Structural themes

Although helices are uncommon in manmade arehiteeture, they are a common structural theme in biological maeromole-eules—proteins, nucleic acids, and even polysaeeharides. (Loretta Chapet, Santa Fe, NM/ Q Sarbo)... 

The functions of a large proportion of the proteins encoded by the human genome are presently unknown. Recent advances in bioinformatics permit researchers to compare amino acid sequences to discover clues to potential properties, physiologic roles, and mechanisms of action of proteins. Algorithms exploit the tendency of nature to employ variations of a structural theme to perform similar functions in several proteins (eg, the Rossmarm nucleotide binding fold to bind NAD(P)H,... 

In addition to their varied biological roles, non-heme iron proteins contain a magnificent assortment of iron sites having a multitude of chemical and structural properties. Indeed, the catalog of iron centers is a bit like the taxonomy of insects—a seemingly limitless variation of a few structural themes, yet each new form sufficiently different to define a new species. It is beyond the scope of any review of non-heme iron proteins to be inclusive, and there are excellent recent reviews which detail selected topics. Rather, it is our intention to provide in one chapter an overview of the major classes with an emphasis on proteins for which a crystal structure is available. This review begins with a survey of the types of protein iron structures and a discussion of some methods and problems associated with establishing the iron center type. This should provide an introduction to readers less familiar with the area. Sections II to IV include the current status and recent developments for a limited number of proteins from the major iron classes. These have been chosen in the subjective vein of a limited review the omission of a topic does not indicate its relative importance or interest, only the limitation of space. The purpose of this section is to emphasize the diversity of iron center structures and functions. 

W. Nitschke and A. Rutherford, Trends Biochem. Sci. 16,241-245 (1991). Photosynthetic Reaction Centres Variations on a Common Structural Theme. ... 

A rich variety of crystal structures are made possible by hydrogen bonding. The variety is comparable to that found amongst the silicate minerals, and it is similarly based on a limited number of simple structural themes. We illustrate a few of the pattern-types revealed by crystal-structure analysis. 

IV. Common Structural Themes in Network-Forming Collagens. 396... 

Variations on the basic structural theme of 1 have led to a plethora of unusual macrocyclic systems, collectively known as porphyrin analogs or porphyrinoids. These molecules, often nontrivial to synthesize, exhibit remarkable physical and chemical properties and their chemistry has been extensively reviewed [2-18], With the impressive range of structural modifications introduced so far, the term porphyrinoid has ultimately expanded to encompass a wide range of often exotic macrocycles, some of which contain no pyrrole rings at all, or have a structural outline barely resembling that of porphyrin. Some of the generic modification types are shown in Fig. 1. Combination of these design concepts provides a virtually inexhaustible source of structural diversity. 

In almost all of the series of binary and ternary compounds known, there are examples of the dominant structural theme in the crystalline halide compounds—the [MnCl ] octahedron. These octahedra are derived, according to the point of view, from Mn2+ (and the other M+) fitting into appropriate holes in close-packed halide lattices, or from face-, edge- or corner-sharing of interconnected octahedra, forming polymers, In the hydrates and the other solvates, other octahedra, containing molecules of solvent, occur. 

The repertoire of membrane lipids is extensive, perhaps even bewildering, at first sight. However, they possess a critical common structural theme membrane lipids are amphipathic molecules (amphiphilic molecules). A membrane lipid contains both a hydrophilic and a hydrophobic moiety. 

Intuitively, it seems evident that this kind of hierarchic interrelation should be entered into the structure of chemical sets, with not only the nudei but also the electrons of the partides composing them being taken into account. Let us consider now a major structural theme in coordination chemistry - the evolution of dusters having the general formula BL. Each duster is formed from a central atom of the element E bonded to a number of ligands L (n is the coordination number) and each is characterized by a certain formal... 

The number of binary compounds alone is evidently considerable, and there is an indefinitely large number of compounds built of atoms of three or more elements. It seems logical to concentrate our attention first on the simplest compounds such as binary halides, chalconides, etc., for it would appear unlikely that we could understand the structures of more complex compounds unless the structures of the simpler ones are known and understood. However, it should be noted that simplicity of chemical formula may be deceptive, for the structures of many compounds with simple chemical formulae present considerable problems in bonding, and indeed the structures of some elements are incomprehensibly complex (for example, B and red P). On the other hand, there are compounds with complex formulae which have structures based on an essentially simple pattern, as are the numerous structures described in Chapter 3 which are based on the diamond net, one of the simplest 3-dimensional frameworks. We shall make a point of looking for the simple underlying structural themes in the belief that Nature prefers simplicity to complexity and also because structures are most easily understood if reduced to their simplest terms. 

The diamond net (Pig. 3.35(a)) is well suited to showing how a very simple structural theme may serve as the basis of the structures of a variety of compounds of increasing complexity. We saw on p. 75 that the simplest three-dimensional framework in which every point is joined to four others is a system of puckered hexagons. Any atom or group which can form bonds to four similar atoms or... 

Both of these compounds possess a /3-phen-ethylamine framework, a common structural theme that occurs in many related CNS stimulants. In general, these compounds have similar mechanisms of action. 

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