RESEARCH ARTICLE


Investigating the Conformation of S100β Protein Under Physiological Parameters Using Computational Modeling: A Clue for Rational Drug Design



Elvis K. Tiburu1, 3, *, Ibrahim Issah1, Mabel Darko1, Robert E. Armah-Sekum1, Stephen O. A. Gyampo1, Nadia K. Amoateng1, Samuel K. Kwofie1, 2, 3, Gordon Awandare2, 3
1 Department of Biomedical Engineering, College of Basic and Applied Sciences, University of Ghana, P. O. Box LG 25, Legon, Ghana
2 Department of Biochemistry, Cell and Molecular Biology, University of Ghana, P. O. Box LG 25, Legon, Ghana
3 West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, P. O. Box LG 25, Legon, Ghana


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© 2018 Tiburu et al.

open-access license: This is an open access article distributed under the terms of the Creative Commons Attribution 4.0 International Public License (CC-BY 4.0), a copy of which is available at: https://creativecommons.org/licenses/by/4.0/legalcode. This license permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

* Address correspondence to this author at the Department of Biomedical Engineering, College of Basic and Applied Sciences, University of Ghana, Legon, Ghana; Tel: +233559585194; E-mail: etiburu@ug.edu.gh


Abstract

Background:

Physiochemical factors such as temperature, pH and cofactors are well known parameters that confer conformational changes in a protein structure. With S100β protein being a metal binding brain-specific receptor for both extracellular and intracellular functions, a change in conformation due to the above-mentioned factors, can compromise their cellular functions and therefore result in several pathological conditions such as Alzheimer’s disease, Ischemic stroke, as well as Myocardial Infarction.

Objective:

The studies conducted sought to elucidate the effect of these physiological factors on the conformational dynamics of S100β protein using computational modeling approaches.

Method:

Temperature-dependent and protein-cofactor complexes molecular dynamics simulations were conducted by varying the temperature from 100 to 400K using GROMACS 5.0.3. Additionally, the conformational dynamics of the protein was studied by varying the pH at 5.0, 7.4 and 9.0 using Ambertools17. This was done by preparing the protein molecule, solvating and minimizing its energy level as well as heating it to the required temperature, equilibrating and simulating under desired conditions (NVT and NPT ensembles).

Results:

The results show that the protein misfolds as a function of increasing temperature with alpha helical content at 100K and 400K being 57.8% and 43.3%, respectively. However, the binding sites of the protein was not appreciably affected by temperature variations. The protein displayed high conformational instability in acidic medium (pH ~5.0). The binding sites of Ca2+, Mg2+ and Zn2+ were identified and each exhibited different groupings of the secondary structural elements (binding motifs). The secondary structure analysis revealed different conformational changes with the characteristic appearance of two beta hairpins in the presence of Zn2+and Mg2+.

Conclusion:

High temperatures, different cofactors and acidic pH confer conformational changes to the S100β structure and these results may inform the design of novel drugs against the protein.


Keywords: S100β Protein, Molecular Dynamics, Cofactors, Energy Minimization, Physiological Parameters, Alzheimer's.