Three-dimensional structures, animating

The materials capable of stimulating the lymphoid tissues to produce antibodies are termed antigens and comprise bacterial and viruses as well as some smaller molecular entities. However, the response is not to the intact organisms but rather to some specific parts which have characteristic three-dimensional structures, the epitopes, and this sensitivity to structure is a characteristic feature of the immune response. Once an animal is in contact with an epitope the response can be in the circulatory or humoral system or directly as a cell-mediated response, but it is exquisitely sensitive to the specific antigen and rarely to any other. 

Figure 3.1 Three-dimensional structure of the animal cell membrane. Proteins (A) are interspersed in the phospholipid bilayer (B).

In bacteria some cytochromes b and dt serve as terminal electron carriers able to react with 02, nitrite, or nitrate, while others act as carriers between redox systems.141-1433 The aldehyde heme a is utilized by animals and by some bacteria in cytochrome c oxidase, a complex enzyme whose three-dimensional structure is known (see Fig. 18-10) and which is discussed further in Chapter 18. 

The last systematic description of heme peroxidases was published in 1999 by Brian Dunford, from the University of Alberta in Canada. The book Heme peroxidases covers discussion on three-dimensional structure, reaction mechanism, kinetics, and spectral properties of representative enzymes from bacterial, plant, fungal, and animal origin. Since 1999, vast information on basic but also applied aspects of heme peroxidases has been generated. We believe fusion of these two aspects will benefit research of those dedicated to development of biocatalytic process. The aim of this book is to present recent advances on basic aspects such as evolution, structure-function relation, and catalytic mechanism, as well as applied aspects, such as bioreactor and protein engineering, in order to provide the tools for rational design of enhanced biocatalysts and biocatalytic processes. The book does not include an exhaustive listing of references but rather a selected collection to enrich discussion and to allow envisioning future directions for research. 

Since the steroidal molecules are highly asymmetric, the resulting hierarchical assemblies may have the corresponding three-dimensional structures with supramolecular chirality. Starting from molecular chirality, each assembly must be chiral. In this context, we encountered a new problem, how we describe such molecular and supramolecular chirality. The first idea is that the steroidal molecules are analogous to a vertebrate animal which has three-axial chirality based on three directions such as head-leg, right-left, and belly-back. The three-axial chirality enables us to determine the three-axes of the hierarchical assemblies, as in the case of the helices of proteins and DNA. 

Figure 1. Antiparallel and parallel P-sheet structures. (Three-dimensional structures of this as well as of structures occurring e.g. in Figures 2, 22, 26, and Scheme 4 can be seen as animated views with the help of CHIME etc. from our website httpy/www.uni-sb.de/matfak/fbll/schneidei).

Cellulose is a polysaccharide found in plant cell walls. Cellulose forms the fibrous part of the plant cell wall. In terms of human diets, cellulose is indigestible, and thus forms an important, easily obtained part of dietary fiber. As compared to starch and glycogen, which are each made up of mixtures of a and (3 glucoses, cellulose (and the animal structural polysaccharide chitin) are made up of only (3 glucoses. The three-dimensional structure of the structural polysaccharides is thus constrained into straight microfibrils by the uniform nature of the glucoses, which resist the actions of enzymes (such as amylase) that breakdown storage polysaccharides (such a starch). 

Fortunately, however, certain types of bacteria manufacture an enzyme called phospho-triesterase (PTE) that inactivates sarin and other organophosphate molecules like it, some of which are found in certain insecticides but are hundreds of times less toxic to people. Certain organophosphates, such as the common insecticide malathion, kill insects because, unlike animals, bugs lack an enzyme that breaks down this chemical. For many years Frank Raushel of Texas A M University in College Station has studied the PTE enzyme, and recently he and his colleague Hazel Holden of the University of Wisconsin-Madison cleared a substantial hurdle They identified the three-dimensional structure— a molecular snapshot —of what this enzyme looks like. This information will help scientists understand how the enzyme works—and could reveal how to engineer one that works even better. 

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