Conformational Ensembles from Experimental Data and Computer Simulations

Conformational Ensembles from Experimental Data

and Computer Simulations

Poster Abstracts

145

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

University of Lethbridge, Lethbridge, AB, Canada,

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

), 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.