Proteins
display a wealth of dynamical motions that can be probed
using both experiments and simulations. We present an approach to
integrate side-chain NMR relaxation measurements with molecular dynamics
simulations to study the structure and dynamics of these motions.
The approach, which we term ABSURDer (average block selection using
relaxation data with entropy restraints), can be used to find a set
of trajectories that are in agreement with relaxation measurements.
We apply the method to deuterium relaxation measurements in T4 lysozyme
and show how it can be used to integrate the accuracy of the NMR measurements
with the molecular models of protein dynamics afforded by the simulations.
We show how fitting of dynamic quantities leads to improved agreement
with static properties and highlight areas needed for further improvements
of the approach.
Proteins display a wealth of dynamical motions that can be probed using both experiments and simulations. We present an approach to integrate side chain NMR relaxation measurements with molecular dynamics simulations to study the structure and dynamics of these motions. The approach, which we term ABSURDer (Average Block Selection Using Relaxation Data with Entropy Restraints) can be used to find a set of trajectories that are in agreement with relaxation measurements. We apply the method to deuterium relaxation measurements in T4 lysozyme, and show how it can be used to integrate the accuracy of the NMR measurements with the molecular models of protein dynamics afforded by the simulations. We show how fitting of dynamic quantities leads to improved agreement with static properties, and highlight areas needed for further improvements of the approach.
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