Close Search Advanced
Journals
Resources
About Us
Open Access

How the Antimicrobial Peptides Kill Bacteria: Computational Physics Insights

How the Antimicrobial Peptides Kill Bacteria: Computational Physics Insights
Preview
Add to basket

Year:    2012

Communications in Computational Physics, Vol. 11 (2012), Iss. 3 : pp. 709–725

Abstract

In the present article, coarse grained Dissipative Particle Dynamics simulation with implementation of electrostatic interactions is developed in constant pressure and surface tension ensemble to elucidate how the antimicrobial peptide molecules affect bilayer cell membrane structure and kill bacteria. We find that peptides with different chemical-physical properties exhibit different membrane obstructing mechanisms. Peptide molecules can destroy vital functions of the affected bacteria by translocating across their membranes via worm-holes, or by associating with membrane lipids to form hydrophilic cores trapped inside the hydrophobic domain of the membranes. In the latter model, the affected membranes are strongly buckled, in accord with very recent experimental observations [G. E. Fantner et al., Nat. Nanotech., 5 (2010), pp. 280-285].

Submit Article

You do not have full access to this article.

Already a Subscriber? Sign in as an individual or via your institution

Journal Article Details

Publisher Name:    Global Science Press

Language:    English

DOI:    https://doi.org/10.4208/cicp.071210.240511a

Communications in Computational Physics, Vol. 11 (2012), Iss. 3 : pp. 709–725

Published online:    2012-01

AMS Subject Headings:    Global Science Press

Copyright:    COPYRIGHT: © Global Science Press

Pages:    17

Keywords:   

  1. Suppressing membrane height fluctuations leads to a membrane-mediated interaction among proteins

    Sapp, Kayla | Maibaum, Lutz

    Physical Review E, Vol. 94 (2016), Iss. 5

    https://doi.org/10.1103/PhysRevE.94.052414 [Citations: 8]
  2. Advances in Artificial Life, Evolutionary Computation and Systems Chemistry

    Models for the Prediction of Antimicrobial Peptides Activity

    Parisi, Rosaura | Moccia, Ida | Sessa, Lucia | Di Biasi, Luigi | Concilio, Simona | Piotto, Stefano

    2016

    https://doi.org/10.1007/978-3-319-32695-5_8 [Citations: 1]

  3. Theoretical Insight into the Relationship between the Structures of Antimicrobial Peptides and Their Actions on Bacterial Membranes

    Chen, Licui | Li, Xiaoxu | Gao, Lianghui | Fang, Weihai

    The Journal of Physical Chemistry B, Vol. 119 (2015), Iss. 3 P.850

    https://doi.org/10.1021/jp505497k [Citations: 39]

  4. Sequestered Alkaloid Defenses in the Dendrobatid Poison Frog Oophaga pumilio Provide Variable Protection from Microbial Pathogens

    Hovey, Kyle J. | Seiter, Emily M. | Johnson, Erin E. | Saporito, Ralph A.

    Journal of Chemical Ecology, Vol. 44 (2018), Iss. 3 P.312

    https://doi.org/10.1007/s10886-018-0930-8 [Citations: 25]

  5. Beyond the Young-Laplace model for cluster growth during dewetting of thin films: Effective coarsening exponents and the role of long range dewetting interactions

    Constantinescu, Adi | Golubović, Leonardo | Levandovsky, Artem

    Physical Review E, Vol. 88 (2013), Iss. 3

    https://doi.org/10.1103/PhysRevE.88.032113 [Citations: 11]

  6. Structure and Formation Mechanism of Antimicrobial Peptides Temporin B- and L-Induced Tubular Membrane Protrusion

    Zhang, Shan | Ma, Ming | Shao, Zhuang | Zhang, Jincheng | Fu, Lei | Li, Xiangyuan | Fang, Weihai | Gao, Lianghui

    International Journal of Molecular Sciences, Vol. 22 (2021), Iss. 20 P.11015

    https://doi.org/10.3390/ijms222011015 [Citations: 9]

  7. Electrostatic interactions in dissipative particle dynamics—Ewald-like formalism, error analysis, and pressure computation

    Vaiwala, Rakesh | Jadhav, Sameer | Thaokar, Rochish

    The Journal of Chemical Physics, Vol. 146 (2017), Iss. 12

    https://doi.org/10.1063/1.4978809 [Citations: 17]

  8. Dissipative particle dynamics simulations for biological systems: From protein structures to cell mechanics

    Tang, Zihan | Li, Xuejin | Li, Dechang

    Chinese Science Bulletin, Vol. 68 (2023), Iss. 7 P.741

    https://doi.org/10.1360/TB-2022-0913 [Citations: 1]
  9. Biophysics of Infection

    Neutron Reflectivity as a Tool for Physics-Based Studies of Model Bacterial Membranes

    Barker, Robert D. | McKinley, Laura E. | Titmuss, Simon

    2016

    https://doi.org/10.1007/978-3-319-32189-9_16 [Citations: 6]

  10. Peptide-Lipid Interaction Sites Affect Vesicles’ Responses to Antimicrobial Peptides

    Shi, Yu | Wan, Mingwei | Fu, Lei | Zhang, Shan | Wang, Shiyuan | Gao, Lianghui | Fang, Weihai

    Biophysical Journal, Vol. 115 (2018), Iss. 8 P.1518

    https://doi.org/10.1016/j.bpj.2018.08.040 [Citations: 17]

  11. Bacteriocin AS-48 binding to model membranes and pore formation as revealed by coarse-grained simulations

    Cruz, Victor L. | Ramos, Javier | Melo, Manuel N. | Martinez-Salazar, Javier

    Biochimica et Biophysica Acta (BBA) - Biomembranes, Vol. 1828 (2013), Iss. 11 P.2524

    https://doi.org/10.1016/j.bbamem.2013.05.036 [Citations: 34]

  12. Treatment of microbial biofilms in the post-antibiotic era: prophylactic and therapeutic use of antimicrobial peptides and their design by bioinformatics tools

    Di Luca, Mariagrazia | Maccari, Giuseppe | Nifosì, Riccardo

    Pathogens and Disease, Vol. 70 (2014), Iss. 3 P.257

    https://doi.org/10.1111/2049-632X.12151 [Citations: 79]
  13. Computational Peptidology

    In Silico Design of Antimicrobial Peptides

    Maccari, Giuseppe | Di Luca, Mariagrazia | Nifosì, Riccardo

    2015

    https://doi.org/10.1007/978-1-4939-2285-7_9 [Citations: 20]

  14. Defensins are natural peptide antibiotics of higher eukaryotes

    Grishin, D. V. | Sokolov, N. N.

    Biochemistry (Moscow) Supplement Series B: Biomedical Chemistry, Vol. 8 (2014), Iss. 1 P.11

    https://doi.org/10.1134/S1990750814010077 [Citations: 3]

  15. Tension-compression asymmetry in the binding affinity of membrane-anchored receptors and ligands

    Xu, Guang-Kui | Liu, Zishun | Feng, Xi-Qiao | Gao, Huajian

    Physical Review E, Vol. 93 (2016), Iss. 3

    https://doi.org/10.1103/PhysRevE.93.032411 [Citations: 5]

  16. Mesoscale modeling: solving complex flows in biology and biotechnology

    Mills, Zachary Grant | Mao, Wenbin | Alexeev, Alexander

    Trends in Biotechnology, Vol. 31 (2013), Iss. 7 P.426

    https://doi.org/10.1016/j.tibtech.2013.05.001 [Citations: 65]

  17. Effects of Antimicrobial Peptide Revealed by Simulations: Translocation, Pore Formation, Membrane Corrugation and Euler Buckling

    Chen, Licui | Jia, Nana | Gao, Lianghui | Fang, Weihai | Golubovic, Leonardo

    International Journal of Molecular Sciences, Vol. 14 (2013), Iss. 4 P.7932

    https://doi.org/10.3390/ijms14047932 [Citations: 16]

  18. Distinct profiling of antimicrobial peptide families

    Khamis, Abdullah M. | Essack, Magbubah | Gao, Xin | Bajic, Vladimir B.

    Bioinformatics, Vol. 31 (2015), Iss. 6 P.849

    https://doi.org/10.1093/bioinformatics/btu738 [Citations: 28]

  19. Peripheral Antimicrobial Peptide Gomesin Induces Membrane Protrusion, Folding, and Laceration

    Zhang, Shan | Fu, Lei | Wan, Mingwei | Song, Junjie | Gao, Lianghui | Fang, Weihai

    Langmuir, Vol. 35 (2019), Iss. 40 P.13233

    https://doi.org/10.1021/acs.langmuir.9b02175 [Citations: 8]