Trans-scale Granular Modelling of Cytoskeleton: aMini-Review

Free to read Living cells are the functional unit of organs that controls reactions to their exterior. However, the mechanics of living cells can be difficult to characterize due to the crypticity of their microscale structures and associated dynamic cellular processes. Fortunately, multiscale modelling provides a powerful simulation tool that can be used to study the mechanical properties of these soft hierarchical, biological systems. This paper reviews recent developments in hierarchical multiscale modeling technique that aimed at understanding cytoskeleton mechanics. Discussions are expanded with respects to cytoskeletal components including: intermediate filaments, microtubules and microfilament networks. The mechanical performance of difference cytoskeleton components are discussed with respect to their structural and material properties. Explicit granular simulation methods are adopted with different coarse-grained strategies for these cytoskeleton components and the simulation details are introduced in this review.

[1]  M. Omary,et al.  Intermediate filament proteins and their associated diseases. , 2004, The New England journal of medicine.

[2]  A. Erdemir,et al.  Multiscale modeling in computational biomechanics , 2009, IEEE Engineering in Medicine and Biology Magazine.

[3]  K Weber,et al.  Intermediate filaments: structure, dynamics, function, and disease. , 1994, Annual review of biochemistry.

[4]  David A Weitz,et al.  The cell as a material. , 2007, Current opinion in cell biology.

[5]  L. C. Zhang,et al.  A Concurrent Multiscale Method Based on the Meshfree Method and Molecular Dynamics Analysis , 2006, Multiscale Model. Simul..

[6]  M. Selman,et al.  Cell size, cell cycle, and α-smooth muscle actin expression by primary human lung fibroblasts. , 1998, American journal of physiology. Lung cellular and molecular physiology.

[7]  Tao Wu,et al.  Molecular simulation of protein adsorption and desorption on hydroxyapatite surfaces. , 2008, Biomaterials.

[8]  M. Omary,et al.  "Heads and tails" of intermediate filament phosphorylation: multiple sites and functional insights. , 2006, Trends in biochemical sciences.

[9]  Ravi Iyengar,et al.  Multiscale modeling of cell shape from the actin cytoskeleton. , 2014, Progress in molecular biology and translational science.

[10]  T. Yanagida,et al.  Direct measurement of stiffness of single actin filaments with and without tropomyosin by in vitro nanomanipulation. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[11]  J. Berg,et al.  Molecular dynamics simulations of biomolecules , 2002, Nature Structural Biology.

[12]  Prasad K. Yarlagadda,et al.  Hierarchical multiscale model for biomechanics analysis of microfilament networks , 2013 .

[13]  S. Almo,et al.  Structure and dynamics of the actin filament. , 2005, Biochemistry.

[14]  R. Ritchie,et al.  Bioinspired structural materials. , 2014, Nature Materials.

[15]  Roger D Kamm,et al.  Dynamic role of cross-linking proteins in actin rheology. , 2011, Biophysical journal.

[16]  Umberto Morbiducci,et al.  Biomechanics of actin filaments: a computational multi-level study. , 2011, Journal of biomechanics.

[17]  S. Suresh,et al.  Cell and molecular mechanics of biological materials , 2003, Nature materials.

[18]  Julia E. Sero,et al.  The forces of cancer , 2019, Philosophical Transactions of the Royal Society B.

[19]  M. Buehler,et al.  Computational and theoretical modeling of intermediate filament networks: Structure, mechanics and disease , 2012 .

[20]  Gang-Yu Liu,et al.  Cell mechanics using atomic force microscopy-based single-cell compression. , 2006, Langmuir : the ACS journal of surfaces and colloids.

[21]  P. Janmey,et al.  Cell mechanics: integrating cell responses to mechanical stimuli. , 2007, Annual review of biomedical engineering.

[22]  Ilpo Vattulainen,et al.  Strain hardening, avalanches, and strain softening in dense cross-linked actin networks. , 2008, Physical review. E, Statistical, nonlinear, and soft matter physics.

[23]  J. Howard,et al.  Flexural rigidity of microtubules and actin filaments measured from thermal fluctuations in shape , 1993, The Journal of cell biology.

[24]  D. Ingber Tensegrity I. Cell structure and hierarchical systems biology , 2003, Journal of Cell Science.

[25]  D. Hartmann A multiscale model for red blood cell mechanics , 2010, Biomechanics and modeling in mechanobiology.

[26]  Xi-Qiao Feng,et al.  Coarse-grained mechanochemical model for simulating the dynamic behavior of microtubules. , 2011, Physical review. E, Statistical, nonlinear, and soft matter physics.

[27]  Adekunle Oloyede,et al.  Molecular investigation of the mechanical properties of single actin filaments based on vibration analyses , 2014, Computer methods in biomechanics and biomedical engineering.

[28]  C Zhu,et al.  Cell mechanics: mechanical response, cell adhesion, and molecular deformation. , 2000, Annual review of biomedical engineering.

[29]  Andreas R. Bausch,et al.  A bottom-up approach to cell mechanics , 2006 .

[30]  Yuichiro Maéda,et al.  The nature of the globular- to fibrous-actin transition , 2009, Nature.

[31]  Peng Chen,et al.  Strain stiffening induced by molecular motors in active crosslinked biopolymer networks , 2010, 1009.0548.

[32]  D. Weitz,et al.  Elastic Behavior of Cross-Linked and Bundled Actin Networks , 2004, Science.

[33]  Taiji Adachi,et al.  Multiscale modeling and mechanics of filamentous actin cytoskeleton , 2012, Biomechanics and modeling in mechanobiology.

[34]  Alberto Redaelli,et al.  Hierarchical structure and nanomechanics of collagen microfibrils from the atomistic scale up. , 2011, Nano letters.

[35]  E. Shakhnovich,et al.  Understanding hierarchical protein evolution from first principles. , 2001, Journal of molecular biology.

[36]  S T Quek,et al.  Mechanical models for living cells--a review. , 2006, Journal of biomechanics.

[37]  Markus J. Buehler,et al.  Robustness-Strength Performance of Hierarchical Alpha-Helical Protein Filaments , 2009 .

[38]  Roger D. Kamm,et al.  Computational Analysis of a Cross-linked Actin-like Network , 2009 .

[39]  P. Janmey,et al.  Viscoelasticity of F-actin and F-actin/gelsolin complexes. , 1988, Biochemistry.

[40]  Markus J Buehler,et al.  A multi-scale approach to understand the mechanobiology of intermediate filaments. , 2010, Journal of biomechanics.

[41]  Markus J. Buehler,et al.  Alpha-Helical Protein Networks Are Self-Protective and Flaw-Tolerant , 2009, PloS one.

[42]  A. Shahsavari,et al.  Multiscale modeling of semiflexible random fibrous structures , 2013, Comput. Aided Des..

[43]  P. Matsudaira,et al.  Bending stiffness of a crystalline actin bundle. , 2004, Journal of molecular biology.

[44]  K. Holmes Structural biology: Actin in a twist , 2009, Nature.

[45]  H E Huxley,et al.  X-ray diffraction measurements of the extensibility of actin and myosin filaments in contracting muscle. , 1994, Biophysical journal.

[46]  T. Pollard,et al.  Cellular Motility Driven by Assembly and Disassembly of Actin Filaments , 2003, Cell.

[47]  T. Pollard Mechanics of cytokinesis in eukaryotes. , 2010, Current opinion in cell biology.

[48]  R. Himeno,et al.  Biomechanical characterization of ventricular-arterial coupling during aging: a multi-scale model study. , 2009, Journal of biomechanics.

[49]  George Em Karniadakis,et al.  Probing red blood cell mechanics, rheology and dynamics with a two-component multi-scale model , 2014, Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences.

[50]  Gregory A Voth,et al.  Coarse-grained modeling of the actin filament derived from atomistic-scale simulations. , 2006, Biophysical journal.

[51]  Tong Li,et al.  A stochastic thermostat algorithm for coarse-grained thermomechanical modeling of large-scale soft matters: Theory and application to microfilaments , 2014, J. Comput. Phys..

[52]  Gregory A Voth,et al.  Multiscale modeling of biomolecular systems: in serial and in parallel. , 2007, Current opinion in structural biology.

[53]  S. Cowin,et al.  A model for strain amplification in the actin cytoskeleton of osteocytes due to fluid drag on pericellular matrix. , 2001, Journal of biomechanics.

[54]  D A Weitz,et al.  Stress-dependent elasticity of composite actin networks as a model for cell behavior. , 2006, Physical review letters.

[55]  Mohammad R K Mofrad,et al.  Computational modeling of axonal microtubule bundles under tension. , 2012, Biophysical journal.

[56]  U Aebi,et al.  Exploring the mechanical behavior of single intermediate filaments. , 2005, Journal of molecular biology.

[57]  Ning Wang,et al.  Mechanics of vimentin intermediate filaments , 2004, Journal of Muscle Research & Cell Motility.

[58]  F. Migliavacca,et al.  Multiscale modelling in biofluidynamics: application to reconstructive paediatric cardiac surgery. , 2006, Journal of biomechanics.

[59]  Gerald H Pollack,et al.  Mechanics of F-actin characterized with microfabricated cantilevers. , 2002, Biophysical journal.

[60]  Anthony A. Hyman,et al.  Dynamics and mechanics of the microtubule plus end , 2022 .

[61]  D Stamenović,et al.  Contribution of intermediate filaments to cell stiffness, stiffening, and growth. , 2000, American journal of physiology. Cell physiology.

[62]  Masaki Hojo,et al.  Evaluation of extensional and torsional stiffness of single actin filaments by molecular dynamics analysis. , 2010, Journal of biomechanics.

[63]  Marco Viceconti,et al.  Are spontaneous fractures possible? An example of clinical application for personalised, multiscale neuro-musculo-skeletal modelling. , 2012, Journal of biomechanics.

[64]  Multiscale modeling of the nanomechanics of microtubule protofilaments. , 2012, The journal of physical chemistry. B.

[65]  Daniel A. Fletcher,et al.  Cell mechanics and the cytoskeleton , 2010, Nature.

[66]  Ueli Aebi,et al.  Intermediate filaments: from cell architecture to nanomechanics , 2007, Nature Reviews Molecular Cell Biology.

[67]  Mischa Schmidt,et al.  Destruction of cancer cells by laser-induced shock waves: recent developments in experimental treatments and multiscale computer simulations. , 2014, Soft matter.

[68]  P. Yarlagadda,et al.  Continuum mechanics modelling of microfilament networks with different architectures based on molecular investigation of single F-actin , 2012 .

[69]  Junru Wu,et al.  Actin filament mechanics in the laser trap , 1997, Journal of Muscle Research & Cell Motility.

[70]  Daniel A. Fletcher,et al.  Reversible stress softening of actin networks , 2007, Nature.

[71]  Thomas D. Pollard,et al.  Actin, a Central Player in Cell Shape and Movement , 2009, Science.

[72]  Masaki Hojo,et al.  Coarse-grained modeling and simulation of actin filament behavior based on Brownian dynamics method. , 2009, Molecular & cellular biomechanics : MCB.

[73]  George Oster,et al.  Force generation by actin polymerization II: the elastic ratchet and tethered filaments. , 2003, Biophysical journal.

[74]  Andrea Acquaviva,et al.  Multiscale modeling of cellular actin filaments: From atomistic molecular to coarse‐grained dynamics , 2012, Proteins.

[75]  Paul Martin,et al.  Wound Healing--Aiming for Perfect Skin Regeneration , 1997, Science.