Indirect recognition

Jones DA Takemoto D (2004) Plant innate immunity direct and indirect recognition of general and specific pathogen-associated molecules. Curr Opin Immunol 16 48-62... 

Indirect recognition The DNA sequence can predetermine a particular conformation, which is a prerequisite for specific protein binding. Alternative DNA conformations will not be boimd and recognized. We speak here of an indirect recognition of a sequence ... 

N. Inohara and G. Nunez, TSfods intracellular proteins involved in inflammation and apoptosis, Nature Reviews Immunology, 3, 2003, 371-82 D. A. Jones and D. Takemoto, Plant innate immunity - direct and indirect recognition of general and specific pathogen-associated molecules, Current Opinion in Immunology, 16, 2004, 48-62. 

Also on the nucleic acid field, it has been shown95 that the distribution pattern of NH2/NH3 + /OH groups in natural aminoglycosides could indirectly influence their RNA binding properties and therefore their antibiotic functions. Indeed, the number and location of these polar groups is essential to modulate the conformation and dynamics of the glycoside with the concomitant implication for the RNA recognition process. 

Chiral separation of drng molecules and of their precursors, in the case of synthesis of enantiomerically pure drugs, is one of the important application areas of HPLC in pharmaceutical analysis. Besides HPLC, capillary electrophoresis (CE) is another technique of choice for chiral separations. Chapter 18 provides an overview of the different modes (e.g., direct and indirect ones) of obtaining a chiral separation in HPLC and CE. The direct approaches, i.e., those where the compound of interest is not derivatized prior to separation, are discussed in more detail since they are cnrrently the most frequently used techniques. These approaches require the use of the so-called chiral selectors to enable enantioselective recognition and enantiomeric separation. Many different molecnles have been nsed as chiral selectors, both in HPLC and CE. They can be classified into three different groups, based on their... 

Several recent and often sophisticated methods allow to make measurements of interfaciai recognition. These methods, performed either on Langmuir-Blodgett (LB) films or on vesicles allow the direct or indirect measurement of the binding... 

The contact between protein and DNA can also be transmitted via boimd water molecules. In the crystal structure of the complex of the bacterial Trp-repressor and the cognate operator sequence are foimd only a few direct H-bonds between the amino acid residues of the protein and the bases of the recognition sequence. Rather, the contacts between protein and nucleic acid are frequently established indirectly by a chain of well-defined bound water molecules which contact the protein and the bases, and thereby function as transmitter between the protein and DNA. 

While there is usually only one El enzyme, many species of E2 proteins and multiple families of E3 enzymes or E3 multiprotein complexes exist. Selection of substrates for ubiquitin-ligation occurs mainly by specific E3 enzymes which target substrate proteins that contain specific recognition signals (fig. 2.15B). E3 enzymes also can bind indirectly to the substrate, via an adaptor protein. 

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