LETTER

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

  • Yonghui Zhang 1 ,
  • Bin Wen 1 ,
  • Junhui Peng 1 ,
  • Xiaobing Zuo 2 ,
  • Qingguo Gong 1 ,
  • Zhiyong Zhang , 1
Expand
  • 1. Hefei National Laboratory for Physical Science at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei 230026, China
  • 2. Advanced Photon Source, Argonne National Laboratory, Chicago, IL 60437, USA

Published date: 05 Aug 2015

Copyright

2014 This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Cite this article

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[J]. Protein & Cell, 2015 , 6(8) : 619 -623 . DOI: 10.1007/s13238-015-0162-4

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

DOI

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

DOI

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

DOI

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

DOI

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

DOI

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

DOI

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

DOI

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

DOI

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

DOI

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

DOI

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

DOI

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

DOI

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

DOI

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

DOI

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

DOI

Outlines

/