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Article

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

1
Institute of Applied and Computational Mathematics (IACM), Foundation for Research and Technology Hellas (FORTH), IACM/FORTH, GR-71110 Heraklion, Crete, Greece
2
Department of Mathematics and Applied Mathematics, University of Crete, GR-71409 Heraklion, Crete, Greece
3
Department of Biology, University of Crete, GR-71409 Heraklion, Crete, Greece
4
Institute of Molecular Biology and Biotechnology, Foundation of Research and Technology, GR-70013 Heraklion, Crete, Greece
5
Computation-Based Science and Technology Research Center, The Cyprus Institute, 2121 Nicosia, Cyprus
*
Author to whom correspondence should be addressed.
Academic Editor: David Pérahia
Int. J. Mol. Sci. 2021, 22(11), 5931; https://doi.org/10.3390/ijms22115931
Received: 23 April 2021 / Revised: 23 May 2021 / Accepted: 25 May 2021 / Published: 31 May 2021
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. View Full-Text
Keywords: biomolecules; Rop; RM6; proteins; molecular dynamics simulations; mutations; thermostability; secondary structure biomolecules; Rop; RM6; proteins; molecular dynamics simulations; mutations; thermostability; secondary structure
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MDPI and ACS Style

Arnittali, M.; Rissanou, A.N.; Amprazi, M.; Kokkinidis, M.; Harmandaris, V. Structure and Thermal Stability of wtRop and RM6 Proteins through All-Atom Molecular Dynamics Simulations and Experiments. Int. J. Mol. Sci. 2021, 22, 5931. https://doi.org/10.3390/ijms22115931

AMA Style

Arnittali M, Rissanou AN, Amprazi M, Kokkinidis M, Harmandaris V. Structure and Thermal Stability of wtRop and RM6 Proteins through All-Atom Molecular Dynamics Simulations and Experiments. International Journal of Molecular Sciences. 2021; 22(11):5931. https://doi.org/10.3390/ijms22115931

Chicago/Turabian Style

Arnittali, Maria, Anastassia N. Rissanou, Maria Amprazi, Michael Kokkinidis, and Vagelis Harmandaris. 2021. "Structure and Thermal Stability of wtRop and RM6 Proteins through All-Atom Molecular Dynamics Simulations and Experiments" International Journal of Molecular Sciences 22, no. 11: 5931. https://doi.org/10.3390/ijms22115931

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