Bound-ligand conformations

FIGURE 15.9 Monod-Wyman-Changeux (MWC) model for allosteric transitions. Consider a dimeric protein that can exist in either of two conformational states, R or T. Each subunit in the dimer has a binding site for substrate S and an allosteric effector site, F. The promoters are symmetrically related to one another in the protein, and symmetry is conserved regardless of the conformational state of the protein. The different states of the protein, with or without bound ligand, are linked to one another through the various equilibria. Thus, the relative population of protein molecules in the R or T state is a function of these equilibria and the concentration of the various ligands, substrate (S), and effectors (which bind at f- or Fj ). As [S] is increased, the T/R equilibrium shifts in favor of an increased proportion of R-conformers in the total population (that is, more protein molecules in the R conformational state). 

Fig. 8.3 Calculated conformational energy display values less than 2kcalmol ligands penalties of the protein-bound ligands 1-36. with five to eight rotors display values less The energy penalty increases with the number than 4kcalmol and ligands with eight to 11 of rotors. Ligands with one to four rotors rotors display values less than 6kcal mol. ...

Bostrom, J., Norrby, P.-O., Liljefors, T. Conformational energy penalties of protein-bound ligands. /. Comput.-Aided. Mol. Des. 1998, 12, 383-396. 

Due to the fact that cross-correlated relaxation depends linearly on the correlation time, it can be used to determine the conformation of ligands when bound to target molecules, provided that the off rate is fast enough to enable detection of the cross-correlated relaxation rate via the free ligand [33, 34]. The conditions under which such an experiment can be performed are similar to those found for transferred NOEs [35], and, for Kd values... 

CCR is easily measured by heteronuclear NMR experiments of isotopically labeled molecules. The information extracted from these experiments will significantly improve the resolution of NMR structures, especially bound conformations of weakly bound ligands, since /-couplings cannot be used in this case. The reason is the fact that the nonbound conformation significantly contributes to the averaged values of the coupling constant. 

Bostrom J. 2001. Reproducing the conformations of protein-bound ligands a critical evaluation of several popular conformational searching tools. J Comput Aided Mol Des 15(12) 1137-1152. 

Keywords STD-NMR CORCEMA-ST SICO Bound ligand conformation Structure-based drug design... 

Fig.1 CORCEMA-ST protocol for calculating STD-NMR intensities and for optimizing the bound-ligand conformation. Reprinted from [49] 2004, with permission from Elsevier...

In conclusion, using high-quality STD-NMR data on UDP-Gal weakly binding to 34 GalTl, we demonstrated that it is possible to refine the crystal structure (or any computer-docked structure in the proper orientation that serves as the starting structure) to obtain a global-minimum conformation for the bound ligand in solution. 

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