Binding complementarity

The binding by cryptand 1 of the nonspherical ammonium eation was observed, but not surprisingly, the receptor-substrate binding complementarity is poor, and therefore. 

The complex presents a high degree of structural and binding complementarity between the guest NH4 and receptor (92). The NH4 is held inside the cavity by a tetrahedral array of hydrogen bonds and by... 

Desjarlais R L, R P Sheridan, G L Seibel, J S Dixon, ID Kuntz and R Venkataraghavan 1988. Using Shap Complementarity as an Initial Screen in Designing Ligands for a Receptor Binding Site of Know Three-Dimensional Structure. Journal of Medicinal Chemistry 31 722-729. 

Information may be stored in the architecture of the receptor, in its binding sites, and in the ligand layer surrounding the bound substrate such as specified in Table 1. It is read out at the rate of formation and dissociation of the receptor—substrate complex (14). The success of this approach to molecular recognition ties in estabUshing a precise complementarity between the associating partners, ie, optimal information content of a receptor with respect to a given substrate. 

Complementarity. To a first approximation, complementarity should take two forms (Fig. 1). Firstiy, the shape and size of the receptor cavity must complement the form of the substrate. Secondly, there must be a chemical complementarity between the binding groups lining the interior of the cavity and the external chemical features of the substrate (15). 

In conclusion, one important factor that contributes to the strong affinity of TBP proteins to TATA boxes is the large hydrophobic interaction area between them. Major distortions of the B-DNA structure cause the DNA to present a wide and shallow minor groove surface that is sterically complementary to the underside of the saddle structure of the TBP protein. The complementarity of these surfaces, and in addition the six specific hydrogen bonds between four side chains from TBP and four hydrogen bond acceptors from bases in the minor groove, are the main factors responsible for causing TBP to bind to TATA boxes 100,000-fold more readily than to a random DNA sequence. 

How do the mutations identified by phage display improve binding specificity There is as yet no direct stmctural information on the phage-selected inhibitors however they can be modeled using data from the crystal structures of other Kunitz domains bound to serine proteinases. These studies lead to the conclusion that the mutations identified by phage display improve binding specificity by maximizing complementarity between the... 

HIV Protease. Docking of the 3D structures of the Cambridge Structural Database into the HIV protease binding site, by shape and to some extent by chemical complementarity, was performed with an early version of the... 

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