-
1
-
-
0021755973
-
-
J. Deisenhofer, O. Epp, K. Miki, R. Huber, H. Michel, J. Mol. Biol. 180, 385 (1984); R. Henderson et al., ibid. 213, 899 (1990); G. F. X. Schertler, C. Villa, R. Henderson, Nature 362, 770 (1993); W. Kuhlbrandt, D. G. Wang, Y. Fujiyoshi, ibid. 367, 614 (1994); H.-W. Park, S.-T. Kim, A. Sancar, J. Deisenhofer, Science 268, 1866 (1995).
-
(1984)
J. Mol. Biol.
, vol.180
, pp. 385
-
-
Deisenhofer, J.1
Epp, O.2
Miki, K.3
Huber, R.4
Michel, H.5
-
2
-
-
0025292355
-
-
J. Deisenhofer, O. Epp, K. Miki, R. Huber, H. Michel, J. Mol. Biol. 180, 385 (1984); R. Henderson et al., ibid. 213, 899 (1990); G. F. X. Schertler, C. Villa, R. Henderson, Nature 362, 770 (1993); W. Kuhlbrandt, D. G. Wang, Y. Fujiyoshi, ibid. 367, 614 (1994); H.-W. Park, S.-T. Kim, A. Sancar, J. Deisenhofer, Science 268, 1866 (1995).
-
(1990)
J. Mol. Biol.
, vol.213
, pp. 899
-
-
Henderson, R.1
-
3
-
-
0027190359
-
-
J. Deisenhofer, O. Epp, K. Miki, R. Huber, H. Michel, J. Mol. Biol. 180, 385 (1984); R. Henderson et al., ibid. 213, 899 (1990); G. F. X. Schertler, C. Villa, R. Henderson, Nature 362, 770 (1993); W. Kuhlbrandt, D. G. Wang, Y. Fujiyoshi, ibid. 367, 614 (1994); H.-W. Park, S.-T. Kim, A. Sancar, J. Deisenhofer, Science 268, 1866 (1995).
-
(1993)
Nature
, vol.362
, pp. 770
-
-
Schertler, G.F.X.1
Villa, C.2
Henderson, R.3
-
4
-
-
0028147508
-
-
J. Deisenhofer, O. Epp, K. Miki, R. Huber, H. Michel, J. Mol. Biol. 180, 385 (1984); R. Henderson et al., ibid. 213, 899 (1990); G. F. X. Schertler, C. Villa, R. Henderson, Nature 362, 770 (1993); W. Kuhlbrandt, D. G. Wang, Y. Fujiyoshi, ibid. 367, 614 (1994); H.-W. Park, S.-T. Kim, A. Sancar, J. Deisenhofer, Science 268, 1866 (1995).
-
(1994)
Nature
, vol.367
, pp. 614
-
-
Kuhlbrandt, W.1
Wang, D.G.2
Fujiyoshi, Y.3
-
5
-
-
0028812143
-
-
J. Deisenhofer, O. Epp, K. Miki, R. Huber, H. Michel, J. Mol. Biol. 180, 385 (1984); R. Henderson et al., ibid. 213, 899 (1990); G. F. X. Schertler, C. Villa, R. Henderson, Nature 362, 770 (1993); W. Kuhlbrandt, D. G. Wang, Y. Fujiyoshi, ibid. 367, 614 (1994); H.-W. Park, S.-T. Kim, A. Sancar, J. Deisenhofer, Science 268, 1866 (1995).
-
(1995)
Science
, vol.268
, pp. 1866
-
-
Park, H.-W.1
Kim, S.-T.2
Sancar, A.3
Deisenhofer, J.4
-
8
-
-
0023152468
-
-
_, E. Yakali, M. A. Cusanovich, G. Tollin, Biochemistry 26, 418 (1987); T. E. Meyer, G. Tollin, J. H. Hazzard, M. A. Cusanovich, Biophys. J. 56, 559 (1989).
-
(1987)
Biochemistry
, vol.26
, pp. 418
-
-
Yakali, E.1
Cusanovich, M.A.2
Tollin, G.3
-
9
-
-
0024730905
-
-
_, E. Yakali, M. A. Cusanovich, G. Tollin, Biochemistry 26, 418 (1987); T. E. Meyer, G. Tollin, J. H. Hazzard, M. A. Cusanovich, Biophys. J. 56, 559 (1989).
-
(1989)
Biophys. J.
, vol.56
, pp. 559
-
-
Meyer, T.E.1
Tollin, G.2
Hazzard, J.H.3
Cusanovich, M.A.4
-
10
-
-
0027324441
-
-
W. W. Sprenger, W. D. Hoff, J. P. Armitage, K. J. Hellingwerf, J. Bacteriol. 175, 3096 (1993).
-
(1993)
J. Bacteriol.
, vol.175
, pp. 3096
-
-
Sprenger, W.W.1
Hoff, W.D.2
Armitage, J.P.3
Hellingwerf, K.J.4
-
11
-
-
0023028920
-
-
D. E. McRee, T. E. Meyer, M. A. Cusanovich, H. E. Parge, E. D. Getzoff, J. Biol. Chem. 261, 13850 (1986).
-
(1986)
J. Biol. Chem.
, vol.261
, pp. 13850
-
-
McRee, D.E.1
Meyer, T.E.2
Cusanovich, M.A.3
Parge, H.E.4
Getzoff, E.D.5
-
13
-
-
0025910866
-
-
T. E. Meyer, G. Tollin, T. P. Causgrove, P. Cheng, R. E. Blankenship, Biophys. J. 59, 988 (1991); W. D. Hoff et al., ibid. 67, 1691 (1994).
-
(1991)
Biophys. J.
, vol.59
, pp. 988
-
-
Meyer, T.E.1
Tollin, G.2
Causgrove, T.P.3
Cheng, P.4
Blankenship, R.E.5
-
14
-
-
0028100905
-
-
T. E. Meyer, G. Tollin, T. P. Causgrove, P. Cheng, R. E. Blankenship, Biophys. J. 59, 988 (1991); W. D. Hoff et al., ibid. 67, 1691 (1994).
-
(1994)
Biophys. J.
, vol.67
, pp. 1691
-
-
Hoff, W.D.1
-
16
-
-
0028577744
-
-
M. Baca et al., Biochemistry 33, 14369 (1994).
-
(1994)
Biochemistry
, vol.33
, pp. 14369
-
-
Baca, M.1
-
17
-
-
0029964634
-
-
W. D. Hoff et al., ibid., p. 13960; R. Kort et al., FEBS Lett. 382, 73 (1996).
-
Biochemistry
, pp. 13960
-
-
Hoff, W.D.1
-
18
-
-
0029964634
-
-
W. D. Hoff et al., ibid., p. 13960; R. Kort et al., FEBS Lett. 382, 73 (1996).
-
(1996)
FEBS Lett.
, vol.382
, pp. 73
-
-
Kort, R.1
-
19
-
-
0028832513
-
-
M. Kim, R. A. Mathies, W. D. Hoff, K. J. Hellingwerf, Biochemistry 34, 12669 (1995).
-
(1995)
Biochemistry
, vol.34
, pp. 12669
-
-
Kim, M.1
Mathies, R.A.2
Hoff, W.D.3
Hellingwerf, K.J.4
-
20
-
-
0023283774
-
-
J. Hajdu et al., EMBO J. 6, 539 (1987); I. Schlichting et al., Nature 345, 309 (1990); B. L. Stoddard et al., Proc. Natl. Acad. Sci. U.S.A. 88, (1991); P. T. Singer, A. Smalas, R. P. Carty, W. F. Mangel, R. M. Sweet, Science 259, 669 (1993); E. M. H. Duke, S. Wakatsuki, A. Hadfield, L. N. Johnson, Protein Sci. 3, 1178 (1994); V. Fülöp et al., Structure 2, 201 (1994); J. M. Bolduc et al., Science 268, 1312 (1995).
-
(1987)
EMBO J.
, vol.6
, pp. 539
-
-
Hajdu, J.1
-
21
-
-
0025275582
-
-
J. Hajdu et al., EMBO J. 6, 539 (1987); I. Schlichting et al., Nature 345, 309 (1990); B. L. Stoddard et al., Proc. Natl. Acad. Sci. U.S.A. 88, (1991); P. T. Singer, A. Smalas, R. P. Carty, W. F. Mangel, R. M. Sweet, Science 259, 669 (1993); E. M. H. Duke, S. Wakatsuki, A. Hadfield, L. N. Johnson, Protein Sci. 3, 1178 (1994); V. Fülöp et al., Structure 2, 201 (1994); J. M. Bolduc et al., Science 268, 1312 (1995).
-
(1990)
Nature
, vol.345
, pp. 309
-
-
Schlichting, I.1
-
22
-
-
0023283774
-
-
J. Hajdu et al., EMBO J. 6, 539 (1987); I. Schlichting et al., Nature 345, 309 (1990); B. L. Stoddard et al., Proc. Natl. Acad. Sci. U.S.A. 88, (1991); P. T. Singer, A. Smalas, R. P. Carty, W. F. Mangel, R. M. Sweet, Science 259, 669 (1993); E. M. H. Duke, S. Wakatsuki, A. Hadfield, L. N. Johnson, Protein Sci. 3, 1178 (1994); V. Fülöp et al., Structure 2, 201 (1994); J. M. Bolduc et al., Science 268, 1312 (1995).
-
(1991)
Proc. Natl. Acad. Sci. U.S.A.
, vol.88
-
-
Stoddard, B.L.1
-
23
-
-
0027411179
-
-
J. Hajdu et al., EMBO J. 6, 539 (1987); I. Schlichting et al., Nature 345, 309 (1990); B. L. Stoddard et al., Proc. Natl. Acad. Sci. U.S.A. 88, (1991); P. T. Singer, A. Smalas, R. P. Carty, W. F. Mangel, R. M. Sweet, Science 259, 669 (1993); E. M. H. Duke, S. Wakatsuki, A. Hadfield, L. N. Johnson, Protein Sci. 3, 1178 (1994); V. Fülöp et al., Structure 2, 201 (1994); J. M. Bolduc et al., Science 268, 1312 (1995).
-
(1993)
Science
, vol.259
, pp. 669
-
-
Singer, P.T.1
Smalas, A.2
Carty, R.P.3
Mangel, W.F.4
Sweet, R.M.5
-
24
-
-
0028031270
-
-
J. Hajdu et al., EMBO J. 6, 539 (1987); I. Schlichting et al., Nature 345, 309 (1990); B. L. Stoddard et al., Proc. Natl. Acad. Sci. U.S.A. 88, (1991); P. T. Singer, A. Smalas, R. P. Carty, W. F. Mangel, R. M. Sweet, Science 259, 669 (1993); E. M. H. Duke, S. Wakatsuki, A. Hadfield, L. N. Johnson, Protein Sci. 3, 1178 (1994); V. Fülöp et al., Structure 2, 201 (1994); J. M. Bolduc et al., Science 268, 1312 (1995).
-
(1994)
Protein Sci.
, vol.3
, pp. 1178
-
-
Duke, E.M.H.1
Wakatsuki, S.2
Hadfield, A.3
Johnson, L.N.4
-
25
-
-
0028773124
-
-
J. Hajdu et al., EMBO J. 6, 539 (1987); I. Schlichting et al., Nature 345, 309 (1990); B. L. Stoddard et al., Proc. Natl. Acad. Sci. U.S.A. 88, (1991); P. T. Singer, A. Smalas, R. P. Carty, W. F. Mangel, R. M. Sweet, Science 259, 669 (1993); E. M. H. Duke, S. Wakatsuki, A. Hadfield, L. N. Johnson, Protein Sci. 3, 1178 (1994); V. Fülöp et al., Structure 2, 201 (1994); J. M. Bolduc et al., Science 268, 1312 (1995).
-
(1994)
Structure
, vol.2
, pp. 201
-
-
Fülöp, V.1
-
26
-
-
0029024462
-
-
J. Hajdu et al., EMBO J. 6, 539 (1987); I. Schlichting et al., Nature 345, 309 (1990); B. L. Stoddard et al., Proc. Natl. Acad. Sci. U.S.A. 88, (1991); P. T. Singer, A. Smalas, R. P. Carty, W. F. Mangel, R. M. Sweet, Science 259, 669 (1993); E. M. H. Duke, S. Wakatsuki, A. Hadfield, L. N. Johnson, Protein Sci. 3, 1178 (1994); V. Fülöp et al., Structure 2, 201 (1994); J. M. Bolduc et al., Science 268, 1312 (1995).
-
(1995)
Science
, vol.268
, pp. 1312
-
-
Bolduc, J.M.1
-
27
-
-
1842363215
-
-
note
-
2 for 200 ms) needed to produce a plateau in crystal bleaching. This wavelength, in the tail of PYP's absorption peak, allowed effective crystal penetration, thus minimizing thermal artifacts (15, 22). After laser shutoff, optical difference spectra were continuously recorded with a single-crystal microspectrophotometer (15) in the 380-to 520-nm range (7). After a variable delay period (2 ms in the reported experiment), a magnetic "alligator" solenoid shutter (16) opened and exposed the crystal to a 10-ms, polychromatic x-ray pulse from the National Synchrotron Light Source (NSLS) beamline X-26C at Brookhaven National Laboratory (23) (300-μm collimator, 200-mm crystal-to-detector distance, 150-μm aluminum filter). After a 30-s period for recovery from transient irradiation effects, the experiment was repeated. Ten to 16 exposures were collected on a single image plate (Fuji), before rotation of the crystal to a new spindle position (4° offset). Crystals were cooled to -12°C (FTS cooling device) to slow down the photocycle. As a control, we collected dark-state diffraction data by repeating the same procedure without laser illumination.
-
-
-
-
28
-
-
0028430176
-
-
Y. Chen, V. Šrajer, K. Ng, A. D. LeGrand, K. Moffat, Rev. Sci. Instrum. 65, 1506 (1994).
-
(1994)
Rev. Sci. Instrum.
, vol.65
, pp. 1506
-
-
Chen, Y.1
Šrajer, V.2
Ng, K.3
LeGrand, A.D.4
Moffat, K.5
-
30
-
-
0039719067
-
-
K. Moffat, Y. Chen, K. Ng, D. McRee, E. D. Getzoff, Philos. Trans. R. Soc. London Ser. A 340, 175 (1992).
-
(1992)
Philos. Trans. R. Soc. London Ser. A
, vol.340
, pp. 175
-
-
Moffat, K.1
Chen, Y.2
Ng, K.3
McRee, D.4
Getzoff, E.D.5
-
31
-
-
1842353488
-
-
note
-
H the structure factors from the monochromatic structure determination. Merging R factors between dark-state and photostationary-state data sets (19) show poor signal-to-noise ratios beyond 1.9 Å resolution, so only data to 1.9 Å were used for structure determination. As a control, data were processed with the Daresbury Laue suite of programs (24). Anisotropically streaked profiles were used for spatial overlap prediction and integration of ∼45,000 reflections per data set in the wavelength range 0.65 to 1.65 Å. Merging of diffraction data by AGROVATA and ROTAVATA [The CCP4 Suite: Programs for Protein Crystallography, Acta Crystallogr. D50, 760 (1994)] gave unweighted merging R factors for native and bleached data sets of 18.9 and 21.2%, respectively. Data were >76% complete overall (12.0 to 2.0 Å) and >57% complete in the highest resolution shell (2.08 to 2.0 Å).
-
-
-
-
32
-
-
0008285604
-
-
Z. Ren and K. Moffat, J. Synchrotron Rad. 1, 78 (1994); J. Appl. Crystallogr. 28, 461 (1995); ibid., p. 482; Z. Ren, K. Ng, G. E. O. Borgstahl, E. D. Getzoff, K. Moffat, ibid. 29, 246 (1996).
-
(1994)
J. Synchrotron Rad.
, vol.1
, pp. 78
-
-
Ren, Z.1
Moffat, K.2
-
33
-
-
1842356425
-
-
Z. Ren and K. Moffat, J. Synchrotron Rad. 1, 78 (1994); J. Appl. Crystallogr. 28, 461 (1995); ibid., p. 482; Z. Ren, K. Ng, G. E. O. Borgstahl, E. D. Getzoff, K. Moffat, ibid. 29, 246 (1996).
-
(1995)
J. Appl. Crystallogr.
, vol.28
, pp. 461
-
-
-
34
-
-
1842341741
-
-
Z. Ren and K. Moffat, J. Synchrotron Rad. 1, 78 (1994); J. Appl. Crystallogr. 28, 461 (1995); ibid., p. 482; Z. Ren, K. Ng, G. E. O. Borgstahl, E. D. Getzoff, K. Moffat, ibid. 29, 246 (1996).
-
J. Appl. Crystallogr.
, pp. 482
-
-
-
35
-
-
0039126743
-
-
Z. Ren and K. Moffat, J. Synchrotron Rad. 1, 78 (1994); J. Appl. Crystallogr. 28, 461 (1995); ibid., p. 482; Z. Ren, K. Ng, G. E. O. Borgstahl, E. D. Getzoff, K. Moffat, ibid. 29, 246 (1996).
-
(1996)
J. Appl. Crystallogr.
, vol.29
, pp. 246
-
-
Ren, Z.1
Ng, K.2
Borgstahl, G.E.O.3
Getzoff, E.D.4
Moffat, K.5
-
36
-
-
1842285342
-
-
note
-
photostationary|, again restricting movement to the 10 selected residues of the bleached structure, gave an R factor of 23.8%. The higher R factor of the selected-atom refinement is due to structural changes away from the active site that reflect systematic errors or changes in experimental conditions between the monochromatic (2) and Laue data sets. Those changes were also observed in refinement of dark-state coordinates against dark-state Laue data (R factor 20.7%) (27). Therefore, compared to the previously published dark-state structure (2), coordinates from the selected-atom refinement better indicate changes due solely to photobleaching and were used for all figures.
-
-
-
-
37
-
-
0025829307
-
-
R. A. Mathies, S. W. Lin, J. B. Ames, W. T. Pollard, Annu. Rev. Biophys. Biophys. Chem. 20, 491 (1991); Q. Wang, R. W. Schoenlein, L. A. Peteneau, R. A. Mathies, C. V. Shank, Science 266, 422 (1994).
-
(1991)
Annu. Rev. Biophys. Biophys. Chem.
, vol.20
, pp. 491
-
-
Mathies, R.A.1
Lin, S.W.2
Ames, J.B.3
Pollard, W.T.4
-
38
-
-
0028519152
-
-
R. A. Mathies, S. W. Lin, J. B. Ames, W. T. Pollard, Annu. Rev. Biophys. Biophys. Chem. 20, 491 (1991); Q. Wang, R. W. Schoenlein, L. A. Peteneau, R. A. Mathies, C. V. Shank, Science 266, 422 (1994).
-
(1994)
Science
, vol.266
, pp. 422
-
-
Wang, Q.1
Schoenlein, R.W.2
Peteneau, L.A.3
Mathies, R.A.4
Shank, C.V.5
-
41
-
-
0001475908
-
-
J. R. Helliwell et al., J. Appl. Crystallogr. 22, 483 (1989); T. J. Greenhough and A. K. Shrive, ibid. 27, 111 (1994); J. W. Campbell, ibid. 28, 228 (1995).
-
(1989)
J. Appl. Crystallogr.
, vol.22
, pp. 483
-
-
Helliwell, J.R.1
-
42
-
-
0028374994
-
-
J. R. Helliwell et al., J. Appl. Crystallogr. 22, 483 (1989); T. J. Greenhough and A. K. Shrive, ibid. 27, 111 (1994); J. W. Campbell, ibid. 28, 228 (1995).
-
(1994)
J. Appl. Crystallogr.
, vol.27
, pp. 111
-
-
Greenhough, T.J.1
Shrive, A.K.2
-
43
-
-
0001405524
-
-
J. R. Helliwell et al., J. Appl. Crystallogr. 22, 483 (1989); T. J. Greenhough and A. K. Shrive, ibid. 27, 111 (1994); J. W. Campbell, ibid. 28, 228 (1995).
-
(1995)
J. Appl. Crystallogr.
, vol.28
, pp. 228
-
-
Campbell, J.W.1
-
44
-
-
0023140814
-
-
A. T. Brünger, J. Kuriyan, M. Karplus, Science 235, 458 (1987); A. T. Brünger, A. Krukowski, J. W. Erickson, Acta Crystallogr. A 46, 585 (1990).
-
(1987)
Science
, vol.235
, pp. 458
-
-
Brünger, A.T.1
Kuriyan, J.2
Karplus, M.3
-
45
-
-
84901961522
-
-
A. T. Brünger, J. Kuriyan, M. Karplus, Science 235, 458 (1987); A. T. Brünger, A. Krukowski, J. W. Erickson, Acta Crystallogr. A 46, 585 (1990).
-
(1990)
Acta Crystallogr. A
, vol.46
, pp. 585
-
-
Brünger, A.T.1
Krukowski, A.2
Erickson, J.W.3
-
46
-
-
0002705842
-
-
D. E. McRee, J. Mol. Graph. 10, 44 (1992); D. E. McRee, Practical Protein Crystallography (Academic Press, San Diego. CA, 1993).
-
(1992)
J. Mol. Graph.
, vol.10
, pp. 44
-
-
McRee, D.E.1
-
48
-
-
1842307293
-
-
unpublished data
-
U. K. Genick et al., unpublished data.
-
-
-
Genick, U.K.1
-
50
-
-
84986486656
-
-
A. Nicholls and B. Honig, J. Comput. Chem. 12, 435 (1991); A. Nicholls, K. A. Sharp, B. Honig, DelPhi (Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 1990).
-
(1991)
J. Comput. Chem.
, vol.12
, pp. 435
-
-
Nicholls, A.1
Honig, B.2
-
51
-
-
84986486656
-
-
Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY
-
A. Nicholls and B. Honig, J. Comput. Chem. 12, 435 (1991); A. Nicholls, K. A. Sharp, B. Honig, DelPhi (Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 1990).
-
(1990)
DelPhi
-
-
Nicholls, A.1
Sharp, K.A.2
Honig, B.3
-
52
-
-
0000217485
-
-
A. D. MacKerell et al., FASEB J. 6, A143 (1992); A. D. MacKerell Jr. et al., in preparation.
-
(1992)
FASEB J.
, vol.6
-
-
MacKerell, A.D.1
-
53
-
-
1842272624
-
-
in preparation
-
A. D. MacKerell et al., FASEB J. 6, A143 (1992); A. D. MacKerell Jr. et al., in preparation.
-
-
-
MacKerell Jr., A.D.1
-
55
-
-
1842352488
-
-
note
-
We thank E. Blum, Y. Chen, A. LeGrand, H. E. Parge, and G. Shea-McCarthy for assistance in designing and constructing apparatus for these experiments and for help with data collection at NSLS, Brookhaven National Laboratory, and previous runs at CHESS, Cornell University; T. Greenhough for help with the Daresbury Laue program suite; J. A. Tainer and M. Baca for valuable discussions; and M. E. Pique for help with AVS figures. Coordinates for the PYP bleached intermediate have been deposited in the Protein Data Bank (accession number 2pyp). Supported by grants from NIH (GM37684 to E.D.G.; GM36452 and RR07707 to K.M.) and the W. M. Keck Foundation (M. Makinen and K.M.), and fellowships from NIH (NRSA GM15820 to G.E.O.B.) and Boehringer Ingelheim Fonds (U.K.G.).
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-
-
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