Proteins theoretical background

The theoretical background to classical electrostatics is first reviewed, beginning with the physical basis for the electrostatic response of a protein/solvent system to a charge distribution, and ways of modelling this response. Consistent classical electrostatic frameworks for describing a protein/solvent system are then described. In addition the methods must be able to model temperature, pH and ionic strength effects if these affect the property of interest. Of particular importance is the way one may extract experimentally observable properties from such models. 

Metal-enzyme complexes, a subgroup of metal-protein complexes, exhibit enzymatic activity consequent to readily dissociable combination with a variety of metal ions. Many of these studies have been performed with unpurified enzymes, and, even when pure enzymes were used, the stoichiometry of the interaction of the metal and enzyme has not been measured. Enhancement of enzymatic activity as a result of the addition of metal ions and its partial loss on their removal has been the chief criterion of assessment of physiological significance. Only in a few instances, e.g., enolase, has the stability and stoichiometry been studied in relation to function (Malmstrom, 1953, 1954). The study of metal complexes and particularly metal chelates (Bjerrum, 1941 Martell and Calvin, 1952 Calvin, 1954) has provided both new experimental and new theoretical backgrounds for the study of metals in relation to the specificity of enzyme action, metal-enzyme (Calvin, 1954), metal-substrate (Najjar, 1951), and metalloenzyme interaction, as well as metal-enzyme inhibition (James, 1953). 

Piezoelectric sensors have become a versatile tool in biosensorics to study protein-protein and protein-small molecule interactions. Here we present theoretical background on piezoelectric sensors and instructions, how to modify their surface with various recognition elements for cholinesterases. These recognition elements comprise an organophosphate (paraoxon), a cocaine derivative (BZE-DADOO), and a tricyclic, aromatic compound (propidium). Additionally, a guide to the kinetic evaluation of the obtained binding curves is given in this chapter. 

Membranes and model membranes exhibit liquid crystalline behavior and this has been exploited in a number of studies to obtain valuable information on the structure and dynamics of membrane associated peptides and proteins as well as on the interaction of the peptides with the membranes themselves. NMR spectroscopy of nuclei such as proton, carbon, deuterium, nitrogen and phosphorus has been utilized for such purposes. Structure elucidation of membrane-associated peptides and proteins in oriented bilayers by solid-state NMR spectroscopy has been reviewed. A survey on the use of static uniaxially oriented samples for structural and topological analysis of membrane-associated polypeptides is available. The theoretical background has been dealt with and a number of examples of applications provided. In addition, ongoing developments combining this method with information from solution NMR spectroscopy and molecular modelling as well as exploratory studies using dynamic nuclear polarization solid-state NMR have been presented. The use of N chemical shift anisotropy, dipolar interactions and the deuterium quadrupolar split-... 

In this subsection, a quick review of what other investigators have done in this area will be presented. Of course, it is to be mentioned here that not all of the relevant pubhshed work will be presented only those that were accessible to us and were reviewed will be presented and we apologize for those whose work was not mentioned hereafter. For a thorough review of protein adsorption, covering both theoretical background and experimentation in a more detail, the reader is advised to read the textbooks by Andrade [8] and Horbett and Brash [6]. 

Molecular dynamic calculations (Gelin and Karplus, 1975 McCammon et al, 1977 Karplus and McCammon, 1979) promise to provide the theoretical background for understanding motions in folded proteins. Time-... 

Electron Spin Echo Envelope Modulation, or ESEEM, is widely used to investigate structure of the immediate surroundings of paramagnetic species. In combination with site-specific spin labeling and selective deuterium substitution, it becomes a helpful tool to study location of proteins and small peptides within membranes, interaction of small molecules with proteins, supramolecular assemblies, water accessibility to specific regions of proteins and water penetration into membranes, protein folding and secondary structures. In this review, experimental approaches and limitations, theoretical background of the method, and recent applications are discussed. 

Altered thermodynamic activity of proteins in solution arises when unreactive (or inert) macromolecules are added to a solution and occupy more than a few percent of total solution volume. Terms such as unreactive , "background, or inert are used to emphasize that the added protein need not exhibit and direct binding interaction with the protein of interest. Instead, the consequences have more to do with molecular crowding, and approximate theoretical models show that this effect depends on the shapes and sizes of the macromolecules. Thus, biological fluids are anything but ideal or dilute solutions. 

As with the first two editions, the book is organized into two parts I. Theory and Experimental Techniques and II. Experiments. Part I introduces students to theoretical and background material for the experiments. This part may also serve as a supplement for instructors who use their own experiments. In Part II there are 15 experiments that represent all areas of biochemistry, including working with proteins and nucleic acid isolation and characterization. The number of experiments has been reduced from earlier editions at the request of instructors and students who believed the book had more experiments than needed for a typical one-semester course. There are, however, still sufficient experiments for a two-semester course sequence. The reduction in the number of experiments has also been achieved by combining some experiments. 

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