Conformational change, mechanism

Figure 17. Molecular motor reverse conformational changes (mechanical energy) stimulated by oxidation or reduction of the polymeric chain, a) reduced chain b) oxidized chain.

FIGURE 16.5 Molecular motor Reverse conformational changes (mechanical energy) stimulated by oxidation or reduction of the polymeric chain in an electrolyte, (a) reduced chain, (b) oxidized chain. (From Otero, T.F., Modem Aspects of Electrochemistry, Kluwer Academic, New York, 1999. With permission.)... 

Figure 15.6 Suggested conformational change mechanism for the operation of transport proteins...

These conclusions are not final, because they may be affected by the mechanical constraints exerted by the surroundings may play a leading role in such conformational changes (mechanical embedding). More elaborated studies, including the whole of the protein in actual QM/M studies, are necessary to confirm or reject the latter proposal. 

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. 

A minimal mechanism for Na, K -ATPase postulates that the enzyme cycles between two principal conformations, denoted Ej and Eg (Figure 10.11). El has a high affinity for Na and ATP and is rapidly phosphorylated in the presence of Mg to form Ei-P, a state which contains three oeeluded Na ions (occluded in the sense that they are tightly bound and not easily dissociated from the enzyme in this conformation). A conformation change yields Eg-P, a form of the enzyme with relatively low affinity for Na, but a high affinity for K. This state presumably releases 3 Na ions and binds 2 ions on the outside of the cell. Dephosphorylation leaves EgKg, a form of the enzyme with two... 

The Coupling Mechanism ATP Hydrolysis Drives Conformation Changes in the Myosin Heads... 

FIGURE 17.23 The mechanism of skeletal muscle contraction. The free energy of ATP hydrolysis drives a conformational change in the myosin head, resulting in net movement of the myosin heads along the actin filament. Inset) A ribbon and space-filling representation of the actin—myosin interaction. (SI myosin image courtesy of Ivan Rayment and Hazel M. Holden, University of Wiseonsin, Madison.)... 

Another particularly unique aspect of allosteric mechanisms is that they can be very probe specific (i.e., a conformational change that is catastrophic for one receptor... 

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