Inherent backbone dynamics fine-tune the functional plasticity of Tudor domains

Ashish A Kawale,Björn M Burmann

doi:10.1016/j.str.2021.06.007

Abstract

Tudor domains are crucial for mediating a diversity of protein-protein or protein-DNA interactions involved in nucleic acid metabolism. Using solution NMR spectroscopy, we assess the comprehensive understanding of the dynamical properties of the respective Tudor domains from four different bacterial (Escherichia coli) proteins UvrD, Mfd, RfaH, and NusG involved in different aspects of bacterial transcription regulation and associated processes. These proteins are benchmarked to the canonical Tudor domain fold from the human SMN protein. The detailed analysis of protein backbone dynamics and subsequent analysis by the Lipari-Szabo model-free approach revealed subtle differences in motions of the amide-bond vector on both pico- to nanosecond and micro- to millisecond timescales. On these timescales, our comparative approach reveals the usefulness of discrete amplitudes of dynamics to discern the different functionalities for Tudor domains exhibiting promiscuous binding, including the metamorphic Tudor domain included in the study.

Highlights

Proteins, the fundamental building blocks of cellular life, exhibit a wide range of structural variations and are involved in a myriad of different cellular functions
A defining feature of the canonical Tudor domain is an aromatic cage formed by key aromatic residues to recognize covalent modifications of positively charged amino acid side chains, such as lysine or arginine residues, via cation-p interactions mediated through conserved aromatic residues (Botuyan and Mer, 2016; Cote and Richard, 2005)
Analysis of fast timescale backbone dynamics To achieve the required in-depth understanding of domain motions embedded in the Tudor domains of Survival motor neuron (SMN), NusG, Mfd, UvrD, and RfaH proteins, we measured the 15N relaxation parameters by using solution nuclear magnetic resonance (NMR) spectroscopy at two different static magnetic field strengths, 700 MHz (16.4 T) and 800 MHz (18.8 T), respectively, which were available for the current study

Summary

Introduction

The fundamental building blocks of cellular life, exhibit a wide range of structural variations and are involved in a myriad of different cellular functions. To understand the details underlying biological function, an in-depth understanding of the static three-dimensional structures together with the dynamic motions embedded within these biomolecules is mandatory. In this context, nuclear magnetic resonance (NMR) spectroscopy is an extremely powerful technique, playing a key role in discerning these inherent dynamical processes ranging from picosecond to second and minute regimes at atomic resolution under close to physiological conditions (Kovermann et al, 2016; Markwick et al, 2008). Recent studies point to a broader substrate specificity highlighting their involvement in a variety of nucleic acid and general protein-protein interactions (Bauer et al, 2019; Gao et al, 2019; Hossain et al, 2008)

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Discussion

Conclusion