D. R. Beniac, G. J. Czarnota, T. A. Barlett, B. R. Rutherford, F. P. Ottensmeyer, and G. Harauz, "Challenges of three-dimensional reconstruction of ribonucleoprotein complexes from electron spectroscopic images: Reconstructing ribosomal RNA," Scan. Microsc., vol. 11, pp. 301-322, 1997.
Y. Hiraoka, J. R. Swedlow, M. R. Paddy, D. A. Agard, and J. W. Sedat, "Three-dimensional multiple-wavelenght fluorescence microscopy for the structural analysis of biological phenomena," Sem. Cell. Biol., vol. 2, pp. 153-165, 1991.
R. Foisner, F. E. Leichfried, H. Herrmann, J. V. Small, D. Lawson, and G. Wiche, "Cytoskeleton-associated plectin: In situ localization, in vitro reconstitution, and binding to immobilized intermediate filament proteins," J. Cell. Biol., vol. 106, pp. 723-733, 1988.
E. Aamodt and J. G. Culotti, "Microtubules and microtubule-associated proteins from the nematode caenorhabditis elegans: Periodic cross-links connect microtubules in vitro," J. Cell. Biol., vol. 103, pp. 23-31, 1986.
M. Jaumot, X. Grana, A. Giordano, P. V. Reddy, N. Agell, and O. Bachs, "Cyclin/cdk2 complexes in the nucleus of hela cells," Biochem. Biophys. Res. Commun., vol. 203, pp. 1527-1534, 1994.
K. Oakata, S. Hisanaga, J. C. Bulinski, H. Murofushi, H. Aizawa, T. J. Itoh, H. Hotani, E. Okumura, K. Tachibana, and T. Kishimoto, "Cyclin B interaction with microtubule-associated protein 4 (MAP4) targets p34cdc2 kinase to microtubules and is a potential regulator of M-phase microtubule dynamics," J. Cell Biol., vol. 128, pp. 849-862, 1995.
B. Buchwitz, K. Ahmad, L. L. Moore, M. B. Roth, and S. Henikoff, "Cell division: A histone-H3-like protein in C. elegans," Nature, vol. 401, pp. 547-548, 1999.
T. Nguyen-Ngoc, K. Afshar, and P. Gonczy, "Coupling of cortical dynein and ga proteins mediates spindle position in caenorhabditis elegans," Nat. Cell. Biol., vol. 9, pp. 1294-1302, 2007.
L. Zhang, M. S. Anglesio, M. O’sullivan, F. Zhang, G. Yang, R. Sarao, M. Ngheim, S. Cronin, H. Hara, N. Melnyk, L. Li, T. Wada, P. Liu, J. Farrar, R. Arceci, P. Sorensen, and J. Penninger, "The E3 ligase HACE1 is a critical chromosome 6q21 tumor suppressor involved in multiple cancers," Nat. Med., vol. 13, pp. 1060-1069, 2007.
A. Deniset-Besseau, S. Lévêque-Fort, M. P. Fontaine-Aupart, G. Roger, and P. Georges, "Three-dimentional time-resolved fluorescence imaging by multifocal multiphoton microscopy for a photosensitizer study in living cells," Appl. Opt., vol. 46, pp. 8045-8051, 2007.
K. Frick, P. Marnitz, and A. Munk, "Statistical multiresolution dantzig estimation in imaging: Fundamental concepts and algorithmic network," Electr. J. Statist., vol. 6, pp. 231-268, 2012.
K. Frick, P. Marnitz, and A. Munk, "Statistical multiresolution estimation for variational imaging: With an application of poisson-biophotonics," J. Math. Imag. Vis., vol. 46, pp. 370-387, 2013.
B. J. Kopek, G. Shtengel, C. S. Xu, D. A. Clayton, and H. F. Hess, "Correlative 3D supperresolution fluorescence and electron microscopy reveal the relationship of mitochondrial nucleoids to membranes," Proc. Natl. Acad. Sci. U.S.A, vol. 106, pp. 6136-6141, 2012.
H. Ma, Q. Jiang, S. Han, Y. Wu, J. C. Tomshine, D. Wang, Y. Gan, G. Zou, and X. J. Liang, "Multicellular tumor spheroids as an in vitro-like tumor model for three-dimensional imaging of chemotherapeutic and nano material cellular penetration," Molec. Imag., vol. 11, pp. 487-498, 2012.
N. Maghelli and I. M. Toli?-Nørrelykke, "Optical trapping and laser ablation of microtubules in fission yeast," Meth. Cell. Biol., vol. 97, pp. 173-183, 2010.
J. Goncalves, M. Graos, and A. X. C. N. Valente, "Polar mapper: Computational tool for integrated visualization of protein interaction networks and mRNA expression data," Nat. Preced., vol. 6, pp. 881-896, 2009.
P. Gönczy, C. Echeverri, K. Oegema, A. Coulson, S. J. M. Jones, R. R. Copley, J. Duperon, J. Oegema, M. Brehm, E. Cassin, E. Hannak, M. Kirkham, S. Pichler, K. Flohrs, A. Goessen, S. Leidel, A. M. Alleaume, C. Martin, N. Ozlu, P. Bork, and A. A. Hyman, "Functional genomica analysis of cell division in C. elegans using RNAi of genes in chromosome III. ," Nature, vol. 408, pp. 331-336, 2000.
Y. Ding, H. Xie, T. Peng, Y. Lu, D. Jin, J. Teng, Q. Ren, and P. Xi, "Laser oblique scanning optical microscopy (LOSOM) for phase relief imaging," Opt. Soc. Am., vol. 20, pp. 14100-14108, 2012.
L. Schermelleh, P. M. Carlton, S. Haase, L. Shao, L. Winoto, P. Kner, B. Burke, C. M. Cardoso, D. A. Agard, M. G. L. Gustafsson, H. Leonhardt, and J. W. Sedat, "Subdiffraction multicolor imaging of the nuclear periphery with 3D structured illumination microscopy," Science, vol. 320, pp. 1332-1336, 2008.
S. R. Swift and L. Trinkle-Mulcahy, "Basic principles of FRAP, FLIM and FRET," Proc. Royal Mic. Soc., vol. 39, pp. 3-10, 2004.
E. Torregianni, G. Lisignoli, C. Manferdini, E. Lambertini, L. Penolazzi, R. Vacchiatini, P. Chieco, A. Facchini, R. Gambari, and R. Piva, "Role of slug transcription factor in human mesenchymal stem cells," J. Cell. Mol. Med., vol. 16, pp. 740-751, 2012.
L. Yu, S. Mohanty, J. Zhang, S. Genc, M. K. Kim, M. W. Berns, and Z. Chen, "Digital cholographic microscopy for quantitative cell dynamic evaluation during laser microsurgery," Opt. Soc. Am., vol. 17, pp. 12031-12038, 2009.
B. Kemper, P. Langehanenberg, and G. Von Bally, "Digital holographic microscopy," Optik & Photonik, vol. 2, pp. 41–44, 2007.
P. P. McDonnald, A. Bald, and M. A. Cassatella, "Activation of NF-kappaB pathway by inflammatory stimuli in human neutrophils," Blood, vol. 89, pp. 3421-3433, 1997.
J. El Benna, J. Han, J. W. Park, E. Schmid, R. J. Ulevitch, and B. M. Babior, "Activation of p38 in stimulated human neutrophils: Phosphorylation of the oxidase component p47phox by p38 and ERK but not by JNK," Arch. Biochem. Biophys., vol. 334, pp. 395-400, 1986.
R. E. Rowland and E. M. Nickless, "Confocal microscopy opens the door to 3-dimensional analysis of cells," Bioscience, vol. 26, pp. 3-7, 2000.
H. Niioka, N. I. Smith, K. Fujita, Y. Inouye, and S. Kawata, "Femtosecond laser nano-ablation in fixed and non-fixed cultured cells," Opt. Soc. Am., vol. 16, pp. 14476-14495, 2008.
Sainova, I. Valkova, V. Pavlova, and E. Nikolova, "Development of improved methods for protein separation and identification," Int. J. Electron. Commun. Comput. Eng., vol. 4, pp. 415-417, 2013.
M. Fischer, I. Haase, E. Simmeth, G. Gerisch, and A. Müller-Taubenberger, "A brilliant monomeric red fluorescent protein to visualize cytoskeleton dynamics in dictyostelium," FEBS Lett., vol. 577, pp. 227-232, 2004.
Sainova, I. Vavrek, V. Pavlova, T. Daneva, I. Iliev, L. Yossifova, E. Gardeva, and E. Nikolova, "Experimental in vitro-stem cell models for balanced activity of oncogenes and tumor-suppressor genes from mouse and human," Adv. Biores., vol. 3, pp. 69-72, 2012.
Iskra V Sainova , Ilina P Valkova , Bistra Alexieva , Elena B Nikolova , Angel Baldzhiev , Daniela Karashanova , Biliana Georgieva , Angel Alishev , Marin Nenchev (2016). A Pilot Study of Methods about Detection of Inter-Molecular Interactions As Individual Units of Intra-Cellular Structures, Intra- And Extra-Cellular Cascade Regulatory Pathways. World Journal of Molecular Research, 1(1): 1-13. DOI: 10.18488/journal.505/2016.1.1/505.1.1.13
Different methods for investigation on the mechanisms of participation of cell proteins in direct and/or indirect intra- and extra-cellular inter-molecular (protein-lipid, protein-protein, protein-RNA, protein-DNA interactions, etc.), by cascade regulatory pathways were developed and tested. These bio-molecules (in particular microtubule proteins and cyclins) have been found as parts from different complex structures from the nuclear, cytoskeleton and membrane cell fractions, as mitotic spindle, endocytosis vesicles, cell organelles, membrane structures, which are important for basic cell functions. The techniques, developed in the current study, could be useful for identification of the proteins/peptides, participating in the composition of these structures, but also of the interactions between them, on molecular and intra-molecular levels. For confirmation of the results obtained and the reliability of the applied methods, routine techniques as scanning electron microscopy (SEM) and transmission electron microscopy (TEM) assays were used. In all cases, the main goal is directed to search of molecules, participating in the control of cell growth and proliferation, as well as of such, which determine the further cell fate during cell differentiation and maturation.
The current study contributes in the existing literature with confirmation of the inter-molecular interactions for the cell differentiation direction. The current paper underlines the relationship between the changes in three different levels: cell morphology; intra-cellular organelles structure, and bio-molecules, by application of novel detection methods.
M. Nznojil, "The perturbated sine-gordon equation," ACTA Physica Polonica, vol. B 10, pp. 951-958, 1979.
A. M. Dikande, "Kink dislocations in layered lattices with periodic interlayer substrate interactions," Phys. Stat. Sol., vol. 208, pp. 5-14, 1998.
S. Rainer, K. S. Yuri, S. Angel, and B. R. Alan, "Sine-gordon kink-antikink generation on spatially periodic potentials generation," Phys. Rev. A, vol. 45, pp. R5369-R5372, 1992.
V. Anna and K. G. Panayotis, "Dynamics of phase transitions in a piecewise linear diatomic chain," J. Nonlinear Sci., vol. 22, pp. 107-134, 2012.
N. A. S. Tchakoutio and T. C. Kofane, "Soliton patterns and breakup thresholds in hydrogen-bonded chains," Eur. Phys. J. B, vol. 57, pp. 411–422, 2007.
V. M. Karpan, Y. Zolotaryuk, P. L. Christiansen, and A. V. Zolotaryuk, "Discrete kink dynamics in hydrogen-bonded chains: The two-component model," Phys. Rev., vol. E 70, pp. 1-11, 2004.
A. V. Zolotaryuk, M. Peyrard, and K. H. Spatschek, "Collective proton transport with weak proton-proton coupling," Phys. Rev. E, vol. 62, pp. 1-5, 2000.
R. Grauer, K. H. Spatschek, and A. V. Zolotaryuk, "Chaotic proton dynamics in the hydrogen bond," Phys. Rev. E, vol. 47, pp. 236-247, 1993.
B. Malin, W. Jakob, H. E. Michael, and B. W. John, "Simulation studies of the insolubility of cellulose," Carbohydrate Research, vol. 345, pp. 2060–2066, 2010.
W. A. Colin, "Chance and design—proton transfer in water, channels and bioenergetic proteins," Biochimica et Biophysica Acta, vol. 1757, pp. 886–912, 2006.
G. W. Ford, J. T. Lewis, and R. F. O’connell, "Quantum langevin equation," Phys. Rev. A, vol. 37, pp. 4419-4428, 1988.
P. Elie, "Variational transition state of reaction rate in dissipative system," Phys. Rev. Lett., vol. 67, pp. 1399-1402, 1990.
H. H. Risken, The Fokker-Planck equation. Springer series in synergetics vol. 18. Berlin: Springer-Verlag, 1934.
M. Tchoffoet, "Kinematical brownian motion and time dependent entropy," Far East Journal of Applied Mathematics, vol. 68, pp. 21-28, 2012.
P. Elie, G. Hermann, and H. Peter, "Theory of activated rate process for arbitrary frequency dependent friction: Solution of the turnover problem," J. Chem. Phys., vol. 84, pp. 4073-4087, 1986.
J. C. Latorre, G. A. Pavliotis, and P. R. Kramer, "Corrections to einstein’s relation for Brownian motion in a tilted periodic potential," J. Stat. Phys., pp. 1-28. Doi: 10.1007/s10955-013-0692-1, 2012.
H. Peter and H. Waldemar, "Tunneling in reaction theory: The effect of memory friction," Physica Scripta, vol. 37, pp. 559-563, 1988.
L. J. Kelth and K. M. Chrlstlne, "The development of transition-state theory," J. Phys. Chem., vol. 87, pp. 2657-2664, 1983.
G. Hermann, "Escape from a metastable well: The Kramers turnover problem," Phys. Rev. Lett., vol. 61, pp. 1683-1686, 1988.
M. J. R. Antonio and H. Peter, "Escape from a fluctuating double well," Phys. Rev. E, vol. 51, pp. 3849-3861, 1995.
C. Srabanti and C. J. Binny, "Approximate first passage time distribution for barrier crossing in a double well under fractional Gaussian noise," J. Chem. Phys., vol. 125, pp. 1-8, 2006.
L. Benjamin, "Correlations in the sequence of residence times," Phys. Rev. Lett., vol. 98, pp. 1-4, 2007.
J. L. Vega, R. Guantes, and S. Miret-Arte´s, "Mean first passage time and the Kramers turnover theory in activated atom–surface diffusion," Phys. Chem. Chem. Phys., vol. 4, pp. 4985–4991, 2002.
C. T. William, K. P. Yuri, and T. V. Sergey, "Thermally activated escape rate for the Brownian motion of a fixed axis rotator in a double well potential for all values of the dissipation," J. Chem. Phys., vol. 120, pp. 9199-9211, 2004.
L.C. Fai , J.C.Ngana. Kuetche , G.C. Fouokeng , M. Tchoffo , E.A. Ngwa (2016). Thermal Activationprocess in Hydrogen Bonds. World Journal of Molecular Research, 1(1): 14-26. DOI: 10.18488/journal.505/2016.1.1/505.1.14.26
We study the Markovian process on parameterized approximate nonlinear one-dimensional double Morse potentials, used to describe the collective proton dynamics in one dimensional network of hydrogen bonds. Using Kramer’s method, the first and second moment of the proton’s dynamic is evaluated respectively in the case of over damping, intermediate damping and very low damping limit. We found out that in the case of an over damping limit and intermediate damping, the dynamics of the proton decrease when the curvature parameter increases. In the case of very low damping limit, the motion of the proton in the well became independent on the curvature parameter.
This study is one of very few studies which have investigated on the interaction between the heat bath and the hydrogen bonds chain subject to parameterized nonlinear one-dimensional double Morse potentials more precisely the dependence of some physicals quantities with the curvature parameter.