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Front. Mol. Biosci. | doi: 10.3389/fmolb.2018.00115

Why The Energy Landscape of Barnase is Hierarchical

Maya J. Pandyaa1, Stefanie Schiffers1, Andrea M. Hounslow1, Nicola J. Baxter1 and  Mike P. Williamson1, 2*
  • 1Department of Molecular Biology and Biotechnology, University of Sheffield, United Kingdom
  • 2University of Sheffield, United Kingdom

We have used NMR and computational methods to characterize the dynamics of the ribonuclease barnase over a wide range of timescales in free and inhibitor-bound states. Using temperature- and denaturant-dependent measurements of chemical shift, we show that barnase undergoes frequent and highly populated hinge bending. Using relaxation dispersion, we characterize a slower and less populated motion with a rate of 750 ± 200 s-1, involving residues around the lip of the active site, which occurs in both free and bound states and therefore suggests conformational selection. Normal mode calculations characterize correlated hinge bending motions on a very rapid timescale. These three measurements are combined with previous measurements and molecular dynamics calculations on barnase to characterize its dynamic landscape on timescales from picoseconds to milliseconds and length scales from 0.1 to 2.5 nm. We show that barnase has two different large-scale fluctuations: one on a timescale of 10-9 to 10-6 s that has no free energy barrier and is a hinge bending that is determined by the architecture of the protein; and one on a timescale of milliseconds (ie 750 s-1) that has a significant free energy barrier and starts from a partially hinge-bent conformation. These two motions can be described as hierarchical, in that the more highly populated faster motion provides a platform for the slower (less probable) motion. The implications are discussed. The use of temperature and denaturant is suggested as a simple and general way to characterize motions on the intermediate ns-us timescale.

Keywords: protein dynamics, nuclear magnetic resonance (NMR), biophysics, structural biology, molecular dynamics, conformational selection, relaxation dispersion, Protein dynamic, NMR, Biophysics, Structural Biology, molecular dynamics, Conformational selection, relaxation dispersion

Received: 27 Aug 2018; Accepted: 07 Dec 2018.

Edited by:

Piero A. Temussi, University of Naples Federico II, Italy

Reviewed by:

Alfonso De Simone, Imperial College London, United Kingdom
Gian Gaetano Tartaglia, Catalan Institution for Research and Advanced Studies, Spain  

Copyright: © 2018 Pandyaa, Schiffers, Hounslow, Baxter and Williamson. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence: Prof. Mike P. Williamson, University of Sheffield, Sheffield, United Kingdom, m.williamson@sheffield.ac.uk