Specific binding, to proteins

Without highly specific binding to proteins on the chip, thorough washing of the array may remove specific binders as well as non-specific binders. Protein bindings cannot offer a universal detection scheme like hybridization used in DNA arrays, which makes it difficult to discover enough probes for proteomics. 

It is important to realize however that these antisense molecules were not specifically targeted to the endothehum. Consequently, the contribution of the endothelial cells to the effects observed is unknown. Furthermore, in these studies adequate control experiments with mismatched ohgonucleotides are essential, since polyanionic agents such as antisense oligonucleotides can exert a broad range of non-specific antisense effects due to non-specific binding to proteins [117]. 

Sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) is one of the most important separation techniques for proteins. The addition of an anionic detergent, SDS, to the sample causes denaturation of proteins. Detergent donates the negative charge to the protein, which is proportional to the polypeptide chain length. SDS specifically binds to proteins in a mass ratio of 1.4 1. In this type of separation, migration rate of proteins exclusively depends on their molecular masses and not on other factors, listed previously. Such a system allows for the separation of molecules... 

Protems can be physisorbed or covalently attached to mica. Another method is to innnobilise and orient them by specific binding to receptor-fiinctionalized planar lipid bilayers supported on the mica sheets [15]. These surfaces are then brought into contact in an aqueous electrolyte solution, while the pH and the ionic strength are varied. Corresponding variations in the force-versus-distance curve allow conclusions about protein confomiation and interaction to be drawn [99]. The local electrostatic potential of protein-covered surfaces can hence be detemiined with an accuracy of 5 mV. 

A typical force curve showing the specific avidin-biotin interaction is depicted in figure Bl.20.10. The SFA revealed the strong influence of hydration forces and membrane undulation forces on the specific binding of proteins to membrane-bound receptors [81]. 

Food vitamin B 2 appears to bind to a saUvary transport protein referred to as the R-protein, R-binder, or haptocorrin. In the stomach, R-protein and the intrinsic factor competitively bind the vitamin. Release from the R-protein occurs in the small intestine by the action of pancreatic proteases, leading to specific binding to the intrinsic factor. The resultant complex is transported to the ileum where it is bound to a cell surface receptor and enters the intestinal cell. The vitamin is then freed from the intrinsic factor and bound to transcobalamin II in the enterocyte. The resulting complex enters the portal circulation. 

Figure 9.19 shows the sequence of the DNA that was used for the structure determination of the p53-DNA complex the bases involved in sequence-specific binding to the protein are shaded. One molecule of the DNA-bind-ing domain of p53 binds to the minor and the major grooves of the DNA making sequence-specific interactions with both strands (Figure 9.20). 

The subtilisin mutants described here illustrate the power of protein engineering as a tool to allow us to identify the specific roles of side chains in the catalytic mechanisms of enzymes. In Chapter 17 we shall discuss the utility of protein engineering in other contexts, such as design of novel proteins and the elucidation of the energetics of ligand binding to proteins. 

Oblimersen sodium is a DNA antisense oligonucleotide designed to specifically bind to human bcl-2 mRNA, resulting in catalytic degradation of bcl-2. This results in decreased translation of the protein Bcl-2, which is a cellular antiapoptotic protein. Thus, oblimersen enhances sensitivity to chemotherapy by shifting the intracellular balance to a state in which the cells are more likely to be killed by apoptosis. Currently, it is used in combination chemotherapy for treating advanced melanoma. 

In the cAMP-bound conformation, cAMP-GEFs specifically bind to Ras-like small GTPases and activate these proteins by profoundly accelerating the exchange of GDP for GTP. 

Conventional and novel PKC isozymes are potently activated by phorbol esters, heterocyclic compounds found in the milky sap exuded by plants of the Euphorbiaccae family. This sap was used medicinally as a counterirritant and cathartic agent over the millennia we now know that the active ingredients, phorbol esters, specifically bind to the Cl domain, the diacylglycerol sensor described above. In fact, their ability to recruit PKC to membranes is so effective that phorbol esters cause maximal activation of conventional PKCs, bypassing the requirement for Ca2+. This module is found in a number of other proteins in addition to PKC, so the profound effects of phorbol esters on cells are mediated by other proteins in addition to PKC. 

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