Ping Xie

Summary

Affiliation: Institute of Physics
Country: China

Publications

  1. doi Ubiquitin ligase Smurf1 targets TRAF family proteins for ubiquitination and degradation
    Shan Li
    State Key Laboratory of Proteomics, Department of Genomics and Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, China
    Mol Cell Biochem 338:11-7. 2010
  2. doi On the pathway of ribosomal translocation
    Ping Xie
    Key Laboratory of Soft Matter Physics and Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China Electronic address
    Int J Biol Macromol 92:401-415. 2016
  3. doi Processivity of nucleic acid unwinding and translocation by helicases
    Ping Xie
    Key Laboratory of Soft Matter Physics and Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
    Proteins 84:1590-1605. 2016
  4. doi Dynamics of monomeric and hexameric helicases
    Ping Xie
    Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China Electronic address
    Biophys Chem 211:49-58. 2016
  5. pmc Dwell-Time Distribution, Long Pausing and Arrest of Single-Ribosome Translation through the mRNA Duplex
    Ping Xie
    Key Laboratory of Soft Matter Physics and Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
    Int J Mol Sci 16:23723-44. 2015
  6. doi A unified model of nucleic acid unwinding by the ribosome and the hexameric and monomeric DNA helicases
    Ping Xie
    Key Laboratory of Soft Matter Physics and Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China Electronic address
    J Theor Biol 380:359-66. 2015
  7. doi Dynamics of tRNA translocation, mRNA translocation and tRNA dissociation during ribosome translation through mRNA secondary structures
    Ping Xie
    Key Laboratory of Soft Matter Physics and Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
    Eur Biophys J 43:229-40. 2014
  8. doi An explanation of biphasic characters of mRNA translocation in the ribosome
    Ping Xie
    Key Laboratory of Soft Matter Physics and Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China Electronic address
    Biosystems 118:1-7. 2014
  9. pmc Dynamics of forward and backward translocation of mRNA in the ribosome
    Ping Xie
    Key Laboratory of Soft Matter Physics and Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China
    PLoS ONE 8:e70789. 2013
  10. doi A dynamical model of programmed -1 ribosomal frameshifting
    Ping Xie
    Key Laboratory of Soft Matter Physics and Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China Electronic address
    J Theor Biol 336:119-31. 2013

Collaborators

  • Wei Li
  • Shuo Xing Dou
  • Jun Chen
  • Liang Chen
  • Lingqiang Zhang
  • Hui Li
  • Hong Shen
  • Jun He
  • Dan Yang
  • Xu Guang Xi
  • Xi Yang
  • Jian Wang
  • Jun Xu
  • Peng Ye Wang
  • Xuwei Deng
  • Wei Chi Wang
  • Xing Dong Zhang
  • Hong Yan Zhang
  • Yu Ru Liu
  • Zhimei Ma
  • Chao Ji
  • Fei Zhou Chen
  • Zhao Wen Duan
  • Zhihua Liu
  • Zhi Xin Ke
  • Gaodao Liang
  • Min Qi
  • Meng Zhang
  • Qiong Xiao
  • Shan Li
  • Te Cao
  • Xi Miao Hou
  • Ai Ping Wu
  • Tianpeng Zhang
  • Xiushan Yin
  • Fuchu He
  • Zhi Pan
  • Jun Qian
  • Yan Li
  • Li Li
  • Xia Zhang
  • Yu Ying Liu
  • Wei Min Zeng
  • Qingjie Li
  • Min Tao
  • Yuan Niu
  • Xiaobo Sun
  • Qiong Zhou
  • Yan Jiang
  • Long Gen Guo
  • Xu Zeng
  • Guibo Sun
  • Guomin Ren
  • Yaqin Liu
  • Zhengqi Wang
  • Leyi Ni
  • Li Ping Wang
  • Xiao Zhen Jiao
  • Xiao yu Liu
  • Kefeng Lu
  • Qian Wu
  • Hui Chen
  • Yu Cui
  • Liguo An
  • Guichun Xing
  • Guiwen Yang
  • Yongna Fan
  • Shi Kai Wu
  • Le Yi Ni
  • Jizhi Jiang
  • Juntao Yang
  • Jin Shan Hu
  • Jingyun Fang
  • Kun Zhao
  • Shuqing Zhao
  • Yan Ling Li
  • Hui juan Tang
  • Ni Chun Guo
  • Hong Liu
  • Jian hui Qin
  • Si Xin Li
  • Hua Wei Yin
  • Hui Ping Song
  • Shu Hua Chen
  • Mei Lian Liu
  • Yapeng Gu
  • Huiping Song
  • Weimin Zeng
  • Jianjun Huang

Detail Information

Publications84

  1. doi Ubiquitin ligase Smurf1 targets TRAF family proteins for ubiquitination and degradation
    Shan Li
    State Key Laboratory of Proteomics, Department of Genomics and Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, China
    Mol Cell Biochem 338:11-7. 2010
    ..Consequently, Smurf1 interfered with the functions of TRAFs in NF-kappaB signaling under stimulation or not. These results suggested a new role of Smurf1 in inflammation and immunity through controlling the degradation of TRAFs...
  2. doi On the pathway of ribosomal translocation
    Ping Xie
    Key Laboratory of Soft Matter Physics and Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China Electronic address
    Int J Biol Macromol 92:401-415. 2016
    ..Moreover, we study the kinetics of 30S head rotation in the presence of EF-G mutants, providing predicted results. These have significant implications for the molecular mechanism and pathway of ribosomal translocation...
  3. doi Processivity of nucleic acid unwinding and translocation by helicases
    Ping Xie
    Key Laboratory of Soft Matter Physics and Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
    Proteins 84:1590-1605. 2016
    ..Proteins 2016; 84:1590-1605. © 2016 Wiley Periodicals, Inc...
  4. doi Dynamics of monomeric and hexameric helicases
    Ping Xie
    Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China Electronic address
    Biophys Chem 211:49-58. 2016
    ..Our studies indicate that although the monomeric and hexameric helicases show very different features on the dependence of NA unwinding speed upon the external force, they use much similar active mechanisms to unwind NA duplex. ..
  5. pmc Dwell-Time Distribution, Long Pausing and Arrest of Single-Ribosome Translation through the mRNA Duplex
    Ping Xie
    Key Laboratory of Soft Matter Physics and Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
    Int J Mol Sci 16:23723-44. 2015
    ....
  6. doi A unified model of nucleic acid unwinding by the ribosome and the hexameric and monomeric DNA helicases
    Ping Xie
    Key Laboratory of Soft Matter Physics and Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China Electronic address
    J Theor Biol 380:359-66. 2015
    ....
  7. doi Dynamics of tRNA translocation, mRNA translocation and tRNA dissociation during ribosome translation through mRNA secondary structures
    Ping Xie
    Key Laboratory of Soft Matter Physics and Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
    Eur Biophys J 43:229-40. 2014
    ..The reduced translation rate through the mRNA secondary structure is induced by the slow mRNA translocation rather than the slow tRNA dissociation...
  8. doi An explanation of biphasic characters of mRNA translocation in the ribosome
    Ping Xie
    Key Laboratory of Soft Matter Physics and Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China Electronic address
    Biosystems 118:1-7. 2014
    ..Thus, Model II could be the appropriate one for the kinetic pathway of mRNA translocation. ..
  9. pmc Dynamics of forward and backward translocation of mRNA in the ribosome
    Ping Xie
    Key Laboratory of Soft Matter Physics and Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China
    PLoS ONE 8:e70789. 2013
    ..The theoretical results provide quantitative explanations of a lot of different, independent experimental data, and also provide testable predictions. ..
  10. doi A dynamical model of programmed -1 ribosomal frameshifting
    Ping Xie
    Key Laboratory of Soft Matter Physics and Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China Electronic address
    J Theor Biol 336:119-31. 2013
    ..Our theoretical results provide a consistent explanation of a lot of independent experimental data and also provide predicted results. ..
  11. doi Translocation dynamics of tRNA-mRNA in the ribosome
    Ping Xie
    Key Laboratory of Soft Matter Physics and Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China Electronic address
    Biophys Chem 180:22-8. 2013
    ..GTP can also bind to the classical non-rotated pretranslocation state and the greater potency of GTP hydrolysis in facilitating translocation of tRNA-mRNA complex derives from its effects on the second step of the translocation process. ..
  12. doi Model of ribosome translation and mRNA unwinding
    Ping Xie
    Key Laboratory of Soft Matter Physics and Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
    Eur Biophys J 42:347-54. 2013
    ....
  13. doi Dynamics of DNA polymerase I (Klenow fragment) under external force
    Ping Xie
    Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
    J Mol Model 19:1379-89. 2013
    ..These results can be tested easily by future experiments and are aid our understanding of the chemomechanical coupling mechanism and polymerization dynamics of high-fidelity DNAP...
  14. doi Dynamics of tRNA occupancy and dissociation during translation by the ribosome
    Ping Xie
    Key Laboratory of Soft Matter Physics and Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
    J Theor Biol 316:49-60. 2013
    ..GTP and aminoacyl-tRNA.EF-Tu.GTP complex, the mean time for occupancy of three tRNA molecules is in the order of milliseconds in one translation cycle, which is much shorter than the in vitro mean translation time of about 1s...
  15. doi A dynamic model for processive transcription elongation and backtracking long pauses by multisubunit RNA polymerases
    Ping Xie
    Key Laboratory of Soft Matter Physics and Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
    Proteins 80:2020-34. 2012
    ..Moreover, some testable predictions are presented...
  16. doi Modeling translocation dynamics of strand displacement DNA synthesis by DNA polymerase I
    Ping Xie
    Key Laboratory of Soft Matter Physics and Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China
    J Mol Model 18:1951-60. 2012
    ....
  17. doi Dynamics of strand passage catalyzed by topoisomerase II
    Ping Xie
    Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, 100190, Beijing, China
    Eur Biophys J 39:1251-9. 2010
    ..On the basis of these theoretical results and previous experimental data, a modified two-gate model for chemomechanical coupling of the topoisomerase II enzyme is proposed...
  18. doi A model for dynamics of primer extension by eukaryotic DNA primase
    Ping Xie
    Key Laboratory of Soft Matter Physics and Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China
    Eur Biophys J 40:1157-65. 2011
    ..The model also predicts some data such as the binding affinities of the primase for the DNA template and for the RNA primer...
  19. pmc A nucleotide binding rectification Brownian ratchet model for translocation of Y-family DNA polymerases
    Ping Xie
    Key Laboratory of Soft Matter Physics and Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
    Theor Biol Med Model 8:22. 2011
    ..Moreover, we compare the effect of the external force on the DNA synthesis rate of the Y-family polymerase with that of the replicative DNA polymerase...
  20. doi A model for the dynamics of mammalian family X DNA polymerases
    Ping Xie
    Key Laboratory of Soft Matter Physics and Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
    J Theor Biol 277:111-22. 2011
    ..The theoretical results on the polymerization processivities are also in agreement with the available experimental data...
  21. doi A modified model for translocation events of processive nucleotide and repeat additions by the recombinant telomerase
    Ping Xie
    Institute of Physics, Chinese Academy of Sciences, Beijing, China
    Biophys Chem 153:83-96. 2010
    ..Their effects on the repeat addition processivity are theoretically studied. The theoretical results are in agreement with the available experimental data...
  22. doi A model for processive movement of single-headed myosin-IX
    Ping Xie
    Institute of Physics, Chinese Academy of Sciences, Beijing, China
    Biophys Chem 151:71-80. 2010
    ..The experimental results on the motility of myosin-IX such as the step size, large forward/backward stepping ratio, run length, stall force, etc, are explained well...
  23. doi A possible mechanism of processive nucleotide and repeat additions by the telomerase
    Ping Xie
    Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
    Biosystems 97:168-78. 2009
    ..A large difference in free energy corresponds to a low repeat addition processivity while a small difference in free energy corresponds to a high repeat addition processivity...
  24. doi A polymerase-site-jumping model for strand transfer during DNA synthesis by reverse transcriptase
    Ping Xie
    Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Zhongguancun Sourth Street No 3, Haidian District, Beijing 100190, China
    Virus Res 144:65-73. 2009
    ..The theoretical results are in agreement with the available experimental data. Moreover, some predicted results of the dependence of negative interference on the ratio of polymerase over RNase H rates are presented...
  25. doi A possible mechanism for the dynamics of transition between polymerase and exonuclease sites in a high-fidelity DNA polymerase
    Ping Xie
    Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100790, China
    J Theor Biol 259:434-9. 2009
    ..Moreover, we also give some predictive results for the transfer rate of DNA containing only A:T base pairs and that of DNA containing only G:C base pairs...
  26. doi On chemomechanical coupling of the F(1)-ATPase molecular motor
    Ping Xie
    Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
    Biochim Biophys Acta 1787:955-62. 2009
    ..The theoretical results obtained with only three adjustable parameters reproduce the available experimental data well...
  27. ncbi Processive hand-over-hand motion of homodimeric nanomotors induced by interaction between two monomeric components and thermal noise
    Ping Xie
    Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
    Phys Rev E Stat Nonlin Soft Matter Phys 79:011920. 2009
    ..Using detailed analyses and numerical simulations, it is shown that the homodimeric nanowalker walks hand over hand along the track with a high efficiency and a high stall force...
  28. doi Dynamics of backtracking long pauses of RNA polymerase
    Ping Xie
    Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
    Biochim Biophys Acta 1789:212-9. 2009
    ..The results are in agreement with the available experimental data and, moreover, some predicted results are presented. In addition, using this V(0) we study the processivity of RNA polymerase under no and sideways forces...
  29. doi A thermal ratchet model of tRNA-mRNA translocation by the ribosome
    Ping Xie
    Institute of Physics, Chinese Academy of Sciences, Beijing, China
    Biosystems 96:19-28. 2009
    ..Also, the model is consistent with other available experimental results such as the suppression of EF-G-dependent translocation in cross-linked ribosomes and frameshifting under some conditions...
  30. doi Stepping behavior of two-headed kinesin motors
    Ping Xie
    Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100080, China
    Biochim Biophys Acta 1777:1195-202. 2008
    ..the actual time taken by the ADP head to transit from the trailing to leading positions, is on the time scale of microseconds under any backward load smaller than the stall force. This is consistent with available experimental results...
  31. ncbi Model for kinetics of wild-type and mutant kinesins
    Ping Xie
    Laboratory of Soft Matter Physics, Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100080, China
    Biosystems 84:24-38. 2006
    ..The puzzling dynamic behaviours of mutant homodimeric and heterodimeric kinesins become understandable...
  32. ncbi Model for kinetics of myosin-V molecular motors
    Ping Xie
    Laboratory of Soft Matter Physics, Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100080, China
    Biophys Chem 120:225-36. 2006
    ....
  33. ncbi A hand-over-hand diffusing model for myosin-VI molecular motors
    Ping Xie
    Laboratory of Soft Matter Physics, Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100080, China
    Biophys Chem 122:90-100. 2006
    ..The processive movement of mutant myosin-V with its neck domains truncated to only one IQ motif can also be explained by using this hand-over-hand diffusing model...
  34. ncbi Mechanochemical couplings of kinesin motors
    Ping Xie
    Laboratory of Soft Matter Physics, Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China
    Biophys Chem 123:58-76. 2006
    ..We have tested this model using various available experimental results on different samples and obtained a good agreement between the theory and the experiments...
  35. ncbi Model for unidirectional movement of axonemal and cytoplasmic dynein molecules
    Ping Xie
    Laboratory of Soft Matter Physics, Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100080, China
    Acta Biochim Biophys Sin (Shanghai) 38:711-24. 2006
    ....
  36. ncbi Model for forward polymerization and switching transition between polymerase and exonuclease sites by DNA polymerase molecular motors
    Ping Xie
    Department of Physics, Zhejiang Sci Tech University, Xiasha College Park, Hangzhou, Zhejiang, China
    Arch Biochem Biophys 457:73-84. 2007
    ..The switching rates between the two sites are analyzed. All the results show good quantitative agreement with the available experimental results...
  37. ncbi Model for helicase translocating along single-stranded DNA and unwinding double-stranded DNA
    Ping Xie
    Department of Physics, Zhejiang Sci Tech University, Xiasha College Park, Hangzhou, Zhejiang 310018, China
    Biochim Biophys Acta 1764:1719-29. 2006
    ..The interaction force between ssDNA and helicases in weakly-ssDNA-bound state determines whether monomeric helicases such as PcrA can unwind dsDNA or dimeric helicases such as Rep are required to unwind dsDNA...
  38. ncbi Limping of homodimeric kinesin motors
    Ping Xie
    Laboratory of Soft Matter Physics, Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China
    J Mol Biol 366:976-85. 2007
    ..We predict that a high degree of limping will correlate strongly with a high sensitivity of ATP turnover rate to upwards force...
  39. doi A dynamic model for transcription elongation and sequence-dependent short pauses by RNA polymerase
    Ping Xie
    Department of Physics, Renmin University of China, Beijing 100872, China
    Biosystems 93:199-210. 2008
    ....
  40. ncbi Processivity of single-headed kinesin motors
    Ping Xie
    Department of Physics, Renmin University of China, Beijing 100872, China
    Biochim Biophys Acta 1767:1418-27. 2007
    ..This local conformational change of the microtubule may also play important roles in the processive movement of conventional two-headed kinesins. An experiment to verify the model is suggested...
  41. ncbi On translocation mechanism of ring-shaped helicase along single-stranded DNA
    Ping Xie
    Department of Physics, Renmin University of China, Beijing 100872, China
    Biochim Biophys Acta 1774:737-48. 2007
    ....
  42. ncbi Model for RuvAB-mediated branch migration of Holliday junctions
    Ping Xie
    Department of Physics, Renmin University of China, Beijing 100872, China
    J Theor Biol 249:566-73. 2007
    ..Using the model, the relationship between the power-stroke size, the step size of DNA translocation and the ratio of the rotational rate of DNA over that of RuvB relative to RuvA is predicted...
  43. ncbi Escherichia coli RecQ is a rapid, efficient, and monomeric helicase
    Xing Dong Zhang
    Laboratory of Soft Matter Physics, Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100080, China
    J Biol Chem 281:12655-63. 2006
    ..These kinetic results not only further support our previous conclusion that E. coli RecQ functions as a monomer but also suggest that some of the Superfamily 2 helicases may function through an "inchworm" mechanism...
  44. ncbi Brownian dynamics simulation of the effect of histone modification on nucleosome structure
    Wei Li
    Laboratory of Soft Matter Physics, Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China
    Phys Rev E Stat Nonlin Soft Matter Phys 75:051915. 2007
    ..Though the simulation study may only give a coarse grained view of the DNA unwrapping process for the modified histone octamer, it may provide insight into the mechanism of DNA repair...
  45. ncbi Off-flavor compounds from decaying cyanobacterial blooms of Lake Taihu
    Zhimei Ma
    Freshwater Ecology and Biotechnology of China, Institute of Hydrobiology, Chinese Academy of Sciences, Donghu South Road 7, Wuhan 430072, China
    J Environ Sci (China) 25:495-501. 2013
    ..The experimental results suggested that preventing the anaerobic decomposition of cyanobacterial blooms is an important strategy against the recurrence of a malodor crisis in Lake Taihu...
  46. ncbi Brownian dynamics simulation of directional sliding of histone octamers caused by DNA bending
    Wei Li
    Laboratory of Soft Matter Physics, Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100080, China
    Phys Rev E Stat Nonlin Soft Matter Phys 73:051909. 2006
    ..The DNA loop size is an important factor affecting the process of directional sliding of the histone octamer...
  47. pmc Oxaliplatin and its enantiomer induce different condensation dynamics of single DNA molecules
    Hong Yan Zhang
    Key Laboratory of Soft Matter Physics, Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China
    PLoS ONE 8:e71556. 2013
    ..The study has strong implications for the understanding of the effect of chirality on the interaction between Pt-DACH and DNA and the kinetics of DNA condensation induced by platinum complexes. ..
  48. ncbi RecQ helicase-catalyzed DNA unwinding detected by fluorescence resonance energy transfer
    Xing Dong Zhang
    Laboratory of Soft Matter Physics, Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100080, China
    Acta Biochim Biophys Sin (Shanghai) 37:593-600. 2005
    ..We showed that this method could be used to determine the polarity of DNA unwinding. This assay should greatly facilitate further study of the mechanism for RecQ-catalyzed DNA unwinding...
  49. doi Microwave-assisted purge-and-trap extraction device coupled with gas chromatography and mass spectrometry for the determination of five predominant odors in sediment, fish tissues, and algal cells
    Xuwei Deng
    Donghu Experimental Station of Lake Ecosystems, State Key Laboratory of Freshwater Ecology and Biotechnology of China, Chinese Academy of Sciences, Wuhan, Hubei, China
    J Chromatogr A 1219:75-82. 2012
    ..The relative standard deviations were between 2.65% and 7.29% (n=6). Thus the proposed design is ready for rapid translation into a standard analytical tool and is useful for multiple applications in the analysis of off-flavors...
  50. ncbi Formation of DNA toroids inside confined droplets adsorbed on mica surfaces
    Xi Miao Hou
    Laboratory of Soft Matter Physics, Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
    Phys Rev E Stat Nonlin Soft Matter Phys 79:051912. 2009
    ..The simulation reveals that the toroid formation is sensitive to not only the microdroplet size, but also the DNA stiffness...
  51. doi Transplatin enhances effect of cisplatin on both single DNA molecules and live tumor cells
    Yu Ru Liu
    Key Laboratory of Soft Matter Physics, Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
    Arch Biochem Biophys 536:12-24. 2013
    ..The results of the present study provide a new clue for understanding the stepwise reactions of DNA with platinum drugs and might serve as a basis for the development of a new antitumor strategy. ..
  52. pmc Effects of paclitaxel on EGFR endocytic trafficking revealed using quantum dot tracking in single cells
    Hui Li
    Key Laboratory of Soft Matter Physics, Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China
    PLoS ONE 7:e45465. 2012
    ..The present study may shed light on the mechanism of the effect of PTX on the treatment of lung cancer...
  53. pmc CHIP represses myocardin-induced smooth muscle cell differentiation via ubiquitin-mediated proteasomal degradation
    Ping Xie
    Department of Pathology and National Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, 5 Dong Dan San Tiao, Beijing, China
    Mol Cell Biol 29:2398-408. 2009
    ....
  54. ncbi Elastic response and length change of single DNA molecules induced by a combination of cisplatin and transplatin
    Wei Li
    Key Laboratory of Soft Matter Physics, Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
    Phys Rev E Stat Nonlin Soft Matter Phys 85:021918. 2012
    ..Moreover, abrupt length changes were also observed when DNA was treated with a mixture of cisplatin and transplatin at high concentrations. A model was proposed to qualitatively explain well these results...
  55. ncbi Negative effects of Microcystis blooms on the crustacean plankton in an enclosure experiment in the subtropical China
    Fei Zhou Chen
    Donghu Experimental Station of Lake Ecosystems, State Key Laboratory for Freshwater Ecology and Biotechnology of China, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
    J Environ Sci (China) 17:775-81. 2005
    ..cornuta and D. brachyurum by late August. It appears that dense Microcystis blooms exert strong negative effects on the herbivorous cladocerans and the predaceous cyclopoids...
  56. doi The role of GSH in microcystin-induced apoptosis in rat liver: Involvement of oxidative stress and NF-κB
    Liang Chen
    Donghu Experimental Station of Lake Ecosystems, State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
    Environ Toxicol 31:552-60. 2016
    ..Our data will provide a new perspective for understanding the mechanisms of MC-induced liver injury...
  57. doi Microcystis aeruginosa/Pseudomonas pseudoalcaligenes interaction effects on off-flavors in algae/bacteria co-culture system under different temperatures
    Xi Yang
    Donghu Experimental Station of Lake Ecosystems, State Key Laboratory of Freshwater Ecology and Biotechnology of China, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China Wuhan Fisheries Science Research Institute, Wuhan 430207, China The University of Chinese Academy of Sciences, Beijing 100049, China Electronic address
    J Environ Sci (China) 31:38-43. 2015
    ..aeruginosa. Our results also provide some insights into understanding the relationship between cyanobacteria and heterotrophic bacteria. ..
  58. doi Mapping intracellular diffusion distribution using single quantum dot tracking: compartmentalized diffusion defined by endoplasmic reticulum
    Hui Li
    Key Laboratory of Soft Matter Physics, Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
    J Am Chem Soc 137:436-44. 2015
    ..These results shed new light on the diffusive movements of macromolecules in the cell, and the mapping of intracellular diffusion distribution may be used to develop strategies for nanoparticle-based drug deliveries and therapeutics. ..
  59. pmc Are coiled-coils of dimeric kinesins unwound during their walking on microtubule?
    Zhao Wen Duan
    Key Laboratory of Soft Matter Physics and Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China
    PLoS ONE 7:e36071. 2012
    ..Thus, we concluded that the coiled-coils of kinesin-1, Ncd and Kar3/Vik1 are almost impossible to unwind during their walking on the microtubule...
  60. ncbi Decrease of NH4+-N by bacterioplankton accelerated the removal of cyanobacterial blooms in aerated aquatic ecosystem
    Xi Yang
    Donghu Experimental Station of Lake Ecosystems, State Key Laboratory of Freshwater Ecology and Biotechnology of China, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
    J Environ Sci (China) 25:2223-8. 2013
    ..The present study demonstrated that bacterioplankton can play crucial roles in aerated ecosystems, which could control the impact of cyanobacterial blooms in eutrophicated fresh water systems...
  61. ncbi [Effects of large bio-manipulation fish pen on community structure of crustacean zooplankton in Meiliang Bay of Taihu Lake]
    Zhi Xin Ke
    Key Laboratory of Marine Bio resource Sustainable Utilization, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
    Ying Yong Sheng Tai Xue Bao 23:2270-6. 2012
    ..Canonical correspondence analysis showed that water transparency, temperature, and phytoplankton biomass were the most important factors affecting the seasonal succession of the crustacean...
  62. doi Atrogin-1/MAFbx enhances simulated ischemia/reperfusion-induced apoptosis in cardiomyocytes through degradation of MAPK phosphatase-1 and sustained JNK activation
    Ping Xie
    Department of Pathology and National Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Beijing, China
    J Biol Chem 284:5488-96. 2009
    ....
  63. ncbi A model for biased diffusion of collagenase along collagen fibrils
    Jun Qian
    Laboratory of Soft Matter Physics, Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100080, China
    J Theor Biol 243:322-7. 2006
    ..We calculate the correlation function and the mean transport velocity for both wild-type and mutant collagenases along collagen fibrils, the results of which are consistent with the previous experiments...
  64. pmc CKIP-1 regulates macrophage proliferation by inhibiting TRAF6-mediated Akt activation
    Luo Zhang
    1 State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Collaborative Innovation Center for Cancer Medicine, Beijing, China 2 Department of Biomedical Engineering, Chinese PLA 307 Hospital, Beijing, China
    Cell Res 24:742-61. 2014
    ..Together, these data demonstrate that CKIP-1 plays a critical role in the regulation of macrophage homeostasis by inhibiting TRAF6-mediated Akt activation. ..
  65. pmc Ischemia/reperfusion-induced MKP-3 impairs endothelial NO formation via inactivation of ERK1/2 pathway
    Dan Yang
    Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
    PLoS ONE 7:e42076. 2012
    ....
  66. pmc A model for transition of 5'-nuclease domain of DNA polymerase I from inert to active modes
    Ping Xie
    Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China
    PLoS ONE 6:e16213. 2011
    ..We thus conclude that the latter model rather than the former one is reasonable to describe the cooperation of the PolI's polymerase and 5'-3' exonuclease activities. Moreover, predicted results for the latter model are presented...
  67. doi Ammonium, microcystins, and hypoxia of blooms in eutrophic water cause oxidative stress and C-N imbalance in submersed and floating-leaved aquatic plants in Lake Taihu, China
    Meng Zhang
    Donghu Experimental Station of Lake Ecosystems, State Key Laboratory for Freshwater Ecology and Biotechnology of China, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
    Chemosphere 82:329-39. 2011
    ..The findings of this study provide mainly field evidence that reveals the physical, chemical, and biological stresses on aquatic plants in bloom-prevailed eutrophic lakes...
  68. pmc Mechanism of processive movement of monomeric and dimeric kinesin molecules
    Ping Xie
    Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
    Int J Biol Sci 6:665-74. 2010
    ..Here, we attempt to present a comprehensive review of these models. We further propose a new hybrid model for the dimeric kinesin by combining the existing models and provide a framework for future studies in this subject...
  69. ncbi The function study on the interaction between Grb2 and AMPK
    Zhi Pan
    State Key Laboratory of Proteomics, Beijing Proteomics Research Center, Beijing Institute of Radiation Medicine, Beijing, China
    Mol Cell Biochem 307:121-7. 2008
    ..Furthermore, Grb2 function as a factor which mediates phosphorylation of AMPK at Thr172, and potentially involves in metabolism pathways and AMPK-TSC2-mTOR cell growth pathway through regulating the activation of AMPK...
  70. doi Simultaneous determination of eight common odors in natural water body using automatic purge and trap coupled to gas chromatography with mass spectrometry
    Xuwei Deng
    Donghu Experimental Station of Lake Ecosystems, State Key Laboratory of Freshwater Ecology and Biotechnology of China, Institute of Hydrobiology, Chinese Academy of Sciences, Donghu South Road 7, Wuhan, Hubei 430072, China
    J Chromatogr A 1218:3791-8. 2011
    ..38% and 8.59% (n=5) and recoveries of the analytes from water samples of a eutrophic lake are between 80.54% and 114.91%. This method could be widely employed for monitoring these eight odors in natural waters...
  71. ncbi Ionic effect on combing of single DNA molecules and observation of their force-induced melting by fluorescence microscopy
    Yu Ying Liu
    Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Science, Beijing 100080, China
    J Chem Phys 121:4302-9. 2004
    ..The effects of sodium and magnesium ions and pH of the DNA solution were investigated. Interestingly, we observed force-induced melting of single DNA molecules...
  72. doi MiR-106b and MiR-15b modulate apoptosis and angiogenesis in myocardial infarction
    Zhihua Liu
    Center for Computational Biology and Bioinformatics, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
    Cell Physiol Biochem 29:851-62. 2012
    ..To make a better understanding towards functional roles of miRNAs in MI, useful information was mined through bioinformatic techniques...
  73. ncbi Present status and changes of the phytoplankton community after invasion of Neosalanx taihuensis since 1982 in a deep oligotrophic plateau lake, Lake Fuxian in the subtropical China
    Xia Zhang
    Donghu Experimental Station of Lake Ecosystems, State Key Laboratory for Freshwater Ecology and Biotechnology of China, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
    J Environ Sci (China) 17:389-94. 2005
    ....
  74. ncbi Land-cover changes in an urban lake watershed in a mega-city, Central China
    Yan Li
    Department of Ecology, College of Environmental Sciences, and Key Laboratory for Earth Surface Processes of the Ministry of Education, Peking University, Beijing, China
    Environ Monit Assess 115:349-59. 2006
    ..These alterations had resulted in significant negative environmental consequences, including decline of lakes, deterioration of water and air quality, and loss of biodiversity...
  75. doi Trends of superoxide dismutase and soluble protein of aquatic plants in lakes of different trophic levels in the middle and lower reaches of the Yangtze River, China
    Ai Ping Wu
    Donghu Experimental Station of Lake Ecosystems, The State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
    J Integr Plant Biol 51:414-22. 2009
    ....
  76. doi Phylogenetic analysis of vertebrate CXC chemokines reveals novel lineage specific groups in teleost fish
    Jun Chen
    Scottish Fish Immunology Research Centre, School of Biological Sciences, University of Aberdeen, Aberdeen AB24 2TZ, UK
    Dev Comp Immunol 41:137-52. 2013
    ..These molecules increased the relative expression of CD4 and MCSFR in migrated cells in an in vitro chemotaxis assay. ..
  77. doi Concise total synthesis of largazole
    Qiong Xiao
    Peking Union Medical College and Chinese Academy of Medical Sciences, Institute of Materia Medica, Beijing, China
    J Asian Nat Prod Res 12:940-9. 2010
    ..The key step included the use of the Nagao thiazolidinethione auxiliary for the diastereoselective acetate aldol reaction and it acts as an acylating agent for the peptide formation...
  78. doi Epigallocatechin-3-gallate enhances ischemia/reperfusion-induced apoptosis in human umbilical vein endothelial cells via AKT and MAPK pathways
    Tianpeng Zhang
    Department of Pathology, Chinese Academy of Medical Sciences, 100005, Beijing, China
    Apoptosis 14:1245-54. 2009
    ....
  79. ncbi In vivo studies on toxin accumulation in liver and ultrastructural changes of hepatocytes of the phytoplanktivorous bighead carp i.p.-injected with extracted microcystins
    Li Li
    Donghu Experimental Station of Lake Ecosystems, State Key Laboratory for Freshwater Ecology and Biotechnology of China, Institute of Hydrobiology, The Chinese Academy of Sciences, Wuhan 430072, People s Republic of China
    Toxicon 46:533-45. 2005
    ..The temporal dynamics of MCs in the liver suggest that bighead carp may have a mechanism to degrade or bind MC-LR actively after it enters the blood system...
  80. ncbi Effects of nonylphenol on the growth and microcystin production of Microcystis strains
    Jingxian Wang
    Donghu Experimental Station of the Lake Ecosystems, The State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China
    Environ Res 103:70-8. 2007
    ..aeruginosa in the field and may play a subtle role in affecting cyanobacterial blooms and microcystin production in natural waters...
  81. ncbi Polymorphisms and functions of the aldose reductase gene 5' regulatory region in Chinese patients with type 2 diabetes mellitus
    Qingjie Li
    Department of Biochemistry, Xiangya School of Medicine of Central South University, Changsha 410078, China
    Chin Med J (Engl) 115:209-13. 2002
    ..To screen the 5' regulatory region of the aldose reductase (AR) gene for genetic variabilities causing changes in protein expression and affecting the promoter function...
  82. ncbi Roles of TNF receptor-associated factor 3 in signaling to B lymphocytes by carboxyl-terminal activating regions 1 and 2 of the EBV-encoded oncoprotein latent membrane protein 1
    Ping Xie
    Department of Microbiology, University of Iowa, Iowa City, IA 52242, USA
    J Immunol 173:5546-55. 2004
    ..Together, our findings highlight the central importance of TRAF3 in LMP1-mediated signaling, which is critical for EBV persistent infection and EBV-associated pathogenesis...
  83. ncbi [Variation of insulin receptor substrate-2 gene 3'-untranslated region in patients with type 2 diabetes mellitus]
    Wei Min Zeng
    Department of Biochemistry, Xiangya Medical School, Central South University, Changsha 410078, China
    Yi Chuan Xue Bao 30:785-9. 2003
    ..1% vs 4.0%, x2 = 7.748, P = 0.005). These results indicate that the T4064-->C in IRS-2 gene 3'-UTR may be related to Chinese patients with T2DM...
  84. ncbi Effect of a novel mutation in 5'-regulatory region of aldose reductase gene on its expression
    Ping Xie
    Department of Biochemistry, Xiangya School of Medicine, Central South University, Changsha 410078, China
    Sheng Wu Hua Xue Yu Sheng Wu Wu Li Xue Bao (Shanghai) 35:904-8. 2003
    ..1%) (P<0.01), and the mobility shift of mutant was also slower than that of wild type. The results indicated the mutation C(-167) -->A in AR gene might prevent or delay the development of DC by repressing the expression of AR gene...