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Modeling Behavior of a Chain of Protein as a Bionanorobot by Changing Environmental Condition | ||
| AUT Journal of Mechanical Engineering | ||
| مقاله 12، دوره 1، شماره 1، شهریور 2017، صفحه 109-116 اصل مقاله (4.64 M) | ||
| نوع مقاله: Research Article | ||
| شناسه دیجیتال (DOI): 10.22060/mej.2016.757 | ||
| نویسندگان | ||
| A. Gaffari1؛ A. Khodayari* 2؛ Sh. Movasagh1 | ||
| 1Faculty of Mechanical Engineering, K. N. Toosi University of Technology, Tehran, Iran | ||
| 2Faculty of Mechanical Engineering, Pardis Branch Islamic Azad University, Tehran, Iran | ||
| چکیده | ||
| In this paper, the behavior of one chain of small heat shock protein based on molecular dynamic simulation is modeled by the nonlinear identifier. Molecular dynamic simulation is timeconsuming due to the high load of calculations, and providing a model of system behavior facilitates utilizing protein as a bio nano robot in a shorter time. The ARC1 is a molecular Chaperone with swarm structure containing 12 chains. Each chain of small heat shock protein contains two sections; arm and the central cavity which is introduced as a bionanorobot for their special biological structure and their reaction to external forces. The conformational changes of protein with one chain due to external excitation have been analyzed. In addition to system identification of one chain of small heat shock protein, the effect of temperature, pH, and content of solvent are examined on the behavior of bionanorobot arm and a central cavity in a wide range of variation. The results show that minimum number of error is relevant to the adaptive neuro fuzzy system identifier. Modeling the behavior of one chain provides a suitable condition to control the central cavity and bionanorobot arm in a shorter period of time compared to the molecular dynamic simulation. | ||
تازه های تحقیق | ||
[1] R.J.K. T. Hogg, Mobile micro scopic sensors for high resolution in vivo diagnostics, Nano medicine: Nano technology, Biology and Medicine, 2(4) (2006) 239-247. [2] A. Requicha, Instrumented cellular systems, Nanomedicine: Nanotechnology, Biology and Medicine, 2(4) (2006) 278-287. [3] B.S. A. Calvacanti, R. Freitas,T. Hogg, Nanorobot architecture for medical target identification, Nanotechnology, 19(1) (2008) 1-15. [4] A.F. M. Hamdi, DNA nanorobotics, Microelectronics Journal, 39(8) (2008) 1051-1059. [5] C.B.K. E. Steager, J. Patel, S. Bith,C. Naik, L. Reber,M. J. Kim Control of microfabricated structures powered by flagellated bacteria using phototaxis, Applied Physics Letters, 90(26) (2006) 263901-263903. [6] B.J.N. L.X. Dong, T. Fukuda, F. Arai, 2006. “Towards linear nano servomotors”. , 3(3), pp. 228–235., , IEEE Transactions on Automation Science and Engineering, 3(3) (2006) 228-235. [7] L.X.D. A. Subramanian, B. J. Nelson, Batch fabrication of carbon nanotube bearings, Nanotechnology, 18(7) (2007) 075703. [8] K.K. G.S. Chirikjian, C. Mavroidis Analysis and design of protein based nanodevices: challenges and opportunities in mechanical design, Journal of Mechanical Design, 127(4) (2005) 695–698. [9] O.M.A. R. T. Richardson, G. Grossman, et al, Nuclear Autoantigenic Sperm Protein (NASP), a Linker Histone Chaperone That is required for Cell Proliferation, Journal of Biological Chemistry, 281(30) (2006) 21526–21534. [10] S.M.v.d.V. R. J. Ellis, Molecular Chaperones, Annual review of biochemistry, 60(1) (1991) 321–347. [11] A.S. A. Ghaffari, R. Hasanzadeh Ghasemi, Capturing and releasing a nano cargo by Prefoldin nano actuator, Sensors and Actuators B: Chemical, 171-172(1) (2012) 1199-1206. [12] A.S. A. Ghaffari, R. Hasanzadeh Ghasemi, Design and simulation of a novel bio nano actuator by Prefoldin, in: 10th IEEE Conference on Nanotechnology, 2010, pp. 885-888. [13] A.S. A. Ghaffari, R. Hasanzadeh Ghasemi, Prefoldin: A nano actuator for carrying the various size nano drugs, Journal of Computational and Theoretical Nanoscience, 8(10) (2011) 2078-2086. [14] C.S. R. Van Montfort, E. Vierling, Structure and function of the small heat shock protein /α-crystallin family of molecular chaperones, Advances in Protein Chemistry 59(1) (2001) 105–156. [15] F. Narberhaus, Mechanism of chaperone function in small heat shock proteins, Microbiology and Molecular Biology Reviews, 66(1) (2002) 64–93. [16] J.L.P.B. C. K. Kennaway, U. Gohlke, L. Wang, E. V. rlova, C. V. Robinson, H. R. Saibil, N. H. Keep, Dodecameric structure of the small heat shock protein Acr1 from Mycobacterium tuberculosis, Journal of Biological Chemistry, 280(39) (2005) 33419–33425. [17] D. Shugar, Dynamics of Proteins and Nucleic Acids, FEBS Letters, 253(1) (1987) 248. [18] D.v.d.S. B. Hess, E. Lindahl, et al, GROMACS USER MANUAL Version 4.5.6, Department of Biophysical Chemistry, University of Groningen & 2001–2010: The GROMACS development teams at the Royal Institute of Technology and Uppsala University, Sweden, 1991- 2000. [19] A.E.M. T. A. Wassenaar, The Effect of Box Shape on the Dynamic Properties of Proteins Simulated under Periodic Boundary Conditions, Journal of computational chemistry, 27(3) (2006) 316-325. [20] K. Pauwels, Chaperoning Anfinsen: The Steric Foldases, Molecular Microbiology, 64(4) (2007) 917-922. [21] G. Dorffner, Neural Networks for Time Series Processing, Neural Network World, 6(4) (1996) 447-468. [22] G.B.O. G. Montavon, K. R. Muller, Neural Networks: Tricks of the Trade, Berlin, Springer., 2012. [23] S.A.B. S. Chen, Neural network for nonlinear dynamic system modeling and identification, International Journal of Control, 56(2) (1992) 319–346. | ||
| کلیدواژه‌ها | ||
| Chaperone protein؛ Bionanorobot؛ GROMACS؛ Molecular dynamic؛ Nonlinear identifier | ||
| مراجع | ||
|
[1] R.J.K. T. Hogg, Mobile micro scopic sensors for high resolution in vivo diagnostics, Nano medicine: Nano technology, Biology and Medicine, 2(4) (2006) 239-247.
[2] A. Requicha, Instrumented cellular systems, Nanomedicine: Nanotechnology, Biology and Medicine, 2(4) (2006) 278-287.
[3] B.S. A. Calvacanti, R. Freitas,T. Hogg, Nanorobot architecture for medical target identification, Nanotechnology, 19(1) (2008) 1-15.
[4] A.F. M. Hamdi, DNA nanorobotics, Microelectronics Journal, 39(8) (2008) 1051-1059.
[5] C.B.K. E. Steager, J. Patel, S. Bith,C. Naik, L. Reber,M. J. Kim Control of microfabricated structures powered by flagellated bacteria using phototaxis, Applied Physics Letters, 90(26) (2006) 263901-263903.
[6] B.J.N. L.X. Dong, T. Fukuda, F. Arai, 2006. “Towards linear nano servomotors”. , 3(3), pp. 228–235., , IEEE Transactions on Automation Science and Engineering, 3(3) (2006) 228-235.
[7] L.X.D. A. Subramanian, B. J. Nelson, Batch fabrication of carbon nanotube bearings, Nanotechnology, 18(7) (2007) 075703.
[8] K.K. G.S. Chirikjian, C. Mavroidis Analysis and design of protein based nanodevices: challenges and opportunities in mechanical design, Journal of Mechanical Design, 127(4) (2005) 695–698.
[9] O.M.A. R. T. Richardson, G. Grossman, et al, Nuclear Autoantigenic Sperm Protein (NASP), a Linker Histone Chaperone That is required for Cell Proliferation, Journal of Biological Chemistry, 281(30) (2006) 21526–21534.
[10] S.M.v.d.V. R. J. Ellis, Molecular Chaperones, Annual review of biochemistry, 60(1) (1991) 321–347.
[11] A.S. A. Ghaffari, R. Hasanzadeh Ghasemi, Capturing and releasing a nano cargo by Prefoldin nano actuator, Sensors and Actuators B: Chemical, 171-172(1) (2012) 1199-1206.
[12] A.S. A. Ghaffari, R. Hasanzadeh Ghasemi, Design and simulation of a novel bio nano actuator by Prefoldin, in: 10th IEEE Conference on Nanotechnology, 2010, pp. 885-888.
[13] A.S. A. Ghaffari, R. Hasanzadeh Ghasemi, Prefoldin: A nano actuator for carrying the various size nano drugs, Journal of Computational and Theoretical Nanoscience, 8(10) (2011) 2078-2086.
[14] C.S. R. Van Montfort, E. Vierling, Structure and function of the small heat shock protein /α-crystallin family of molecular chaperones, Advances in Protein Chemistry 59(1) (2001) 105–156.
[15] F. Narberhaus, Mechanism of chaperone function in small heat shock proteins, Microbiology and Molecular Biology Reviews, 66(1) (2002) 64–93.
[16] J.L.P.B. C. K. Kennaway, U. Gohlke, L. Wang, E. V. rlova, C. V. Robinson, H. R. Saibil, N. H. Keep, Dodecameric structure of the small heat shock protein Acr1 from Mycobacterium tuberculosis, Journal of Biological Chemistry, 280(39) (2005) 33419–33425.
[17] D. Shugar, Dynamics of Proteins and Nucleic Acids, FEBS Letters, 253(1) (1987) 248.
[18] D.v.d.S. B. Hess, E. Lindahl, et al, GROMACS USER MANUAL Version 4.5.6, Department of Biophysical Chemistry, University of Groningen & 2001–2010: The GROMACS development teams at the Royal Institute of Technology and Uppsala University, Sweden, 1991- 2000.
[19] A.E.M. T. A. Wassenaar, The Effect of Box Shape on the Dynamic Properties of Proteins Simulated under Periodic Boundary Conditions, Journal of computational chemistry, 27(3) (2006) 316-325.
[20] K. Pauwels, Chaperoning Anfinsen: The Steric Foldases, Molecular Microbiology, 64(4) (2007) 917-922.
[21] G. Dorffner, Neural Networks for Time Series Processing, Neural Network World, 6(4) (1996) 447-468.
[22] G.B.O. G. Montavon, K. R. Muller, Neural Networks: Tricks of the Trade, Berlin, Springer., 2012.
[23] S.A.B. S. Chen, Neural network for nonlinear dynamic system modeling and identification, International Journal of Control, 56(2) (1992) 319–346. | ||
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