Macromolecular recognition

Ko DY, Lee HJ, Jeong B. Surface-imprinted, thermosensitive, core-shell nanosphere for molecular recognition. Macromolecular Rapid Communications 2006, 27, 1367-1372. 

In a biocatalytic biosensor the molecular recognition component is an enzyme. Enzymes, macromolecular catalysts that are manufactured by plants and animals, affect the rates of biochemical reactions. Virtually all of the millions of chemical reactions involved in Hfe processes have associated enzymes controlling the rates. CoUectively, there are several thousand enzymes known and perhaps many thousand more yet to be discovered. 

An understanding of a wide variety of phenomena concerning conformational stabilities and molecule-molecule association (protein-protein, protein-ligand, and protein-nucleic acid) requires consideration of solvation effects. In particular, a quantitative assessment of the relative contribution of hydrophobic and electrostatic interactions in macromolecular recognition is a problem of central importance in biology. 

Recently, it has become clear to the author that cyclodextrin is one of the promising hosts for macromolecular recognition, with the finding that the cylindrical channel formed when it is stacked in a linear row is able to accommodate one or more long-chain guests. Thus, he and his coworkers launched a series of experiments to explore the formation of inclusion complexes between... 

CDs and polymers, and have accumulated a lot of information that they believe is basically significant and interesting for the elucidation of macromolecular recognition. This paper summarizes the main findings and conclusions from their efforts, along with the related important contributions from other authors. 

D. Page, D. Zanini, and R. Roy, Macromolecular recognition Effect of multivalency in the inhibition of binding of yeast mannan to concanavalin A and pea lectins by mannosylated dendrimers, Bioorg. Med. Chem., 4 (1996) 1949-1961. 

Fig. 1. Preparation of configurational biomimetic imprinted networks for molecular recognition of biological substrates. A Solution mixture of template, functional monomer(s) (triangles and circles), crosslinking monomer, solvent, and initiator (I). B The prepolymerization complex is formed via covalent or noncovalent chemistry. C The formation of the network. D Wash step where original template is removed. E Rebinding of template. F In less crosslinked systems, movement of the macromolecular chains will produce areas of differing affinity and specificity (filled molecule is isomer of template).

Lipoproteins (Table 5.2) are macromolecular aggregates with varying proportions of triglycerides and cholesterol (with some phosphoacylglycerols) and apoproteins. The apoproteins act as recognition flags for receptor binding, for example apo B and apo E,... 

Different classifications for the chiral CSPs have been described. They are based on the chemical structure of the chiral selectors and on the chiral recognition mechanism involved. In this chapter we will use a classification based mainly on the chemical structure of the selectors. The selectors are classified in three groups (i) CSPs with low-molecular-weight selectors, such as Pirkle type CSPs, ionic and ligand exchange CSPs, (ii) CSPs with macrocyclic selectors, such as CDs, crown-ethers and macrocyclic antibiotics, and (iii) CSPs with macromolecular selectors, such as polysaccharides, synthetic polymers, molecular imprinted polymers and proteins. These different types of CSPs, frequently used for the analysis of chiral pharmaceuticals, are discussed in more detail later. 

In excerpt I5D, Walker begins with a statement of the topic (solvation at hydrophobic and hydrophilic solid-liquid interfaces) and then moves directly to the signihcance of the work. He emphasizes the need for information on interfacial phenomena and points out possible applications of his work for other areas of science (molecular recognitions, electron transfer, and macromolecular self-assembly). He goes on to describe his experimental methods, focusing on three aspects of his approach (in order of difficulty) equilibrium measurements, time-resolved studies, and distance-dependent measurements of solvation strength. 

Motivating the research is the need for systematic, quantitative information about how different surfaces and solvents affect the structure, orientation, and reactivity of adsorbed solutes. In particular, the question of how the anisotropy imposed by surfaces alters solvent-solute interactions from their bulk solution limit will be explored. Answers to this question promise to affect our understanding of broad classes of interfacial phenomena including electron transfer, molecular recognition, and macromolecular self assembly. By combining surface sensitive, nonlinear optical techniques with methods developed for bulk solution studies, experiments will examine how the interfacial environment experienced by a solute changes as a function of solvent properties and surface composition. 

In macromolecular crystallography the optimization problems are too complex so that hardly any existing package could be used as a black box without considerable development and specification. Below we outline how some basic crystallographic problems in refinement and modelling are addressed starting from a foundation of pattern recognition. 

Morris, R. J. (2004). Statistical pattern recognition for macromolecular crystallographers. Actu Crystallogr. D 60, 2133-2143. 

Shenhar R, Sanyal A, Uzun O, Nakade H, Rotello VM. Integration of recognition elements with macromolecular scaffolds effects on polymer self-assembly in the solid state. 

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