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1.
1. K. Moffat, “ Time-resolved macromolecular crystallography,” Annu. Rev. Biophys. Biophys. Chem. 18, 309 (1989).
http://dx.doi.org/10.1146/annurev.bb.18.060189.001521
2.
2. M. Schmidt, “ Structure based enzyme kinetics by time-resolved x-ray crystallography,” Ultrashort Laser Pulses in Medicine and Biology, edited by W. Zinth, M. Braun, and P. Gilch ( Springer, Berlin, New York, Germany, 2008).
3.
3. W. A. Barletta, J. Bisognano, J. N. Corlett, P. Emma, Z. Huang, K. J. Kim, R. Lindberg, J. B. Murphy, G. R. Neil, D. C. Nguyen, C. Pelligrini, R. A. Rimmer, F. Sannibale, G. Stupakov, R. P. Walker, and A. A. Zholents, “ Free electron lasers: Present status and future challenges,” Nucl. Instrum. Methods Phys. Res., Sect. A 618, 69 (2010).
http://dx.doi.org/10.1016/j.nima.2010.02.274
4.
4. P. Emma et al., “ First lasing and operation of an angstrom-wavelength free-electron laser,” Nat. Photonics 4, 641647 (2010).
http://dx.doi.org/10.1038/nphoton.2010.176
5.
5. K. Tanaka and T. Shintake, “ SCSS x-fel conceptual design report,” RIKEN Harima Institute, Hyogo, Japan, 2005.
6.
6. J. C. H. Spence, U. Weierstall, and H. N. Chapman, “ X-ray lasers for structural and dynamic biology,” Rep. Prog. Phys. 75, 102601 (2012).
http://dx.doi.org/10.1088/0034-4885/75/10/102601
7.
7. R. Neutze and K. Moffat, “ Time-resolved structural studies at synchrotrons and x-ray free electron lasers: Opportunities and challenges,” Curr. Opin. Struct. Biol. 22, 651659 (2012).
http://dx.doi.org/10.1016/j.sbi.2012.08.006
8.
8. H. N. Chapman et al., “ Femtosecond x-ray protein nano crystallography,” Nature 470, 7381 (2011).
http://dx.doi.org/10.1038/nature09750
9.
9. J. Tenboer et al., “ Time-resolved serial crystallography captures big-resolution intermediates of photoactive yellow protein,” Science 346, 12421246 (2014).
http://dx.doi.org/10.1126/science.1259357
10.
10. A. McPherson, Crystallization of Biological Macromolecules ( Cold Spring Harbor Laboratory Press, NY, 1999).
11.
11. M. Schmidt, V. Srajer, R. Hening, H. Ihee, N. Purwar, J. Tenboer, and S. Tripathi, “ Protein energy landscapes determined by five-dimensional crystallography,” Acta Crystallogr., Sect. D: Biol. Crystallogr. 69, 2534 (2013).
http://dx.doi.org/10.1107/S0907444913025997
12.
12. O. F. Lange, “ Determination of solution structures of proteins up to 40 kda using cs-rosetta with sparse nmr data from depurated samples,” Proc. Natl. Acad. Sci. U. S. A. 109, 1087310878 (2012).
http://dx.doi.org/10.1073/pnas.1203013109
13.
13. C. M. T. Spahn and P. A. Penczek, “ Exploring conformational modes of macromolecular assemblies by multi particle cryo-em,” Curr. Opin. Struct. Biol. 19, 623631 (2009).
http://dx.doi.org/10.1016/j.sbi.2009.08.001
14.
14. R. M. Glaser and R. J. Hall, “ Reaching the information limit in cryo-em of biological macromolecule: Experimental aspects,” Biophys. J. 100, 23312337 (2011).
http://dx.doi.org/10.1016/j.bpj.2011.04.018
15.
15. Z. Kam, “ Determination of macromolecular structure in solution by spatial correlation of scattering fluctuations,” Macromolecules 10, 927934 (1977).
http://dx.doi.org/10.1021/ma60059a009
16.
16. D. Svergun and H. B. Stuhrmann, “ New developments in direct shape determination from small-angle scattering 1. Theory and model calculations,” Acta Crystallogr., Sect. A: Found. Crystallogr. 47, 736744 (1991).
http://dx.doi.org/10.1107/S0108767391006414
17.
17. D. K. Saldin, V. L. Shneerson, R. Fung, and A. Ourmazd, “ Structure of isolated biomolecules obtained from ultrashort x-ray pulses: Exploiting the symmetry of random orientations,” J. Phys.: Condens. Matter 21, 134014 (2009).
http://dx.doi.org/10.1088/0953-8984/21/13/134014
18.
18. H. C. Poon, P. Schwander, M. Uddin, and D. K. Saldin, “ Fiber diffraction without fibers,” Phys. Rev. Lett. 110, 265505 (2013).
http://dx.doi.org/10.1103/PhysRevLett.110.265505
19.
19. H. Liu, B. K. Poon, A. J. E. M. Janssen, and P. H. Zwart, “ Computation of fluctuation scattering profiles via three-dimensional zernike polynomials,” Acta Crystallogr., Sect. A: Found. Crystallogr. 68, 561567 (2012).
http://dx.doi.org/10.1107/S0108767312029637
20.
20. H. Liu, B. K. Poon, D. K. Saldin, J. C. H. Spence, and P. H. Zwart, “ Three-dimensional single-particle imaging using angular correlations from x-ray laser data,” Acta Crystallogr., Sect. A: Found. Crystallogr. 69, 365373 (2013).
http://dx.doi.org/10.1107/S0108767313006016
21.
21. K. Pande, P. Schwander, M. Schmidt, and D. K. Saldin, “ Deducing fast electron density changes in randomly oriented uncrystallized biomolecules in a pump-probe experiment,” Philos. Trans. R. Soc., B 369, 20130332 (2014).
http://dx.doi.org/10.1098/rstb.2013.0332
22.
22. S. Krinsky and R. Gluckstern, “ Analysis of statistical correlations and intensity spiking in the self-amplified spontaneous-emission free-electron laser,” Phys. Rev. Spec. Top.--Accel. Beams 6, 050701 (2003).
http://dx.doi.org/10.1103/PhysRevSTAB.6.050701
23.
23. R. A. Kirian, K. E. Schmidt, X. Wang, R. B. Doak, and J. C. H. Spence, “ Signal, noise, and resolution in correlated fluctuations from snapshot small angle x-ray scattering,” Phys. Rev. E 84, 011921 (2011).
http://dx.doi.org/10.1103/PhysRevE.84.011921
24.
24. L. Lovisolo and E. A. B. da Silva, “ Uniform distribution of points on a hyper-sphere with applications to vector bit-plane encoding,” IEE Proc. Vis. Image Signal Process. 148, 187193 (2001).
http://dx.doi.org/10.1049/ip-vis:20010361
25.
25. P. C. Hansen, “ The truncated svd as a method for regularization,” BIT Numer. Math. 27, 534553 (1987).
http://dx.doi.org/10.1007/BF01937276
26.
26. K. Pearson, “ Notes on regression and inheritance in the case of two parents,” Proc. R. Soc. London 58, 240242 (1895).
http://dx.doi.org/10.1098/rspl.1895.0041
27.
27. G. Geloni, E. Saldin, L. Samoylova, E. Schneidmiller, H. Sinn, Th. Tschentscher, and M. Yurkov, “ Coherent properties of the European XFEL,” New J. Phys. 12, 035021 (2010).
http://dx.doi.org/10.1088/1367-2630/12/3/035021
28.
28. M. Born and E. Wolf, Principles of Optics ( Pergamon Press, Oxford, 1980).
29.
29. M. M. Siebert et al., “ Single mimivirus particles intercepted and imaged with an x-ray laser,” Nature 470, 7882 (2011).
http://dx.doi.org/10.1038/nature09748
30.
30. P. H. Zwart, private communication (2015).
31.
31. R. Fung, V. Shneerson, D. K. Saldin, and A. Ourmazd, “ Structure from fleeting illumination of faint spinning objects in flight,” Nat. Phys. 5, 6467 (2009).
http://dx.doi.org/10.1038/nphys1129
32.
32. D. Arnlund et al., “ Visualizing a protein quake with time-resolved x-ray scattering at a free electron laser,” Nat. Methods 11, 923 (2014).
http://dx.doi.org/10.1038/nmeth.3067
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/content/aca/journal/sdy/2/2/10.1063/1.4916980
2015-04-10
2016-09-26

Abstract

Determination of fast structural changes of biomolecules is usually performed on crystalline samples in a time-resolved pump-probe experiment. Changes in the structure are found by the difference Fourier method using phases of a known reference structure. As we showed recently, such changes can also be determined from diffraction of uncrystallized molecules in random orientations. In this case, the difference in the angular correlations of the diffraction patterns is used to find structural changes. Similar to the difference Fourier method, there is no need for iterative phasing. We validated this approach previously with simulations in the absence of noise. In this paper, we show that the effects of noise can be adequately suppressed by averaging over a sufficiently large ensemble as they can be obtained using an X-ray free electron laser.

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