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Annual Meeting of the Bulgarian Section of SIAM

BGSIAM 2017: Advanced Computing in Industrial Mathematics pp 257–265Cite as

Molecular Dynamics Study of the Solution Behaviour of Antimicrobial Peptide Indolicidin

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Part of the book series: Studies in Computational Intelligence ((SCI,volume 793))

Abstract

Understanding the mechanism of action of antimicrobial peptides (AMPs) on bacterial cells requires detailed knowledge of how AMPs interact with bacterial membranes. Our hypothesis is that the peptides do not interact with the membrane as monomers, but rather form clusters, that collectively approach the cell and attack the membrane. In this paper we investigate the behavior of the antimicrobial peptide indolicidin in solution, prior to their interaction with the bacterial membrane, by means of coarse grain molecular dynamics simulations (CG-MD). We show that indolicidin in particular and, probably, charged linear AMPs in general tend to aggregate in solution, forming globular amphipathic clusters with a central hydrophobic core. The dependence of the clusters size on the peptide concentration and on the temperature is studied, as well as the influence of the finite size of the simulation box. Our results manifest the investigation of the AMPs behavior in solution prior to membrane impact as an indispensable element in revealing the mechanism of their antimicrobial activity.

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Acknowledgements

The simulations were performed on the supercomputer Avitohol at BAS and on the HPC Cluster at the Faculty of Physics of Sofia University St. Kl. Ohridski. This work was supported in part by National Science Fund under Grant DNTS-China-01/9/2014.

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Authors and Affiliations

  1. Faculty of Physics, Sofia University St. Kl. Ohridski, 5 James Bourchier Blvd., 1164, Sofia, Bulgaria

    Rositsa Marinova, Peicho Petkov & Leandar Litov

  2. Institute of Information and Communication Technologies, Bulgarian Academy of Sciences, 25A, Acad. G. Bonchev Str., 1113, Sofia, Bulgaria

    Nevena Ilieva & Elena Lilkova

Authors
  1. Rositsa Marinova
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  2. Peicho Petkov
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  3. Nevena Ilieva
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  4. Elena Lilkova
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  5. Leandar Litov
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Corresponding author

Correspondence to Rositsa Marinova .

Editor information

Editors and Affiliations

  1. Institute of Information and Communication Technology, Bulgarian Academy of Sciences, Sofia, Bulgaria

    Krassimir Georgiev

  2. Faculty of Applied Mathematics and Informatics, Technical University of Sofia, Sofia, Bulgaria

    Michail Todorov

  3. Institute of Mathematics and Informatics and Institute of Information and Communication Technologies, Bulgarian Academy of Sciences, Sofia, Bulgaria

    Ivan Georgiev

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Marinova, R., Petkov, P., Ilieva, N., Lilkova, E., Litov, L. (2019). Molecular Dynamics Study of the Solution Behaviour of Antimicrobial Peptide Indolicidin. In: Georgiev, K., Todorov, M., Georgiev, I. (eds) Advanced Computing in Industrial Mathematics. BGSIAM 2017. Studies in Computational Intelligence, vol 793. Springer, Cham. https://doi.org/10.1007/978-3-319-97277-0_21

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