Structure and Thermal Stability of wtRop and RM6 Proteins through All-Atom Molecular Dynamics Simulations and Experiments

Maria Arnittali,Vagelis Harmandaris,Anastassia N. Rissanou,Michael Kokkinidis,Maria Amprazi

doi:10.3390/ijms22115931

Abstract

In the current work we study, via molecular simulations and experiments, the folding and stability of proteins from the tertiary motif of 4-α-helical bundles, a recurrent motif consisting of four amphipathic α-helices packed in a parallel or antiparallel fashion. The focus is on the role of the loop region in the structure and the properties of the wild-type Rop (wtRop) and RM6 proteins, exploring the key factors which can affect them, through all-atom molecular dynamics (MD) simulations and supporting by experimental findings. A detailed investigation of structural and conformational properties of wtRop and its RM6 loopless mutation is presented, which display different physical characteristics even in their native states. Then, the thermal stability of both proteins is explored showing RM6 as more thermostable than wtRop through all studied measures. Deviations from native structures are detected mostly in tails and loop regions and most flexible residues are indicated. Decrease of hydrogen bonds with the increase of temperature is observed, as well as reduction of hydrophobic contacts in both proteins. Experimental data from circular dichroism spectroscopy (CD), are also presented, highlighting the effect of temperature on the structural integrity of wtRop and RM6. The central goal of this study is to explore on the atomic level how a protein mutation can cause major changes in its physical properties, like its structural stability.

Highlights

Engineering functional materials at the nanometer scale is a fundamental challenge for nanotechnology [1]
The results reveal a decrease in the number of HBs within the protein molecule by raising the temperature for both proteins
A detailed investigation of structural conformational and physicochemical properties of wild-type repressor of primer (Rop) (wtRop) and its RM6 mutation is presented in the current study

Summary

Introduction

Engineering functional materials at the nanometer scale is a fundamental challenge for nanotechnology [1]. Protein folding is linked to a number of different problems including: (i) the thermodynamic balance of intra and intermolecular forces that dictate protein structure for a given amino acid sequence [3]; (ii) the predictability of protein structure from its amino acid sequence, and (iii) the accessible folding pathways that give rise to the observed folding rates of proteins In view of these complex issues, selected recurrent motifs of protein structure have been frequently used as convenient model systems, which lend themselves, both for understanding aspects of protein folding and stability, and for the development of rational protein design methods for bio-inspired materials. Simulations using all-atom models provide atomistic details in the predicted conformational changes resulting from, e.g., the introduction of mutations or changes in the protein environment (i.e., temperature, pH), etc

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Conclusion