Clusters of segments

A more realistic model of this solution was developed in 1950 by Rory and Krigbaum, and assumes that the polymer consists of approximately spherical clusters of segments. These clusters have a maximum density of segments at their centre and this density decreases with distance from the centre in an approximately Gaussian distribution. 

Flory-Krigbaum Theory A theory of dilute polymer solutions which describes the distribution of polymer segments as clusters of segments separated by regions of pure solvent. A model for this structure is used which takes account of the excluded volume within the coils. 

In many cases, it is also helpful to have the path repel itself so that the transition pathway is self-avoiding. An acmal dynamic trajectory may oscillate about a minimum energy configuration prior to an activated transition. In the computed restrained, selfavoiding path, there will be no clusters of intermediates isolated in potential energy minima and no loops or redundant segments. The self-avoidance restraint reduces the wasted effort in the search for a characteristic reaction pathway. The constraints and restraints are essential components of the computational protocol. 

A helix bundle is a protein composed of a series of rodlike helical domains linked by flexible segments and inserted into a membrane to form a cluster of helices roughly parallel to one another and perpendicular to the plane of the membrane. 

Fig. 37.2. Principal components loading plot of 7 physicochemical substituent parameters, as obtained from the correlations in Table 37.5 [39,40]. The horizontal and vertical axes account for 46 and 31%, respectively, of the correlations. Most of the residual correlation is along the perpendicular to the plane of the diagram. The line segments define clusters of parameters that have been computed by means of cluster analysis.

The elasticity of thermoplastic polyurethane rubbers (which are also known as thermoplastic urethanes or TPUs) is a function of their morphology which comprises hard and soft phases. The hard phases consist of hydrogen bonded clusters of chain segments, which are linked by flexible chain segments that make up the soft phase. The hard blocks, which are the minor phase, exist as separate domains within a continuous matrix of the majority soft phase, as shown schematically in Fig. 25.9. 

The thicker lines represent the sequences of hard urethane segments, and the clusters of these effectively act as crosslinks, making the material act as a conventional elastomer. When the temperature is raised high enough, the clusters disassociate and the material can be made to flow when subsequently cooled, the clusters can reform and the material again exhibits elastomeric properties. Thus these materials show elastomeric behaviour at room temperature, but can be processed as thermoplastics. Hence the name of the material class - thermoplastic elastomers. 

The transmembrane domain in the RPTK is a hydrophobic segment of 22-26 amino acids inserted in the cell membrane. It is flanked by a proline-rich region in the N-terminus and a cluster of basic amino acids in the C-ter-minus. This combination of structures secures the transmembrane domain within the lipid bilayer. There is a low degree of homology in the transmembrane domain, even between two closely related RPTKs, suggesting that the primary sequence contains little information for signal transduction. 

Javitch, J. A., Ballesteros, J. A., Weinstein, H., and Chen, J. (1998) A cluster of aromatic residues in the sixth membrane-spanning segment of the dopamine D2 receptor is accessible in the binding site crevice. Biochemistry 37, 998-1006. 

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