Changes in conformational dynamics of basic side chains upon protein-DNA association.

B. Montgometry Pettitt,Alexandre Esadze,Chuanying Chen,Sourav Roy,Levani Zandarashvili,Junji Iwahara

doi:10.1093/nar/gkw531

B. Montgometry Pettitt, Alexandre Esadze + Show 4 more

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https://doi.org/10.1093/nar/gkw531

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Abstract

Basic side chains play major roles in recognition of nucleic acids by proteins. However, dynamic properties of these positively charged side chains are not well understood. In this work, we studied changes in conformational dynamics of basic side chains upon protein–DNA association for the zinc-finger protein Egr-1. By nuclear magnetic resonance (NMR) spectroscopy, we characterized the dynamics of all side-chain cationic groups in the free protein and in the complex with target DNA. Our NMR order parameters indicate that the arginine guanidino groups interacting with DNA bases are strongly immobilized, forming rigid interfaces. Despite the strong short-range electrostatic interactions, the majority of the basic side chains interacting with the DNA phosphates exhibited high mobility, forming dynamic interfaces. In particular, the lysine side-chain amino groups exhibited only small changes in the order parameters upon DNA-binding. We found a similar trend in the molecular dynamics (MD) simulations for the free Egr-1 and the Egr-1–DNA complex. Using the MD trajectories, we also analyzed side-chain conformational entropy. The interfacial arginine side chains exhibited substantial entropic loss upon binding to DNA, whereas the interfacial lysine side chains showed relatively small changes in conformational entropy. These data illustrate different dynamic characteristics of the interfacial arginine and lysine side chains.

Highlights

Table S1. 15N NMR relaxation data for the Arg side-chain Nε-Hε groups of the free Egr-1 protein at 25 ̊C
Corresponding 15N relaxation data for the Lys NH3+ groups of the Egr-1–DNA complex at 10 ̊C were reported in our previous paper: Chen et al [2015] J Phys Chem Lett 6, 2733-7
A SB contact is defined as a state with the distance between two charged atoms being less than 2.8 Å

Summary

Introduction

Table S1. 15N NMR relaxation data for the Arg side-chain Nε-Hε groups of the free Egr-1 protein at 25 ̊C. 15N NMR relaxation data for the Arg side-chain Nε-Hε groups of the free Egr-1 protein at 25 ̊C. 15N NMR relaxation data for Lys side-chain NH3+ groups of the free Egr-1 protein at 5 ̊C. Corresponding 15N relaxation data for the Lys NH3+ groups of the Egr-1–DNA complex at 10 ̊C were reported in our previous paper: Chen et al [2015] J Phys Chem Lett 6, 2733-7.

Results

Conclusion