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    Interaction of L-Alanine and L-Valine Aminoacid Molecules With Phospholipid Bilayer. Molecular Dynamics Simulation

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    Miguel Ángel Canal
    The document summarizes a molecular dynamics simulation of the interactions between L-alanine and L-valine amino acid molecules with a phospholipid bilayer. The simulation used molecules of L-alanine and L-valine interacting with a bilayer composed of 128 dipalmitoylphosphatidylcholine molecules and 3655 water molecules. Key results included a decrease in bilayer area and thickness after amino acid addition, as well as deeper penetration of L-valine into the bilayer compared to L-alanine due to hydrophobicity differences. The simulations provide insight into amino acid-bilayer interactions at an atomic level.

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    Interaction of L-Alanine and L-Valine Aminoacid Molecules With Phospholipid Bilayer. Molecular Dynamics Simulation

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    Miguel Ángel Canal
    23 views10 pages
    The document summarizes a molecular dynamics simulation of the interactions between L-alanine and L-valine amino acid molecules with a phospholipid bilayer. The simulation used molecules of L-alanine and L-valine interacting with a bilayer composed of 128 dipalmitoylphosphatidylcholine molecules and 3655 water molecules. Key results included a decrease in bilayer area and thickness after amino acid addition, as well as deeper penetration of L-valine into the bilayer compared to L-alanine due to hydrophobicity differences. The simulations provide insight into amino acid-bilayer interactions at an atomic level.

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    The document summarizes a molecular dynamics simulation of the interactions between L-alanine and L-valine amino acid molecules with a phospholipid bilayer. The simulation used molecules of L-alanine and L-valine interacting with a bilayer composed of 128 dipalmitoylphosphatidylcholine molecules and 3655 water molecules. Key results included a decrease in bilayer area and thickness after amino acid addition, as well as deeper penetration of L-valine into the bilayer compared to L-alanine due to hydrophobicity differences. The simulations provide insight into amino acid-bilayer interactions at an atomic level.

    Copyright:

    © All Rights Reserved
    Download as PPTX, PDF, TXT or read online from Scribd
    Download as pptx, pdf, or txt
    23 views10 pages

    Interaction of L-Alanine and L-Valine Aminoacid Molecules With Phospholipid Bilayer. Molecular Dynamics Simulation

    Uploaded by

    Miguel Ángel Canal
    The document summarizes a molecular dynamics simulation of the interactions between L-alanine and L-valine amino acid molecules with a phospholipid bilayer. The simulation used molecules of L-alanine and L-valine interacting with a bilayer composed of 128 dipalmitoylphosphatidylcholine molecules and 3655 water molecules. Key results included a decrease in bilayer area and thickness after amino acid addition, as well as deeper penetration of L-valine into the bilayer compared to L-alanine due to hydrophobicity differences. The simulations provide insight into amino acid-bilayer interactions at an atomic level.

    Copyright:

    © All Rights Reserved
    Download as PPTX, PDF, TXT or read online from Scribd
    Download as pptx, pdf, or txt
    of 10

    INTERACTION OF L-ALANINE AND L-VALINE AMINOACID MOLECULES

    WITH PHOSPHOLIPID BILAYER.


    MOLECULAR DYNAMICS SIMULATION

    S. A. Aramyan , A. H. Poghosyan ,
    Cor. Member of NAS RA A. A. Shahinyan

    Institute of Applied Problems of Physics of National Academy of Sciences of


    Armenia,
    Hr. Nersisian 25, 0014, Yerevan, Republic of Armenia; Tel.: (+374 10) 245 896; e-
    mail: sona_aramyan@yahoo.com;

    International Scientific and Educational Center of National Academy of Sciences


    of Armenia,
    Marshal Baghramian Ave. 24d, 0019 Yerevan, Republic of Armenia; Tel.: (+374
    10) 583 691
    ABSTRACT

    It is well known the importance of investigations of interactions between


    proteins and phospholipid bilayers. We decided to give a deeper sight to this
    problem by the determination of ways of interactions between aminoacids
    and phospholipid bilayers using computer simulation methods. By means of
    simulation, remarkable progress is being made in the understanding of
    protein folding, lipid bilayer behavior and peptide-lipid interactions. There
    were used the molecules of L-alanine and L-valine and phospholipids bilayer
    consisting of 128 Dipalmitoylphosphatidylcholine (dppc) molecules and 3655
    water molecules, which corresponds to fully hydrated state of dppc bilayer.
    For the computer experiment the GROMACS simulation package and
    GROMOS force fields were used. There were done two main simulations of
    systems containing L-ala and bilayer and correspondingly L-val and bilayer.
    Both simulations were done with the duration of 15 ns and under the same
    conditions with same parameters.
    INTRODUCTION
    During last decades the accumulation of biological information is continuing,
    besides this during last years it is accumulating in forms of electronic versions,
    such as texts, images and so on. Because of the presence of this huge amount of
    information is rising a problem of systematization and adequate usage of this
    amount of experimental data.

    Bioinformatical methods give an appropriate salvation to these problems. Besides


    systematization, during last decade, it gives an opportunity to make models and
    investigate complex biological and chemical molecules and processes.

    The aim of this work was to determine the ways of interaction of aminoacids with
    phospholipid bilayers using computer simulation methods. Particularly for these
    simulations the method of molecular dynamics was used. It was interesting to
    find out in details the ways of aminoacid-phospholipids bilayer interactions in
    atomic scale. There were used molecules of L-alanine and L-valine with the bilayer
    consisting of 128 dipalmitoilphosphatidilcholine (dppc) and 3655 water molecules.
    In this experiment there are elucidated many nuances of aminoacid behavior and
    bilayer property changes during aminoacid addition to bilayer.
    METHODS

    The molecular dynamics simulations were carried out using GROMACS


    simulation package (version 3.2.1, single
    precision) [4]. Simulations were performed on Armcluster, which was
    founded in Institute of Informatics and
    Automatization Problems of NAS RA by ISTC A-823 project. The VMD
    package [5] was used for visualization and molecular graphics.
    The interactions between, L-valine/bilayer, L-alanine/bilayer were
    examined. There were investigated two systems consisting of L-alanine, and
    L-valine molecules and phospholipid bilayers (128 DPPC and 3655 water
    molecules, which corresponds to fully hydrated state of phospholipid
    bilayer) (Fig. 1). For the system preparation water was removed
    from bilayer and then the aminoacid molecule was added right onto the
    bilayer surface. After aminoacid addition water
    was palced back onto its starting configuration.
    BILAYER PROPERTIES

    For the description of bilayer properties there were


    measured some parameters such as area per lipid
    and bilayer thickness. In most of cases
    measurements were done on the nearest to
    aminoacid part of bilayer. On Fig. 2 you can see
    changes of area per lipid (on the aminoacid
    neighboring part of bilayer) during simulation time.
    From the real physical experiment this value was
    received as 0.62 nm2 [14]. As you can see this
    value is decreasing up to approximately 0.4 nm2.
    This means that lipids are getting closer to each
    other after aminoacid addition. On Fig. 3 are
    presented the changes of bilayer thickness
    measured as a distance between aminoacid
    neighboring lipid headgroup phosphorus of upper
    and lower layers.
    This value from real experiment was 3.7 nm
    but you can see that thickness is decreasing
    too during simulation to ~3.5 nm [14].
    There were also measured total energies of
    bilayers (Fig.4). From this value we can see
    whether system is stable or not. As you can see
    after 1.5 ns system stabilizes and there are
    little changes in energy after this time.

    Aminoacid behavior
    In Fig. 5 you can see the permeation of
    aminoacid into the bilayer. During simulation
    aminoacids are entering to bilayer from their
    starting point until phosphorus level (7.5 ns)
    and then even go deeper then average
    phosphors. From figure it is clear that at the
    end of simulation, starting from 12 ns till end,
    L-valine penetrates deeper then L-alanine,
    which can be explained by L-valines more
    hydrophobicity compared with L-alanine.
    CONCLUSIONS

    • In conclusion we can say that we have modeled for the first time
    the above mentioned aspect of interaction between phospholipid
    bilayer and aminoacids.
    • Several parameters, describing the structure of the bilayer, such as
    area per lipid on the surface of bilayer, thickness of bilayer,
    arrangement of aminoacid molecules in the bilayer were
    investigated.
    • We have got that areas per lipid for the aminoacid neighboring part
    of bilayer are decreasing from 0.62 to 0.4 nm2. And the bilayers
    thicknesses again for the aminoacid neighboring part of bilayers are
    decreasing from 3.7 to 3.5 nm.
    • Aminoacids center of masses are penetrating into the bilayer
    deeper then lipids average phosphorus for 0.3 nm, furthermore L-
    valine is penetrating deeper than L-alanine.
    REFERENCES

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    unoiiented bilayers of gel phase
    dipalmitoylphosphatidylcholine / Phys. Rev. E, v. 49, №5: 4665-4676.
    [2] Benz R.W., Castro-Roman F., Tobias D. J., White S.H., 2005. Experimental validation of
    molecular dynamics simulations of
    lipid bilayers: a new approach / Biophysical J., v. 88: 805-817.
    [3] Rog T., Murzyn K., Pasenkiewicz-Gierula M., 2003. Molecular dynamics simulations of
    charged and neutral lipid bilayers:
    treatment of electrostatic interactions / Acta Biophisica Polonica, v. 50, №3: 789-798.
    [4] Gromacs 3.1.3 or 3.0
    [5] Humphrey W., Dalke A., Schulten K., 1996. VMD - Visual Molecular Dynamics / J. Molec.
    Graphics, 14.1: 33-38.
    [6] Berger O., Edholm O., Jahnig F., 1997. Molecular dynamics simulations of a fluid bilayer of
    dipalmitoylphosphatidylcholine at
    full hydration, constant pressure, and constant temperature / Biophys. J., 72: 2002–2013.
    [7] Berendsen H.J.C., Postma J.P.M., van Gunsteren W.F., Hermans J., 1981. Interaction models
    for water in relation to protein
    hydration. In Intermolecular Forces / B. Pullman, ed. D. Reidel Publishing Company, Dordrecht,
    The Netherlands: 331-342.
    [8] Ryckaert J.P., Ciccotti G., Berendsen H.J.C., 1977. Numerical integration of the Cartesian
    equations of motion of a system
    with constraints; molecular dynamics of n-alkanes / J. Comp. Phys, 23: 327–341.
    [9] Nos´e S., 1984. A molecular dynamics method for simulations in the canonical ensemble /
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    [10] Hoover W.G., 1985. Canonical dynamics: equilibrium phase-space distributions / Phys. Rev.,
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    [11] Parrinello M., Rahman A., 1981. Polymorphic transitions in single crystals: A new molecular
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    [12] Nos´e S., Klein M.L., 1983. Constant pressure molecular dynamics for molecular systems /
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    [13] Gromacs manual
    [14] Tieleman D.P., Berendsen H.J.C., 1996. Molecular dynamics simulations of a fully hydrated
    dipalmitoylphosphatidylcholine
    bilayer with different macroscopic boundary conditions and parameters / J. Chem. Phys. 105:
    4871–4880.

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