Protein basic interactions

This experiment provides a nice example of the application of spectroscopy to biochemistry. After presenting the basic theory for the spectroscopic treatment of protein-ligand interactions, a procedure for characterizing the binding of methyl orange to bovine serum albumin is described. 

A few basic interactions are responsible for holding proteins together. The properties of water are intimately involved in these interactions. 

In metal-containing biological catalysts it is the protein matrix surrounding the metal centres that provides the unique environment for the Fe and Ni atoms which allows hydrogenases to function properly, selectively and effectively. Therefore, a major goal of hydrogenase basic research is to understand the protein-metal interaction. 

We need to have drugs, antidotes, and cures for the weapons of mass destruction that terrorists are likely to use. To develop medicinal countermeasures, the basic science involved must first be understood. For both chemical and biological weapons, the process of molecular recognition by elements of the human body is of utmost importance. However, we do not have a clear understanding of protein surface interactions, the relationship of genes to protein function, and how viruses infect and replicate. All of these processes are chemical in nature and caimot be solved without knowledge of the chemical sciences. 

Immunoprecipitation can be used to study protein-DNA interactions (Kuo and Allis 1999). For instance, the basic chromatin immunoprecipitation technique is remarkably versatile and has now been used in a wide range of cell types, including budding yeast, fly, and human cells. This technique has been successfully employed to map the boundaries of specifically modified (e.g., acetylated) histones along target... 

A situation that commonly occurs with food foams and emulsions is that there is a mixture of protein and low-molecular-weight surfactant available for adsorption at the interface. The composition and structure of the developing adsorbed layer are therefore strongly influenced by dynamic aspects of the competitive adsorption between protein and surfactant. This competitive adsorption in turn is influenced by the nature of the interfacial protein-protein and protein-surfactant interactions. At the most basic level, what drives this competition is that the surfactant-surface interaction is stronger than the interaction of the surface with the protein (or protein-surfactant complex) (Dickinson, 1998 Goff, 1997 Rodriguez Patino et al., 2007 Miller et al., 2008 Kotsmar et al., 2009). 

The induction of a change in one protein by interaction with another protein is a phenomenon that is met also in the construction of microtubules, ribosomes, cilia, and myofibrillar assemblies of muscle. It is basic to the assembly of the many labile but equally real cascade systems of protein-protein interactions such as that involved in the clotting of blood (Chapter 12) and signaling at membrane surfaces. 

In this chapter we introduced some of the basic principles that govern protein structure. The discussion of protein structures begun in this chapter is continued in many other chapters in this text in which we consider structures designed for specific purposes. In chapter 5 we examine the protein structures for two systems the protein that transports oxygen in the blood and the proteins that constitute muscle tissue. In chapters 8 and 9 we discuss structures of specific enzymes. In chapters 17 and 24 we consider proteins that interact with membranes. In chapters 30 and 31 we study regulatory proteins that interact with specific sites on the DNA. And finally, in supplement 3 we examine the structures of immuno-globin molecules. 

We assume that, after the protein has entered the proteasome, the protein-proteasome interaction is characterized by a spatially periodic asymmetric potential U(x) with the period P equal to the distance between amino adds in the protein. In reality there is a basic periodicity, namely the periodidty of the protein (or peptide) backbone, that is superposed by a nonperiodic (in our sense irregular) part that is attributed to the amino add-spedfic residues. Below we consider also the influence of the nonperiodic constituent. The spatial asymmetry results from breaking the symmetry by entering the proteasome from one end, as well as from the C — N asymmetry of the protein (or peptide) backbone. Figure 14.3 (left) plots several examples of such asymmetric periodic potential. The detailed form of the asymmetric periodic interaction potential is of less importance for this qualitative study. 

Although a few general guidelines exist, the design of such mentioned extraction schemes is still a trial-and-error proposition. Consequently, more basic information on the nature of the lipid -protein - surfactant interactions is still required. It should also be noted that in most instances, the micellar "extraction" step is merely the prelude to further fractionation (usually by electrophoretic, column or hydrophobic chromatographic techniques) and purification of the desired biological components (402-404). 

Cholesterol and membrane proteins, including structural ones such as glycophorin and myelin basic protein and functional ones such as -ATPase, bacteriorhodopsin, and cytochrome c, are important components of biological membranes. Cholesterol-lipid and a number of protein-lipid interactions have therefore been extensively investigated by vibrational spectroscopy. Interactions of hormones and toxins with phospholipid bilayers were also investigated. 

Understanding those components that influence the interfacial binding properties in protein/protein and protein/ligand interactions is of basic importance in protein chemistry. In this report, we have defined a system that should allow the dissection of those chemical properties that influence primary interactions via an evaluation of the transition-state thermodynamic components. 

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