Abstract
A realistic model for the potential energy for the diffusion of N-H vectors in a protein is proposed, massively modifying the simplistic models currently used in the literature. In particular, a quantitative and analytical connection between the order parameter of the N-H vector diffusion in a protein and the number of potential minima is established, offering a significant insight into the longstanding question of how protein dynamics is affected by the potential-energy landscape. The largest number of potential minima in a protein is estimated to be no more than around 25. In addition, the conformational entropies derived from classical statistical mechanics and quantum statistical mechanics are proved to be identical. Based on the presented theoretical formula, the number of potential minima for each residue of five representative proteins is evaluated and shows a good correlation between local structural flexibility and the number of potential minima.
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