It Ligands

Both the AFM rupture experiments as well as our simulation studies focussed on the streptavidin-biotin complex as a model system for specific ligand binding. Streptavidin is a particularly well-studied protein and binds its ligand biotin with high affinity and specificity [51]. Whereas previous experiments (see references in Ref. [49]) and simulation studies [52] referred only to bound/unbound states and the associated kinetics, the recent AFM... 

In order to handle the stereochemistry by permutation groups, the molecule is separated at each stereocenter into a skeleton and its ligands (Figure 2-74). 

Figure 2-74. Basic stages for describing a stereoisomer by a permutation descriptor. At the stereocenter, the molecule is separated into the skeleton and its ligands. Both are then numbered independently, with the indices of the skeleton in italics, the indices of the ligands in bold.

The H2 Receptor and Its Ligands. The discovery of H2 receptors and antagonists occurred in 1972. This topic, including therapeutic implications, is considered in more detail elsewhere (see GASTROINTESTINAL AGENTS). 

The calculation of E] and X from computational methods is the focus here. Generally, the energetics of these quantities are separated into contributions from the inner and outer shells. For transfer between small molecules, the inner shell generally is defined as the entire solutes A and D, and the outer shell is generally defined as only the solvent. However, in a more practical approach for proteins, the inner shell is defined as only the redox site, which consists of the metal plus its ligands no further than atoms of the side chains that are directly coordinated to the metal, and the outer shell is defined as the rest of the protein plus the surrounding solvent. Thus... 

Bosanac I et al (2002) Structure of the inositol 1,4,5-trisphosphate receptor binding core in complex with its ligand. Nature 420 696-701... 

Signaling by PKC is terminated by concentrations of its ligands dropping to basal levels (i.e., Ca2+ and diacylglycerol) and by dephosphorylation of the three processing sites. Dephosphorylation is controlled, in part, by a recently discovered hydrophobic phosphorylation motif phosphatase. This phosphatase, PHLPP (for PH domain Leucine-rich repeat Protein Phosphatase) dephosphorylates conventional and novel PKC isozymes, initiating their downregulation. 

Limitations. Of the three methods, polarization has the lowest signal-to-noise ratio, and is most limited in its ligand concentration range. It works best when a significant fraction of the ligand is bound to the receptor. For FLPEP and cells the practical range is 0.5 to 3 njy (X L R). This method works best when free L is substantially depleted by the binding process. 

Fig. 11. FeMoco, its ligands, and some surrounding amino acids, mutagenesis of which causes changes in substrate specificity.

Ray P. Krishnamoorthy N. Ray A Emerging functions of c-kit and its ligand stem cell factor in dendritic cells regulators of T cell differentiation. Cell Cycle 2008 7 2826-2832. 

Complex ions, also called coordination complexes, have well-defined stoichiometries and structural arrangements. Usually, the formula of a coordination complex is enclosed in brackets to show that the metal and all its ligands form a single structural entity. When an ionic coordination complex is isolated from aqueous solution, the product is composed of the complex ion and enough counter-ions to give a neutral salt. In the chemical formula, the counter-ions are shown outside the brackets. Examples include the sulfate salt of [Ni (NH3)g, ... 

Aiuti A, Turchetto L, Cota M, Cipponi A, Brambilla A, Arcelloni C, Paroni R, Vicenzi E, Bordignon C, Poh G (1999) Human CD34(+) cells express CXCR4 and its ligand stromal cell-derived factor-1. Implications for infection by T-ceU tropic human immunodeficiency virus. Blood 94(l) 62-73... 

Xia M, Qin S, McNamara M, Mackay C, Hyman BT (1997) lnterleukin-8 receptor B immunore-activity in brain and neuritic plaques of Alzheimer s disease. Am J Pathol 150 1267-1274 Xia MQ, Bacskai BJ, Knowles RB, Qin SX, Hyman BT (2000) Expression of the chemokine receptor CXCR3 on neurons and the elevated expression of its ligand IP-10 in reactive astrocytes in vitro ERKl/2 activation and role in Alzheimer s disease. J Neuroimmunol 108 227-235 Xia MQ, Qin SX, Wu LJ, Mackay CR, Hyman BT (1998) Immunohistochemical study of the beta-chemokine receptors CCR3 and CCR5 and their Ugands in normal and Alzheimer s disease brains. Am J Pathol 153 31-37... 

Barbero S, Bajetto A, Bonavia R, Porcile C, Piccioli P, Pirani P, Ravetti JL, Zona G, Spaziante R, Florio T, Schettini G (2002) Expression of the chemokine receptor CXCR4 and its ligand stromal cell-derived factor 1 in human brain tumors and their involvement in glial proliferation in vitro. Ann NY Acad Sci 973 60-69... 

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