Developing a Protocol for Ensemble and Vibrational Probe-Containing Molecular Dynamics Simulations of the Nipah Ntail-XD Complex

Abstract

Intrinsically disordered proteins (IDPs) prove difficult to characterize using typical protein secondary structure indicators, such as CD and NMR spectroscopy, because of their dynamic nature. Molecular Dynamics (MD) simulations can be adapted for use in highly dynamic systems such as IDPs through enhanced sampling techniques. This project involves the characterization of the “fuzzy” Nipah Virus nucleo- and phosphoprotein bound complex by using MD simulations and vibrational probes. In order to run MD simulations on IDPs, a viable structural ensemble must be generated; this can be done by varying the simulation temperature to overcome energy boundaries and exchanging high-energy structures with those generated at low temperature (“replica exchange”). Once an ensemble of structures is generated, shorter simulations can be run in which a site-specific thiocyanate probe is incorporated into each structure. Eventually, an infrared (IR) lineshape can be simulated from the conformational ensemble for each label site and directly compared to experimental data. Progress towards each step of this multi-step simulation protocol will be discussed, as well as the prospects for a hybrid spectroscopic-theoretical determination of the conformational distribution of “fuzzy” bound complexes.