Ligands receptor/ligand binding

In the case of liganded NRs, ligand binding is the first and ciucial molecular event that switches the function of these transcription factors from inactive to active state by inducing a conformational change in the LBD of the receptor (Fig. 1). This specific conformation allows the second step of NR activation that corresponds to the recruitment of coregulatoiy complexes, which contain chromatin-modifying enzymes required for transcription. The transcriptional coactivators are very diverse and have expanded to more than hundred in number. These include the pi 60 family of proteins,... 

To illustrate these methods, we consider the main biological problems that have motivated their development. The problems that have received the most attention are the receptor-ligand binding problem [12-16] and the calculation of proton binding affinities (pKa shifts) [17-20], The methods described can also be applied to many related problems, such as redox protein behavior, protein-protein association, protein folding, or membrane insertion. 

The study of receptor-ligand binding is one of the most important applications of free energy simulations [1]. To approach this problem theoretically, one must first partition the conformational space into bound and unbound states. There is no unique way to do this, but in practical situations there is often a natural choice. The equilibrium binding constant is... 

Figure 10.2 The GM-CSF receptor. Ligand binding appears to promote the phosphorylation of various cytoplasmic polypeptide substrates (at least in part via an associated JAK2), leading to signal transduction...

Armstrong, N., Sun,Y., Chen, G. Q. and Gouaux, E. Structure of a glutamate-receptor ligand-binding core in complex with kainate. Nature 395 913-917,1998. 

Gronemeyer, H. (2000) Nuclear receptor ligand-binding domains three-dimensional structures, molecular interactions and pharmacological implications. Trends in Pharmacological Sciences, 21, 381-388. 

B. and Willson, T.M. (2003) X-ray crystal structure of the liver X receptor (> ligand binding domain regulation by a histidine-tryptophan switch. The Journal of Biological Chemistry, 278, 27138-27143. 

Pandini, A., Denison, M.S., Song, Y., Soshilov, A.A. and Bonati, L. (2007) Structural and functional characterization of the aryl hydrocarbon receptor ligand binding domain by homology modeling and mutational analysis. Biochemistry, 46, 696-708. 

Affinity capillary electrophoresis (ACE), reviewed by Shimura and Kasai,42 is a method for studying receptor-ligand binding in free solution using CE. The technique depends upon a shift in the electrophoretic mobility of the receptor upon complexation with a charged ligand. Pure receptor preparations or accurate concentration values are not required because only migration times are measured. 

Sine SM, Wang HL, Bren NH. 2002. Lysine scanning mutagenesis delinates structural model of the nicotinic receptor ligand binding domain. J Biol Chem 277 29210-292... 

S. Chesla, P. Selvaraj, and C. Zhu Measuring Two-Dimensional Receptor-Ligand Binding Kinetics by Micropipette. Biophys. J. 75, 1553 (1998). 

Receptor-Ligand Binding Assay Drug Discovery ... 

Figure 14-1. Signaling via G protein-coupled receptors. Ligand binding to its cell-surface receptor initiates interaction of the receptor with the heterotrimeric G protein for which it is specific. A conformational change in the G protein brought about by binding of the ligand-receptor complex promotes exchange of GDP for GTP. The activated Gd-GTP dissociates from the Gp complex and both can interact with effectors, which carry on the signal to the mechanism that implements the cellular response.

Gestwicki JE, Cairo CW, Strong LE, Oetjen KA, Kiessling LL. Influencing receptor-ligand binding mechanisms with multivalent ligand architecture. J Am Chem Soc 2002 124 14922-14933. 

So S-S. and M. Karplus (1999). A comparative study of ligand-receptor complex binding affinity prediction methods based on glycogen phosphorylase inhibitors. Journal of Computer Aided Molecular Design 13 243-258. 

---