Journal of Mechanical Science and Technology

, Volume 22, Issue 11, pp 2203–2212 | Cite as

AFM-based identification of the dynamic properties of globular proteins: simulation study

  • Deok-Ho Kim
  • Jungyul Park
  • Moon K. Kim
  • Keum-Shik Hong
Article

Abstract

Nowadays a mathematical model-based computational approach is getting more attention as an effective tool for understanding the mechanical behaviors of biological systems. To find the mechanical properties of the proteins required to build such a model, this paper investigates a real-time identification method based on an AFM nanomanipulation system. First, an AFM-based bio-characterization system is introduced. Second, a second-order time-varying linear model representing the interaction between an AFM cantilever and globular proteins in a solvent is presented. Finally, we address a real-time estimation method in which the results of AFM experiments are designed to be inputs of the state estimator proposed here. Our attention is restricted to a theoretical feasibility analysis of the proposed methodology. We simply set the mechanical properties of the particular protein such as mass, stiffness, and damping coefficient in the system model prior to running the simulation. Simulation results show very good agreement with the preset properties. We anticipate that the realization of the AFM-based bio-characterization system will also provide an experimental validation of the proposed identification procedure in the future. This methodology can be used to determine a model of protein motion for the purpose of computer simulation and for a real-time modification of protein deformation.

Keywords

Nanomechanics AFM cantilever Proteins Dynamic parameters System identification 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. [1]
    G. Bao, Mechanics of biomolecules, Journal of Mechanics and Physics of Solids. 50 (2002) 2237–2274.MATHCrossRefGoogle Scholar
  2. [2]
    D. H. Kim, P. K. Wong, J. Y. Park, A. Levchenko and Y. Sun, Microengineered Platforms for Cell Mechanobiology, Annual Review of Biomedical Engineering, to appear, 2009.Google Scholar
  3. [3]
    H. J. Chizeck, S. Chang, R. B. Stein, A. Scheiner and D. C. Ferencz, Identification of electrically stimulated quadriceps muscles in paraplegic subjects, IEEE Transactions on Biomedical Engineering. 46 (1999) 51–61.CrossRefGoogle Scholar
  4. [4]
    R. E. Kearney, R.B. Stein and L. Parameswaran, Identification of intrinsic and reflex contributions to human ankle stiffness dynamics, IEEE Transactions on Biomedical Engineering. 44 (1997) 493–504.CrossRefGoogle Scholar
  5. [5]
    A. Ikai, A. Idiris, H. Sekiguchi, H. Arakawa and S. Nishida, Intra- and intermolecular mechanics of proteins and polypeptides studied by AFM: with applications, Applied Surface Science. 188 (2002) 1–7.CrossRefGoogle Scholar
  6. [6]
    K. Mitsui, K. Nakajima, H. Arakawa, M. Hara and A. Ikai, Dynamic measurement of single protein’s mechanical properties, Biochemical and Biophysical Research Communications. 272 (2000) 55–63.CrossRefGoogle Scholar
  7. [7]
    A. E. Garcia, Large amplitude nonlinear motion in proteins, Physical Review Letters. 68 (1992) 2696–2699.CrossRefGoogle Scholar
  8. [8]
    B. Alakent, M. C. Camurdan and P. Doruker, Hierarchical structure of the energy landscape of proteins revisited by time series analysis. I. Mimicking protein dynamics in different time scales, The Journal of Chemical Physics. 123 (2005) 144910.Google Scholar
  9. [9]
    M. R. Falvo, S. Washburn, R. Superfine, M. Finch, F.P. Brooks, V. Chi and R.M. Taylor, Manipulation of individual viruses: friction and mechanical properties, Biophysical Journal. 72 (1997) 1396–1403.CrossRefGoogle Scholar
  10. [10]
    D. R. Baselt, G. U. Lee and R. J. Colton, Biosensor based on force microscope technology, Journal of Vacuum Science and Technology B. 14 (1996) 789–793.CrossRefGoogle Scholar
  11. [11]
    L. Dong, F. Arai and T. Fukuda, Destructive constructions of nanostructures with carbon nanotubes through nanorobotic manipulation, IEEE/ASME Transactions on Mechatronics. 9 (2004) 350–357.CrossRefGoogle Scholar
  12. [12]
    M. Sitti, Atomic force microscope probe based controlled pushing for nanotribological characterization, IEEE/ASME Transactions on Mechatronics. 9 (2004) 343–349.CrossRefGoogle Scholar
  13. [13]
    D. Bensimon, A. J. Simon, V. Croquette and A. Bensimon, Stretching DNA with a receding meniscus: experiments and models, Physical Review Letters. 74 (1995) 4754–4757.CrossRefGoogle Scholar
  14. [14]
    M. R. Falvo, G. J. Clary, R. M. Taylor, V. Chi, F.P. Brooks, S. Washburn and R. Superfine, Bending and buckling of carbon nanotubes under large strain, Nature. 389 (1997) 582–584.CrossRefGoogle Scholar
  15. [15]
    M. Guthold, G. Matthews, A. Negishi, R. M. Taylor, D. Erie, F.P. Brooks and R. Superfine, Quantitative manipulation of DNA and viruses with the nanomanipulator scanning force microscope, Surface Interface Analysis. 27 (1999) 437–443.CrossRefGoogle Scholar
  16. [16]
    J. L. Alonso and W. H. Goldmann, Feeling the forces: atomic force microscopy in cell biology, Life Sciences, 72 (2003) 2553–2560.CrossRefGoogle Scholar
  17. [17]
    M. Radmacher and M. Radmacher, Measuring the elastic properties of biological samples with the AFM, Engineering in Medicine and Biology Magazine, IEEE, 16 (1997) 47–57.CrossRefGoogle Scholar
  18. [18]
    F. Arai, G. U. Lee and R. J. Colton, Integrated microendeffector for micromanipulation, IEEE/ASME Transactions on Mechatronics. 3 (1998) 17–23.CrossRefGoogle Scholar
  19. [19]
    J. Dargahi, M. Parameswaran and S. Payandeh, A micromachined piezoelectric tactile sensor for an endoscopic grasper-theory, fabrication and experiments, Journal of Microelectromechanical Systems. 9 (2000) 329–335.CrossRefGoogle Scholar
  20. [20]
    D. H. Kim, B. Kim and J. O. Park, Implementation of a piezoresistive MEMS cantilever for nanoscale force measurements in micro/nano robotic applications, KSME International Journal. 18 (2004) 789–797.Google Scholar
  21. [21]
    J. Y. Park, D. H. Kim, T. S. Kim, B. Kim and K. I. Lee, Design and Performance Evaluation of a 3-DOF Mobile Microrobot for Micro Manipulation, KSME International Journal, 17(9) (2003) 1268–1275.Google Scholar
  22. [22]
    J. Y. Park, S. M. Kim, D. H. Kim, B. Kim, S. J. Kwon, J. -O. Park and K. I. Lee, Identification and Control of a Sensorized Microgripper for Micromanipulation, IEEE/ASME Transactions on Mechatronics, 10(5) (2005) 601–606.CrossRefGoogle Scholar
  23. [23]
    G. Y. Chen, R. J. Warmack, T. Thundat, D. P. Allison and A. Huang, Resonance response of scanning force microscopy cantilevers, Review of Scientific Instrument. 65 (1994) 2532–2537.CrossRefGoogle Scholar
  24. [24]
    L. D. Landau and E. M. Lifshitz, Fluid Mechanics, Pergamon, New York, 1959.Google Scholar
  25. [25]
    O. Wagner, J. Zinke, P. Dancker, W. Grill and J. Bereiter-Hahn, Viscoelastic properties of f-actin, microtubules, f-actin/a-actinin, and factin/hexokinase determined in microliter volumes with a novel nondestructive method, Biophysical Journal. 76 (1999) 2784–2796.CrossRefGoogle Scholar
  26. [26]
    R. E. Mahaffy, S. Park, E. Gerde, J. Kas and C. K. Shih, Quantitative analysis of the viscoelastic properties of thin regions of fibroblasts using atomic force microscopy, Biophysical Journal. 86 (2004) 1777–1793.CrossRefGoogle Scholar
  27. [27]
    L. Ljung, System Identification: Theory for the User, 2nd Edition, Prentice Hall PTR, 1999.Google Scholar
  28. [28]
    J. Howard, Mechanics of Motor Proteins and the Cytoskeleton, Sinauer Associates, Sunderland, MA. 2001.Google Scholar

Copyright information

© The Korean Society of Mechanical Engineers and Springer-Verlag GmbH 2008

Authors and Affiliations

  • Deok-Ho Kim
    • 1
  • Jungyul Park
    • 2
  • Moon K. Kim
    • 3
  • Keum-Shik Hong
    • 4
  1. 1.Department of Biomedical EngineeringJohns Hopkins UniversityBaltimoreUSA
  2. 2.Department of Mechanical EngineeringSogang UniversitySeoulKorea
  3. 3.School of Mechanical EngineeringSungkyunkwan UniversitySuwonKorea
  4. 4.School of Mechanical EngineeringPusan National UniversityBusanKorea

Personalised recommendations