Dynamic Simulation and Mechanical Properties of Microtubules
الموضوعات :
M Motamedi
1
(Faculty of Engineering, University of Shahreza, P. O. Box 86149-56841, Isfahan, Iran)
M Mosavi Mashhadi
2
(Department of Mechanical Engineering, University of Tehran, P.O. Box 11365-4563, Tehran, , Iran)
الکلمات المفتاحية: Finite Element, Mechanical Properties, Microtubules, Molecular dynamic,
ملخص المقالة :
This work is conducted to obtain mechanical properties of microtubule. For this aim, interaction energy in alpha-beta, beta-alpha, alpha-alpha, and beta-beta dimers was calculated using the molecular dynamic simulation. Force-distance diagrams for these dimers were obtained using the relation between potential energy and force. Afterwards, instead of each tubulin, one sphere with 55 KDa weight connecting to another tubulin with a nonlinear connection such as nonlinear spring could be considered. The mechanical model of microtubule was used to calculate Young’s modulus based on finite element method. Obtained Young’s modulus has good agreement with previous works. Also, natural frequency of microtubules was calculated based on finite element method.
[1] Yiting D., Zhiping X., 2011, Mechanics of microtubules from a coarse-grained model, BioNanoScience 1: 173-182.
[2] Downing K.H. , Nogales E., 1998, New insights into microtubule structure and function from the atomic model of tubulin, European Biophysics Journal 27: 431-436.
[3] David S., Nathan A., Andrew J., 2003, The physical basis of microtubule structure and stability, Protein Science 12: 2257-2261.
[4] Lin Y., Gijsje H., Frederick C., David A., 2007, Viscoelastic properties of microtubule networks, Macromolecules 40: 7714-7720.
[5] Chretien D., Fuller S.D., 2000, Microtubules switch occasionally into unfavorable configurations during elongation, Journal of Molecular Biology 298: 663-676.
[6] Iva M.T., 2008, Push-me-pull-you: how microtubules organize the cell interior, European Biophysics Journal 37: 1271-1278.
[7] Chrétien D., Wade R.H., 1991, New data on the microtubule surface lattice, Biology of the Cell 71: 161-174.
[8] Nogales E., Wolf S. G., Downing K. H., 1998, Structure of the α, β tubulin dimer by electron crystallography, Nature 391: 199-203.
[9] Li H., DeRosier D.J., Nicholson W.V., Nogales E., Downing K.H., 2002, Microtubule structure at 8 Å resolution, Structure 10: 1317-1328.
[10] Löwe J., Li H., Downing K. H., Nogales E., 2001, Refined structure of αβ-tubulin at 3.5 Å resolutions, Journal of Molecular Biology 313: 1045-1057.
[11] De Pablo P.J., Schaap I. A.T., MacKintosh F.C., Schmidt C. F., 2003, Deformation and collapse of microtubules on the nanometer scale, Physical Review Letters 91: 098101.
[12] Ja´nosi M., Chre´tien D., Flyvbjerg H., 2002, Structural microtubule cap: stability, catastrophe, rescue, and third state, Biophysical Journal 83: 1317-1330.
[13] Ying X., Dong X., Jie L., 2007, Computational Methods for Protein Structure Prediction and Modeling, Basic Characterization, Springer Science. NewYork.
[14] Karplus M., McCammon J.A., 2002, Molecular dynamics simulations of biomolecules, Nature Structural Biology 9: 646 - 652
[15] Zeiger A.S., Layton B.E., 2008, Molecular modeling of the axial and circumferential elastic moduli of tubulin, Biophysical Journal 95: 3606-3618.
[16] Bekir A., Ömer C., 2014, Mechanical analysis of isolated microtubules based on a higher-order shear deformation beam theory, Composite Structures 118: 9-18.
[17] Kis A., Kasas S., Babic B., Kulik A.J., Benoit W., 2002, Nanomechanics of microtubules, Physical Review Letters 89: 248101.
[18] Kasas S., Kis A., Riederer B. M., Forro L., Dietler G., Catsicas S., 2004, Mechanical properties of microtubules explored using the finite elements method, ChemPhysChem 5: 252-257.
[19] Nogales E., Whittaker M., Milligan R. A., Downing K. H., 1999, High-resolution model of the microtubule, Cell 96: 79-88.
[20] Howard J., 2001, Mechanics of Motor Proteins and the Cytoskeleton, Sinauer, Sunderland.
[21] Dominguez C., Boelens R., Bonvin A.M.J.J., 2003, HADDOCK: a protein-protein docking approach based on biochemical or biophysical information, Journal of the American Chemical Society 125: 1731-1737.
[22] Pronk S., Páll S., Schulz R., Larsson P., Bjelkmar P., Apostolov R., Shirts M.R., Smith J.C., Kasson P.M., Vander Spoel D., Hess B., Lindahl E., 2013, GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit, Bioinformatics 29: 845-854.
[23] Walter R.P., Philippe H. , Ilario G., Alan E., Salomon R., Jens F., Andrew E., Thomas H., Peter K., Wilfred F., 1999, The GROMOS biomolecular simulation program package, The Journal of Physical Chemistry A 103: 3596-3607.
[24] Berendsen H.J.C., Postma J.P.M., DiNola A., Haak J.R., 1984, Molecular dynamics with coupling to an external bath, The Journal of Chemical Physics 81:3684.
[25] Meriam J., Kraige L., 2012, Engineering Mechanics-Dynamic, Wiley, 7 edition.
[26] Russell C., 2013, Mechanics of Materials, Prentice Hall, 9 edition.
[27] Gitte F., Mickey B., Nettleton J., Howard J., 1993, Flexural rigidity of microtubules and actin filaments measured from thermal fluctuations in shape, The Journal of Cell Biology 120: 923-934.
[28] Mickey B., Howard J., 1995, Rigidity of microtubules is increased by stabilizing agent, The Journal of Cell Biology 130: 909-917.
