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Dynamical contribution into enzyme catalytic efficiency

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  • Sitnitsky, A.E.

Abstract

A realistic physical model for the so-called rate-promoting vibration (RPV) at enzyme action is constructed. The origin of the RPV is assumed to be an oscillating electric field produced by long-lived localized vibrational modes in protein dynamics, namely, by the so-called discrete breather (DB) in secondary structure. The strength of interaction of the RPV with the reaction coordinate is evaluated and its effect on the reaction acceleration is assessed within the framework of modern theory for thermally activated escape rate at periodic driving. We reveal the phenomenon of resonant activation in our model elucidating why the frequency of the RPV in the range 100÷200cm-1 was chosen by the evolution of enzymes as an optimal one. The effect of the RPV on the reaction acceleration is shown to vary from moderate one (up to 103÷104) in the case of three-site DB to enormous (up to 106÷108) in the case of five-site DB and thus can significantly contribute into enzyme catalytic efficiency. Also the model is shown to be compatible with the known functional dependence of enzymatic reaction rates on solvent viscosity.

Suggested Citation

  • Sitnitsky, A.E., 2006. "Dynamical contribution into enzyme catalytic efficiency," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 371(2), pages 481-491.
    • Handle: RePEc:eee:phsmap:v:371:y:2006:i:2:p:481-491
    DOI: 10.1016/j.physa.2006.03.039
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    Cited by:

    1. Sitnitsky, A.E., 2008. "Solvent viscosity dependence for enzymatic reactions," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 387(22), pages 5483-5497.

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