Proteins ligand-induced changes

Fradera X, De La Cruz X, Silva CH, et al. Ligand-induced changes in the binding sites of proteins. Bioinformatics 2002 18 939-948. 

The binding site of ligands on proteins can be mapped by either monitoring ligand induced changes in chemical shift of the amide groups or in their solvent exchange... 

Small changes in protein fluorescence resulting from ligand-induced changes [see (c) above] in the environment of tryptophans could be evidenced by the quenching in protein fluorescence of the ternary NAD... 

CD changes provide a convenient spectroscopic method for following protein-ligand interactions. CD bands arising from the ligand can be conveniently monitored in the visible and near-UV. Ligand-induced changes in tertiary and quaternary structure can be detected in the near-UV CD,... 

Van Aalten, D.M.F., Findlay, J.B.C., Amadei, A., Berendsen,H.J.C. Essential dynamics of the cellular retinol-binding protein. Evidence for ligand-induced conformational changes. Protein Engin. 8 (1995) 1129-1136. 

The elegant genetic studies by the group of Charles Yanofsky at Stanford University, conducted before the crystal structure was known, confirm this mechanism. The side chain of Ala 77, which is in the loop region of the helix-turn-helix motif, faces the cavity where tryptophan binds. When this side chain is replaced by the bulkier side chain of Val, the mutant repressor does not require tryptophan to be able to bind specifically to the operator DNA. The presence of a bulkier valine side chain at position 77 maintains the heads in an active conformation even in the absence of bound tryptophan. The crystal structure of this mutant repressor, in the absence of tryptophan, is basically the same as that of the wild-type repressor with tryptophan. This is an excellent example of how ligand-induced conformational changes can be mimicked by amino acid substitutions in the protein. 

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