Nucleic Acid-Protein Systems

The first topic is usually treated in terms of the familiar nucleic acid-protein systems with which we are familiar today. However, a novel proposal for evolution... 

Abstract This chapter updates but mostly supplements the author s Ange-wandte Review,111 setting in context recent advances based on protein and nucleic acid engineering. Systems qualify as a true enzyme mimics if there is experimental evidence for both the initial binding interaction and catalysis with turnover, generally in the shape of saturation kinetics. They are discussed under five broad headings mimics based on natural enzymes, on other proteins, on other biopolymers, on synthetic macromolecules and on small-molecule host-guest interactions. 

The three major classes of biopolymers found in eukaryotic systems are nucleic acids, proteins, and polysaccharides. The latter class is the most complex with respect to structural and stereochemical diversity. Polysaccharides indeed possess a massive information content. Furthermore, polysaccharides are commonly found in nature covalently attached (conjugated) to other biomolecules such as proteins, isoprenoids, fatty acids, and lipids.1... 

The molecules that form the foundation of living systems are often organized into four categories. They are the primary metabolites nucleic acids, proteins, carbohydrates, and lipids. The categories can be grouped together in different ways, based on features that they have in common. For example, nucleic acids, proteins, and polysaccharides are polymeric. Nucleic acids and proteins are further related because they are templated polymers. Other classification systems are also possible.1 Interest in the development of size-expanded versions of biomolecules has grown over the past... 

Detection of the sites of hybridization-dependent binding of biotinylated probe to the filters is most readily conducted with commercially available kits. Favorable results have been obtained with the BluGene Nonradioactive Nucleic Acid Detection System from BRL. Follow the manufacturer s instructions when carrying out the following steps. After washing, sequentially expose the filters to streptavidin and biotinylated alkaline phosphatase (or to a conjugate of these two proteins) This causes the immobilization of alkaline phosphatase at sites of positive hybridization... 

Mid-IR has also been demonstrated for real-time concentration monitoring of a fermentation using a standard transmission cell, and the spectral response was similar, regardless of whether the broth was filtered or not.38 A PLS regression was used to perform quantitation of the substrate, the lactic acid bacterium, and the major metabolites. In another article describing quantitative mid-IR for fermentation studies, a model system was investigated under various fermentation conditions.39 The mid-IR provided insight into the relative concentrations of carbohydrates, nucleic acids, proteins and lipids in the host cells. Mid-IR has also been demonstrated for multi-component quantitation... 

In conventional MM the potential energy function (PEF) is parameterized and these optimized parameters are called force-field parameters. Such methods are widely applied in the studies of nucleic acids, proteins, their complexes and other biomolecular systems. A typical, simple force field of a molecular system is defined by the following equation ... 

In 1980-1982 comprehensive reviews on Raman and resonance Raman studies of biological and biochemical systems appeared in the literature (Carey and Solares, 1980 Carey, 1982). Particularly work on protein conformation, natural, protein-bound chro-mophores, resonance Raman labels (as already mentioned above), nucleic acids and nucleic acid-protein complexes as well as on lipids, membranes, and carbohydrates were reviewed. 

In biological systems, atoms tend to form very large molecules called macromolecules, which can be segregated into four groups carbohydrates, nucleic acids, proteins, and lipids. 

We see that DFT is increasingly used to model a wide range of weak interactions in protein-ligand and nucleic acid-ligand systems. Often, DFT is the only method that can incorporate all electron correlated calculations and that can be applied in... 

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