A dynamic model for the p53 stress response networks under ion radiation

Summary.P53 controls the cell cycle arrest and cell apoptosis through interaction with the downstream genes and their signal pathways. To stimulate the investigation into the complicated responses of p53 under the circumstance of ion radiation (IR) in the cellular level, a dynamic model for the p53 stress response networks is proposed. The model can be successfully used to simulate the dynamic processes of generating the double-strand breaks (DSBs) and their repairing, ataxia telangiectasia mutated (ATM) activation, as well as the oscillations occurring in the p53-MDM2 feedback loop.

[1]  M. Ritter,et al.  The role of p53 in radiation therapy outcomes for favorable-to-intermediate-risk prostate cancer. , 2002, International journal of radiation oncology, biology, physics.

[2]  Bimolecular reactions with a reactive site on a spherical particle: A Hamiltonian formulation , 1988 .

[3]  C. Zhang,et al.  A graphic approach to analyzing codon usage in 1562 Escherichia coli protein coding sequences. , 1994, Journal of molecular biology.

[4]  G M Maggiora,et al.  Solitary wave dynamics as a mechanism for explaining the internal motion during microtubule growth , 1994, Biopolymers.

[5]  Junying Yuan,et al.  Solution Structure of BID, an Intracellular Amplifier of Apoptotic Signaling , 1999, Cell.

[6]  K C Chou,et al.  Kinetics of processive nucleic acid polymerases and nucleases. , 1994, Analytical biochemistry.

[7]  A. Levine,et al.  Surfing the p53 network , 2000, Nature.

[8]  G. Zhou,et al.  An extension of Chou's graphic rules for deriving enzyme kinetic equations to systems involving parallel reaction pathways. , 1984, The Biochemical journal.

[9]  K. Chou,et al.  Prediction of the tertiary structure of a caspase‐9/inhibitor complex , 2000, FEBS letters.

[10]  Arnold Kristjuhan,et al.  ARF and ATM/ATR cooperate in p53-mediated apoptosis upon oncogenic stress. , 2005, Biochemical and biophysical research communications.

[11]  K. Chou,et al.  Role of the protein outside active site on the diffusion-controlled reaction of enzymes , 1982 .

[12]  Paul Van Houtte,et al.  NF-kappaB modulation and ionizing radiation: mechanisms and future directions for cancer treatment. , 2006, Cancer letters.

[13]  K. Chou,et al.  The biological functions of low‐frequency vibrations (phonons). VI. A possible dynamic mechanism of allosteric transition in antibody molecules , 1987, Biopolymers.

[14]  G M Maggiora,et al.  Quasi-continuum models of twist-like and accordion-like low-frequency motions in DNA. , 1989, Biophysical journal.

[15]  C. Zhang,et al.  Diagrammatization of codon usage in 339 human immunodeficiency virus proteins and its biological implication. , 1992, AIDS research and human retroviruses.

[16]  K. Chou,et al.  Graphic rules in steady and non-steady state enzyme kinetics. , 1989, The Journal of biological chemistry.

[17]  K. Chou,et al.  Low-frequency vibrations of DNA molecules. , 1984, The Biochemical journal.

[18]  Karl Otto Greulich,et al.  After double-strand break induction by UV-A, homologous recombination and nonhomologous end joining cooperate at the same DSB if both systems are available , 2004, Journal of Cell Science.

[19]  W. Han.  The influence of dipole—dipole interaction on the low-frequency vibrations in alpha-helix proteins , 1992 .

[20]  Meng Wang,et al.  A new nucleotide-composition based fingerprint of SARS-CoV with visualization analysis. , 2005, Medicinal chemistry (Shariqah (United Arab Emirates)).

[21]  K. Chou,et al.  Low-frequency resonance and cooperativity of hemoglobin. , 1989, Trends in biochemical sciences.

[22]  Zachariah Sinkala,et al.  Soliton/exciton transport in proteins. , 2006, Journal of theoretical biology.

[23]  C. Kuo-chen,et al.  Studies on the rate of diffusion-controlled reactions of enzymes. Spatial factor and force field factor. , 1974, Scientia Sinica.

[24]  K. Neet,et al.  Demonstration of a slow conformational change in liver glucokinase by fluorescence spectroscopy. , 1990, The Journal of biological chemistry.

[25]  W. Zhong,et al.  Diffusion‐Controlled Reactions of Enzymes , 2005 .

[26]  K. Chou,et al.  Collective motion in DNA and its role in drug intercalation , 1988, Biopolymers.

[27]  J. Tyson,et al.  Regulation of the eukaryotic cell cycle: molecular antagonism, hysteresis, and irreversible transitions. , 2001, Journal of theoretical biology.

[28]  S. Forsén,et al.  Graphical rules for enzyme-catalysed rate laws. , 1980, The Biochemical journal.

[29]  Michael Weller,et al.  Predicting response to cancer chemotherapy: the role of p53 , 1998, Cell and Tissue Research.

[30]  K. Chou,et al.  Prediction of the tertiary structure and substrate binding site of caspase‐8 , 1997, FEBS letters.

[31]  J. Chou,et al.  Steady-state kinetic studies with the non-nucleoside HIV-1 reverse transcriptase inhibitor U-87201E. , 1993, The Journal of biological chemistry.

[32]  J A Purdy,et al.  Treatment planning in radiation oncology and impact on outcome of therapy. , 1998, Rays.

[33]  Yongsheng Ding,et al.  An application of gene comparative image for predicting the effect on replication ratio by HBV virus gene missense mutation. , 2005, Journal of theoretical biology.

[34]  K D Watenpaugh,et al.  A model of the complex between cyclin-dependent kinase 5 and the activation domain of neuronal Cdk5 activator. , 1999, Biochemical and biophysical research communications.

[35]  Guo-Ping Zhou,et al.  Biological functions of soliton and extra electron motion in DNA structure , 1989 .

[36]  Zhen-De Huang,et al.  A novel fingerprint map for detecting SARS-CoV , 2005, Journal of Pharmaceutical and Biomedical Analysis.

[37]  The vibrational normal modes of β-barrels in an IgG antibody molecule , 1992 .

[38]  Chou Kuo-Chen,et al.  GRAPH THEORY OF ENZYME KINETICS I.STEADY-STATE REACTION SYSTEMS , 1979 .

[39]  G Zhou,et al.  Diffusion-controlled reactions of enzymes. An approximate analytic solution of Chou's model. , 1983, Biophysical chemistry.

[40]  Gilbert Chu,et al.  Processing of DNA for nonhomologous end‐joining by cell‐free extract , 2005, The EMBO journal.

[41]  M. Kastan,et al.  DNA damage activates ATM through intermolecular autophosphorylation and dimer dissociation , 2003, Nature.

[42]  Diffusion-controlled reactions of enzymes. A comparison between Chou's model and Alberty-Hammes-Eigen's model. , 1982, European journal of biochemistry.

[43]  Fayza Daboussi,et al.  DNA double-strand break repair signalling: the case of RAD51 post-translational regulation. , 2002, Cellular signalling.

[44]  Yves Pommier,et al.  Molecular interaction map of the p53 and Mdm2 logic elements, which control the Off-On switch of p53 in response to DNA damage. , 2005, Biochemical and biophysical research communications.

[45]  K. Chou,et al.  THE BIOLOGICAL FUNCTIONS OF LOW-FREQUENCY PHONONS , 1977 .

[46]  M. Oren,et al.  Decision making by p53: life, death and cancer , 2003, Cell Death and Differentiation.

[47]  Uri Alon,et al.  Dynamics of the p53-Mdm2 feedback loop in individual cells , 2004, Nature Genetics.

[48]  John Jeremy Rice,et al.  A plausible model for the digital response of p53 to DNA damage. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[49]  K. Chou.  Structural bioinformatics and its impact to biomedical science. , 2004, Current medicinal chemistry.

[50]  P. Kuzmič,et al.  Mixtures of tight-binding enzyme inhibitors. Kinetic analysis by a recursive rate equation. , 1992, Analytical biochemistry.

[51]  C. Zhang,et al.  An analysis of base frequencies in the anti-sense strands corresponding to the 180 human protein coding sequences , 1996, Amino Acids.

[52]  J. Levine,et al.  Surfing the p53 network , 2000, Nature.

[53]  P Martel,et al.  Biophysical aspects of neutron scattering from vibrational modes of proteins. , 1992, Progress in biophysics and molecular biology.

[54]  L. Resnick,et al.  The quinoline U-78036 is a potent inhibitor of HIV-1 reverse transcriptase. , 1993, The Journal of biological chemistry.

[55]  K. Chou.  Applications of graph theory to enzyme kinetics and protein folding kinetics. Steady and non-steady-state systems. , 2020, Biophysical chemistry.

[56]  K. Chou,et al.  Low-frequency collective motion in biomacromolecules and its biological functions. , 1988, Biophysical chemistry.

[57]  J. Tyson,et al.  Models of cell cycle control in eukaryotes. , 1999, Journal of biotechnology.

[58]  U Alon,et al.  Generation of oscillations by the p53-Mdm2 feedback loop: a theoretical and experimental study. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[59]  E. L. King,et al.  A Schematic Method of Deriving the Rate Laws for Enzyme-Catalyzed Reactions , 1956 .

[60]  Kai Rothkamm,et al.  Pathways of DNA Double-Strand Break Repair during the Mammalian Cell Cycle , 2003, Molecular and Cellular Biology.

[61]  Kuo-Chen Chou,et al.  A probability cellular automaton model for hepatitis B viral infections. , 2006, Biochemical and biophysical research communications.