SM1 group

 

a)        Abstract

Our research is focused on dynamics of DNA and proteins, including interactions among them. One of our main aim is to explore the physical mechanisms of bio-molecular interactions in the single-molecular level. Experimentally, we use fluorescence microscopy and single-molecular method combined with fast-reaction kinetics for observation and manipulation. Theoretically, we use Brownian dynamics and molecular dynamics for simulations.

 

b)        Research directions and contents

                         i.              One of our research areas is to study the interactions between DNA and histones and to investigate the key factors that affect this complex. Theoretically, we use Brownian dynamics to simulate the process of nucleosome formation and disruption under stretching force. Experimentally, we use molecular combing combined with fluorescence microscopy for observation. We also study the behaviors of single DNA molecules, such as DNA melting, under stretching force with this method.

                       ii.              Our second research area is to study the dynamics of molecular motors including kinesin, myosin and helicase. For kinesin and myosin, we expect to build physical models for their movement mechanisms. For helicase, we focus on investigating the features of RecQ, a human helicase that of important physiological functions. We experimentally investigate, in vitro, its binding properties to DNA, processivity, run length, moving velocity, etc. The experimental methods for this investigation include fast-reaction kinetics, fluorescence anisotropy, fluorescence microscopy, atomic force microscopy, molecular combing, single-molecular manipulation, etc.

 

c)        Recent progress in the lab build up

                         i.            We have built a wet lab for preparing biological materials, including nucleic acids and proteins. We have built a fluorescence microscope, including a sensitive CCD imagining system, a laser exciting system and an evanescent light luminated flow cell, for the single-molecular study of nucleic acids and proteins. We have developed softwares, including Brownian dynamics method, Monte Carlo method, for simulations of dynamical behaviors of biological macromolecules. We have collaborated with internationally well-known scientists.

 

d)        Research team members

                         i.              Professors: Peng-Ye Wang, Shuo-Xing Dou, Wei-Chi Wang, Ping Xie, Wei Li, Ling-Yun Zhang

                       ii.              Collaborator: Dr. Xu-Guang Xi (CNRS, France)

                      iii.            Postdocs and Ph.D. Students: Kai-Ge Wang, Hui-Jie Zhang, Yu-Ying Liu, Jun Qian, Xing-Dong Zhang, Hong Wang, Xi-Miao Hou, Ye Yang, Zhi-Qiang Sun, Bing-Yi Pan, Chao Ji, Zhi-Qiang Zhang, Zhao-Wen Duan, Hui Li

 

e)        Research funding sources

                         i.              National Natural Science Foundation of China.

                       ii.              Chinese Academy of Sciences

 

f)         Main research equipments

                         i.              Our laboratory is equipped with the state-of-art equipment for studying kinetics of proteins, nucleic acids and their interactions. We have a newly installed stopped-flow system from Bio-Logic (SF-400) with absorbance spectrum, CD, fluorescence anisotropy, and automatic titration (MOS-450). We have a fluorescence microscope from Olympus equipped with a cooled CCD (CoolSNAP-HQ, Roper Scientific) and an intensified CCD (I-PentaMAX, Roper Scientific) and a diode-pumped solid-state laser (Verdi-V2, Coherent). A MetaMorph software (Universal Imaging) is used for the system control, data acquisition and data processing. In addition, we share a large common wet lab with other groups. We can use the parallel supercomputer (IBM Sp690 Regatta, 64´1.25G CUPs, 128G-RAM) for simulations.

 

g)        Current and future research plans

                         i.              First, we would like to combine the molecular combing with fluorescence to study the stretching dynamics of DNA single molecules and the interaction between DNA and histones. We expect to observe the assembling process of nucleosomes and their rupture under stretching force. In addition, combining with the experimental results, we will theoretically investigate this system with Brownian dynamics and molecular dynamics simulations.

                       ii.              Second, we will study the dynamics of some biological molecular motors, especially RecQ helicase, at the single-molecular level. Although some pure samples have been obtained, their dynamical features, such as processivity, run length, velocity, etc., are not completely known. The physical originations of the movement are also open questions. We will make our efforts, with single-molecular techniques, fluorescence microscopy and fast-reaction kinetics, to investigate these features.

 

h)        Group leader

                                        Dr. Peng-Ye Wang. EDUCATION: Shandong University, Physics, B.A.(1978-1982); Institute of Physics, Chinese Academy of Sciences, Physics, M.S.(1982-1985), Ph.D.(1985-1988); VISITING EXPERIENCES: Istituto Nazionale di Ottica, Firenze, Italy (ICTP program 1989-1991); Universite des Sciences et Technologies de Lille, France (CNRS Associate Researcher 1991-1992); Visiting scholar (Risø National Lab, Danmark 1998-1999; Heriot-Watt University, UK 1999-2000; Stanford University, USA 2006.5-8); PROFESSIONAL EXPERIENCE: Institute of Physics, Chinese Academy of Sciences, Group Leader (2000-present), Professor (2000-present), Director of the Laboratory of Soft Matter Physics (2001-present), Director of the Soft Matter Physics Division, Beijing National Laboratory for Condensed Matter Physics (2004-present). AWARDS: The fourth award of the National Natural Science Prize of China; The second award of the Science and Technology Advance Prize of CAS; The National Science Fund for Distinguished Young Scholars. PUBLICATIONS: Published over 100 scientific papers, such as Physical Review Letters paper in nonlinear science and The Journal of Biological Chemistry paper in biology. CURRENT RESEARCH DIRECTIONS: Single-molecular and fluorescence study of DNA/DNA, DNA/protein, protein/protein interactions, such as DNA/histone interactions in nucleosomes; Dynamics of biological molecular motors, such as helicase; Brownian dynamics and molecular dynamics simulations of nucleic acids and proteins.

 

i)        Selected recent publications

  1. “Brownian dynamics simulation of the effect of histone modification on nucleosome structure”

Wei Li, Shuo-Xing Dou, Ping Xie, and Peng-Ye Wang

Phys. Rev. E 75, 051915 (2007).

  1.  “The arginine finger of the Bloom syndrome protein: its structural organization and its role in energy coupling”

Hua Ren, Shuo-Xing Dou, Pascal Rigolet, Ye Yang, Peng-Ye Wang, Mounira Amor-Gueret and Xu Guang Xi

Nucleic Acids Research, 35, 6029–6041 (2007).

  1.  “Structural and functional analyses of disease-causing missense mutations in Bloom syndrome protein”

Rong-Bing Guo, Pascal Rigolet, Hua Ren, Bo Zhang, Xing-Dong Zhang, Shuo-Xing Dou, Peng-Ye Wang, Mounira Amor-Gueret and Xu Guang Xi

Nucleic Acids Research, 35, 6297–6310 (2007).

  1.  “Study the effects of divalent metallic ions on the combination of DNA and histones with fluorescence anisotropy assays”

LIU YuYing, WANG PengYe, DOU ShuoXing, XIE Ping, XI XuGuang

Chinese Science Bulletin, 52, 1166-1171 (2007).

  1. Processivity of single-headed kinesin motors”

Ping Xie, Shuo-Xing Dou and Peng-Ye Wang

Biochimica et Biophysica Acta 1767, 1418–1427 (2007).

  1.  “Limping of Homodimeric Kinesin Motors”

Ping Xie, Shuo-Xing Dou and Peng-Ye Wang

J. Mol. Biol. 366, 976–985 (2007).

  1.  “Brownian dynamics simulation of directional sliding of histone octamers caused by DNA bending”

Wei Li, Shuo-Xing Dou, Ping Xie, Peng-Ye Wang

Phys. Rev. E 73, 051909 (2006).

  1.  “Model for kinetics of wild-type and mutant kinesins

Ping Xie, Shuo-Xing Dou, Peng-Ye Wang

BioSystems 84, 24 (2006).

  1. “Manipulating DNA molecules in nanofluidic channels”

Kai-Ge Wang, Shuanglin Yue, Lei Wang, Aizi Jin, Changzhi Gu, Peng-Ye Wang, Yuchun Feng, Yuncheng Wang, Hanben Niu

Microfluid Nanofluid 2, 85 (2006).

  1.  “A hand-over-hand diffusing model for myosin-VI molecular motors”

Ping Xie, Shuo-Xing Dou, Peng-Ye Wang

Biophysical Chemistry 122, 90 (2006).

  1. E. coli RecQ is a rapid, efficient and monomeric helicase

Xing-Dong Zhang, Shuo-Xing Dou, Ping Xie, Jin-Shan Hu, Peng-Ye Wang, Xu Guang Xi

J. Biol. Chem. 281, 12655 (2006).

  1. Mechanochemical couplings of kinesin motors”

Ping Xie, Shuo-Xing Dou, Peng-Ye Wang

Biophysical Chemistry 123, 58 (2006).

  1. A model for biased diffusion of collagenase along collagen fibrils

Jun Qian, Ping Xie, Shuo-Xing Dou, Peng-Ye Wang

J. Theor. Biol. 243, 322 (2006).

  1.  The histone octamer influences the wrapping direction of DNA on it: Brownian dynamics simulation of the nucleosome chirality

Wei Li, Shuo-Xing Dou, Peng-Ye Wang

J. Theor. Biol. 235, 365 (2005).

  1. RecQ Helicase-catalyzed DNA Unwinding Detected by Fluorescence Resonance Energy Transfer

Xing-Dong ZHANG, Shuo-Xing DOU, Ping XIE, Peng-Ye WANG, Xu Guang XI

Acta Biochimica et Biophysica Sinica 37, 593 (2005).

  1. A model for processivity of molecular motors

Ping Xie, Shuo-Xing Dou, and Peng-Ye Wang

Chin. Phys. 13, 1569 (2004).

  1. “Brownian dynamics simulation of nucleosome formation and disruption under stretching”

Wei Li, Shuo-Xing Dou, Peng-Ye Wang

J. Theor. Biol. 230, 375-383 (2004).

  1. “Ionic effect on combing of single DNA molecules and observation of their force-induced melting by fluorescence microscopy”

Yu-Ying Liu, Peng-Ye Wang, Shuo-Xing Dou, Wei-Chi Wang, Ping Xie, Hua-Wei Yin, Xing-Dong Zhang, Xu Guang Xi

J. Chem. Phys. 121, 4302-4309 (2004).

  1. “The Zinc Finger Motif of Escherichia coli RecQ Is Implicated in Both DNA Binding and Protein Folding”

Jie Lin Liu, Pascal Rigolet, Shuo-Xing Dou, Peng-Ye Wang, and Xu Guang Xi

J. Biol. Chem. 279,  42794-42802 (2004).

  1. The DNA Binding Properties of the Escherichia coli RecQ Helicase

Shuo-Xing Dou, Peng-Ye Wang, Hou Qiang Xu, and Xu Guang Xi

J. Biol. Chem. 279,  6354-6363 (2004).[ Abstract ]

  1.  “Control of spiral waves and turbulent states in a cardiac model by travelling-wave perturbations”

Peng-Ye Wang, Ping Xie, and Hua-Wei Yin

Chin. Phys. 12, 674 (2003). [ PDF ( 258kB ) ]

  1.  “Interactions between DNA and histones - a dynamic process of nucleosome formation”

Wei Li, Peng-Ye Wang, Shuo-Xing Dou, and Pei-Qing Tong

Chin. Phys. 12, 226 (2003). [ PDF ( 258kB ) ], [ PS(WinZip) ( 365kB ) ], [PS ( 6.7GB ) ]