Limited binding site

Fig. 3.5 Schematic flow-chart of antibody degradation by proteases combined with the protection by Fc-Rn in phagosomes. (1) IgG molecules are transported to the extracellular space (= interstitial fluid). (2) IgG molecules enter a cell by receptor-mediated endocytosis where the Fc region of the antibody is bound to the limited binding sites of Fc-Rn.

Thus, molecular recognition of poly(bola-amphiphile)s mainly depends on the structure of one limited binding site and not on the structure of the polymer as a whole. Consequently, the knowledge about molecular recognition of monomeric bola-amphiphiles can be brought forward to understand molecular recognition of polymeric bola-amphiphiles. 

With limited amount of Ab, the unlabeled antigen (analyte) competes with the labeled antigen Ag for limited binding sites. Bound fraction (AgAb) is separated from free (Ab), and the signal [Ag Ab] complex (the Ab fraction not occupied by the analyte) is measured. The amount of analyte is inversely proportional to the bound [Ag Ab] complex in a hyperbolic function as in Fig. 1. Methods for transforming or linearizing these functions are presented in the section on data reduction (Sec. V). 

It is not known whether magnesium pyrophosphate and the 3 -hydroxyl group of a nick in DNA share a common acceptor binding site of DNA ligase, in analogy to the acceptors in reactions (35a), (36a), and (37a) discussed above. It seems unlikely that a limited binding site could acconunodate such diverse ac-... 

Immunoassay techniques generally involve a competitive reaction between an analyte antigen and a standard antigen that has been tagged, for limited binding sites on the antibody to that antigen. The tag may be a radioactive tracer, an enzyme, or a fiuorophore. We describe below the immunoassay technique as well... 

Figure 7.7 Total tissue concentration as a function of free drug concentration. Total drug concentration (solid lines) and bound drug concentration (dashed lines) are shown for two different models of binding (a) linear binding with no saturation if = 0.5, Equation 7-27) and (b) binding with limited binding sites ( o = 10 M,...

Other nonlinear relationships are known in addition to nonlinear lipophilicity-activity relationships. Most common are nonlinear dependences on molar refractivity e.g. resulting from a limited binding site at the receptor for examples see chapter 7.1), but also other types of nonlinear relationships, e.g. with steric parameters, are frequently obtained. Even electronic parameters (eq. 48 chapter 3.5) or molecular weight terms (eq. 56 chapter 3.7) have been used in nonlinear equations. 

Radioisotope dilution assays are based on the principle of competition between radioactive labeled ( Co) vitamin B 2 and cobalamins extracted from matrices for binding sites on the intrinsic factor (a glycoprotein). Binding is in proportion to the concentration of the radioactive and nonradio active B 2 with the concentration of intrinsic factor as the limiting factor. Free cobalamins are separated from those bound on the intrinsic factor by absorption... 

In the elucidation of retention mechanisms, an advantage of using enantiomers as templates is that nonspecific binding, which affects both enantiomers equally, cancels out. Therefore the separation factor (a) uniquely reflects the contribution to binding from the enantioselectively imprinted sites. As an additional comparison the retention on the imprinted phase is compared with the retention on a nonimprinted reference phase. The efficiency of the separations is routinely characterized by estimating a number of theoretical plates (N), a resolution factor (R ) and a peak asymmetry factor (A ) [19]. These quantities are affected by the quality of the packing and mass transfer limitations, as well as of the amount and distribution of the binding sites. 

Cleavage occur s at the scissile bond. Residues in the substrate towards the N-terminus are numbered PI, P2, P3, etc, whereas residues towards the C-terminus are numbered PI, P2, P3 etc. Cleavage occurs between PI and P1. For a peptidase with limited specificity, only the residue in PI or PI is important for specificity. A peptidase with an extended substrate binding site will have a preference for residues in other positions. For example cathepsin L prefers substrates with phenylalanine in P2 and arginine in PI. However, this is a preference only, and cathepsin L cleaves substrates after other amino acids. Caspase-3 has a preference for Asp in both P4 and PI, but it is unusual for substrate specificity to extend much further from the scissile bond. The peptidase with the most extended substrate specificity may be mitochondrial intermediate peptidase that removes an octopeptide targeting signal from the N-terminus of cytoplasmically synthesized proteins that are destined for import into the mitochondrial lumen. 

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