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arXiv · 1001.3540

Local transition gradients determine the global attributes of protein energy landscapes

Francesco Rao
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Abstract

The dynamical characterization of proteins is crucial to understand protein function. From a microscopic point of view, protein dynamics is governed by the local atomic interactions that, in turn, trigger the functional conformational changes. Unfortunately, the relationship between local atomic fluctuations and global protein rearrangements is still elusive. Here, atomistic molecular dynamics simulations in conjunction with complex network analysis show that fast peptide relaxations effectively build the backbone of the global free-energy landscape, providing a connection between local and global atomic rearrangements. A minimum-spanning-tree representation, built on the base of transition gradients networks, results in a high resolution mapping of the system dynamics and thermodynamics without requiring any a priori knowledge of the relevant degrees of freedom. These results suggest the presence of a local mechanism for the high communication efficiency generally observed in complex systems.

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Francesco Rao. 2010-01-20. Local transition gradients determine the global attributes of protein energy landscapes. https://arxiv.org/abs/1001.3540

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