Skip to main content

News about Scitation

In December 2016 Scitation will launch with a new design, enhanced navigation and a much improved user experience.

To ensure a smooth transition, from today, we are temporarily stopping new account registration and single article purchases. If you already have an account you can continue to use the site as normal.

For help or more information please visit our FAQs.

banner image
No data available.
Please log in to see this content.
You have no subscription access to this content.
No metrics data to plot.
The attempt to load metrics for this article has failed.
The attempt to plot a graph for these metrics has failed.
The full text of this article is not currently available.
/content/aca/journal/sdy/1/2/10.1063/1.4869472
1.
1. T. Graber, S. Anderson, H. Brewer, Y. S. Chen, H. S. Cho, N. Dashdorj, R. W. Henning, I. Kosheleva, G. Macha, M. Meron, R. Pahl, Z. Ren, S. Ruan, F. Schotte, V. Srajer, P. J. Viccaro, F. Westferro, P. Anfinrud, and K. Moffat, “BioCARS: A synchrotron resource for time-resolved X-ray science,” J. Synchrotron Radiat. 18, 658670 (2011).
http://dx.doi.org/10.1107/S0909049511009423
2.
2. M. Schmidt, V. Srajer, R. Henning, H. Ihee, N. Purwar, J. Tenboer, and S. Tripathi, “Protein energy landscapes determined by five-dimensional crystallography,” Acta Crystallogr. D 69, 25342542 (2013).
http://dx.doi.org/10.1107/S0907444913025997
3.
3. M. Schmidt, “Mix and inject, reaction initiation by diffusion for time-resolved macromolecular crystallography,” Adv. Condens. Matter Phys. 2013, 110.
http://dx.doi.org/10.1155/2013/167276
4.
4. M. Schmidt, K. Achterhold, V. Prusakov, and F. G. Parak, “Protein dynamics of a beta-sheet protein,” Eur. Biophys. J. 38, 687700 (2009).
http://dx.doi.org/10.1007/s00249-009-0427-z
5.
5. F. Parak, E. W. Knapp, and D. Kucheida,“Protein dynamics. Mossbauer spectroscopy on deoxymyoglobin crystals,” J. Mol. Biol. 161, 177194 (1982).
http://dx.doi.org/10.1016/0022-2836(82)90285-6
6.
6. F. Schotte, H. S. Cho, V. R. Kaila, H. Kamikubo, N. Dashdorj, E. R. Henry, T. J. Graber, R. Henning, M. Wulff, G. Hummer, M. Kataoka, and P. A. Anfinrud, “Watching a signaling protein function in real time via 100-ps time-resolved Laue crystallography,” Proc. Natl. Acad. Sci. U. S. A. 109, 1925619261 (2012).
http://dx.doi.org/10.1073/pnas.1210938109
7.
7. H. C. Poon, M. Schmidt, and D. K. Saldin, “Extraction of fast changes in the structure of a disordered ensemble of photoexcited biomolecules,” Adv. Condens. Matter Phys. 2013, 750371.
http://dx.doi.org/10.1155/2013/750371
8.
8. J. I. Steinfeld, J. S. Francisco, and W. L. Hase, Chemical Kinetics and Dynamics, 2nd ed. (Prentience Hall, 1985).
9.
9. Y. O. Jung, J. H. Lee, J. Kim, M. Schmidt, K. Moffat, V. Srajer, and H. Ihee, “Volume-conserving trans-cis isomerization pathways in photoactive yellow protein visualized by picosecond X-ray crystallography,” Nat. Chem. 5, 212220 (2013).
http://dx.doi.org/10.1038/nchem.1565
10.
10. U. Hensen, O. F. Lange, and H. Grubmuller, “Estimating absolute configurational entropies of macromolecules: The minimally coupled subspace approach,” PloS one 5, e9179 (2010).
http://dx.doi.org/10.1371/journal.pone.0009179
11.
11. J. Schlitter, “Estimation of absolute and relative entropies of macromolecules using the covariance-matrix,” Chem. Phys. Lett. 215, 617621 (1993).
http://dx.doi.org/10.1016/0009-2614(93)89366-P
12.
12. A. A. Polyansky, A. Kuzmanic, M. Hlevnjak, and B. Zagrovic, “On the contribution of linear correlations to quasi-harmonic conformational entropy in proteins,” J. Chem. Theo. Comput. 8, 38203829 (2012).
http://dx.doi.org/10.1021/ct300082q
13.
13. F. Parak and E. W. Knapp, “A consistent picture of protein dynamics,” Proc. Natl. Acad. Sci. U. S. A. 81, 70887092 (1984).
http://dx.doi.org/10.1073/pnas.81.22.7088
14.
14. M. Akke, R. Bruschweiler, and A. G. Palmer, “Nmr order parameters and free-energy - an analytical approach and its application to cooperative ca2+ binding by calbindin-D(9k),” J. Am. Chem. Soc. 115, 98329833 (1993).
http://dx.doi.org/10.1021/ja00074a073
15.
15. J. Fitter, “A measure of conformational entropy change during thermal protein unfolding using neutron spectroscopy,” Biophys. J. 84, 39243930 (2003).
http://dx.doi.org/10.1016/S0006-3495(03)75120-0
16.
16. M. Karplus, T. Ichiye, and B. M. Pettitt, “Configurational entropy of native proteins,” Biophys. J. 52, 10831085 (1987).
http://dx.doi.org/10.1016/S0006-3495(87)83303-9
17.
17. R. M. Stroud and J. S. Finer-Moore, “Conformational dynamics along an enzymatic reaction pathway: Thymidylate synthase,” "the movie”, Biochemistry 42, 239247 (2003).
http://dx.doi.org/10.1021/bi020598i
18.
18. I. Schlichting, J. Berendzen, K. Chu, A. M. Stock, S. A. Maves, D. E. Benson, B. M. Sweet, D. Ringe, G. A. Petsko, and S. G. Sligar, “The catalytic pathway of cytochrome P450cam at atomic resolution,” Science 287, 16151622 (2000).
http://dx.doi.org/10.1126/science.287.5458.1615
19.
19. R. M. Daniel, R. V. Dunn, J. L. Finney, and J. C. Smith, “The role of dynamics in enzyme activity,” Annu. Rev. Biophys. Biomol. Struct. 32, 6992 (2003).
http://dx.doi.org/10.1146/annurev.biophys.32.110601.142445
20.
20. C. N. Pace, B. A. Shirley, M. McNutt, and K. Gajiwala, “Forces contributing to the conformational stability of proteins,” Faseb. J. 10, 7583 (1996).
21.
21. K. Ghosh and K. A. Dill, “Computing protein stabilities from their chain lengths,” Proc. Natl. Acad. Sci. U. S. A. 106, 1064910654 (2009).
http://dx.doi.org/10.1073/pnas.0903995106
22.
22. A. D. Robertson and K. P. Murphy, “Protein structure and the energetics of protein stability,” Chem. Rev. 97, 12511267 (1997).
http://dx.doi.org/10.1021/cr960383c
23.
23. D. W. Li, S. A. Showalter, and R. Bruschweiler, “Entropy localization in proteins,” J. Phys. Chem. B 114, 1603616044 (2010).
http://dx.doi.org/10.1021/jp109908u
24.
24. M. E. van Brederode, T. Gensch, W. D. Hoff, K. J. Hellingwerf, and S. E. Braslavsky, “Photoinduced volume change and energy storage associated with the early transformations of the photoactive yellow protein from Ectothiorhodospira halophila,” Biophys. J. 68, 11011109 (1995).
http://dx.doi.org/10.1016/S0006-3495(95)80284-5
25.
25. M. E. Van Brederode, W. D. Hoff, I. H. Van Stokkum, M. L. Groot, and K. J. Hellingwerf, “Protein folding thermodynamics applied to the photocycle of the photoactive yellow protein,” Biophys. J. 71, 365380 (1996).
http://dx.doi.org/10.1016/S0006-3495(96)79234-2
26.
26. F. G. Parak, K. Achterhold, S. Croci, and M. Schmidt, “A physical picture of protein dynamics and conformational changes,” J. Biol. Phys. 33, 371387 (2007).
http://dx.doi.org/10.1007/s10867-008-9102-3
27.
27. K. Takeshita, Y. Imamoto, M. Kataoka, F. Tokunaga, and M. Terazima, “Themodynamic and transport properties of intermediate states of the photocyclic reaction of photoactive yellow protein,” Biochemistry 41, 30373048 (2002).
http://dx.doi.org/10.1021/bi0110600
28.
28. F. Parak, K. Achterhold, C. Keppler, U. vonBurck, W. Potzel, P. SchindelMann, E. W. Knapp, B. Melchers, R. Ruffer, A. I. Chumakov, and A. Q. R. Baron, “The myoglobin phonon-spectrum obtained from X-ray scattering analyzed by Mossbauer effect,” Prog. Biophys. Mol. Bio. 65, Pa322Pa322 (1996).
29.
29. W. Doster, S. Cusack, and W. Petry, “Dynamical transition of myoglobin revealed by inelastic neutron-scattering,” Nature 337, 754756 (1989).
http://dx.doi.org/10.1038/337754a0
30.
30. F. G. Parak, K. Achterhold, M. Schmidt, V. Prusakov, and S. Croci, “Protein dynamics on different timescales,” J. Non-Cryst. Solids 352, 43714378 (2006).
http://dx.doi.org/10.1016/j.jnoncrysol.2006.01.106
31.
31. R. H. Austin, K. W. Beeson, L. Eisenstein, H. Frauenfelder, and I. C. Gunsalus, “Dynamics of ligand binding to myoglobin,” Biochemistry 14, 53555373 (1975).
http://dx.doi.org/10.1021/bi00695a021
32.
32. H. Frauenfelder, G. Chen, J. Berendzen, P. W. Fenimore, H. Jansson, B. H. McMahon, I. R. Stroe, J. Swenson, and R. D. Young, “A unified model of protein dynamics,” Proc. Natl. Acad. Sci. U. S. A. 106, 51295134 (2009).
http://dx.doi.org/10.1073/pnas.0900336106
33.
33. R. D. Young, H. Frauenfelder, and P. W. Fenimore, “Mossbauer effect in proteins,” Phys. Rev. Lett. 107, 158102 (2011).
http://dx.doi.org/10.1103/PhysRevLett.107.158102
34.
34. H. Frauenfelder, F. Parak, and R. D. Young, “Conformational substrates in proteins,” Ann. Rev. Biophys. Biophys. Chem. 17, 451479 (1988).
http://dx.doi.org/10.1146/annurev.bb.17.060188.002315
35.
35. K. Achterhold, C. Keppler, U. vanBurck, W. Potzel, P. Schindelmann, E. W. Knapp, B. Melchers, A. I. Chumakov, A. Q. R. Baron, R. Ruffer, and F. Parak, “Temperature dependent inelastic X-ray scattering of synchrotron radiation on myoglobin analyzed by the Mossbauer effect,” Eur. Biophys. J. Biophys. 25, 4346 (1996).
http://dx.doi.org/10.1007/s002490050015
36.
36. B. Melchers, E. W. Knapp, F. Parak, L. Cordone, A. Cupane, and M. Leone, “Structural fluctuations of myoglobin from normal-modes, Mossbauer, Raman, and absorption spectroscopy,” Biophys. J. 70, 20922099 (1996).
http://dx.doi.org/10.1016/S0006-3495(96)79775-8
37.
37. S. H. Chong, Y. Joti, A. Kidera, N. Go, A. Ostermann, A. Gassmann, and F. Parak, “Dynamical transition of myoglobin in a crystal: comparative studies of X–ray crystallography and Mossbauer spectroscopy,” Eur. Biophys. J. 30, 319329 (2001).
http://dx.doi.org/10.1007/s002490100152
38.
38. C. Tetreau, L. Mouawad, S. Murail, P. Duchambon, Y. Blouquit, and D. Lavalette, “Disentangling ligand migration and heme pocket relaxation in cytochrome P450cam,” Biophys. J. 88, 12501263 (2005).
http://dx.doi.org/10.1529/biophysj.104.050104
39.
39. D. Lavalette, C. Tetreau, and L. Mouawad, “Ligand migration and escape pathways in haem proteins,” Biochem. Soc. Trans. 34, 975978 (2006).
http://dx.doi.org/10.1042/BST0340975
40.
40. J. L. Martin, A. Migus, C. Poyart, Y. Lecarpentier, R. Astier, and A. Antonetti, “Femtosecond photolysis of CO-ligated protoheme and hemoproteins: Appearance of deoxy species with a 350-fsec time constant,” Proc. Natl. Acad. Sci. U. S. A. 80, 173177 (1983).
http://dx.doi.org/10.1073/pnas.80.1.173
41.
41. G. Groenhof, M. Bouxin-Cademartory, B. Hess, S. P. De Visser, H. J. Berendsen, M. Olivucci, A. E. Mark, and M. A. Robb, “Photoactivation of the photoactive yellow protein: why photon absorption triggers a trans-to-cis Isomerization of the chromophore in the protein,” J. Am. Chem. Soc. 126, 42284233 (2004).
http://dx.doi.org/10.1021/ja039557f
42.
42. G. Groenhof, M. F. Lensink, H. J. Berendsen, and A. E. Mark, “Signal transduction in the photoactive yellow protein. II. Proton transfer initiates conformational changes,” Proteins 48, 212219 (2002).
http://dx.doi.org/10.1002/prot.10135
43.
43. G. Groenhof, M. F. Lensink, H. J. Berendsen, J. G. Snijders, and A. E. Mark, “Signal transduction in the photoactive yellow protein. I. Photon absorption and the isomerization of the chromophore,” Proteins 48, 202211 (2002).
http://dx.doi.org/10.1002/prot.10136
44.
44. G. Groenhof, L. V. Schafer, M. Boggio-Pasqua, H. Grubmuller, and M. A. Robb, “Arginine52 controls the photoisomerization process in photoactive yellow protein,” J. Am. Chem. Soc. 130, 32503251 (2008).
http://dx.doi.org/10.1021/ja078024u
45.
45. S. Anderson, S. Crosson, and K. Moffat, “Short hydrogen bonds in photoactive yellow protein,” Acta Crystallogr D 60, 10081016 (2004).
http://dx.doi.org/10.1107/S090744490400616X
46.
46. S. Anderson, V. Srajer, R. Pahl, S. Rajagopal, F. Schotte, P. Anfinrud, M. Wulff, and K. Moffat, “Chromophore conformation and the evolution of tertiary structural changes in photoactive yellow protein,” Structure 12, 10391045 (2004).
http://dx.doi.org/10.1016/j.str.2004.04.008
47.
47. M. Schmidt, R. Pahl, V. Srajer, S. Anderson, Z. Ren, H. Ihee, S. Rajagopal, and K. Moffat, “Protein kinetics: Structures of intermediates and reaction mechanism from time-resolved x-ray data,” Proc. Natl. Acad. Sci. U. S. A. 101, 47994804 (2004).
http://dx.doi.org/10.1073/pnas.0305983101
48.
48. H. Ihee, S. Rajagopal, V. Srajer, R. Pahl, S. Anderson, M. Schmidt, F. Schotte, P. A. Anfinrud, M. Wulff, and K. Moffat, “Visualizing reaction pathways in photoactive yellow protein from nanoseconds to seconds,” Proc. Natl. Acad. Sci. U. S. A. 102, 71457150 (2005).
http://dx.doi.org/10.1073/pnas.0409035102
49.
49. C. N. Lincoln, A. E. Fitzpatrick, and J. J. van Thor, “Photoisomerisation quantum yield and non-linear cross-sections with femtosecond excitation of the photoactive yellow protein,” Phys. Chem. Chem. Phys. 14, 1575215764 (2012).
http://dx.doi.org/10.1039/c2cp41718a
50.
50. I. H. van Stokkum, D. S. Larsen, and R. van Grondelle, “Global and target analysis of time—resolved spectra,” Biochim. Biophys. Acta 1657, 82104 (2004).
http://dx.doi.org/10.1016/j.bbabio.2004.04.011
51.
51. T. E. Meyer, “Isolation and characterization of soluble cytochromes, ferredoxins and other chromophoric proteins from the halophilic phototrophic bacterium Ectothiorhodospira halophila,” Biochim. Biophys. Acta 806, 175183 (1985).
http://dx.doi.org/10.1016/0005-2728(85)90094-5
52.
52. T. E. Meyer, G. Tollin, T. P. Causgrove, P. Cheng, and R. E. Blankenship, “Picosecond decay kinetics and quantum yield of fluorescence of the photoactive yellow protein from the halophilic purple phototrophic bacterium, ectothiorhodospira-halophila,” Biophys. J. 59, 988991 (1991).
http://dx.doi.org/10.1016/S0006-3495(91)82313-X
53.
53. W. D. Hoff, I. H. van Stokkum, H. J. van Ramesdonk, M. E. van Brederode, A. M. Brouwer, J. C. Fitch, T. E. Meyer, R. van Grondelle, and K. J. Hellingwerf, “Measurement and global analysis of the absorbance changes in the photocycle of the photoactive yellow protein from Ectothiorhodospira halophila,” Biophys. J. 67, 16911705 (1994).
http://dx.doi.org/10.1016/S0006-3495(94)80643-5
54.
54. L. Ujj, S. Devanathan, T. E. Meyer, M. A. Cusanovich, G. Tollin, and G. H. Atkinson, “New photocycle intermediates in the photoactive yellow protein from Ectothiorhodospira halophila: picosecond transient absorption spectroscopy,” Biophys. J. 75, 406412 (1998).
http://dx.doi.org/10.1016/S0006-3495(98)77525-3
55.
55. R. Kort, H. Vonk, X. Xu, W. D. Hoff, W. Crielaard, and K. J. Hellingwerf, “Evidence for trans-cis isomerization of the p-coumaric acid chromophore as the photochemical basis of the photocycle of photoactive yellow protein,” Febs. Lett. 382, 7378 (1996).
http://dx.doi.org/10.1016/0014-5793(96)00149-4
56.
56. A. Xie, W. D. Hoff, A. R. Kroon, and K. J. Hellingwerf, “Glu46 donates a proton to the 4-hydroxycinnamate anion chromophore during the photocycle of photoactive yellow protein,” Biochemistry 35, 1467114678 (1996).
http://dx.doi.org/10.1021/bi9623035
57.
57. G. E. Borgstahl, D. R. Williams, and E. D. Getzoff, “1.4 A structure of photoactive yellow protein, a cytosolic photoreceptor: unusual fold, active site, and chromophore,” Biochemistry 34, 62786287 (1995).
http://dx.doi.org/10.1021/bi00019a004
58.
58. U. K. Genick, G. E. Borgstahl, K. Ng, Z. Ren, C. Pradervand, P. M. Burke, V. Srajer, T. Y. Teng, W. Schildkamp, D. E. McRee, K. Moffat, and E. D. Getzoff, “Structure of a protein photocycle intermediate by millisecond time-resolved crystallography,” Science 275, 14711475 (1997).
http://dx.doi.org/10.1126/science.275.5305.1471
59.
59. M. Schmidt, S. Rajagopal, Z. Ren, and K. Moffat, “Application of singular value decomposition to the analysis of time-resolved macromolecular x-ray data,” Biophys. J. 84, 21122129 (2003).
http://dx.doi.org/10.1016/S0006-3495(03)75018-8
60.
60. S. Rajagopal, M. Schmidt, S. Anderson, H. Ihee, and K. Moffat, “Analysis of experimental time-resolved crystallographic data by singular value decomposition,” Acta crystallogr. D 60, 860871 (2004).
http://dx.doi.org/10.1107/S0907444904004160
61.
61. L. Mendonca, F. Hache, P. Changenet-Barret, P. Plaza, H. Chosrowjan, S. Taniguchi, and Y. Imamoto, “Ultrafast carbonyl motion of the photoactive yellow protein chromophore probed by femtosecond circular dichroism,” J. Am. Chem. Soc. 135, 1463714643 (2013).
http://dx.doi.org/10.1021/ja404503q
62.
62. J. Liu, A. Yabushita, S. Taniguchi, H. Chosrowjan, Y. Imamoto, K. Sueda, N. Miyanaga, and T. Kobayashi, “Ultrafast time-resolved pump-probe spectroscopy of PYP by a sub-8 fs pulse laser at 400 nm,” J. Phys. Chem. B 117, 48184826 (2013).
http://dx.doi.org/10.1021/jp4001016
63.
63. A. Xie, L. Kelemen, J. Hendriks, B. J. White, K. J. Hellingwerf, and W. D. Hoff, “Formation of a new buried charge drives a large-amplitude protein quake in photoreceptor activation,” Biochemistry 40, 15101517 (2001).
http://dx.doi.org/10.1021/bi002449a
64.
64. S. Yeremenko, I. H. van Stokkum, K. Moffat, and K. J. Hellingwerf, “Influence of the crystalline state on photoinduced dynamics of photoactive yellow protein studied by ultraviolet-visible transient absorption spectroscopy,” Biophys. J. 90, 42244235 (2006).
http://dx.doi.org/10.1529/biophysj.105.074765
65.
65. K. Ng, E. D. Getzoff, and K. Moffat, “Optical studies of a bacterial photoreceptor protein, photoactive yellow protein, in single-crystals,” Biochemistry 34, 879890 (1995).
http://dx.doi.org/10.1021/bi00003a022
66.
66. H. Eyring, “The activated complex in chemical reaction,” J. Chem. Phys. 3, 107115 (1935).
http://dx.doi.org/10.1063/1.1749604
67.
67. P. Hanggi, P. Talkner, and M. Borkovec, “Reaction-rate theory—50 years after kramers,” Rev. Mod. Phys. 62, 251341 (1990).
http://dx.doi.org/10.1103/RevModPhys.62.251
68.
68. H. S. Chung and W. A. Eaton, “Single-molecule fluorescence probes dynamics of barrier crossing,” Nature 502, 685 (2013).
http://dx.doi.org/10.1038/nature12649
69.
69. D. Bourgeois, B. Vallone, A. Arcovito, G. Sciara, F. Schotte, P. A. Anfinrud, and M. Brunori, “Extended subnanosecond structural dynamics of myoglobin revealed by Laue crystallography,” Proc. Natl. Acad. Sci. U. S. A. 103, 49244929 (2006).
http://dx.doi.org/10.1073/pnas.0508880103
70.
70. M. Schmidt, K. Nienhaus, R. Pahl, A. Krasselt, S. Anderson, F. Parak, G. U. Nienhaus, and V. Srajer, “Ligand migration pathway and protein dynamics in myoglobin: A time-resolved crystallographic study on L29W MbCO,” Proc. Natl. Acad. Sci. U. S. A. 102, 1170411709 (2005).
http://dx.doi.org/10.1073/pnas.0504932102
71.
71. M. H. Lim, T. A. Jackson, and P. A. Anfinrud, “Nonexponential protein relaxation—Dynamics of conformational change in myoglobin,” Proc. Natl. Acad. Sci. U. S. A. 90, 58015804 (1993).
http://dx.doi.org/10.1073/pnas.90.12.5801
72.
72. K. Moritsugu and J. C. Smith, “Langevin model of the temperature and hydration dependence of protein vibrational dynamics,” J. Phys. Chem. B 109, 1218212194 (2005).
http://dx.doi.org/10.1021/jp044272q
73.
73. M. Schmidt, T. Graber, R. Henning, and V. Srajer, “Five-dimensional crystallography,” Acta Crystallogr. Sect. A 66, 198206 (2010).
http://dx.doi.org/10.1107/S0108767309054166
74.
74. P. Schwander, D. Giannakis, C. H. Yoon, and A. Ourmazd, “The symmetries of image formation by scattering. II. Applications,” Opt. Express 20, 1282712849 (2012).
http://dx.doi.org/10.1364/OE.20.012827
75.
75. K. Pande, P. Schwander, M. Schmidt, and D. K. Saldin, “Deducing fast electron density changes in randomly orientated uncrystallized biomolecules in a pump-probe experiment,” Philos. Trans. R. Soc. B (in press).
76.
76. D. K. Saldin, H. C. Poon, V. L. Shneerson, M. Howells, H. N. Chapman, R. A. Kirian, K. E. Schmidt, and J. C. H. Spence, “Beyond small-angle x-ray scattering: Exploiting angular correlations,” Phys. Rev. B 81, 174105 (2010).
http://dx.doi.org/10.1103/PhysRevB.81.174105
77.
77. H. Liu, B. K. Poon, D. K. Saldin, J. C. Spence, and P. H. Zwart, “Three-dimensional single-particle imaging using angular correlations from X-ray laser data,” Acta Crystallogr. Sect. A 69, 365373 (2013).
http://dx.doi.org/10.1107/S0108767313006016
78.
78. 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
79.
79. D. K. Saldin, H. C. Poon, P. Schwander, M. Uddin, and M. Schmidt, “Reconstructing an icosahedral virus from single-particle diffraction experiments,” Opt. Express 19, 1731817335 (2011).
http://dx.doi.org/10.1364/OE.19.017318
80.
80. 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
81.
81. 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
82.
82. G. Rubinstenn, G. W. Vuister, F. A. Mulder, P. E. Dux, R. Boelens, K. J. Hellingwerf, and R. Kaptein, “Structural and dynamic changes of photoactive yellow protein during its photocycle in solution,” Nat. Struct. Biol. 5, 568570 (1998).
http://dx.doi.org/10.1038/823
83.
83. P. L. Ramachandran, J. E. Lovett, P. J. Carl, M. Cammarata, J. H. Lee, Y. O. Jung, H. Ihee, C. R. Timmel, and J. J. van Thor, “The short-lived signaling state of the photoactive yellow protein photoreceptor revealed by combined structural probes,” J. Am. Chem. Soc. 133, 93959404 (2011).
http://dx.doi.org/10.1021/ja200617t
84.
84. R. A. Kirian, K. E. Schmidt, X. Wang, R. B. Doak, and J. C. 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
85.
85. R. A. Kirian, “Structure determination through correlated fluctuations in x-ray scattering,” J. Phys. B At. Mol. Opt. Phys. 45, 223001 (2012).
http://dx.doi.org/10.1088/0953-4075/45/22/223001
86.
86. M. Porro, L. Andricek, S. Aschauer, M. Bayer, J. Becker, L. Bombelli, A. Castoldi, G. De Vita, I. Diehl, F. Erdinger, S. Facchinetti, C. Fiorini, P. Fischer, T. Gerlach, H. Graafsma, C. Guazzoni, K. Hansen, P. Kalavakuru, H. Klar, A. Kugel, P. Lechner, M. Lemke, G. Lutz, M. Manghisoni, D. Mezza, D. Muntefering, U. Pietsch, E. Quartieri, M. Randall, V. Re, C. Reckleben, C. Sandow, J. Soldat, L. Struder, J. Szymanski, G. Weidenspointner, and C. B. Wunderer, “Development of the depfet sensor with signal compression: A large format x-ray imager with mega-frame readout capability for the European XFEL,” IEEE Trans. Nucl. Sci. 59, 33393351 (2012).
http://dx.doi.org/10.1109/TNS.2012.2217755
87.
87. P. Nissen, J. Hansen, N. Ban, P. B. Moore, and T. A. Steitz, “The structural basis of ribosome activity in peptide bond synthesis,” Science 289, 920930 (2000).
http://dx.doi.org/10.1126/science.289.5481.920
88.
88. N. Ban, P. Nissen, J. Hansen, P. B. Moore, and T. A. Steitz, “The complete atomic structure of the large ribosomal subunit at 2.4 angstrom resolution,” Science 289, 905920 (2000).
http://dx.doi.org/10.1126/science.289.5481.905
89.
89. J. Harms, F. Schluenzen, R. Zarivach, A. Bashan, S. Gat, I. Agmon, H. Bartels, F. Franceschi, and A. Yonath, “High resolution structure of the large ribosomal subunit from a mesophilic Eubacterium,” Cell 107, 679688 (2001).
http://dx.doi.org/10.1016/S0092-8674(01)00546-3
90.
90. M. Selmer, C. M. Dunham, F. V. Murphy, A. Weixlbaumer, S. Petry, A. C. Kelley, J. R. Weir, and V. Ramakrishnan, “Structure of the 70S ribosome complexed with mRNA and tRNA,” Science 313, 19351942 (2006).
http://dx.doi.org/10.1126/science.1131127
91.
91. A. Yonath, “Antibiotics targeting ribosomes: Resistance, selectivity, synergism, and cellular regulation,” Annu. Rev. Biochem. 74, 649679 (2005).
http://dx.doi.org/10.1146/annurev.biochem.74.082803.133130
92.
92. S. R. Adams and R. Y. Tsien, “Controlling Cell Chemistry with Caged Compounds,” Annu. Rev. Physiol. 55, 755784 (1993).
http://dx.doi.org/10.1146/annurev.ph.55.030193.003543
http://aip.metastore.ingenta.com/content/aca/journal/sdy/1/2/10.1063/1.4869472
Loading
/content/aca/journal/sdy/1/2/10.1063/1.4869472
Loading

Data & Media loading...

Loading

Article metrics loading...

/content/aca/journal/sdy/1/2/10.1063/1.4869472
2014-03-27
2016-12-05

Abstract

With recent technological advances at synchrotrons [Graber , J. Synchrotron Radiat. , 658–670 (2011)], it is feasible to rapidly collect time-resolved crystallographic data at multiple temperature settings [Schmidt , Acta Crystallogr. D , 2534–2542 (2013)], from which barriers of activation can be extracted. With the advent of fourth generation X-ray sources, new opportunities emerge to investigate structure and dynamics of biological macromolecules in real time [M. Schmidt, Adv. Condens. Matter Phys. , 1–10] in crystals and potentially from single molecules in random orientation in solution [Poon , Adv. Condens. Matter Phys. , 750371]. Kinetic data from time-resolved experiments on short time-scales must be interpreted in terms of chemical kinetics [Steinfeld , , 2nd ed. (Prentience Hall, 1985)] and tied to existing time-resolved experiments on longer time-scales [Schmidt , Acta Crystallogr. D , 2534–2542 (2013); Jung , Nat. Chem. , 212–220 (2013)]. With this article, we will review and outline steps that are required to routinely determine the energetics of reactions in biomolecules in crystal and solution with newest X-ray sources. In eight sections, we aim to describe concepts and experimental details that may help to inspire new approaches to collect and interpret these data.

Loading

Full text loading...

/deliver/fulltext/aca/journal/sdy/1/2/1.4869472.html;jsessionid=1bkYPm8n7vjKc8lQKDw8Uw72.x-aip-live-03?itemId=/content/aca/journal/sdy/1/2/10.1063/1.4869472&mimeType=html&fmt=ahah&containerItemId=content/aca/journal/sdy

Most read this month

Article
content/aca/journal/sdy
Journal
5
3
Loading

Most cited this month

+ More - Less
true
true

Access Key

  • FFree Content
  • OAOpen Access Content
  • SSubscribed Content
  • TFree Trial Content
752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
/content/realmedia?fmt=ahah&adPositionList=
&advertTargetUrl=//oascentral.aip.org/RealMedia/ads/&sitePageValue=sd.aip.org/1/2/10.1063/1.4869472&pageURL=http://scitation.aip.org/content/aca/journal/sdy/1/2/10.1063/1.4869472'
Right1,Right2,Right3,