Abstract
The stochastic energy transition of peptide-bond (PB) in enzyme-substrate-complex (ESC) is investigated. By introducing a coupled Pippard system and thermal fluctuation as the noise, the two important mechanisms of enhancing PB breaking rate, i.e., the Fermi resonance and the reduction of potential barrier height are studied. The necessary frequency ratio 1:2 for Fermi resonance is verified by using the deterministic averaging method. With the noise terms present, the average energy transition rate of PB is predicted by using the stochastic averaging method. The comparison of the analytical results and Monte Carlo simulation results shows that the stochastic averaging method is promising for predicting the PB breaking rate. A preliminary work to investigate the possible influence of the oxygen ion on the PB is presented. The Morse potential model is introduced to describe the potential landscape of the oxygen ion oscillator, which is coupled with the Pippard system. Monte Carlo simulation results for PB energy transition rate are obtained for the coupled system, and they agree well with the theoretical results in the range of low potential barrier.
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Deng, M.L., Zhu, W.Q. (2011). Energy Transition Rate at Peptide-Bond Using Stochastic Averaging Method. In: Zhu, W.Q., Lin, Y.K., Cai, G.Q. (eds) IUTAM Symposium on Nonlinear Stochastic Dynamics and Control. IUTAM Bookseries, vol 29. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-0732-0_2
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DOI: https://doi.org/10.1007/978-94-007-0732-0_2
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