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Computer Simulations of Homocysteine Molecules Embedded in High-Density Lipoprotein

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Nanophysics, Nanophotonics, Surface Studies, and Applications

Part of the book series: Springer Proceedings in Physics ((SPPHY,volume 183))

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Abstract

Excessive level of homocysteine is a factor increasing the risk for cardiovascular diseases and other ailments. In this paper we applied molecular dynamics method to study the homocysteine system embedded in high-density lipoprotein. HDL aggregate removes cholesterol from artery walls. We fill the aggregate with almost 700 biologically important homocysteine molecules.

The calculations were performed in the physiological temperature T = 310 K. HDL container was simulated both, in water environment and without water, to estimate the impact of water on the dynamics of the molecules inside HDL aggregate. Moreover, the behaviour of homocysteine molecules in HDL was compared with their dynamics in a free cluster consisted of the same number of homocysteine molecules, as placed inside the lipoprotein.

The structural and dynamical observables (mean square displacement, diffusion coefficient, second-rank order parameter, Lindemann index and radial distribution function) are discussed. We have found that although the dynamics of homocysteine molecules does not strongly depend on the presence of water surrounding HDL, the differences in dynamics of homocysteine molecules in the free cluster and these embedded in HDL are clearly observed.

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Acknowledgment

Calculations were performed at ICM University of Warsaw, Grant no. G53-6.

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Authors and Affiliations

  1. Institute of Physics, University of Silesia, Uniwersytecka 4, 40-007, Katowice, Poland

    Zygmunt Gburski & Przemysław Raczyński

Authors
  1. Zygmunt Gburski
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  2. Przemysław Raczyński
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Correspondence to Zygmunt Gburski .

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Editors and Affiliations

  1. Institute of Physics of National Academy of Sciences of Ukraine, Kiev, Ukraine

    Olena Fesenko

  2. Institute of Physics of National Academy of Sciences of Ukraine, Kiev, Ukraine

    Leonid Yatsenko

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Gburski, Z., Raczyński, P. (2016). Computer Simulations of Homocysteine Molecules Embedded in High-Density Lipoprotein. In: Fesenko, O., Yatsenko, L. (eds) Nanophysics, Nanophotonics, Surface Studies, and Applications. Springer Proceedings in Physics, vol 183. Springer, Cham. https://doi.org/10.1007/978-3-319-30737-4_26

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