Cooperative templating mechanisms

In vitro, fibril formation by several proteins displays an initial lag phase, followed by a rapid increase in aggregation (reviewed in Rochet and Lansbury, 2000). Introduction of fibrillar seeds eliminates the lag phase. These cooperative aggregation kinetics suggest that fibril formation begins with the formation of a nucleus and proceeds by fibril extension. The structure of the nucleus must therefore act as a template for the protein s conformation in the fibril. As the structural requirements for templating are unclear, it is difficult to assess the consistency of the model classes with this feature of fibril formation. We have described one possible templating mechanism for the cross-/ spine of GNNQQNY (Nelson et al., 2005). 

Figure 3.4 Formation of mesoporous materials by structure-directing agents (a) true liquid-crystal template mechanism, (b) cooperative liquid-crystal template mechanism.

This generalization is useful, especially when other types of inorganic-organic interactions are considered. This mechanism is also suitable for the formation of nonsilicon mesoporous materials. The success of the cooperative templating model was illustrated by the diverse compositions of organic-inorganic mesostructures found to be possible. 

All authors conclude that carbons with adjusted pore size distribution in the entire range of the nanopores can be obtained, depending the synthesis conditions and cationic surfactants used as templates. Despite this, it is an effective pathway to obtain porous carbons, even though the pore formation mechanism is not well understood. Hence, different mechanisms are used to explain its effect emerged, such as liquid crystal templating mechanism, cooperative self-assembly, electrostatic interaction between cationic surfactant molecules and the anionic RF polymer chain and micelles as nanoreactors to produce RF nanoparticles [51, 70]. In these cases, the simple mold effect from the globular form and the RF polymerization around it is insufficient to explain the structuring of the material by the template, where spherical closed pores would be expected. 

Figure 18.1 Synthesis of periodic mesoporous materiais assisted by SDAs (A). Route 1 true liquid crystal templating mechanism. Route 2 cooperative self-assembly mechanism. (Adapted from Refs [44,45].)...

These template polymerizations suffer from three fundamental problems (i) In most cases the binding of the polymer to the template is stronger than the binding of the monomer due to the cooperativity of the interaction between the polymers. As a consequence the newly formed macromolecules are not released from the template and multiple replication is not possible without multiple separation steps, (ii) We lack the possibility to start the polymerisation reaction at the terminal group of the monomer-template complex, (iii) While a weak interaction between the template and the monomer is favourable to allow easy separation of the template and the newly formed macromolecule, it leads to incomplete complexation of the template and interraption of the polymerisation along the chain. A solution of these problems would require a relatively strong complexation of the monomers in combination with sufficient anticooperativity in the complexation of the polymer. The latter however would inevitably impede the polymerisation reaction and require therefore a living polymerisation mechanism which does not suffer from a slowed down rate of polymerisation. 

Pol V is upregulated from <15 to 200 copies per cell approximately 45 minutes after SOS induction. Pol V is a heterotrimer with a subunit composition of UmuD 2C (see Fig. 6a). UmuC contains the catalytic domain of Pol V. UmuD is the product of RecA-mediated proteolytic cleavage of UmuD. Importantly, Pol V function requires RecA, and the mechanism by which RecA stimulates Pol V activity has been under investigation for several years (57). Recent data indicate that RecA nucleoprotein filaments act in trans to stimulate Pol V (see Fig. 6a) (57, 58). Interestingly, RecA hlaments in cis (immediately 5 to Pol V on the DNA template) do not stimulate Pol V (59). Pol V and SSB may cooperate to displace RecA from DNA (57, 60). Alternatively, recent data indicate that RecA may be removed by UvrD helicase, as UvrD is also induced during the SOS response, but whether UvrD plays a direct role in translesion synthesis is currently an open question (61, 62). 

With these template monomers very careful investigations on the mechanism of the imprinting procedure have been performed by Shea s group. The influence of the cooperativity of binding sites, of the shape of the cavity, and of the occurrence of one- or two-point binding has been taken into consideration. 

Figure 1. Schematic pathway for preparing surfactant-templated mesoporous silicas, illustrating a formation mechanism based on preformed liquid crystal (LC) mesophase (route A) or a cooperative process (route B). Reprinted from [20], Copyright (2008) WILEY-VCH Verlag GmbH Co.

Formation Mechanism of Mesostructure Liquid-crystal Template and Cooperative Self-assembly... 

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