Transition States: Substrate‐induced Conformational Transitions

Abstract

Substrate binding produces a variety of conformational changes in an enzyme that result in favourable substrate–protein interactions and influence catalysis in different ways. The altered form of the enzyme often appears to be more active in catalysis. A specific conformational change that continues into the transition state complex is the basis for substrate specificity.

Keywords: induced‐fit mechanism; transition state; substrate specificity; ground state destabilization; entropy of activation; concentrated protein motions; conformational dynamics

Figure 1.

The effect on free energy of substrate‐induced conformational change leading to enzymatic activation. The free energy of the enzyme–substrate ground state and transition state, and the free energy of the catalytic rate constant kcat and kcat/KM are indicated. Features of the low probability state E–S are shown in blue. (a) The substrate‐induced changes stabilize the ground state and transition state by an equal amount Δ. The free energy of kcat is uneffected, while that of kcat/KM is lowered and this rate increases. (b) The transition state is stabilized more than the ground state. The free energy of both kcat and kcat/KM is lowered, and both rates increase.

Figure 2.

Thermodynamic binding cycle to represent an induced‐fit process. In the physical process, the substrate S binds E and induces the change to the catalytically active form Eact. The energetically equivalent, albeit hypothetical, process factors out the conformational activation of the inactive enzyme E to the active form Eact with the equilibrium Kact << 1.0. This step is followed by S binding Eact with the dissociation constant KS.

Figure 3.

Schematic representation of a substrate‐induced fit that confers specificity because the specific changes in the enzyme E exist into the transition state. The enzyme structure in the transition state of the good substrate produces an optimum environment for catalysing the chemical step and has high catalytic efficiency. The enzyme form in the transition state for the poor substrate differs and solvates the bond making/bond breaking in the transition state less well. The chemical transformation is rate‐limiting for both substrates and occurs in the dark blue moiety of the good substrate. Binding of the poor substrate, which is the reactive fragment of the good substrate, induces a small closing of the enzyme active site. The change in E to form the optimum transition state environment requires the additional binding interactions of the light blue fragment.

close

References

Bernstein BE, Michels PAM and Hol WGJ (1997) Synergistic effects of substrate‐induced conformational changes in phosphoglycerate kinase activation. Nature (London) 385(6613): 275–278.

Fersht A (1985) Enzyme Structure and Mechanism. New York: WH Freeman.

Gerstein M, Lesk AM and Chothia C (1994) Structural mechanisms for domain movements in proteins. Biochemistry 33(22): 6739–6749.

Herschlag D (1988) The role of induced fit and conformational changes of enzymes in specificity and catalysis. Bioorganic Chemistry 16: 62–96.

Karplus M (2000) Aspects of protein reaction dynamics: deviations from simple behavior. Journal of Physical Chemistry B 104: 11–27.

Koshland DE Jr (1958) Application of a theory of enzyme specificity to protein synthesis. Proceedings of the National Academy of Sciences of the USA 44: 98–104.

Pompliano DL, Peyman A and Knowles JR (1990) Stabilization of a reaction intermediate as a catalytic device: definition of the functional role of the flexible loop in triosephosphate isomerase. Biochemistry 29(13): 3186–3194.

Post CB and Ray WJ Jr (1995) Reexamination of induced fit as a determinant of substrate specificity in enzymic reactions. Biochemistry 34(49): 15881–15885.

Radkiewicz JL and Brooks CL (2000) Protein dynamics in enzymatic catalysis: exploration of dihydrofolate reductase. Journal of the American Chemical Society 122(2): 225–231.

Ray WJ Jr and Long JW (1976) Thermodynamics and mechanism of the PO3 [phosphoester dianion] transfer process in the phosphoglucomutase reaction. Biochemistry 15(18): 3993–4006.

Taylor FR, Bixler SA, Budman JI et al. (1999) Induced fit activation mechanism of the exceptionally specific serine protease, complement Factor D. Biochemistry 38(9): 2849–2859.

Villa J and Warshel A (2001) Energetics and dynamics of enzymatic reactions. Journal of Physical Chemistry B 105(33): 7887–7907.

Young L and Post CB (1996) Catalysis by entropic guidance from enzymes. Biochemistry 35(48): 15129–15133.

Contact Editor close
Submit a note to the editor about this article by filling in the form below.

* Required Field

How to Cite close
Post, Carol B(May 2003) Transition States: Substrate‐induced Conformational Transitions. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1038/npg.els.0000604]