Many proteins involved in regulation and binding events are either highly dynamic or intrinsically disordered.  One example of an intrinsically disordered domain whose binding to another protein is central to organismal function is the C-terminus of the nucleoprotein (N<sub>TAIL</sub>) of paramyxoviruses, which binds to the structured X-domain of the viral phosphoprotein in assembly of the viral replicative complex.  We have collected data from thiocyanate infrared probe groups located throughout the XD-binding region of N<sub>TAIL</sub>, and we are using a strategy of replica exchange molecular dynamics as well as short probe-included MD trajectories to constitute and then then directly compare a simulated ensemble to the spectroscopic data set, which in principle contains the entire conformational ensemble of the complex. Our experimental and simulation methodologies and the way that they are connected through vibrational frequency calculations will be discussed.

Conformational ensembles of viral protein complexes from molecular dynamics and vibrational probe data

256th National Meeting (2018)

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