Interaction mechanisms binding sites

In general the relevance of predictions of structure-function relationships based on molecular modeling and structural bioinformatics are threefold. First they can be used to answer the question of which partners (proteins) could interact. Second, predictions generate new hypotheses about binding site, about molecular mechanisms of activation and interaction between two partners, and can lead to new ideas for pharmacological intervention. The third aim is to use the predictions for structure-based drug design. 

B. Studies of Equilibria and Reactions.—N.m.r. spectroscopy is being increasingly employed to study the mode and course of reactions. Thus n.m.r. has been used to unravel the mechanism of the reaction of phosphorus trichloride and ammonium chloride to give phosphazenes, and to follow the kinetics of alcoholysis of phosphoramidites. Its use in the study of the interaction of nucleotides and enzymes has obtained valuable information on binding sites and conformations and work on the line-widths of the P resonance has enabled the calculation of dissociation rate-constants and activation energies to be performed. 

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