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.
Article PDF
Similar content being viewed by others
References
IW Althaus JJ Chou AJ Gonzales MR Diebel KC Chou FJ Kezdy DL Romero PA Aristoff WG Tarpley F Reusser (1993a) ArticleTitleSteady-state kinetic studies with the non-nucleoside HIV-1 reverse transcriptase inhibitor U-87201E J Biol Chem 268 6119–6124 Occurrence Handle1:CAS:528:DyaK3sXitVCktbo%3D
IW Althaus AJ Gonzales JJ Chou MR Diebel KC Chou FJ Kezdy DL Romero PA Aristoff WG Tarpley F Reusser (1993b) ArticleTitleThe quinoline U-78036 is a potent inhibitor of HIV-1 reverse transcriptase J Biol Chem 268 14875–14880 Occurrence Handle1:CAS:528:DyaK2cXksFagsw%3D%3D
CJ Bakkenist MB Kastan (2003) ArticleTitleDNA damage activates ATM through intermolecular autophosphorylation and dimer dissociation Nature 421 499–506 Occurrence Handle12556884 Occurrence Handle10.1038/nature01368 Occurrence Handle1:CAS:528:DC%2BD3sXntFSqsQ%3D%3D
J Budman G Chu (2005) ArticleTitleProcessing of DNA for nonhomologous end-joining by cell-free extract Embo J 24 849–860 Occurrence Handle15692565 Occurrence Handle10.1038/sj.emboj.7600563 Occurrence Handle1:CAS:528:DC%2BD2MXhsFWlsbc%3D
JJ Chou H Li GS Salvessen J Yuan G Wagner (1999a) ArticleTitleSolution structure of BID, an intracellular amplifier of apoptotic signalling Cell 96 615–624 Occurrence Handle10.1016/S0092-8674(00)80572-3 Occurrence Handle1:CAS:528:DyaK1MXitVChsro%3D
KC Chou (1984) ArticleTitleLow-frequency vibration of DNA molecules Biochem J 221 27–31 Occurrence Handle6466317 Occurrence Handle1:CAS:528:DyaL2cXkvVGrtb4%3D
KC Chou (1987) ArticleTitleThe biological functions of low-frequency phonons: 6. A possible dynamic mechanism of allosteric transition in antibody molecules Biopolymers 26 285–295 Occurrence Handle3828475 Occurrence Handle10.1002/bip.360260209 Occurrence Handle1:CAS:528:DyaL2sXhvFCgsr0%3D
KC Chou (1988) ArticleTitleReview: Low-frequency collective motion in biomacromolecules and its biological functions Biophys Chem 30 3–48 Occurrence Handle3046672 Occurrence Handle10.1016/0301-4622(88)85002-6 Occurrence Handle1:CAS:528:DyaL1cXks1yru7k%3D
KC Chou (1989a) ArticleTitleGraphical rules in steady and non-steady enzyme kinetics J Biol Chem 264 12074–12079 Occurrence Handle1:CAS:528:DyaL1MXkslekt7o%3D
KC Chou (1989b) ArticleTitleLow-frequency resonance and cooperativity of hemoglobin Trends Biochem Sci 14 212 Occurrence Handle10.1016/0968-0004(89)90026-1 Occurrence Handle1:CAS:528:DyaL1MXkvFamsbk%3D
KC Chou (1990) ArticleTitleReview: Applications of graph theory to enzyme kinetics and protein folding kinetics. Steady and non-steady state systems Biophys Chem 35 1–24 Occurrence Handle2183882 Occurrence Handle10.1016/0301-4622(90)80056-D Occurrence Handle1:CAS:528:DyaK3cXhslCntro%3D
KC Chou (2004) ArticleTitleReview: Structural bioinformatics and its impact to biomedical science Curr Med Chem 11 2105–2134 Occurrence Handle15279552 Occurrence Handle1:CAS:528:DC%2BD2cXlslWltbw%3D
KC Chou NY Chen (1977) ArticleTitleThe biological functions of low-frequency phonons Sci Sin 20 447–457 Occurrence Handle1:CAS:528:DyaE2sXlsl2nt78%3D
KC Chou S Forsen (1980) ArticleTitleGraphical rules for enzyme-catalyzed rate laws Biochem J 187 829–835 Occurrence Handle7188428 Occurrence Handle1:CAS:528:DyaL3cXls1ensbw%3D
KC Chou SP Jiang (1974) ArticleTitleStudies on the rate of diffusion-controlled reactions of enzymes Sci Sin 17 664–680
KC Chou SP Jiang WM Liu CH Fee (1979) ArticleTitleGraph theory of enzyme kinetics: 1. Steady-state reaction system Sci Sin 22 341–358 Occurrence Handle1:CAS:528:DyaE1MXhvF2msbY%3D
KC Chou D Jones RL Heinrikson (1997) ArticleTitlePrediction of the tertiary structure and substrate binding site of caspase-8 FEBS Lett 419 49–54 Occurrence Handle9426218 Occurrence Handle10.1016/S0014-5793(97)01246-5 Occurrence Handle1:CAS:528:DyaK2sXnvFGlu74%3D
KC Chou FJ Kezdy F Reusser (1994a) ArticleTitleReview: steady-state inhibition kinetics of processive nucleic acid polymerases and nucleases Anal Biochem 221 217–230 Occurrence Handle10.1006/abio.1994.1405 Occurrence Handle1:CAS:528:DyaK2cXmt1Clt7k%3D
KC Chou GM Maggiora B Mao (1989) ArticleTitleQuasi-continuum models of twist-like and accordion-like low-frequency motions in DNA Biophys J 56 295–305 Occurrence Handle2775828 Occurrence Handle1:CAS:528:DyaL1MXlt12iu74%3D Occurrence Handle10.1016/S0006-3495(89)82676-1
KC Chou B Mao (1988) ArticleTitleCollective motion in DNA and its role in drug intercalation Biopolymers 27 1795–1815 Occurrence Handle3233332 Occurrence Handle10.1002/bip.360271109 Occurrence Handle1:CAS:528:DyaL1MXjsFCqsw%3D%3D
KC Chou AG Tomasselli RL Heinrikson (2000) ArticleTitlePrediction of the tertiary structure of a caspase-9/inhibitor complex FEBS Lett 470 249–256 Occurrence Handle10745077 Occurrence Handle10.1016/S0014-5793(00)01333-8 Occurrence Handle1:CAS:528:DC%2BD3cXitVSrurw%3D
KC Chou KD Watenpaugh RL Heinrikson (1999b) ArticleTitleA model of the complex between cyclin-dependent kinase 5(Cdk5) and the activation domain of neuronal Cdk5 activator Biochem Biophys Res Commun 259 420–428 Occurrence Handle10.1006/bbrc.1999.0792 Occurrence Handle1:CAS:528:DyaK1MXjs1Smu7o%3D
KC Chou CT Zhang (1992) ArticleTitleDiagrammatization of codon usage in 339 HIV proteins and its biological implication AIDS Res Hum Retroviruses 8 1967–1976 Occurrence Handle1493047 Occurrence Handle1:STN:280:DyaK3s7lt1aluw%3D%3D Occurrence Handle10.1089/aid.1992.8.1967
KC Chou CT Zhang GM Maggiora (1994b) ArticleTitleSolitary wave dynamics as a mechanism for explaining the internal motion during microtubule growth Biopolymers 34 143–153 Occurrence Handle10.1002/bip.360340114 Occurrence Handle1:CAS:528:DyaK2cXpvF2nug%3D%3D
KC Chou GP Zhou (1982) ArticleTitleRole of the protein outside active site on the diffusion-controlled reaction of enzyme J Am Chem Soc 104 1409–1413 Occurrence Handle10.1021/ja00369a043 Occurrence Handle1:CAS:528:DyaL38XhtVSjtrc%3D
NJ Cotes MG Sceats (1988) ArticleTitleBiomolecular reactions with a reactive site on a spherical particle: a Hamiltonian formulation J Chem Phys 89 2816–2821 Occurrence Handle10.1063/1.454984 Occurrence Handle1:CAS:528:DyaL1cXlsFOht78%3D
F Daboussi A Dumay F Delacote BS Lopez (2002) ArticleTitleDNA double-strand break repair signalling: the case of RAD51 post-translational regulation Cell Signal 14 969–975 Occurrence Handle12359302 Occurrence Handle10.1016/S0898-6568(02)00052-9 Occurrence Handle1:CAS:528:DC%2BD38XnsVahsbk%3D
L Gao YS Ding H Dai SH Shao ZD Huang KC Chou (2006) ArticleTitleA novel fingerprint map for detecting SARS-CoV J Pharm Biomed Anal 41 246–250 Occurrence Handle16289934 Occurrence Handle10.1016/j.jpba.2005.09.031 Occurrence Handle1:CAS:528:DC%2BD28Xis1entb4%3D
WG Han (1992) ArticleTitleThe influence of dipole-dipole interaction on the low-frequency vibrations in alpha-helix proteins Biophys Chem 43 169–173 Occurrence Handle10.1016/0301-4622(92)80031-Y Occurrence Handle1:CAS:528:DyaK3sXhvVWltg%3D%3D
WG Han CD Wang (1992) ArticleTitleThe vibrational normal modes of beta-barrels in an IgG antibody molecule Biophys Chem 44 29–45 Occurrence Handle1420940 Occurrence Handle10.1016/0301-4622(92)85033-Z Occurrence Handle1:CAS:528:DyaK38XlvV2rsLs%3D
EL King C Altman (1956) ArticleTitleA schematic method of deriving the rate laws for enzyme-catalyzed reactions J Phys Chem 60 1375–1378 Occurrence Handle10.1021/j150544a010 Occurrence Handle1:CAS:528:DyaG2sXhslKisQ%3D%3D
KW Kohn Y Pommier (2005) ArticleTitleMolecular interaction map of the p53 and Mdm2 logic elements, which control the Off-On switch of p53 in response to DNA damage Biochem Biophys Res Commun 331 816–827 Occurrence Handle15865937 Occurrence Handle10.1016/j.bbrc.2005.03.186 Occurrence Handle1:CAS:528:DC%2BD2MXjslKjtLo%3D
P Kuzmic KY Ng TD Heath (1992) ArticleTitleMixtures of tight-binding enzyme inhibitors. Kinetic analysis by a recursive rate equation Anal Biochem 200 68–73 Occurrence Handle1595902 Occurrence Handle10.1016/0003-2697(92)90278-F Occurrence Handle1:CAS:528:DyaK38XhsVKlsLg%3D
G Lahav N Rosenfeld A Sigal N Geva-Zatorsky AJ Levine MB Elowitz U Alon (2004) ArticleTitleDynamics of the p53-Mdm2 feedback loop in individual cells Nat Genet 36 147–150 Occurrence Handle14730303 Occurrence Handle10.1038/ng1293 Occurrence Handle1:CAS:528:DC%2BD2cXntlCgtA%3D%3D
R Lev Bar-Or R Maya LA Segel U Alon AJ Levine M Oren (2000) ArticleTitleGeneration of oscillations by the p53-Mdm2 feedback loop: a theoretical and experimental study Proc Natl Acad Sci USA 97 11250–11255 Occurrence Handle11016968 Occurrence Handle10.1073/pnas.210171597 Occurrence Handle1:STN:280:DC%2BD3M%2Fit1Kgtg%3D%3D
SX Lin KE Neet (1990) ArticleTitleDemonstration of a slow conformational change in liver glucokinase by fluorescence spectroscopy J Biol Chem 265 9670–9675 Occurrence Handle2351663 Occurrence Handle1:CAS:528:DyaK3cXkt1SisLk%3D
L Ma J Wagner JJ Rice W Hu AJ Levine GA Stolovitzky (2005) ArticleTitleA plausible model for the digital response of p53 to DNA damage Proc Natl Acad Sci USA 102 14266–14271 Occurrence Handle16186499 Occurrence Handle10.1073/pnas.0501352102 Occurrence Handle1:CAS:528:DC%2BD2MXhtFChu7fJ
N Magne RA Toillon V Bottero C Didelot PV Houtte JP Gerard JF Peyron (2006) ArticleTitleNF-kappaB modulation and ionizing radiation: mechanisms and future directions for cancer treatment Cancer Lett 231 158–168 Occurrence Handle16399220 Occurrence Handle10.1016/j.canlet.2005.01.022 Occurrence Handle1:CAS:528:DC%2BD28XhsFGgsA%3D%3D
P Martel (1992) ArticleTitleBiophysical aspects of neutron scattering from vibrational modes of proteins Prog Biophys Mol Biol 57 129–179 Occurrence Handle1603938 Occurrence Handle10.1016/0079-6107(92)90023-Y Occurrence Handle1:CAS:528:DyaK38XltVOnt78%3D
M Oren (2003) ArticleTitleDecision making by p53: life, death and cancer Cell Death Differ 10 431–442 Occurrence Handle12719720 Occurrence Handle10.1038/sj.cdd.4401183 Occurrence Handle1:CAS:528:DC%2BD3sXjt1GjsLg%3D
S Pauklin A Kristjuhan T Maimets V Jaks (2005) ArticleTitleARF and ATM/ATR cooperate in p53-mediated apoptosis upon oncogenic stress Biochem Biophys Res Commun 334 386–394 Occurrence Handle16004968 Occurrence Handle10.1016/j.bbrc.2005.06.097 Occurrence Handle1:CAS:528:DC%2BD2MXmsVOgsbc%3D
CA Perez JA Purdy (1998) ArticleTitleTreatment planning in radiation oncology and impact on outcome of therapy Rays 23 385–426 Occurrence Handle9932463 Occurrence Handle1:STN:280:DyaK1M7jtFamtw%3D%3D
A Rapp KO Greulich (2004) ArticleTitleAfter double-strand break induction by UV-A, homologous recombination and nonhomologous end joining cooperate at the same DSB if both systems are available J Cell Sci 117 4935–4945 Occurrence Handle15367581 Occurrence Handle10.1242/jcs.01355 Occurrence Handle1:CAS:528:DC%2BD2cXhtVSns7vN
MA Ritter KW Gilchrist M Voytovich RJ Chappell BM Verhoven (2002) ArticleTitleThe role of p53 in radiation therapy outcomes for favorable-to-intermediate-risk prostate cancer Int J Radiat Oncol Biol Phys 53 574–580 Occurrence Handle12062599 Occurrence Handle10.1016/S0360-3016(02)02781-5 Occurrence Handle1:CAS:528:DC%2BD38XksValt7g%3D
K Rothkamm I Kruger LH Thompson M Lobrich (2003) ArticleTitlePathways of DNA double-strand break repair during the mammalian cell cycle Mol Cell Biol 23 5706–5715 Occurrence Handle12897142 Occurrence Handle10.1128/MCB.23.16.5706-5715.2003 Occurrence Handle1:CAS:528:DC%2BD3sXmt1Srt7Y%3D
Z Sinkala (2006) ArticleTitleSoliton/exciton transport in proteins J Theor Biol 241 919–927 Occurrence Handle16516929 Occurrence Handle1:CAS:528:DC%2BD28XntlGhtr8%3D
Sobell HM, Banerjee A, Lozansky ED, Zhou GP, Chou KC (1983) The role of low-frequency (acoustic) phonons in determining the premelting and melting behaviors of DNA. In: Clementi E, Sarma RH (eds) Structure and dynamics: nucleic acids and proteins. New York, pp 181–195
JJ Tyson (1999) ArticleTitleModels of cell cycle control in eukaryotes J Biotechnol 71 239–244 Occurrence Handle10483109 Occurrence Handle10.1016/S0168-1656(99)00027-9 Occurrence Handle1:CAS:528:DyaK1MXltVCmur4%3D
JJ Tyson B Novak (2001) ArticleTitleRegulation of the eukaryotic cell cycle: molecular antagonism, hysteresis, and irreversible transitions J Theor Biol 210 249–263 Occurrence Handle11371178 Occurrence Handle10.1006/jtbi.2001.2293 Occurrence Handle1:CAS:528:DC%2BD3MXjslansL8%3D
B Vogelstein D Lane AJ Levine (2000) ArticleTitleSurfing the p53 network Nature 408 307–310 Occurrence Handle11099028 Occurrence Handle10.1038/35042675 Occurrence Handle1:CAS:528:DC%2BD3cXosVemtrY%3D
M Wang JS Yao ZD Huang ZJ Xu GP Liu HY Zhao XY Wang J Yang YS Zhu KC Chou (2005) ArticleTitleA new nucleotide-composition based fingerprint of SARS-CoV with visualization analysis Med Chem 1 39–47 Occurrence Handle16789884 Occurrence Handle10.2174/1573406053402505
M Weller (1998) ArticleTitlePredicting response to cancer chemotherapy: the role of p53 Cell Tissue Res 292 435–445 Occurrence Handle9582400 Occurrence Handle10.1007/s004410051072 Occurrence Handle1:CAS:528:DyaK1cXivFWgtbw%3D
X Xiao S Shao Y Ding Z Huang X Chen KC Chou (2005) ArticleTitleAn application of gene comparative image for predicting the effect on replication ratio by HBV virus gene missense mutation J Theor Biol 235 555–565 Occurrence Handle15935173 Occurrence Handle10.1016/j.jtbi.2005.02.008 Occurrence Handle1:CAS:528:DC%2BD2MXltVelt7c%3D
X Xiao SH Shao KC Chou (2006) ArticleTitleA probability cellular automaton model for hepatitis B viral infections Biochem Biophys Res Commun 342 605–610 Occurrence Handle16487938 Occurrence Handle10.1016/j.bbrc.2006.01.166 Occurrence Handle1:CAS:528:DC%2BD28XhvVehsLg%3D
CT Zhang KC Chou (1994) ArticleTitleAnalysis of codon usage in 1562 E. Coli protein coding sequences J Mol Biol 238 1–8 Occurrence Handle8145249 Occurrence Handle10.1006/jmbi.1994.1263 Occurrence Handle1:CAS:528:DyaK2cXkt1yjsrg%3D
CT Zhang KC Chou (1996) ArticleTitleAn analysis of base frequencies in the anti-sense strands corresponding to the 180 human protein coding sequences Amino Acids 10 253–262 Occurrence Handle10.1007/BF00807327 Occurrence Handle1:CAS:528:DyaK28XkslKms7Y%3D
G Zhou MT Wong GQ Zhou (1983) ArticleTitleDiffusion-controlled reactions of enzymes. An approximate analytic solution of Chou’s model Biophys Chem 18 125–132 Occurrence Handle6626685 Occurrence Handle10.1016/0301-4622(83)85006-6 Occurrence Handle1:CAS:528:DyaL3sXlslWqsbs%3D
GP Zhou (1989) ArticleTitleBiological functions of soliton and extra electron motion in DNA structure Phys Scripta 40 698–701 Occurrence Handle10.1088/0031-8949/40/5/021 Occurrence Handle1:CAS:528:DyaK3cXjt1amug%3D%3D
GP Zhou MH Deng (1984) ArticleTitleAn extension of Chou’s graphical rules for deriving enzyme kinetic equations to system involving parallel reaction pathways Biochem J 222 169–176 Occurrence Handle6477507 Occurrence Handle1:CAS:528:DyaL2cXls1Khsr0%3D
GQ Zhou WZ Zhong (1982) ArticleTitleDiffusion-controlled reactions of enzymes. A comparison between Chou’s model and Alberty-Hammes-Eigen’s model Eur J Biochem 128 383–387 Occurrence Handle7151785 Occurrence Handle1:CAS:528:DyaL3sXjtVCrsQ%3D%3D Occurrence Handle10.1111/j.1432-1033.1982.tb06976.x
Author information
Authors and Affiliations
Rights and permissions
About this article
Cite this article
Qi, JP., Shao, SH., Li, DD. et al. A dynamic model for the p53 stress response networks under ion radiation. Amino Acids 33, 75–83 (2007). https://doi.org/10.1007/s00726-006-0454-3
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00726-006-0454-3