The flexible nature of protein loops and the timescales of their dynamics are critical for many biologically important events at the molecular level, such as protein interaction and recognition processes. In order to obtain a predictive understanding of the dynamic properties of loops, we classify them into three types, namely fast loops with correlation times &lt; 10 ns, slow loops with correlation times between 10 ns and 500 ns, and loops that are static over the course of the whole trajectory based on the detailed comparison of experimental and predicted NMR chemical shifts and order parameters from 500 ns MD trajectories of 38 different proteins. Chemical and biophysical loop descriptors, such as amino-acid sequence, average 3D structure, charge distribution, hydrophobicity, and local contacts were used to develop and parameterize the algorithm for the prediction of the flexibility and motional timescale of every protein loop. The results demonstrate that loop dynamics with their timescales can be increasingly well predicted, which helps better understand the various roles of protein loops for protein-protein interactions during biomolecular recognition events.

Decoding the dynamics properties of protein loops by the combination of NMR and molecular dynamics simulations

249th National Meeting (2015)

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