Train-like conformation

PAMPS and its random copolymer containing 18-crown-6 (PAMPS -co-crown), are used to further study the nonelectrostatic contribution to desorption force [56]. The primary structures of polymers are shown in Scheme 30.5. As shown in Fig. 30.12, the typical force curves of PAMPS with a plateau are obtained from amino-modified quartz in the buffer of water. The long plateau suggests that the desorption process of the PAMPS chain from the substrate is smooth and that it adopts a train-like conformation at the interface and the desorption force remains about 120 pN. The desorption-adsorption process is in equilibrium in the experimental time scale, which is confirmed by the constant desorption force when changing the stretching velocity. The desorption force of PAMPS from the amino-modified quartz has been... 

Fig. 1. Various conformation models for macromolecules adsorbed on an interface, a) chain lying totally on the interface b) loop-train conformation c) loop-train-tail conformation d) adsorbed at one chain end e) random coil adsorbed at a single point f) rod-like macromolecules adsorbed at one end g) rod-like macromolecules adsorbed located totally on an interface...

In the case of a loosely structured, highly solvated train-loop-tail-like conformation of the adsorbed layer, as is the case with flexible polymers, the density of the adsorbed layer approaches that of the bulk solution and, hence, the contribution from dispersion (London-van der Waals) interactions may be negligibly small. However, for the formation of a compact adsorbed protein layer, dispersion interactions have to be taken into account. 

In a controversial study, Sun [34] was able to use a GA to achieve surprisingly good predictions for very small proteins, like melittin, with 26 residues, and for avian pancreatic polypeptide inhibitor, with 36 residues. The algorithm involved a very complicated scheme and was able to achieve accuracy of less than 2 A versus the native conformation. However, careful analysis of this report suggests that the algorithm took advantage of the fact that the predicted proteins were actually included, in an indirect way, in the training phase that was used to parameterize the fitness function, and in a sense the GA procedure retrieved the known structure rather than predicted it. 

When polymer chains overlap, they take conformations that are different from those of isolated individual chains because monomers interact in a different way. Figure 2.22 schematically shows the conformation of a polymer chain in a concentration well above the overlap concentration. It has a structure like a pearl-necklace a train of blobs (called a concentration blob) made up of groups of monomers connected in sequence. The size of each concentration blob is called the correlation length f. The monomers in the blob are directly in contact with the solvent so that they swell by the excluded-volume effect, in the same way as an isolated random coil does. 

We consider a real chain consisting of N monomers of size b and confined to a cylindrical pore of diameter d. When the chain dimension R in the free solution is smaller than the pore size, the chain does not feel much of the effect of the pore wall. As exceeds d, the chain must adopt a conformation extending along the pore because of the excluded volume effect. As R increases further, the confined chain will look like a train of spheres of diameter d (see Fig. 2.64). The excluded volume effect prohibits the spheres from overlapping with each other. Therefore, the spheres can be arranged only like a shish kebab. The partial chain within each sphere follows a conformation of a real chain in the absence of confinement. The number of monomers in the sphere is then given by... 

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