Ligand binding conformational changes

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. 

Frimurer TM, Peters GH, Iversen LF, Andersen HS, Moller NP, et al. 2003. Ligand-induced conformational changes improved predictions of ligand binding conformations and affinities. Biophys J 84(4) 2273-2281. 

Computer-based techniques for locating and analyzing ligand binding sites on macromolecules. These methods must take into account the steric and electrostatic properties of ligand and receptor as well as ligand-induced conformational changes. 

Ligand Binding Cooperativity Koshland-Nemethy-Filmer Model Scatchard Equation Ligand-Induced Conformational Change... 

Fluorescence spectroscopy S Conformational change with ligand binding induces change in fluorescence properties of intrinsic or extrinsic fluorophore... 

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