施蕴渝实验室 发布论文

Yunyu Shi and Jihui Wu . (2007) Structural basis of protein–protein interaction studied by NMR. Journal of Structural and Functional Genomics. 8(2-3):67-72.

Fangming Wu, Jiahai Zhang, Jianping Sun, Hongda Huang, Peng Ji, Wangsheng Chu, Meijuan Yu, Feifei Yang, Ziyu Wu, Jihui Wu and Yunyu Shi. (2008) Solution structure of human DESR1, a CSL zinc-binding protein. Proteins: Structure, Function, and Bioinformatics. 71(1) 514-518.

Xiaogang Niu, Quan Chen, Jiahai Zhang, Weiqun Shen, Yunyu Shi, and Jihui Wu. (2007) Interesting Structural and Dynamical Behaviors Exhibited by the AF-6 PDZ Domain upon Bcr Peptide Binding. Biochemistry 46 (51):15042 -15053

Qi Hu, Weiqun Shen, Hongda Huang, Jiangxin Liu, Jiahai Zhang, Xiaojuan Huang, Jihui Wu, and Yunyu Shi. (2007) Insight into the Binding Properties of MEKK3 PB1 to MEK5 PB1 from Its Solution Structure. Biochemistry 46(47):13478-89.

Hongda Huang , Jiahai Zhang , Weiqun Shen , Xingsheng Wang , Jiawen Wu , Jihui Wu and Yunyu Shi. (2007) Solution structure of the second bromodomain of Brd2 and its specific interaction with acetylated histone tails. BMC Structural Biology 7:57.

Zhe Shi, Sartaj Tabassum, Wei Jiang, Jiahai Zhang, Suvigya Mathur, Jihui Wu and Yunyu Shi.(2007) Identification of a Potent Inhibitor of Human Dual-Specific Phosphatase, VHR, from Computer-Aided and NMR-Based Screening to Cellular Effects. ChemBioChem. 8(17):2092-2099.

Jiawen Wu, Yinshan Yang, Jiahai Zhang, Peng Ji, Wenjing Du, Peng Jiang, Dinghai Xie, Hongda Huang, Mian Wu, Guangzhao Zhang, Jihui Wu and Yunyu Shi. (2007)Domain-swapped dimerization of the second PDZ domain of ZO2 may provide a structural basis for the polymerization of claudins. Journal of Biological Chemistry 282(49):35988-35999.

Xianju Jin, Jiahai Zhang, Haiming Dai, Hongbin Sun, Dandan Wang, Jihui Wu and Yunyu Shi. (2007)Investigation of the four cooperative unfolding units existing in the MICAL-1 CH domain. Biophysical Chemistry 129, 269-278.

Quan Chen, Xiaogang Niu, Yingqi Xu, Jihui Wu, and Yunyu Shi. (2007) Solution structure and backbone dynamics of the AF-6 PDZ domain/Bcr peptide complex. Protein Science 16, 1053-1062.

Hongbin Sun, Jiangxin Liu, Jiahai Zhang, Weiqun Shen, Hongda Huang, Chao Xu, Haiming Dai, Jihui Wu and Yunyu Shi. (2007) Solution structure of BRD7 bromodomain and its interaction with acetylated peptides from histone H3 and H4. Biochemical and Biophysical Research Communications 358, 435-441.

Jiahai Zhang, Xiang Li, Bo Yao, Weiqun Shen, Hongbin Sun, Chao Xu, Jihui Wu and Yunyu Shi. (2007) Solution structure of the first SH3 domain of human vinexin and its interaction with vinculin peptides. Biochemical and Biophysical Research Communications 357, 931-937.

Weiqun Shen, Chao Xu, Wei Huang, Jiahai Zhang, Justin E. Carlson, Xiaoming Tu, Jihui Wu, and Yunyu Shi.(2007) Solution Structure of Human Brg1 Bromodomain and Its Specific Binding to Acetylated Histone Tails. Biochemistry 46, 2100-2110.

Dandan Wang, Jiahai Zhang, Xianju Jin, Jihui Wu, and Yunyu Shi. (2007) Investigation of the Structural Stability of hUBF HMG Box 5 by Native-State Hydrogen Exchange. Biochemistry 46,1293 -1302.

Bo Yao, Jiahai Zhang, Haiming Dai, Jianping Sun, Yuanyuan Jiao, Yajun Tang, Jihui Wu and Yunyu Shi. (2007) Solution structure of the second SH3 domain of human CMS and a newly identified binding site at the C-terminus of c-Cbl. Biochimica et Biophysica Acta (BBA) - Proteins & Proteomics 1774, 35-43.

Haiming Dai, Wei Huang, Jian Xu, Bo Yao, Shangmin Xiong, Husheng Ding, Yajun Tang, Haiyan Liu, Jihui Wu and Yunyu Shi. (2006) Binding model of human coactosin-like protein with filament actin revealed by mutagenesis. Biochimica et Biophysica Acta (BBA) - Proteins & Proteomics 1764, 1688-700.

Sun, H. B., Dai, H. M., Zhang, J. H., Jin, X. J., Xiong, S. M., Xu, J., Wu, J. H. and Shi, Y. Y. (2006)Solution structure of calponin homology domain of Human MICAL-1. Journal of Biomolecular Nmr 36, 295-300.

Li, X., Zhang, J. H., Cao, Z. X., Wu, J. H. and Shi, Y. Y. (2006) Solution structure of GOPC PDZ domain and its interaction with the C-terminal motif of neuroligin. Protein Science 15, 2149-2158.

Xu, J. J., Zhang, J. H., Wang, L., Zhou, J., Huang, H. D., Wu, J. H., Zhong, Y., and Shi, Y. Y. (2006) Solution structure of Urm1 and its implications for the origin of protein modifiers. Proceedings of the National Academy of Sciences of the United States of America 103, 11625-11630.

Man, N., Cheng, Y. Y., Xu, T. W., Ding, Y., Wang, X. M., Li, Z. W., Chen, Z. C., Huang, G. Y., Shi, Y. Y., and Longping, W. (2006) Dendrimers as potential drug carriers. Part II. Prolonged delivery of ketoprofen by in vitro and in vivo studies. European Journal of Medicinal Chemistry 41, 670-674.

Xu, C., Zhang, J. H., Huang, X. J., Sun, J. P., Xu, Y. Q., Tang, Y. J., Wu, J. H., Shi, Y. Y., Huang, Q. H., and Zhang, Q. H. (2006) Solution structure of human peptidyl prolyl isomerase-like protein 1 and insights into its interaction with SKIP. Journal of Biological Chemistry 281, 15900-15908.

Zhang, X. C., Zhang, J. H., Li, X., Xu, J. J., Huang, H. D., Chen, Q., Wu, J. H., and Shi, Y. Y. (2005) Compact molten globule-like state of hUBF HMG Box1 at extremely low pH. Biochimica Et Biophysica Acta-Proteins and Proteomics 1748, 66-73.

Ding, H. S., Yang, Y. D., Zhang, J. H., Wu, J. H., Liu, H. Y., and Shi, Y. Y. (2005) Structural basis for SUMO-E2 interaction revealed by a complex model using docking approach in combination with NMR data. Proteins-Structure Function and Bioinformatics 61, 1050-1058.

Sun, J. P., Zhang, J. H., Wu, F. M., Xu, C., Li, S. J., Zhao, W., Wu, Z. Y., Wu, J. H., Zhou, C. Z., and Shi, Y. Y. (2005) Solution structure of Kti11p from Saccharomyces cerevisiae reveals a novel zinc-binding module. Biochemistry 44, 8801-8809.

Zhang, X. C., Xu, Y. Q., Zhang, J. H., Wu, J. H., and Shi, Y. Y. (2005) Structural and dynamic characterization of the acid-unfolded state of hUBF HMG box 1 provides clues for the early events in protein folding. Biochemistry 44, 8117-8125.

Xu, C., Zheng, P. Z., Shen, S. H., Xu, Y. Q., Wei, L., Gao, H. J., Wang, S. N., Zhu, C. R., Tang, Y. J., Wu, J. H., Zhang, Q. H., and Shi, Y. Y. (2005) NMR structure and regulated expression in APL cell of human SH3BGRL3. Febs Letters 579, 2788-2794.

Zhou, H. Y., Xu, Y. Q., Yang, Y. D., Huang, A. D., Wu, J. H., and Shi, Y. Y. (2005) Solution structure of AF-6 PDZ domain and its interaction with the C-terminal peptides from neurexin and Bcr. Journal of Biological Chemistry 280, 13841-13847.

Xu, C., Xu, Y. Q., Tang, Y. J., Wu, J. H., Shi, Y. Y., Huang, Q. H., and Zhang, Q. H. (2005) Letter to the Editor: Backbone and side chain assignments of human peptidylprolyl isomerase like 1 (hPPIL1). Journal of Biomolecular Nmr 31, 179-180.

Ding, H. S., Xu, Y. Q., Chen, Q., Dai, H. M., Tang, Y. J., Wu, J. H., and Shi, Y. Y. (2005) Solution structure of human SUMO-3 C47S and its binding surface for Ubc9. Biochemistry 44, 2790-2799.

Wang, C. G., Cai, Z., Lu, W. Y., Wu, J. H., Xu, Y. Q., Shi, Y. Y., and Chi, C. W. (2005) A novel short-chain peptide BmKX from the chinese scorpion Buthus martensi karsch, sequencing, gene cloning and structure determination. Toxicon 45, 309-319.

Dai, H. M., Wu, J. H., Xu, Y. Q., Tang, Y. J., Ding, H. S., and Shi, Y. Y. (2004) Letter to the Editor: H-1, C-13 and N-15 resonance assignments and the secondary structures of human Coactosin like protein (hCLP) D123N. Journal of Biomolecular Nmr 29, 455-456.

Cai, Z., Xu, C. Q., Xu, Y. Q., Lu, W. Y., Chi, C. W., Shi, Y. Y., and Wu, J. H. (2004) Solution structure of BmBKTx1, a new BKCa1 channel blocker from the Chinese scorpion Buthus martensi Karsch. Biochemistry 43, 3764-3771.

Xiao, Y. Z., Chen, Q., Hang, J., Shi, Y. Y., Xiao, Y. Z., Wu, J., Hong, Y. Z., and Wang, Y. P. (2004) Selective induction, purification and characterization of a laccase isozyme from the basidiomycete Trametes sp AH28-2. Mycologia 96, 26-35.

Zhang, J. H., Du, D. Z., and Wu, J. H. (2003) Identification for the hydrogen and carbon spectra of cilnidipine by nuclear magnetic resonance. Chinese Journal of Analytical Chemistry 31, 1044-1047.

Zhu, J., Zhu, Q. Q., Shi, Y. Y., and Liu, H. Y. (2003) How well can we predict native contacts in proteins based on decoy structures and their energies? Proteins-Structure Function and Genetics 52, 598-608.

Zeng, W. Y., Wang, Y. H., Zhang, Y. C., Yang, W. L., and Shi, Y. Y. (2003) Functional significance of conserved glycine 127 in a human dual-specificity protein tyrosine phosphatase. Biochemistry-Moscow 68, 634-638.

Wang, J. H., Zhang, Z. Y., Liu, H. Y., and Shi, Y. Y. (2003) Quasiequilibrium unfolding thermodynamics of a small protein studied by molecular dynamics simulation with an explicit water model. Physical Review E 67.

Xiao, Y. Z., Tu, X. M., Wang, J., Zhang, M., Cheng, Q., Zeng, W. Y., and Shi, Y. Y. (2003) Purification, molecular characterization and reactivity with aromatic compounds of a laccase from basidiomycete Trametes sp strain AH28-2. Applied Microbiology and Biotechnology 60, 700-707.

Wang, Y. H., Zeng, W. Y., and Shi, Y. Y. (2003) Mutation of arginines near the active site Cys(124) of human dual-specificity phosphatase and its effect on the enzymatic activity. Acta Biochimica Et Biophysica Sinica 35, 149-153.

Yang, W. L., Xu, Y. Q., Wu, J. H., Zeng, W. Y., and Shi, Y. Y. (2003) Solution structure and DNA binding property of the fifth HMG box domain in comparison with the first HMG box domain in human upstream binding factor. Biochemistry 42, 1930-1938.

Xu, Y. Q., Yang, W. L. Wu, J. H. and Shi, Y. Y. (2002) Solution Structure of the First HMG Box Domain in Human Upstream Binding Factor. Biochemistry 41, 5415-5420.

Zhu, J., Fan, H., Liu, H. Y., and Shi, Y. Y. (2001) Structure-based ligand design for flexible proteins: Application of new F-DycoBlock. Journal of Computer-Aided Molecular Design 15, 979-996.

Tu, X. M., Wu, J. H., Xu, Y. Q., and Shi, Y. Y. (2001) H-1, C-13 and N-15 resonance assignments and secondary structure of ADR6 DNA-binding domain. Journal of Biomolecular Nmr 21, 187-188.

Liu, S. S., Yin, C. S., Shi, Y. Y., Cai, S. X., and Li, Z. L. (2001) MEDV-13 for QSAR studies on the COX-2 inhibition by indomethacin amides and esters. Chinese Journal of Chemistry 19, 751-756.

Han, J. G., and Shi, Y. Y. (2001) A computational study on geometries, electronic structures and ionization potentials of MSi15 (M = Cr, Mo, W) clusters by density functional method. Chemical Physics 266, 33-40.

Zhang, Z. Y., Zhu, Y. J., and Shi, Y. Y. (2001) Molecular dynamics simulations of urea and thermal-induced denaturation of S-peptide analogue. Biophysical Chemistry 89, 145-162.

Zeng, W. Y., Zhang, X. C., Tu, X. M., Guang, S. H., Xiao, Y. Z., and Shi, Y. Y. (2001) Expression and purification of the DNA-binding domain of the human transcription factor E2F1. Protein Expression and Purification 21, 99-104.

Xu, Y. Q., Wu, J. H., Pei, J. M., Shi, Y. Y., Ji, Y. H., and Tong, Q. C. (2000) Solution structure of BmP02, a new potassium channel blocker from the venom of the Chinese scorpion Buthus martensi Karsch. Biochemistry 39, 13669-13675.

Tu, X. M., Xiao, Y. Z., Zeng, W. Y., and Shi, Y. Y. (2000) Expression and purification of a recombinant DNA-binding domain of ADR6 protein from Escherichia coli and its secondary structure characterization. Biochimica Et Biophysica Acta-Protein Structure and Molecular Enzymology 1481, 167-174.

Lu, B. Z., Wang, C. X., Chen, W. Z., Wan, S. Z., and Shi, Y. Y. (2000) A stochastic dynamics simulation study associated with hydration force and friction memory effect. Journal of Physical Chemistry B 104, 6877-6883.

Han, J. G., Pang, W. M., and Shi, Y. Y. (2000) Theoretical study on the sandwich clusters of Na-n(COT)(m) by density functional method. Chemical Physics 257, 21-28.

Xia, Y. L., Wu, J. H., Guang, S. H., Zhang, H. Y., Liang, S., and Shi, Y. Y. (2000) Proton NMR investigation of heme and surrounding proton in low-spin cyanide-ligated bacterial hemoglobin from Vitreoscilla. Science in China Series C-Life Sciences 43, 57-67.

Guo, Q. X., Liu, H. Y., Ruan, X. Q., Zheng, X. Q., Shi, Y. Y., and Liu, Y. C. (1999) Experimental and theoretical studies on the inclusion complexation of beta-cyclodextrin with phenothiazine derivatives. Journal of Inclusion Phenomena and Macrocyclic Chemistry 35, 487-496.

Tang, Y. Z., Chen, W. Z., Wang, C. X., and Shi, Y. Y. (1999) Constructing the suitable initial configuration of the membrane-protein system in molecular dynamics simulations. European Biophysics Journal with Biophysics Letters 28, 478-488.

Wu, J. H., Kang, Q., Xia, Y. L., and Shi, Y. Y. (1999) The application of watergate technique in DNA. Progress in Biochemistry and Biophysics 26, 376-378.

Liu, H. Y., Duan, Z. H., Luo, Q. M., and Shi, Y. Y. (1999) Structure-based ligand design by dynamically assembling molecular building blocks at binding site. Proteins-Structure Function and Genetics 36, 462-470.

Hu, H., Liu, H. Y., and Shi, Y. Y. (1999) Incorporating density functional potential in classical molecular dynamics simulation. Chinese Science Bulletin 44, 286-287.

Gong, Q. G., Wu, J. H., Liu, Q., Shi, Y. Y., Cui, D. F., Xu, L. G., and Zhang, Y. S. (1998) Solution structure of N-terminal segment of hepatitis B virus surface antigen Pre-S1. Science in China Series C-Life Sciences 41, 530-541.

Xia, W. D., Liu, Q., Wu, J. H., Xia, Y. L., Shi, Y. Y., and Qu, X. M. (1998) Secondary structure of an antibacterial peptide Abp3 studied by two-dimensional proton-NMR. Biochimica Et Biophysica Acta-Protein Structure and Molecular Enzymology 1384, 299-305.

Wan, S. Z., Wang, C. X., and Shi, Y. Y. (1998) Generalized Langevin dynamics simulation: numerical integration and application of the generalized Langevin equation with an exponential model for the friction kernel. Molecular Physics 93, 901-912.

Cheng, W., Wang, C. X., Chen, W. Z., Xu, Y. W., and Shi, Y. Y. (1998) Investigating the dielectric effects of channel pore water on the electrostatic barriers of the permeation ion by the finite difference Poisson-Boltzmann method. European Biophysics Journal with Biophysics Letters 27, 105-112.

You, L. C., Liu, Q., Shi, Y. Y., Wang, C. X., Lahaye, M., and Tran, V. (1997) The conformational study of beta-D-GlcA-(1,4)-L-Rha in solution by NMR and molecular dynamics simulations. Chemical Physics 224, 81-94.

Wan, S. Z., Wang, C. X., Xiang, Z. X., and Shi, Y. Y. (1997) Stochastic dynamics simulation of alanine dipeptide: Including solvation interaction determined by boundary element method. Journal of Computational Chemistry 18, 1440-1449.

Hu, H., Liu, H. Y., and Shi, Y. Y. (1997) The reaction pathway of the isomerization of D-xylose catalyzed by the enzyme D-xylose isomerase: A theoretical study. Proteins-Structure Function and Genetics 27, 545-555.

Wang, C. X., Wan, S. Z., Xiang, Z. X., and Shi, Y. Y. (1997) Incorporating hydration force determined by boundary element method into stochastic dynamics. Journal of Physical Chemistry B 101, 230-235.

Wan, S. Z., Wang, C. S., Xu, Y. W., and Shi, Y. Y. (1996) Molecular dynamics simulations of cis-trans isomerization for a proline-containing tripeptide in solution. Chemical Physics 211, 227-234.

Hu, H., Shi, Y. Y., and Wang, C. X. (1996) Exploring the interaction between D-xylose isomerase and D-xylose by free energy calculation. Proteins-Structure Function and Genetics 26, 157-166.

Xiang, Z. X., Huang, F. H., Shi, Y. Y., and Xu, Y. W. (1995) Incorporating the Protein-Dipole Langevin-Dipole Model into Tanford-Kirkwood Theory. Journal of Computational Chemistry 16, 1468-1473.

Wan, S. Z., Xu, Y. W., Wang, C. X., and Shi, Y. Y. (1995) Analysis of Friction Kernels for N-Butane Isomerization in Water by the Generalized Langevin Equation. Journal of Chemical Physics 102, 4976-4980.

Xiang, Z. X., Shi, Y. Y., and Xu, Y. W. (1995) Calculating the Electric-Potential of Macromolecules - a Simple Method for Molecular-Surface Triangulation. Journal of Computational Chemistry 16, 512-516.

Xiang, Z. X., Shi, Y. Y., and Xu, Y. W. (1995) Solving the Finite-Difference, Nonlinear, Poisson-Boltzmann Equation under a Linear-Approach. Journal of Computational Chemistry 16, 200-206.

Xiang, Z. X., Huang, F. H., and Shi, Y. Y. (1994) Calculation of Solvation Energy with a Combination of the Boundary-Element Method and Pdld Model. Journal of Physical Chemistry 98, 12782-12788.

Liu, H. Y., and Shi, Y. Y. (1994) Combined Molecular Mechanical and Quantum-Mechanical Potential Study of a Nucleophilic-Addition Reaction in Solution. Journal of Computational Chemistry 15, 1311-1318.

Liu, H. Y., and Shi, Y. Y. (1993) Combination of Molecular Dynamic Simulation Program Gromos with Semiempirical Quantum-Chemistry Method Am1. Chinese Science Bulletin 38, 2023-2024.

Shi, Y. Y., Zhao, H. M., and Wang, C. X. (1993) Relative Binding Free-Energy Calculations of DNA to Daunomycin and Its 13-Dihydro Analog. International Journal of Biological Macromolecules 15, 247-251.

Shi, Y. Y., Mark, A. E., Wang, C. X., Huang, F. H., Berendsen, H. J. C., and Vangunsteren, W. F. (1993) Can the Stability of Protein Mutants Be Predicted by Free-Energy Calculations. Protein Engineering 6, 289-295.

Wang, C. X., Shi, Y. Y., Zhou, F., and Wang, L. (1993) Thermodynamic Integration Calculations of Binding Free-Energy Difference for Gly-169 Mutation in Subtilisin Bpn'. Proteins-Structure Function and Genetics 15, 5-9.

Wang, C. X., Shi, Y. Y., and Huang, F. H. (1991) The Relationship between Fractal Dimension and Tertiary Structure of Protein Molecule. Chinese Science Bulletin 36, 499-503.[