Complete relaxation and conformational exchange matrix (CORCEMA) analysis of intermolecular saturation transfer effects in reversibly forming ligand-receptor complexes.
A couple of recent applications of intermolecular NOE (INOE) experiments as applied to biomolecular systems involve the (i) saturation transfer difference NMR (STD-NMR) method and (ii) the intermolecular cross-saturation NMR (ICS-NMR) experiment. STD-NMR is a promising tool for rapid screening of a large library of compounds to identify bioactive ligands binding to a target protein. Additionally, it is also useful in mapping the binding epitopes presented by a bioactive ligand to its target protein. In this latter application, the STD-NMR technique is essentially similar to the ICS-NMR experiment, which is used to map protein-protein or protein-nucleic acid contact surfaces in complexes. In this work, we present a complete relaxation and conformational exchange matrix (CORCEMA) theory (H. N. B. Moseley et al., J. Magn. Reson. B 108, 243-261 (1995)) applicable for these two closely related experiments. As in our previous work, we show that when exchange is fast on the relaxation rate scale, a simplified CORCEMA theory can be formulated using a generalized average relaxation rate matrix. Its range of validity is established by comparing its predictions with those of the exact CORCEMA theory which is valid for all exchange rates. Using some ideal model systems we have analyzed the factors that influence the ligand proton intensity changes when the resonances from some protons on the receptor protein are saturated. The results show that the intensity changes in the ligand signals in an intermolecular NOE experiment are very much dependent upon: (1) the saturation time, (2) the location of the saturated receptor protons with respect to the ligand protons, (3) the conformation of the ligand-receptor interface, (4) the rotational correlation times for the molecular species, (5) the kinetics of the reversibly forming complex, and (6) the ligand/receptor ratio. As an example of a typical application of the STD-NMR experiment we have also simulated the STD effects for a hypothetical trisaccharide bound to a protein. The CORCEMA theory for INOE and the associated algorithm are useful in a quantitative interpretation of the intensity changes in the ligand in both the STD-NMR and ICS-NMR, provided the identity of the receptor protons experiencing direct RF saturation is known. The formalism presented here is likely to be useful in the design of bioactive ligands to a specific target protein and in the quantitative mapping of binding epitopes and interfaces between molecules in complexes.
Jayalakshmi
V
V
Department of Biochemistry and Molecular Genetics, NMR Core Facility, Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, Alabama 35294-2041, USA.
Krishna
N Rama
NR
D000465:Algorithms; D001665:Binding Sites; D002352:Carrier Proteins / Q000737:chemistry*; D037222:Collectins; D003198:Computer Simulation; D008024:Ligands; D046911:Macromolecular Substances; D008956:Models, Chemical; D015394:Molecular Structure; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods*; D011522:Protons; D014312:Trisaccharides / Q000737:chemistry*
D002352:Carrier Proteins; D037222:Collectins; D008024:Ligands; D046911:Macromolecular Substances; D011522:Protons; D014312:Trisaccharides