Conformational Ensembles from Experimental Data and Computer Simulations

Conformational Ensembles from Experimental Data and Computer Simulations

Poster Abstracts

59-POS Board 19 Constructing Ensembles Using Site-Specific Vibrational Spectroscopy Probe Groups Casey H. Londergan , Rosalind J. Xu, Kristen L. Kelly, Shannon R. Dalton, Alice R. Vienneau, Daniel M. Konstantinovsky. Haverford College, Haverford, PA, USA. Vibrational spectroscopy has an inherent advantage over other experimental techniques for ensemble determination due to its very fast intrinsic time scale (10s of fs to a few ps), which means that protein conformational changes are in slow exchange in vibrational spectra and the full conformational distribution is thus present in some form in the spectrum. A recently popularized approach uses functional groups with unique vibrational frequencies (i.e. the CN stretch of nitriles) as reporters of the environment around specific sites in proteins. The infrared or Raman lineshapes of these probe groups contain the local structural distribution, and the fast intrinsic time scale also means that there is a direct match between the decay times of the vibrational correlation functions and the time steps in all-atom molecular dynamics simulations. We have placed the SCN vibrational probe group into several proteins, including model peptides, alpha synuclein, calmodulin, and fuzzy viral complexes. The SCN group in particular is surprisingly non-perturbative in most cases and this lack of perturbation suggests that it could be placed in many systems, including directly along protein-protein and protein-membrane binding interfaces. Our extensive experimental data provides new and previously unreported information about the range of environments around specific sites in these proteins, especially about the dynamic structures of bound protein-protein and protein-membrane complexes. We have also performed initial molecular dynamics simulations intended to provide an interpretive guide to the data, and it appears that there is at least semi-quantitative agreement between simulated probe solvent exposure distributions and the CN frequencies and lineshapes of the SCN group. While there are current challenges associated with making a direct connection between vibrational probe data and simulations, this general two-pronged strategy is a promising new methodology for determining and representing protein ensembles.

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