Investigating the trade-off between folding and function in a multidomain Y-family DNA polymerase.

Xiakun Chu,Zucai Suo,Jin Wang

doi:10.7554/elife.60434

Abstract

The way in which multidomain proteins fold has been a puzzling question for decades. Until now, the mechanisms and functions of domain interactions involved in multidomain protein folding have been obscure. Here, we develop structure-based models to investigate the folding and DNA-binding processes of the multidomain Y-family DNA polymerase IV (DPO4). We uncover shifts in the folding mechanism among ordered domain-wise folding, backtracking folding, and cooperative folding, modulated by interdomain interactions. These lead to 'U-shaped' DPO4 folding kinetics. We characterize the effects of interdomain flexibility on the promotion of DPO4-DNA (un)binding, which probably contributes to the ability of DPO4 to bypass DNA lesions, which is a known biological role of Y-family polymerases. We suggest that the native topology of DPO4 leads to a trade-off between fast, stable folding and tight functional DNA binding. Our approach provides an effective way to quantitatively correlate the roles of protein interactions in conformational dynamics at the multidomain level.

Highlights

Our understanding of protein folding has been deepened by intensive experimental, theoretical, and computational studies focused on single-domain proteins or isolated domains of multidomain proteins (Jackson, 1998)
The essential assumption made by SBMs is that native contacts should determine the protein folding mechanism, which has been confirmed by allatom simulations (Best et al, 2013)
We investigate the effects of temperature on folding kinetics by analyzing kinetic simulations performed at a temperature 0:96Tf, which is the optimal temperature for growth of Sulfolobus solfataricus (Figure 2)

Summary

Introduction

Our understanding of protein folding has been deepened by intensive experimental, theoretical, and computational studies focused on single-domain proteins or isolated domains of multidomain proteins (Jackson, 1998). It is widely recognized that throughout all three kingdoms of life, proteins occur predominately in multidomain forms (Apic et al, 2001; Ekman et al, 2005). As their name indicates, multidomain proteins consist of more than one structural building unit, or domain (Teichmann et al, 1999). Multidomain proteins, which often possess significant domain interfaces, are more prone to aggregation during folding processes than single-domain proteins (Han et al, 2007; Borgia et al, 2011). A ‘divide-andconquer’ scenario has been proposed for in vitro multidomain protein folding, where all domains

Objectives

Methods

Results

Conclusion