Conformational Ensembles from Experimental Data and Computer Simulations

Conformational Ensembles from Experimental Data and Computer Simulations

Poster Abstracts

108-POS Board 28 Should I Stay Or Should I Go – Integrating Molecular Dynamics Simulations and Biochemical Data Provides Insight into the Structural Basis of Biomolecular Decision Making Hans-Joachim Wieden 1,2 , Dylan Girodat 1,2 . 1 University of Lethbridge, Lethbridge, AB, Canada, 2 Alberta RNA Research and Training Institute, Lethbridge, AB, Canada. Gene expression strongly relies on the rapid and accurate responses of a large number of protein and ribonucleoprotein (RNP) complexes to a variety of inputs. Two examples for this are the RNA processing machinery and ribosome-dependent protein synthesis. Their critical role for survival of bacterial cells makes these processes promising targets for antibiotics. On this background, understanding the structural dynamics of the involved proteins and RNP complexes is pivotal for the development of novel antibiotic strategies that utilize the modulation of their structural dynamics. Here we report data from our recent work on RNaseE (1) and Elongation Factor Tu (2,3) using an approach that combines Molecular Dynamics (MD) simulations with experimental methods that provide mechanistic information derived from detailed kinetic studies using rapid-kinetics (stopped-flow), high-throughput biochemical assays, and next generation sequencing. Our findings explain how in RNaseE conformational dynamics contributes to the selection of the cleavage site two nucleotides downstream of a uracil (U +2 ), as well as to triggering its catalytic activity. Furthermore, we demonstrate how structural dynamics is utilized by P-loop GTPases such as Elongation Factor Tu to facilitate nucleotide selection and to fine- tune nucleotide binding properties. In line with the role that structural and conformational dynamics plays for the function of translational GTPases, we also have investigated, by developing computational methods that combine MD simulations with rapid kinetics data, how the conformational ensemble distribution targeted by different types of ligands can provide opportunities to modulate the functional characteristics of the respective biomolecular complex. (1) Chao, Y., et al. (2016) Mol. Cell 65(1): 39-51. (2) De Laurentiis, E.I., (2016) J. Biol. Chem. 291: 23136-48. (3) Mercier, E., et al. (2015) Sci. Rep. 5: 7677.

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