description of the environment surrounding each set of corresponding alpha carbons. We first take a template backbone and mount the sidechains of a new sequence upon the template. Then we can compute a likelihood score for each alpha carbon environment (created by the sidechains as they hang off the template backbone) and sum these to get an overall measure of the compatibility of this sequence to the template backbone. 

The SCWRL program for placing sidechains is able to reproduce crystal structure sidechains to about 2 A RMSD. In early (unpublished) work, we used average side chain rotamers, not dependent on backbone torsion angles, and the resulting scores were much lower than the SCWRL scores. In fact, the template backbones with SCWRL-placed sidechains score as well as template backbones with sidechains taken from the known crystal structure of the query sequence. 

Our scoring method is sensitive to the distance of the template backbone from the actual structure. Up to about 2.9 A, we are able to place sidechains such that the main features of the alpha carbon environments remain recognizable by the program. However, above 3 A, the sidechains are simply... 

Fig> 5-18 Example of attachment of CP monomer (here aniline) to a "template" backbone before polymerization. 

Fig. 5-19 Poly(aniline) and Poly(electrolyte) (template backbone) stnictureresulting from polymerization of the template-pendant monomer shown in Fig. 5-18.

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