Transient helicity in intrinsically disordered Axin-1 studied by NMR spectroscopy and molecular dynamics simulations

Rainer Bomblies,Martin Zacharias,Sandra Scanu,Tobias Madl,Manuel Patrick Luitz

doi:10.1371/journal.pone.0174337

Abstract

Many natural proteins are, as a whole or in part, intrinsically disordered. Frequently, such intrinsically disordered regions (IDRs) undergo a transition to a defined and often helical conformation upon binding to partner molecules. The intrinsic propensity of an IDR sequence to fold into a helical conformation already in the absence of a binding partner can have a decisive influence on the binding process and affinity. Using a combination of NMR spectroscopy and molecular dynamics (MD) simulations we have investigated the tendency of regions of Axin-1, an intrinsically disordered scaffolding protein of the WNT signaling pathway, to form helices in segments interacting with binding partners. Secondary chemical shifts from NMR measurements show an increased helical population in these regions. Systematic application of MD advanced sampling approaches on peptide segments of Axin-1 reproduces the experimentally observed tendency and allows insights into the distribution of segment conformations and free energies of helix formation. The results, however, were found to dependent on the force field water model. Recent water models specifically designed for IDRs significantly reduce the predicted helical content and do not improve the agreement with experiment.

Highlights

The structure–function paradigm of molecular biology, stating that every protein exerting a function requires one specific three-dimensional form, has been under revision since the turn of the century [1]
In this work we investigated the property of intrinsically disordered regions to contain transient helical population with molecular dynamics (MD) simulations and nuclear magnetic resonance (NMR) secondary chemical shifts
Simulations with the traditional TIP3P water model reproduced the trend of increased helicity in the binding regions quite well

Summary

Introduction

The structure–function paradigm of molecular biology, stating that every protein exerting a function requires one specific three-dimensional form, has been under revision since the turn of the century [1]. Evidence has accumulated that some active proteins do not adopt a single stable energy minimum at a folded structure but are intrinsically disordered in solution (intrinsically disordered proteins: IDPs) [2, 3]. Distinct sequence patterns predicted to form intrinsically disordered states in solution have been identified in genome sequences of many forms of life but are more abundant in highly evolved eukaryotes [4, 5]. About 15–45% of eukaryotic proteins have segments of significant disorder [6] where 30 or more consecutive.

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