Determining structural ensembles of flexible multi-domain proteins using small-angle X-ray scattering and molecular dynamics simulations

Yonghui Zhang; Bin Wen; Junhui Peng; Xiaobing Zuo; Qingguo Gong; Zhiyong Zhang

doi:10.1007/s13238-015-0162-4

Protein Cell ›› 2015, Vol. 6 ›› Issue (8) : 619 -623. DOI: 10.1007/s13238-015-0162-4

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Determining structural ensembles of flexible multi-domain proteins using small-angle X-ray scattering and molecular dynamics simulations

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Yonghui Zhang, Bin Wen, Junhui Peng, Xiaobing Zuo, Qingguo Gong, Zhiyong Zhang. Determining structural ensembles of flexible multi-domain proteins using small-angle X-ray scattering and molecular dynamics simulations. Protein Cell, 2015, 6(8): 619-623 DOI:10.1007/s13238-015-0162-4

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References

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[1]	Arkhipov A, Shan Y, Das R, Endres NF, Eastwood MP, Wemmer DE, Kuriyan J, Shaw DE (2013) Architecture and membrane interactions of the EGF receptor. Cell 152: 557-569

[2]	Bedford MT, Reed R, Leder P (1998) WW domain-mediated interactions reveal a spliceosome-associated protein that binds a third class of proline-rich motif: The proline glycine and methionine-rich motif. Proc Natl Acad Sci USA 95: 10602-10607

[3]	Bernadó P, Blackledge M (2010) Proteins in dynamic equilibrium. Nature 468: 1046-1048

[4]	Bernadó P, Mylonas E, Petoukhov MV, Blackledge M, Svergun DI (2007) Structural characterization of flexible proteins using smallangle X-ray scattering. J Am Chem Soc 129: 5656-5664

[5]	Dror RO, Dirks RM, Grossman JP, Xu HF, Shaw DE (2012) Biomolecular simulation: a computational microscope for molecular biology. Annu Rev Biophys 41: 429-452

[6]	Graewert MA, Svergun DI (2013) Impact and progress in small and wide angle X-ray scattering (SAXS and WAXS). Curr Opin Struct Biol 23: 748-754

[7]	Grishaev A, Wu J, Trewhella J, Bax A (2005) Refinement of multidomain protein structures by combination of solution smallangle X-ray scattering and NMR data. J Am Chem Soc 127: 16621-16628

[8]	Huang X, Beullens M, Zhang J, Zhou Y, Nicolaescu E, Lesage B, Hu Q, Wu J, Bollen M, Shi Y (2009) Structure and function of the two tandem WW domains of the pre-mRNA splicing factor FBP21 (Formin-binding protein 21). J Biol Chem 284: 25375-25387

[9]	Ma W, Schulten K (2015) Mechanism of substrate translocation by a ring-shaped ATPase motor at millisecond resolution. J Am Chem Soc 137: 3031-3040

[10]	Pelikan M, Hura GL, Hammel M(2009) Structure and flexibility within proteins as identified through small angle X-ray scattering. Gen Physiol Biophys 28: 174-189

[11]	Różycki B, Kim YC, Hummer G (2011) SAXS ensemble refinement of ESCRT-III CHMP3 conformational transitions. Structure 19: 109-116

[12]	Schneidman-Duhovny D, Kim SJ, Sali A (2012) Integrative structural modeling with small angle X-ray scattering profiles. BMC Struct Biol 12: 17

[13]	Wen B, Peng JH, Zuo XB, Gong QG, Zhang ZY (2014) Characterization of protein flexibility using small-angle X-ray scattering and amplified collective motion simulations. Biophys J 107: 956-964

[14]	Yang S (2014) Methods for SAXS-based structure determination of biomolecular complexes. Adv Mater 26: 7902-7910

[15]	Yang SC, Blachowicz L, Makowski L, Roux B (2010) Multidomain assembled states of Hck tyrosine kinase in solution. Proc Natl Acad Sci USA 107: 15757-15762

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