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Protein structure and function studied by NMR

  • School of Life Science, and Hefei National Laboratory for Physical Sciences at Microscale, University of Science and Technology of China, Hefei 230027, China

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  • Corresponding author: SHI Yun-yu, E-mail: yyshi@ustc.edu.cn
  • Received Date: 30 June 2008
  • Rev Recd Date: 10 July 2008
  • Publish Date: 31 August 2008
    Abstract

  • Abstract

    More than 10 years of research in the Laboratory of Nuclear Magnetic Resonance (NMR) at the School of Life Science, University of Science and Technology of China is reviewed. Our researches have focused on two systems: proteins related to the regulation of gene expression in humans and other eukaryotes, and proteins existing in the cell junction in humans. The majority of proteins selected from these two systems are related to human health and diseases, and some are potential drug targets. We were interested in using NMR to study structural basis of protein-protein interactions. NMR was highly suited for investigating molecular interactions under approximately physiological conditions and was particularly suited for the study of low-affinity, transient complexes. It can provide information of protein interaction surface, complex structure, and dynamic properties during protein recognition. Several examples were given in this paper. NMR was also used to study dynamic properties of protein both in pico-second to nano-second and in micro-second to mili-second time scales. We have studied protein folding and unfolding by NMR together with fluorescence and circular dichroism experiments. Proteins in unfolded states were characterized in detail by NMR. The last example of NMR application is the identification of a novel inhibitor of a human dual-specific phosphatase and the cellular effects of this compound were also studied. Our results demonstrate that our screening strategy, which combines both virtual and NMR-based methods, is feasible and might be employed in the early stage of drug discovery.

    Abstract

    More than 10 years of research in the Laboratory of Nuclear Magnetic Resonance (NMR) at the School of Life Science, University of Science and Technology of China is reviewed. Our researches have focused on two systems: proteins related to the regulation of gene expression in humans and other eukaryotes, and proteins existing in the cell junction in humans. The majority of proteins selected from these two systems are related to human health and diseases, and some are potential drug targets. We were interested in using NMR to study structural basis of protein-protein interactions. NMR was highly suited for investigating molecular interactions under approximately physiological conditions and was particularly suited for the study of low-affinity, transient complexes. It can provide information of protein interaction surface, complex structure, and dynamic properties during protein recognition. Several examples were given in this paper. NMR was also used to study dynamic properties of protein both in pico-second to nano-second and in micro-second to mili-second time scales. We have studied protein folding and unfolding by NMR together with fluorescence and circular dichroism experiments. Proteins in unfolded states were characterized in detail by NMR. The last example of NMR application is the identification of a novel inhibitor of a human dual-specific phosphatase and the cellular effects of this compound were also studied. Our results demonstrate that our screening strategy, which combines both virtual and NMR-based methods, is feasible and might be employed in the early stage of drug discovery.
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    • References(35)
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    [2]
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    Liu Jiangxin, Zhang Jiahai, Yang Yinshan, et al. Conformational change upon ligand binding and dynamics of the PDZ domain from leukemia-associated Rho guanine nucleotide exchange factor[J]. Protein Sci,2008,17(6):1 003-1 014.
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    Xu Yingqi, Wu Jihui, Pei Jiming, et al. Solution structure of BmP02, a new potassium channel blocker form the venom of the Chinese Scorpion Buthus martensi Karsch[J]. Biochemistry, 2000,39:1 369-1 375.
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    Yang Wulin, Xu Yinqi, Wu Jihui, et al. 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[J]. Biochemistry, 2003,42:1 930-1 938.
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    Zhang Xuecheng, Zhang Jiahai, Li Xuan, et al. Compact molten globule-like state of hUBF HMG Box1 at extremely low pH[J]. Biochim Biophys Acta, 2005,1 748(1):66-73.
    [29]
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    [30]
    Englander S W. Protein folding intermediates and pathways studied by hydrogen exchange[J]. Annu Rev Biophys Biomol Struct,2000,29: 213-238.
    [31]
    Wang Dandan, Zhang Jiahai, Jin Xianju, et al. Investigation of the Structural Stability of hUBF HMG Box 5 by native-state hydrogen exchange[J]. Biochemistry, 2007,46(5):1 293-1 302.
    [32]
    Jin Xianju, Zhang Jiahai, Dai Haiming, et al. Investigation of the four cooperative unfolding units existing in the MICAL-1 CH domain[J]. Biophysical Chemistry,2007,129:269-278.
    [33]
    Shi Zhe, Sartaj Tabassum, Jiang Wei, et al. Identification of a potent inhibitor of human dual-specific phosphatase, VHR, from computer-aided and NMR-based screening to cellular effects[J]. Chembiochem,2007,8(17):2 092-2 099.
    [34]
    Shi Yunyu, Wu Jihui. Structural basis of protein-protein interaction studied by NMR[J]. Journal of Structural and Functional Genomics,2007,8:67-72.
    [35]
    Structural Genomics Consortium, Architecture et Fonction des Macrodolécules Biologiques, Berkeley Structural Genomics, China structural Genomics Consortium, et al. Protein Production and purification[J]. Nature Methods, 2008,5(2):135-146.
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    [1]
    Kay L E. NMR studies of protein structure and dynamics[J]. J Magn Reson, 2005,173: 193-207.
    [2]
    Takeuchi K, Wagner G. NMR studies of protein interactions[J]. Curr Opin Struct Biol, 2006,16: 109-117.
    [3]
    Vaynberg J, Qin J. Weak protein-protein interactions as probed by NMR spectroscopy[J]. Trends Biotechnol,2006,24: 22-27.
    [4]
    Shen Weiqun, Xu Chao, Huang Wei, et al. Solution Structure of Human Brg1 Bromodomain and Its Specific Binding to Acetylated Histone Tails[J]. Biochemistry, 2007,46(8):2 100-2 110.
    [5]
    Mujtaba S, Zeng L, Zhou M M. Structure and acetyl-lysine recognition of the bromodmain[J]. Oncogene, 2007,26:5 521-5 527.
    [6]
    Huang Hongda, Zhang Jiahai, Shen Weiqun, et al. Solution structure of the second bromodomain of Brd2 and its specific interaction with acetylated histone tails[J]. BMC Struct Biol,2007,7(1):57.
    [7]
    Liu Ying, Wang Xiqing, Zhang Jiahai, et al. Structural basis and binding properties of the second bromodomain of Brd4 with acetylated histone tails[J]. Biochemistry,2008,47(24):6 403-6 417.
    [8]
    Sun H B, Sun Hongbin, Liu J X, et al. Solution structure of BRD7 bromodomain and its interaction with acetylated peptides from histone H3 and H4[J]. Biochem Bioph Res Co,2007,358(2): 435-441.
    [9]
    Xu Chao, Wu Jihui, Xu Yingqi, et al. Backbone and side chain assignments of human Peptidylprolyl isomerase Like 1 (hPPIL1)[J]. Journal of Biomolecular NMR,2005,31(2):179-180.
    [10]
    Xu Chao, Zhang Jiahai, Huang Xiaojuan, et al. Solution structure of human peptidyl prolyl isomerase like protein 1 and insights into its interaction with SKIP[J]. Journal of Biological Chemistry, 2006,281(23):15 900-15 908.
    [11]
    Ding H, Xu Y, Chen Q, et al. Solution Structure of Human SUMO-3 C47S and Its Binding Surface for Ubc9[J]. Biochemistry, 2005,44(8):2 790-2 799.
    [12]
    Ding Husheng, Yang Yuedong, Zhang Jiahai, et al. Structural basis for SUMO-E2 interaction revealed by a complex model using docking approach in combination with NMR data[J]. Proteins: Structure, Function, and Bioinformatics, 2005,61(4):1 050-1 058.
    [13]
    Xu Junjie, Zhang Jiahai, Wang Li, et al. Solution structure of Urm1 and its implications for the origin of protein modifiers[J]. Proc Natl Acad Sci USA, 2006,103:11 625-11 630.
    [14]
    Sun Jianping, Zhang Jiahai, Wu Fangming, et al. Solution structure of Kti11p from Saccharomyces cerevisiae reveals a novel zinc binding module[J]. Biochemistry, 2005,44:8 801-8 809.
    [15]
    Wu Fangming, Zhang Jiahai, Sun Jianping, et al. Solution structure of human DESR1, a CSL zinc-binding protein[J]. Proteins, 2008,71(1):514-518.
    [16]
    Zhou Heyue, Xu Yingqi, Yang Yuedong, et al. Solution structure of AF-6 PDZ domain and its interaction with the C-terminal peptides from neurexin and Bcr[J]. J Biol Chem, 2005,280:13 841-13 847.
    [17]
    Chen Quan, Niu Xiaogang, Xu Yingqi, et al. Solution structure and backbone dynamics of the AF-6 PDZ domain/Bcr peptide complex[J]. Protein Science,2007,16:1 053-1 062.
    [18]
    Wu Jiawen, Yang Yinshan, Zhang Jiahai, et al. Domain-swapped dimerization of the second PDZ domain of ZO2 may provide a structural basis for the polymerization of claudins[J]. J Biol Chem, 2007,282(49):35 988-35 999.
    [19]
    Li Xiang, Zhang Jiahai, Cao Zanxia, et al. Solution structure of GOPC PDZ domain and its interaction with the C-terminal motif of Neuroligin[J]. Protein Science, 2006,15(9):2 149-2 158.
    [20]
    Mittermaier A, Kay L E. New tools provide new insights in NMR studies of protein dynamics[J]. Science, 2006,312:224-228.
    [21]
    Palmer A G 3rd. NMR characterization of the dynamics of biomacromolecules[J]. Chem Rev,2004,104:3 623-3 640.
    [22]
    Palmer A G, 3rd, Massi F. Characterization of the dynamics of biomacromolecules using rotating-frame spin relaxation NMR spectroscopy[J]. Chem Rev,2006,106:1 700-1 719.
    [23]
    Niu Xiaogang, Chen Quan, Zhang Jiahai, et al. Interesting structural and dynamical behaviors exhibited by the AF-6 PDZ domain upon Bcr peptide binding[J]. Biochemistry, 2007,46(51):15 042-15 053.
    [24]
    Liu Jiangxin, Zhang Jiahai, Yang Yinshan, et al. Conformational change upon ligand binding and dynamics of the PDZ domain from leukemia-associated Rho guanine nucleotide exchange factor[J]. Protein Sci,2008,17(6):1 003-1 014.
    [25]
    Mittag T, Forman-Kay J D. Atomic-level characterization of disordered protein ensembles[J]. Curr Opin Struct Biol,2007,17: 3-14.
    [26]
    Xu Yingqi, Wu Jihui, Pei Jiming, et al. Solution structure of BmP02, a new potassium channel blocker form the venom of the Chinese Scorpion Buthus martensi Karsch[J]. Biochemistry, 2000,39:1 369-1 375.
    [27]
    Yang Wulin, Xu Yinqi, Wu Jihui, et al. 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[J]. Biochemistry, 2003,42:1 930-1 938.
    [28]
    Zhang Xuecheng, Zhang Jiahai, Li Xuan, et al. Compact molten globule-like state of hUBF HMG Box1 at extremely low pH[J]. Biochim Biophys Acta, 2005,1 748(1):66-73.
    [29]
    Zhang Xuecheng, Xu Yingqi, Zhang Jiahai, et al. Structural and dynamic properties of the acid-unfolded state of hUBF HMG Box 1 provide clues for the early events in protein folding[J]. Biochemistry, 2005,44:8 117-8 125.
    [30]
    Englander S W. Protein folding intermediates and pathways studied by hydrogen exchange[J]. Annu Rev Biophys Biomol Struct,2000,29: 213-238.
    [31]
    Wang Dandan, Zhang Jiahai, Jin Xianju, et al. Investigation of the Structural Stability of hUBF HMG Box 5 by native-state hydrogen exchange[J]. Biochemistry, 2007,46(5):1 293-1 302.
    [32]
    Jin Xianju, Zhang Jiahai, Dai Haiming, et al. Investigation of the four cooperative unfolding units existing in the MICAL-1 CH domain[J]. Biophysical Chemistry,2007,129:269-278.
    [33]
    Shi Zhe, Sartaj Tabassum, Jiang Wei, et al. Identification of a potent inhibitor of human dual-specific phosphatase, VHR, from computer-aided and NMR-based screening to cellular effects[J]. Chembiochem,2007,8(17):2 092-2 099.
    [34]
    Shi Yunyu, Wu Jihui. Structural basis of protein-protein interaction studied by NMR[J]. Journal of Structural and Functional Genomics,2007,8:67-72.
    [35]
    Structural Genomics Consortium, Architecture et Fonction des Macrodolécules Biologiques, Berkeley Structural Genomics, China structural Genomics Consortium, et al. Protein Production and purification[J]. Nature Methods, 2008,5(2):135-146.
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