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Evaluation of Protein Electrostatic Potential from Molecular Dynamics Simulations in the Presence of Exogenous Electric Fields: The Case Study of Myoglobin

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Computational Electrostatics for Biological Applications

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Abstract

When studying proteins in solution it is apparent that electrostatic interactions play a role in folding, conformational stability, and other chemical-physical properties. Electrostatics considers the evaluation of the static electrical field that is formed between charged species once a rearrangement of their charge distributions has occurred due to the influence of each other and their local environment. A powerful tool used to follow the many interactions among the polar and/or charged residues is computer simulations, which can provide atomic-scale information on energetic and dynamic contributions of the bio-molecular structure. Here we use molecular dynamics (MD) simulations to map on a three-dimensional space the electrostatic interactions within the protein itself and of the protein with its aqueous environment. The method has been first tested on a simulation domain of water molecules and then applied to the myoglobin-water system. The presence of intense electric fields has also been considered and some representative results are discussed.

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Acknowledgments

This activity is performed in the framework of the Joint IIT-Sapienza LAB on Life-NanoScience Project “Novel strategies for the imaging and treatment of brain tumors through targeting cancer stem cell-specific signaling pathways.”

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Authors and Affiliations

  1. University Sapienza of Rome, Via Eudossiana 18, 00141, Rome, Italy

    P. Marracino, M. Casciola, M. Liberti & F. Apollonio

  2. Istituto Italiano di Tecnologia IIT, Genova, Italy

    M. Casciola

Authors
  1. P. Marracino
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  2. M. Casciola
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  3. M. Liberti
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  4. F. Apollonio
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Corresponding author

Correspondence to F. Apollonio .

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Editors and Affiliations

  1. CONCEPT Lab - CompuNet, Istituto Italiano di Tecnologia, Genova, Italy

    Walter Rocchia

  2. Institute of Applied Mathematics and Inf, National Research Council, Genova, Italy

    Michela Spagnuolo

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Marracino, P., Casciola, M., Liberti, M., Apollonio, F. (2015). Evaluation of Protein Electrostatic Potential from Molecular Dynamics Simulations in the Presence of Exogenous Electric Fields: The Case Study of Myoglobin. In: Rocchia, W., Spagnuolo, M. (eds) Computational Electrostatics for Biological Applications. Springer, Cham. https://doi.org/10.1007/978-3-319-12211-3_13

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