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Dynamics of a nonconserving Davydov monomer
1CCMAR and FCT, University of Algarve, Campus de Gambelas, 8000 Faro, Portugal.
Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics
|October 10, 2006
Summary
The Davydov-Scott model, explaining energy transfer in proteins, is extended to include conformational changes. This modified model accounts for excitation loss, enabling a more dynamic description of hydrogen bond dynamics in alpha helices.
Area of Science:
- Biophysics
- Protein Dynamics
- Molecular Excitation Transfer
Background:
- The Davydov-Scott model explains energy transfer along hydrogen-bonded chains in structures like alpha helices.
- Amide I excitations, potentially from ATP hydrolysis, are hypothesized to be created and sustained within these systems.
- Experimental data confirms amide I excitation persistence for picoseconds in proteins and model systems.
Purpose of the Study:
- To address the limitation of the Davydov-Scott model in describing energy conversion into work due to conserved excitation numbers.
- To develop a non-conserving generalization of the model to describe conformational changes in hydrogen-bonded systems.
- To investigate the time-dependent dynamics of hydrogen bonds adjacent to excitation sites.
Main Methods:
- A non-conserving generalization of the Davydov-Scott model was formulated.
- The model was analyzed to describe the contraction of hydrogen bonds near excitation sites.
- Time-averaged dynamical variables were considered to compare with existing Davydov-Scott model results.
Main Results:
- The generalized model describes a time-dependent contraction of hydrogen bonds adjacent to excitation sites.
- This contraction is a consequence of the non-conservation of excitations, unlike the standard Davydov-Scott model.
- Time-averaged results from the generalized model converge to the established Davydov-Scott model predictions.
Conclusions:
- The non-conserving model provides a more dynamic description of energy transfer and conformational changes in proteins.
- It offers insights into how sustained amide I excitations can lead to functional work, such as protein conformational changes.
- The study bridges the gap between energy transfer mechanisms and their functional consequences in biological systems.
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