The Influence of Calcium toward Order/Disorder Conformation of Repeat-in-Toxin (RTX) Structure of Family I.3 Lipase from Pseudomonas fluorescens AMS8.

Nur Shidaa Mohd Ali,Thean Chor Leow,Abu Bakar Salleh,Mohd Shukuri Mohamad Ali,Raja Noor Zaliha Raja Abd Rahman

doi:10.3390/toxins12090579

Abstract

Calcium-binding plays a decisive role in the folding and stabilization of many RTX proteins, especially for the RTX domain. Although many studies have been conducted to prove the contribution of Ca2+ ion toward the folding and stabilization of RTX proteins, its functional dynamics and conformational structural changes remain elusive. Here, molecular docking and molecular dynamics (MD) simulations were performed to analyze the contribution of Ca2+ ion toward the folding and stabilization of the RTX lipase (AMS8 lipase) structure. AMS8 lipase contains six Ca2+ ions (Ca1–Ca6). Three Ca2+ ions (Ca3, Ca4, and Ca5) were bound to the RTX parallel β-roll motif repeat structure (RTX domain). The metal ion (Ca2+) docking analysis gives a high binding energy, especially for Ca4 and Ca5 which are tightly bound to the RTX domain. The function of each Ca2+ ion is further analyzed using the MD simulation. The removal of Ca3, Ca4, and Ca5 caused the AMS8 lipase structure to become unstable and unfolded. The results suggested that Ca3, Ca4, and Ca5 stabilized the RTX domain. In conclusion, Ca3, Ca4, and Ca5 play a crucial role in the folding and stabilization of the RTX domain, which sustain the integrity of the overall AMS8 lipase structure.

Highlights

Calcium-binding plays a decisive role in the folding and stabilization of many RTX proteins, especially for the RTX parallel β-roll motif repeat structure
The results suggested that Ca5 and Ca4 play a crucial role in the formation and folding of the RTX parallel β-roll motif repeat structure
The RTX parallel β-roll motif repeat structure plays a crucial role in the folding and stabilization of the RTX protein structure

Summary

Introduction

Calcium-binding plays a decisive role in the folding and stabilization of many RTX proteins, especially for the RTX parallel β-roll motif repeat structure. Disorder-to-order conformation plays a crucial role in the biological function of many proteins containing intrinsically disordered domains. This trait is exhibited by the repeat-in-toxin (RTX) protein family [1]. RTX proteins represent a broad and diverse family of pore-forming protein produced by various Gram-negative bacteria. Pseudomonas and Serratia produced RTX lipases of the I.3 subfamily. It contains glycine (G) and aspartate (D) nonapeptide repeats of the consensus sequence GGXGXDXUX (where X can be any amino acid and U represents hydrophobic residue) and involved with the binding of Ca2+ ions

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