Conformation change, ligand

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 first chapter, on Conformational Dynamics, includes discussion of several rather recent computational approaches to treat the dominant slow modes of molecular dynamical systems. In the first paper, SCHULTEN and his group review the new field of steered molecular dynamics (SMD), in which large external forces are applied in order to be able to study unbinding of ligands and conformation changes on time scales accessible to MD... 

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. 

Equation 1.9 indicates that if the ligand has an equal affinity for both the Ri and Ra states (a = 1) then Poo/po will equal unity and no change in the proportion of Ra will result from maximal ligand binding. However, if a > 1, then the presence of the conformationally selective ligand will cause the ratio Poo/Po to be > 1 and the Ra state will be enriched by presence of the ligand. 

Natural or synthethic receptor ligands that induce a conformational change (active conformation) and a signal transduction process upon receptor binding. Agonists may act as typical hormones or neurotransmitters or they may confer paracrine functions, recognize bacterial, viral or other environmental constituents via activating their dedicated receptors. 

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