To macromolecules

In this book, we concentrate largely on methods for the computer manipulation of small and medium-sized molecules, molecules of up to a few hundred or thousand atoms. We do this to develop an understanding of the methods available for the processing of information on chemical compounds and reactions. However, many of these methods can also be applied to macromolecules such as proteins and nucleic acids. 

A key factor determining the performance of ultrafiltration membranes is concentration polarization due to macromolecules retained at the membrane surface. In ultrafiltration, both solvent and macromolecules are carried to the membrane surface by the solution permeating the membrane. Because only the solvent and small solutes permeate the membrane, macromolecular solutes accumulate at the membrane surface. The rate at which the rejected macromolecules can diffuse away from the membrane surface into the bulk solution is relatively low. This means that the concentration of macromolecules at the surface can increase to the point that a gel layer of rejected macromolecules forms on the membrane surface, becoming a secondary barrier to flow through the membrane. In most ultrafiltration appHcations this secondary barrier is the principal resistance to flow through the membrane and dominates the membrane performance. 

The electric field-jump method is applicable to reactions of ions and dipoles. Application of a powerful electric field to a solution will favor the production of ions from a neutral species, and it will orient dipoles with the direction of the applied field. The method has been used to study metal ion complex formation, the binding of ions to macromolecules, and acid-base reactions. 

An alternative method of studying the molecular motions of a polymeric chain is to measure the complex permitivity of the sample, mounted as dielectric of a capacitor and subjected to a sinusoidal voltage, which produces polarization of the sample macromolecules. The storage and loss factor of the complex permitivity are related to the dipolar orientations and the corresponding motional processes. The application of the dielectric thermal analysis (DETA) is obviously limited to macromolecules possessing heteroatomic dipoles but, on the other hand, it allows a range of frequency measurement much wider than DMTA and its theoretical foundations are better established. 

Experimental distances from NOEs/ROEs of small molecules are recommended not to be classified into regions of small, medium, and large as it is often done in the structure determination of large molecules. As opposed to macromolecules, the overall correlation time Tc can be considered constant in small molecules. Thus, it is possible to measure distances in the range between 2 and 5 A with an accuracy of about 10%. Often distances between protons are almost exclusively used for the structure determination. This leads to the fact that molecules with small numbers of hydrogen atoms are more difficult to determine. 

Kuntz ID, Blaney JM, Oatley SJ, Langridge R, Ferrin TE. A geometric approach to macromolecule-ligand interactions. J Mol Biol 1982 161 269-288. 

An understanding of specific and general solvent effects can provide a basis for interpreting the emission spectra of fluorophores that are bound to macromolecules or, in general, are located in different sites of structurally heterogeneous system. 

Several of the postulated roles for nematode-secreted AChEs assume that they gain access to the intestinal mucosa. Several possibilities exist for transport of parasite AChE across the epithelial cell barrier, such as (i) utilization of existing pathways for receptor-mediated transcytosis (ii) a paracellular route facilitated by parasite-secreted proteases as observed for a bacterial elastase (Azghani et al., 1993) and (iii) increased paracellular permeability resulting from inflammatory events in the mucosa. We consider the latter suggestion most likely, as this has been duplicated by ex vivo perfusion with rat mast cell protease II (Scudamore et al., 1995). Moreover, cholinergic stimulation attenuates epithelial barrier properties to macromolecules in rat ileal crypts (Phillips et al., 1987). 

Scudamore, C.L., Thornton, E.M., McMillan, L., Newlands, G.F.J. and Miller, H.R.P. (1995) Release of the mucosal mast cell granule chymase, rat mast cell protease-II, during anaphylaxis is associated with the rapid development of paracellular permeability to macromolecules in rat jejunum. Journal of Experimental Medicine 182, 1871—1881. 

The mechanisms whereby mast cells enhance host protection to H. polygyms and T. spiralis (and whether these are related to the leak-lesion hypothesis) have not yet been fully defined. Certainly, mast cells contribute to intestinal inflammation during infection through the secretion of a range of cytokines (Gordon et al., 1990) and vasoactive substances (see above). In addition, the release of mast cell proteases are known to increase enterocyte permeability to macromolecules in the rat intestine (Scudamore et al., 1995) and regulate epithelial cell functions at other mucosal sites (Cairns and Walls, 1996). 

Lee, J.J. Fuller, G.G. "Elllpsometry Studies of Adsorbed Polymer Chains Subjected to Flow", submitted to Macromolecules. 

Nitroxide attached to macromolecules also induces the living radical polymerization of St. Yoshida and Sugita [252] prepared a polymeric stable radical by the reaction of the living end of the polytetrahydrofuran prepared by cationic polymerization with 4-hydroxy-TEMPO and studied the living radical polymerization of St with the nitroxide-bearing polytetrahydrofuran chain. The nitroxides attached to the dendrimer have been synthesized (Eq. 69) to yield block copolymers consisting of a dendrimer and a linear polymer [250,253]. 

Concentrations of zinc in tissues of aquatic organisms are usually far in excess of that required for normal metabolism. Much of the excess zinc is bound to macromolecules or present as insoluble metal inclusions in tissues (Eisler 1981, 1984, 1993 USEPA 1987). Diet is the most signihcant source of zinc for aquatic organisms and is substantially more important than uptake from seawater (Eisler 1981, 1984). In general, zinc concentrations in sediments and tissues of aquatic organisms are elevated in the vicinity of smelters and other point sources of zinc, and decrease with increasing distance (Ward et al. 1986 Table 9.4). 

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