Structure of amino acid sequence-reversed wtRop protein: insights from atomistic molecular dynamics simulations

Abstract

This study aims to the investigation of the advantages of designing new proteins presume upon a ‘bias’ sequence of amino acids, based on the reversed sequence of parent proteins, such as the retro ones. The structural simplicity of wtRop offers a very attractive model system to study these aspects. The current work is based on all-atom Molecular Dynamics (MD) simulations and corresponding experimental evidence on two different types of reversed wtRop protein, one with a fully reversed sequence of amino acids (rRop) and another with a partially reversed sequence (prRop), where only the five residues of the loop region (30ASP-34GLN) were not reversed. The exploration of the structure of the two retro proteins is performed highlighting the similarities and the differences with their parent protein, by employing various measures. Two models have been studied for both reversed proteins, a dimeric and a monomeric with the former one found to be more stable than the latter. Preferable equilibrium structures that the protein molecule can attain are explored, indicating the equilibration pathway. Simulation findings indicate a disruption of the α-helical structure and the appearance of additional secondary structures for both retro proteins. Reduced structural stability compared to their parent protein (wtRop) is also found. A corruption of the hydrophobic core is observed in the dimeric models. Furthermore, the simulations findings are consistent with the experimental characterization of prRop by circular dichroism spectroscopy (CD) which highlights an unstable, highly α-helical protein.

Communicated by Ramaswamy H. Sarma

Keywords:

• Retro proteins
• amino acid sequence
• heptad pattern
• protein folding
• molecular dynamics
• secondary structure

Acknowledgements

The authors would like to thank the support of this work by computational time granted from Greek Research & Technology Network (GRNET) in the National HPC facility—ARIS for the Project: Molecular Simulations and Free Energy Calculations of Proteins, MDMET. Support to A.K. through funding provided by the Hellenic Foundation for Research and Innovation (H.F.R.I.) in the framework of the OH-C_α project is acknowledged.

Authors contributions

Maria Arnittali: performed simulations, code development, and writing; Anastassia N. Rissanou: planned simulations, analysis methodology, discussions of results, writing, supervision; Vagelis Harmandaris: planned simulations, discussions of results, supervision; Aikaterini Kefala: performed experiments, discussions of experimental results. Michael Kokkinidis: Conceptualization, discussions of results, writing. All authors have read and agreed to the published version of the manuscript.

Consent for publication

All authors consent to submit the manuscript to the Journal of Biomolecular Structure and Dynamics.

Data availability statement

All the data and supplementary material can be made public after publication.

Ethical responsibilities

This manuscript is a core computational biology study, and the research does not involve humans or any other organism physically, so the ethical issues are not applicable.

Disclosure statement

No potential conflict of interest was reported by the authors.

Correction Statement

This article has been corrected with minor changes. These changes do not impact the academic content of the article.

Additional information

Funding

This research has received funding from the European Union’s Horizon 2020 research and innovation program under grant agreement No. 810660.