Macromolecules, interactions

The principle of specific chemical recognition is common to ligand—macromolecule interactions, but this alone does not suffice to define a receptor in the pharmacologic sense. Rather, it is the combination of chemical specificity or recognition and the capacity to initiate biological response or transduction that define the pharmacologic receptor (1,10,11). 

Due to the fact that the nitrile groups interact with the positively charged carbon atoms of the carboxyl or ester groups more easily than the less mobile nitrile groups in the PAN macromolecules interact with each other, the electrophilicity of the nitrile groups in the macromolecules of the copolymers increases to a greater extent, which, naturally, manifests itself in the increase of the rate of hydrogen sulfide addition. 

Jones TA. Diffraction methods for biological macromolecules. Interactive computer graphics FRODO. Methods Enzymol 1985 115 157-71. 

Should the macromolecules interact with each other, then d In yildcj does not vanish. In actual experience, its value is almost always positive, largely because of excluded volume effects. Then, c,[0 In Jt/dc,] will then increase in magnitude as Cj increases and r decreases. Thus, the downward curvature shown in curve B of Figure 21.3 is typical of nonideal behavior. 

J. J. Stezowski, K. Chandrasekhar (1986). X-ray crystallography of drug molecule-macromolecule interactions as an aid to drug design. Annu. Rep. Med. Chem. 21 293-302. 

In the case of adsorption chromatography in contrast to exclusion chromatography, the macromolecules interact with the stationary phase, which makes the method sensitive to both the size of the macromolecule and its local structure, since the interaction of monomer units with the surface is restricted to the distance of several Angstroms. It is one of the ways of solving the above-mentioned problems. This review presents the principal ideas underlying the method of chromatographic... 

A detailed study of the chromatographic behaviour of the lattic-like models of chains in slit-like pores has been performed in Refs. 59 6I), for all chain length N and pore size D ratios and all energies of the interaction of units with pore walls, 0. In Ref. 62 a strict analytical theory has been elaborated for the separation according to the functionality of macromolecules interacting with the surface only by their terminal groups. 

The use of molecular mechanics as an aid in the interpretation of spectroscopic data is outlined in more detail in Chapter 9. One of the most rapidly developing applications of molecular mechanics is the use of the structures to aid in the analysis of multidimensional NMR spectroscopy125,261. This is particularly pertinent to the study of metal-macromolecule interactions where the spectroscopic data often have too low an observation/variable ratio to allow an unequivocal determination of the structure. Therefore, an additional source of structural information is needed. To date, there have been a limited number of studies involving metal ions but this area is likely to become a very important application of structural information from molecular mechanics studies (see also Chapter 9). 

Figure 5.3. A humic acid macromolecule interacting with a surface of a clay mineral. The proposed macromolecular structure of the soil humic acid (HA) is based on the following common average characteristics of humic acids MW 6386 Da elemental analysis (%) C, 53.9 N, 5.0 H, 5.8 0,35.1 S, 0.5 C/N, 10.7 NMR information (%) aliphatic C, 18.1 aromatic C, 20.9 carbohydrate C, 23.7 metoxy C, 4.9 carboxylic C, 8.4 ketone C, 4.5 phenolic C, 4.2 functional groups (cmol/g) carboxyl, 376 phenol, 188 total acidity, 564. The structure was created using the ACD/ChemSketch program. [HA-clay complex Chen s group, unpublished (2008). Individual HA molecule Grinhut et al., 2007.]...

When visualizing ligand-macromolecule interactions, we differentiate between the ligand core molecule) and its immediate environment. The environment consists of all atoms in the macromolecule residing within a distance of up to 5 A from the ligand. 

Sequence analysis is a core area of bioinformatics research. There are four basic levels of biological structure (Table 1), termed primary, secondary, tertiary, and quaternary structure. Primary structure refers to the representation of a linear, hetero-polymeric macromolecule as a string of monomeric units. For example, the primary structure of DNA is represented as a string of nucleotides (G, C, A, T). Secondary structure refers to the local three-dimensional shape in subsections of macromolecules. For example, the alpha- and beta-sheets in protein structures are examples of secondary structure. Tertiary structure refers to the overall three-dimensional shape of a macromolecule, as in the crystal structure of an entire protein. Finally, quaternary structure represents macromolecule interactions, such as the way different peptide chains dimerize into a single functional protein. 

Hammes GG, Roberts PB (1968) Cooperativity of solvent-macromolecule interactions in aqueous solutions of polyethylene glycol and polyethylene glycol-urea. J Am Chem Soc 90(25) 7119-7122... 

Most physiological processes are the consequences of an effector interaction with biomacromolecules (Harding and Chowdhry, 2001 Weber, 1992), such as interactions between enzymes and their substrates, between hormones and hormone receptors, between antigens and antibodies, between inducer and DNA, and so on. In addition, there are macromolecule-macromolecule interactions such as between proteins (Kleanthous, 2000), between protein and nucleic acid (Saenger and Heinemann, 1989), and between protein and cell-surface saccharide. The effector of small molecular weight is normally referred to as the ligand, and the macromolecular combinant is known as the receptor. 

One says that the above results are valid for a chain with non-interacting particles. However, the monomers in a real macromolecule interact with each another, and this ensures, above all, that parts of the molecule cannot occupy the place already occupied by other parts i.e. the probabilities of successive steps are no longer statistically independent, as was assumed in the derivation of the above probability distribution functions and mean end-to-end distance (Flory 1953). So, considering the coarse-grained model, one has to introduce lateral forces of attractive and repulsive interactions. The potential energy of lateral interactions U depends on the differences of the position vectors of all particles of the chain and, in the simplest case, can be written as a sum of pair interactions... 

In the simplest case Equation (4.6) relates the Rayleigh factor to the molecular weight in the absence of solvent-macromolecule and macromolecule-macromolecule interactions. The molecular weight is determined from the slope of a plot of the Rayleigh factor versus weight concentration of macromolecules, c. 

In the case of macromolecule-macromolecule interactions, the relationship between the Rayleigh factor and weight concentration of macromolecules is complicated by the fact that the coefficient B is needed to account for this effect (Equation (4.7)). 

Before we further analyze water micromolecule-macromolecule interactions, it is appropri-... 

With these fundamental aspects of water-micromolecule macromolecule interactions as a background, we now are prepared to analyze why evolutionary processes have led to the generation of the particular types of cellular solutions we find among the three major domains of the tree of life. This analysis will emphasize especially well the principle of unity in diversity that serves as a central theme of this volume. 

The different facets of water-micromolecule-macromolecule interactions discussed up to this point involve several of the most important ways in which water has shaped the characteristics of living systems and the ways in which the internal milieu is defended in the face of water stress. Because of water s pervasive influence on the evolution of virtually all properties of organisms, there are many other imprints of water on biological design that remain to be discussed. Below, we present in somewhat abbreviated manner several of these issues. This discussion will help us to understand more clearly how water establishes the boundary conditions for life and dictates many of the engineering principles that are found in the designs of cells. Of particular importance is the issue of packaging how to accommodate tens of thousands of chemical systems in a minute volume of water. 

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