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Open AccessArticle

Understanding Calcium-Dependent Conformational Changes in S100A1 Protein: A Combination of Molecular Dynamics and Gene Expression Study in Skeletal Muscle

1
Department of Bioengineering, University of Information Science and Technology, St. Paul The Apostle, Ohrid-6000, North Macedonia
2
Department of Medical Biotechnology, Yeungnam University, Gyeongsan 38541, Korea
3
Department of Obstetrics and Gynaecology, Vardhman Mahavir Medical College and Safdarjang Hospital, New Delhi-110029, India
*
Authors to whom correspondence should be addressed.
These authors contributed equally to this work.
Cells 2020, 9(1), 181; https://doi.org/10.3390/cells9010181 (registering DOI)
Received: 25 December 2019 / Revised: 8 January 2020 / Accepted: 8 January 2020 / Published: 10 January 2020
(This article belongs to the Special Issue Bioinformatics and Computational Biology 2019)
The S100A1 protein, involved in various physiological activities through the binding of calcium ions (Ca2+), participates in several protein-protein interaction (PPI) events after Ca2+-dependent activation. The present work investigates Ca2+-dependent conformational changes in the helix-EF hand-helix using the molecular dynamics (MD) simulation approach that facilitates the understanding of Ca2+-dependent structural and dynamic distinctions between the apo and holo forms of the protein. Furthermore, the process of ion binding by inserting Ca2+ into the bulk of the apo structure was simulated by molecular dynamics. Expectations of the simulation were demonstrated using cluster analysis and a variety of structural metrics, such as interhelical angle estimation, solvent accessible surface area, hydrogen bond analysis, and contact analysis. Ca2+ triggered a rise in the interhelical angles of S100A1 on the binding site and solvent accessible surface area. Significant configurational regulations were observed in the holo protein. The findings would contribute to understanding the molecular basis of the association of Ca2+ with the S100A1 protein, which may be an appropriate study to understand the Ca2+-mediated conformational changes in the protein target. In addition, we investigated the expression profile of S100A1 in myoblast differentiation and muscle regeneration. These data showed that S100A1 is expressed in skeletal muscles. However, the expression decreases with time during the process of myoblast differentiation. View Full-Text
Keywords: calcium-binding protein; protein-protein interaction; entry of free calcium ions; molecular dynamics; cell culture calcium-binding protein; protein-protein interaction; entry of free calcium ions; molecular dynamics; cell culture
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Chaturvedi, N.; Ahmad, K.; Yadav, B.S.; Lee, E.J.; Sonkar, S.C.; Marina, N.; Choi, I. Understanding Calcium-Dependent Conformational Changes in S100A1 Protein: A Combination of Molecular Dynamics and Gene Expression Study in Skeletal Muscle. Cells 2020, 9, 181.

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