101
|
Anderson S, Srajer V, Moffat K. Structural heterogeneity of cryotrapped intermediates in the bacterial blue light photoreceptor, photoactive yellow protein. Photochem Photobiol 2004; 80:7-14. [PMID: 15339224 DOI: 10.1562/2004-03-15-ra-115.1] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
We investigate by X-ray crystallographic techniques the cryotrapped states that accumulate on controlled illumination of the blue light photoreceptor, photoactive yellow protein (PYP), at 110 K in both the wild-type species and its E46Q mutant. These states are related to those that occur during the chromophore isomerization process in the PYP photocycle at room temperature. The structures present in such states were determined at high resolution, 0.95-1.05A. In both wild type and mutant PYP, the cryotrapped state is not composed of a single, quasitransition state structure but rather of a heterogeneous mixture of three species in addition to the ground state structure. We identify and refine these three photoactivated species under the assumption that the structural changes are limited to simple isomerization events of the chromophore that otherwise retains chemical bonding similar to that in the ground state. The refined chromophore models are essentially identical in the wild type and the E46Q mutant, which implies that the early stages of their photocycle mechanisms are the same.
Collapse
Affiliation(s)
- Spencer Anderson
- Department of Biochemistry and Molecular Biology, and Consortium for Advanced Radiation Sciences, University of Chicago, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, USA.
| | | | | |
Collapse
|
102
|
Pan D, Philip A, Hoff WD, Mathies RA. Time-resolved resonance raman structural studies of the pB' intermediate in the photocycle of photoactive yellow protein. Biophys J 2004; 86:2374-82. [PMID: 15041675 PMCID: PMC1304086 DOI: 10.1016/s0006-3495(04)74294-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Time-resolved resonance Raman spectroscopy is used to obtain chromophore vibrational spectra of the pR, pB', and pB intermediates during the photocycle of photoactive yellow protein. In the pR spectrum, the C8-C9 stretching mode at 998 cm(-1) is approximately 60 cm(-1) lower than in the dark state, and the combination of C-O stretching and C7H=C8H bending at 1283 cm(-1) is insensitive to D2O substitution. These results indicate that pR has a deprotonated, cis chromophore structure and that the hydrogen bonding to the chromophore phenolate oxygen is preserved and strengthened in the early photoproduct. However, the intense C7H=C8H hydrogen out-of-plane (HOOP) mode at 979 cm(-1) suggests that the chromophore in pR is distorted at the vinyl and adjacent C8-C9 bonds. The formation of pB' involves chromophore protonation based on the protonation state marker at 1174 cm(-1) and on the sensitivity of the COH bending at 1148 cm(-1) as well as the combined C-OH stretching and C7H=C8H bending mode at 1252 cm(-1) to D2O substitution. The hydrogen out-of-plane Raman intensity at 985 cm(-1) significantly decreases in pB', suggesting that the pR-to-pB' transition is the stage where the stored photon energy is transferred from the distorted chromophore to the protein, producing a more relaxed pB' chromophore structure. The C=O stretching mode downshifts from 1660 to 1651 cm(-1) in the pB'-to-pB transition, indicating the reformation of a hydrogen bond to the carbonyl oxygen. Based on reported x-ray data, this suggests that the chromophore ring flips during the transition from pB' to pB. These results confirm the existence and importance of the pB' intermediate in photoactive yellow protein receptor activation.
Collapse
Affiliation(s)
- Duohai Pan
- Department of Chemistry, University of California at Berkeley, Berkeley, California 94720, USA
| | | | | | | |
Collapse
|
103
|
Neutze R, Huldt G, Hajdu J, van der Spoel D. Potential impact of an X-ray free electron laser on structural biology. Radiat Phys Chem Oxf Engl 1993 2004. [DOI: 10.1016/j.radphyschem.2004.04.121] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
|
104
|
Anderson S, Srajer V, Pahl R, Rajagopal S, Schotte F, Anfinrud P, Wulff M, Moffat K. Chromophore conformation and the evolution of tertiary structural changes in photoactive yellow protein. Structure 2004; 12:1039-45. [PMID: 15274923 DOI: 10.1016/j.str.2004.04.008] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2004] [Revised: 04/01/2004] [Accepted: 04/05/2004] [Indexed: 11/29/2022]
Abstract
We use time-resolved crystallography to observe the structural progression of a bacterial blue light photoreceptor throughout its photocycle. Data were collected from 10 ns to 100 ms after photoactivation of the E46Q mutant of photoactive yellow protein. Refinement of transient chromophore conformations shows that the spectroscopically distinct intermediates are formed via progressive disruption of the hydrogen bond network to the chromophore. Although structural change occurs within a few nanoseconds on and around the chromophore, it takes milliseconds for a distinct pattern of tertiary structural change to fully progress through the entire molecule, thus generating the putative signaling state. Remarkably, the coupling between the chromophore conformation and the tertiary structure of this small protein is not tight: there are leads and lags between changes in the conformation of the chromophore and the protein tertiary structure.
Collapse
Affiliation(s)
- Spencer Anderson
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA.
| | | | | | | | | | | | | | | |
Collapse
|
105
|
Cherepanov AV, De Vries S. Microsecond freeze-hyperquenching: development of a new ultrafast micro-mixing and sampling technology and application to enzyme catalysis. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2004; 1656:1-31. [PMID: 15136155 DOI: 10.1016/j.bbabio.2004.02.006] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2003] [Revised: 02/17/2004] [Accepted: 02/17/2004] [Indexed: 11/21/2022]
Abstract
A novel freeze-quench instrument with a characteristic <<dead-time>> of 137 +/- 18 micros is reported. The prototype has several key features that distinguish it from conventional freeze-quench devices and provide a significant improvement in time resolution: (a) high operating pressures (up to 400 bar) result in a sample flow with high linear rates (up to 200 m s(-1)); (b) tangential micro-mixer with an operating volume of approximately 1 nl yields short mixing times (up to 20 micros); (c) fast transport between the mixer and the cryomedium results in short reaction times: the ageing solution exits the mixer as a free-flowing jet, and the chemical reaction occurs "in-flight" on the way to the cryomedium; (d) a small jet diameter (approximately 20 microm) and a high jet velocity (approximately 200 m s(-1)) provide high sample-cooling rates, resulting in a short cryofixation time (up to 30 micros). The dynamic range of the freeze-quench device is between 130 micros and 15 ms. The novel tangential micro-mixer efficiently mixes viscous aqueous solutions, showing more than 95% mixing at eta < or = 4 (equivalent to protein concentrations up to 250 mg ml(-1)), which makes it an excellent tool for the preparation of pre-steady state samples of concentrated protein solutions for spectroscopic structure analysis. The novel freeze-quench device is characterized using the reaction of binding of azide to metmyoglobin from horse heart. Reaction samples are analyzed using 77 K optical absorbance spectroscopy, and X-band EPR spectroscopy. A simple procedure of spectral analysis is reported that allows (a) to perform a quantitative analysis of the reaction kinetics and (b) to identify and characterize novel reaction intermediates. The reduction of dioxygen by the bo3-type quinol oxidase from Escherichia coli is assayed using the MHQ technique. In these pilot experiments, low-temperature optical absorbance measurements show the rapid oxidation of heme o3 in the first 137 micros of the reaction, accompanied by the formation of an oxo-ferryl species. X-band EPR spectroscopy shows that a short-living radical intermediate is formed during the oxidation of heme o3. The radical decays within approximately 1 ms concomitant with the oxidation of heme b, and can be attributed to the PM reaction intermediate converting to the oxoferryl intermediate F. The general field of application of the freeze-quench methodology is discussed.
Collapse
Affiliation(s)
- Alexey V Cherepanov
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
| | | |
Collapse
|
106
|
Baxter RHG, Ponomarenko N, Srajer V, Pahl R, Moffat K, Norris JR. Time-resolved crystallographic studies of light-induced structural changes in the photosynthetic reaction center. Proc Natl Acad Sci U S A 2004; 101:5982-7. [PMID: 15073325 PMCID: PMC395909 DOI: 10.1073/pnas.0306840101] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2003] [Indexed: 11/18/2022] Open
Abstract
Light-induced structural changes in the bacterial reaction center were studied by a time-resolved crystallographic experiment. Crystals of protein from Blastochloris viridis (formerly Rhodopseudomonas viridis) were reconstituted with ubiquinone and analyzed by monochromatic and Laue diffraction, in the dark and 3 ms after illuminating the crystal with a pulsed laser (630 nm, 3 mJ/pulse, 7 ns duration). Refinement of monochromatic data shows that ubiquinone binds only in the "proximal" Q(B) binding site. No significant structural difference was observed between the light and dark datasets; in particular, no quinone motion was detected. This result may be reconciled with previous studies by postulating equilibration of the "distal" and "proximal" binding sites upon extended dark adaption, and in which movement of ubiquinone is not the conformational gate for the first electron transfer between Q(A) and Q(B).
Collapse
Affiliation(s)
- Richard H G Baxter
- Department of Chemistry, University of Chicago, 5735 South Ellis Avenue, Chicago, IL 60637, USA
| | | | | | | | | | | |
Collapse
|
107
|
Techert S, Zachariasse KA. Structure Determination of the Intramolecular Charge Transfer State in Crystalline 4-(Diisopropylamino)benzonitrile from Picosecond X-ray Diffraction. J Am Chem Soc 2004; 126:5593-600. [PMID: 15113231 DOI: 10.1021/ja0379518] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The molecular structure of photoexcited crystalline 4-(diisopropylamino)benzonitrile (DIABN) is determined by time-resolved X-ray diffraction with a time resolution of 70 ps. Spectroscopic results suggest that an ICT state with a lifetime of 3 ns is produced after photoexcitation. According to structural refinement of the X-ray data (powder diffraction), the torsional angle of the diisopropylamino group with respect to the plane of the phenyl ring of DIABN decreases from 14 degrees in the electronic ground state to 10 degrees in the equilibrated ICT state.
Collapse
Affiliation(s)
- Simone Techert
- Max-Planck-Institut für biophysikalische Chemie, Spektroskopie und Photochemische Kinetik, 37070 Goettingen, Germany.
| | | |
Collapse
|
108
|
Knapp JE, Srajer V, Pahl R, Royer WE. Immobilization of Scapharca HbI crystals improves data quality in time-resolved crystallographic experiments. Micron 2004; 35:107-8. [PMID: 15036308 DOI: 10.1016/j.micron.2003.10.039] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Time-resolved crystallography is a powerful technique that allows structural transitions to be followed in real time during the course of a chemical reaction. The extension of the time resolution of this technique to nanosecond and picosecond time scales require a short laser pulse to initiate the transition and a rapid polychromatic X-ray pulse to probe the structural perturbations. Unfortunately, polychromatic diffraction patterns are quite sensitive to subtle crystal movements that can occur from laser pulses used to trigger the structural transition. The immobilization of crystals within capillary tubes dramatically improves data quality and allows the utilization of more intense laser pulses for the initiation step. This leads to an increase in the signal to noise present in the electron density maps.
Collapse
Affiliation(s)
- James E Knapp
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | | | | | | |
Collapse
|
109
|
|
110
|
Siwick BJ, Dwyer JR, Jordan RE, Miller R. Femtosecond electron diffraction studies of strongly driven structural phase transitions. Chem Phys 2004. [DOI: 10.1016/j.chemphys.2003.11.040] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
111
|
Schmidt M, Pahl R, Srajer V, Anderson S, Ren Z, Ihee H, Rajagopal S, Moffat K. Protein kinetics: structures of intermediates and reaction mechanism from time-resolved x-ray data. Proc Natl Acad Sci U S A 2004; 101:4799-804. [PMID: 15041745 PMCID: PMC387328 DOI: 10.1073/pnas.0305983101] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We determine the number of authentic reaction intermediates in the later stages of the photocycle of photoactive yellow protein at room temperature, their atomic structures, and a consistent set of chemical kinetic mechanisms, by analysis of a set of time-dependent difference electron density maps spanning the time range from 5 micros to 100 ms. The successful fit of exponentials to right singular vectors derived from a singular value decomposition of the difference maps demonstrates that a chemical kinetic mechanism holds and that structurally distinct intermediates exist. We identify two time-independent difference maps, from which we refine the structures of the corresponding intermediates. We thus demonstrate how structures associated with intermediate states can be extracted from the experimental, time-dependent crystallographic data. Stoichiometric and structural constraints allow the exclusion of one kinetic mechanism proposed for the photocycle but retain other plausible candidate kinetic mechanisms.
Collapse
Affiliation(s)
- Marius Schmidt
- Physikdepartment E17, Technische Universität München, 85747 Garching, Germany.
| | | | | | | | | | | | | | | |
Collapse
|
112
|
Kort R, Hellingwerf KJ, Ravelli RBG. Initial events in the photocycle of photoactive yellow protein. J Biol Chem 2004; 279:26417-24. [PMID: 15026418 DOI: 10.1074/jbc.m311961200] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The light-induced isomerization of a double bond is the key event that allows the conversion of light energy into a structural change in photoactive proteins for many light-mediated biological processes, such as vision, photosynthesis, photomorphogenesis, and photo movement. Cofactors such as retinals, linear tetrapyrroles, and 4-hydroxy-cinnamic acid have been selected by nature that provide the essential double bond to transduce the light signal into a conformational change and eventually, a physiological response. Here we report the first events after light excitation of the latter chromophore, containing a single ethylene double bond, in a low temperature crystallographic study of the photoactive yellow protein. We measured experimental phases to overcome possible model bias, corrected for minimized radiation damage, and measured absorption spectra of crystals to analyze the photoproducts formed. The data show a mechanism for the light activation of photoactive yellow protein, where the energy to drive the remainder of the conformational changes is stored in a slightly strained but fully cis-chromophore configuration. In addition, our data indicate a role for backbone rearrangements during the very early structural events.
Collapse
Affiliation(s)
- Remco Kort
- Laboratory for Microbiology, Swammerdam Institute for Life Sciences, University of Amsterdam, Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands.
| | | | | |
Collapse
|
113
|
Edman K, Royant A, Larsson G, Jacobson F, Taylor T, van der Spoel D, Landau EM, Pebay-Peyroula E, Neutze R. Deformation of Helix C in the Low Temperature L-intermediate of Bacteriorhodopsin. J Biol Chem 2004; 279:2147-58. [PMID: 14532280 DOI: 10.1074/jbc.m300709200] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
X-ray and electron diffraction studies of specific reaction intermediates, or reaction intermediate analogues, have produced a consistent picture of the structural mechanism of light-driven proton pumping by bacteriorhodopsin. Of central importance within this picture is the structure of the L-intermediate, which follows the retinal all-trans to 13-cis photoisomerization step of the K-intermediate and sets the stage for the primary proton transfer event from the positively charged Schiff base to the negatively charged Asp-85. Here we report the structural changes in bacteriorhodopsin following red light illumination at 150 K. Single crystal microspectrophotometry showed that only the L-intermediate is populated in three-dimensional crystals under these conditions. The experimental difference Fourier electron density map and refined crystallographic structure were consistent with those previously presented (Royant, A., Edman, K., Ursby, T., Pebay-Peyroula, E., Landau, E. M., and Neutze, R. (2000) Nature 406, 645-648; Royant, A., Edman, K., Ursby, T., Pebay-Peyroula, E., Landau, E. M., and Neutze, R. (2001) Photochem. Photobiol. 74, 794-804). Based on the refined crystallographic structures, molecular dynamic simulations were used to examine the influence of the conformational change of the protein that is associated with the K-to-L transition on retinal dynamics. Implications regarding the structural mechanism for proton pumping by bacteriorhodopsin are discussed.
Collapse
Affiliation(s)
- Karl Edman
- Department of Chemistry and Bioscience, Chalmers University of Technology, Box 462, S-40530 Gothenburg, Sweden
| | | | | | | | | | | | | | | | | |
Collapse
|
114
|
Getzoff ED, Gutwin KN, Genick UK. Anticipatory active-site motions and chromophore distortion prime photoreceptor PYP for light activation. Nat Struct Mol Biol 2003; 10:663-8. [PMID: 12872160 DOI: 10.1038/nsb958] [Citation(s) in RCA: 100] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2002] [Accepted: 06/26/2003] [Indexed: 11/08/2022]
Abstract
Protein photoreceptors use small-molecule cofactors called chromophores to detect light. Only under the influence of the receptors' active sites do these chromophores adopt spectral and photochemical properties that suit the receptors' functional requirements. This protein-induced change in chromophore properties is called photochemical tuning and is a prime example for the general--but poorly understood--process of chemical tuning through which proteins shape the reactivity of their active-site groups. Here we report the 0.82-A resolution X-ray structure of the bacterial light receptor photoactive yellow protein (PYP). The unusually precise structure reveals deviations from expected molecular geometries and anisotropic atomic displacements in the PYP active site. Our analysis of these deviations points directly to the intramolecular forces and active-site dynamics that tune the properties of PYP's chromophore to absorb blue light, suppress fluorescence, and favor the required light-driven double-bond isomerization.
Collapse
Affiliation(s)
- Elizabeth D Getzoff
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA.
| | | | | |
Collapse
|
115
|
Kort R, Ravelli RB, Schotte F, Bourgeois D, Crielaard W, Hellingwerf KJ, Wulff M. Characterization of photocycle intermediates in crystalline photoactive yellow protein. Photochem Photobiol 2003; 78:131-7. [PMID: 12945580 DOI: 10.1562/0031-8655(2003)078<0131:copiic>2.0.co;2] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The photocycle in photoactive yellow protein (PYP) crystals was studied by single-crystal absorption spectroscopy with experimental setups for low-temperature and time-resolved measurements. Thin and flat PYP crystals, suitable for light absorption studies, were obtained using special crystallization conditions. Illumination of PYP crystals at 100 K led to the formation of a photostationary state, which includes at least one hypsochromic and one bathochromic photoproduct that resemble PYP(H) and PYP(B), respectively. The effect of temperature, light color and light pulse duration on the occupancy of these low-temperature photoproducts was determined and appeared similar to that observed in solution. At room temperature a blueshifted photocycle intermediate was identified that corresponds to the blueshifted state of PYP (pB). Kinetic studies show that the decay of this blueshifted intermediate is biphasic at -12 degrees C and 15-fold faster than that observed in solution at room temperature. These altered pB decay kinetics confirm a model that holds that the photocycle in crystals takes place in a shortcut version. In this version the key structural events of the photocycle, such as photoisomerization and reversible protonation of the chromophore, take place, but large conformational changes in the surrounding protein are limited by constraints imposed by the crystal lattice.
Collapse
Affiliation(s)
- Remco Kort
- Laboratory for Microbiology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands.
| | | | | | | | | | | | | |
Collapse
|
116
|
Abstract
PURPOSE OF REVIEW Structural biology is one of the most informative disciplines available to biochemical research. It unites technologies that can reveal high-resolution (often atomic) details of the inner workings of biochemical systems. These insights are crucial for an understanding of basic life processes, such as the reaction mechanism of a drug-converting enzyme, signal transduction from one protein to another, activation of a metabolic pathway by a gene effector, action modes of drugs, or the consequences of a mutation on the function of an enzyme. Structural biology is also vital for characterizing the molecular basis of many diseases and often provides a starting platform for the development of specifically tuned therapies, for example by designing drugs that bind to particular targets in order to affect their functionality. An overview of the main techniques as well as some selected case studies are presented. RECENT FINDINGS Recent advances in the three major structure determination techniques (X-ray crystallography, nuclear magnetic resonance spectroscopy, and electron microscopy) have made it possible to obtain three-dimensional structural information on larger systems, at higher resolution and with much less effort than in the past. Because these techniques often provide complementary information, combining them is particularly powerful for gaining comprehensive insights into complex systems, as illustrated by the recent structure determinations of the low-density lipoprotein receptor and the ribosome. SUMMARY Structural biology is no longer exclusive to a few dedicated specialists. Many of its techniques are now easily accessible and can be used as tools in general life science research.
Collapse
Affiliation(s)
- Mischa Machius
- Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, USA.
| |
Collapse
|
117
|
Dugave C, Demange L. Cis-trans isomerization of organic molecules and biomolecules: implications and applications. Chem Rev 2003; 103:2475-532. [PMID: 12848578 DOI: 10.1021/cr0104375] [Citation(s) in RCA: 763] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Christophe Dugave
- CEA/Saclay, Département d'Ingénierie et d'Etudes des Protéines (DIEP), Bâtiment 152, 91191 Gif-sur-Yvette, France.
| | | |
Collapse
|
118
|
Coppens P. What can time-resolved diffraction tell us about transient species?: excited-state structure determination at atomic resolution. Chem Commun (Camb) 2003:1317-20. [PMID: 12841224 DOI: 10.1039/b301371p] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The author describes his work for which he coined the word 'photocrystallography', a technique which consists of using a laser to pump, or excite, a molecular crystal while the X-ray diffractometer probes its structure at the atomic level. The technique is being used to study highly reactive excited molecules that exist for just millionths or even billionths of a second using very intense light sources at the National Synchrotron Light Source at Brookhaven National Laboratory and the Advanced Photon Source at Argonne National Laboratory.
Collapse
Affiliation(s)
- Philip Coppens
- Department of Chemistry, State University of New York at Buffalo, Buffalo, NY 14260-3000, USA.
| |
Collapse
|
119
|
Schmidt M, Rajagopal S, Ren Z, Moffat K. Application of singular value decomposition to the analysis of time-resolved macromolecular x-ray data. Biophys J 2003; 84:2112-29. [PMID: 12609912 PMCID: PMC1302779 DOI: 10.1016/s0006-3495(03)75018-8] [Citation(s) in RCA: 102] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2002] [Accepted: 11/04/2002] [Indexed: 11/20/2022] Open
Abstract
Singular value decomposition (SVD) is a technique commonly used in the analysis of spectroscopic data that both acts as a noise filter and reduces the dimensionality of subsequent least-squares fits. To establish the applicability of SVD to crystallographic data, we applied SVD to calculated difference Fourier maps simulating those to be obtained in a time-resolved crystallographic study of photoactive yellow protein. The atomic structures of one dark state and three intermediates were used in qualitatively different kinetic mechanisms to generate time-dependent difference maps at specific time points. Random noise of varying levels in the difference structure factor amplitudes, different extents of reaction initiation, and different numbers of time points were all employed to simulate a range of realistic experimental conditions. Our results show that SVD allows for an unbiased differentiation between signal and noise; a small subset of singular values and vectors represents the signal well, reducing the random noise in the data. Due to this, phase information of the difference structure factors can be obtained. After identifying and fitting a kinetic mechanism, the time-independent structures of the intermediates could be recovered. This demonstrates that SVD will be a powerful tool in the analysis of experimental time-resolved crystallographic data.
Collapse
Affiliation(s)
- Marius Schmidt
- Physik-Department E17, Technische Universitaet Muenchen, 85747 Garching, Germany.
| | | | | | | |
Collapse
|
120
|
Monitoring initial structural changes in a crystal during photo-induced disappearance of its diffracting properties. Chem Phys 2003. [DOI: 10.1016/s0301-0104(03)00029-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
|
121
|
Rajagopal S, Moffat K. Crystal structure of a photoactive yellow protein from a sensor histidine kinase: conformational variability and signal transduction. Proc Natl Acad Sci U S A 2003; 100:1649-54. [PMID: 12563032 PMCID: PMC149887 DOI: 10.1073/pnas.0336353100] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2002] [Indexed: 11/18/2022] Open
Abstract
Photoactive yellow protein (E-PYP) is a blue light photoreceptor, implicated in a negative phototactic response in Ectothiorhodospira halophila, that also serves as a model for the Per-Arnt-Sim superfamily of signaling molecules. Because no biological signaling partner for E-PYP has been identified, it has not been possible to correlate any of its photocycle intermediates with a relevant signaling state. However, the PYP domain (Ppr-PYP) from the sensor histidine kinase Ppr in Rhodospirillum centenum, which regulates the catalytic activity of Ppr by blue light absorption, may allow such issues to be addressed. Here we report the crystal structure of Ppr-PYP at 2 A resolution. This domain has the same absorption spectrum and similar photocycle kinetics as full length Ppr, but a blue-shifted absorbance and considerably slower photocycle than E-PYP. Although the overall fold of Ppr-PYP resembles that of E-PYP, a novel conformation of the beta 4-beta 5 loop results in inaccessibility of Met-100, thought to catalyze chromophore reisomerization, to the chromophore. This conformation also exposes a highly conserved molecular surface that could interact with downstream signaling partners. Other structural differences in the alpha 3-alpha 4 and beta 4-beta 5 loops are consistent with these regions playing significant roles in the control of photocycle dynamics and, by comparison to other sensory Per-Arnt-Sim domains, in signal transduction. Because of its direct linkage to a measurable biological output, Ppr-PYP serves as an excellent system for understanding how changes in photocycle dynamics affect signaling by PYPs.
Collapse
Affiliation(s)
- Sudarshan Rajagopal
- Department of Biochemistry and Molecular Biology, University of Chicago, 920 East 58th Street, Chicago, IL 60637, USA
| | | |
Collapse
|
122
|
Hendriks J, van Stokkum IHM, Hellingwerf KJ. Deuterium isotope effects in the photocycle transitions of the photoactive yellow protein. Biophys J 2003; 84:1180-91. [PMID: 12547797 PMCID: PMC1302693 DOI: 10.1016/s0006-3495(03)74932-7] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
The Photoactive Yellow Protein (PYP) from Halorhodospira halophila (formerly Ectothiorhodospira halophila) is increasingly used as a model system. As such, a thorough understanding of the photocycle of PYP is essential. In this study we have combined information from pOH- (or pH-) dependence and (kinetic) deuterium isotope effects to elaborate on existing photocycle models. For several characteristics of PYP we were able to make a distinction between pH- and pOH-dependence, a nontrivial distinction when comparing data from samples dissolved in H(2)O and D(2)O. It turns out that most characteristics of PYP are pOH-dependent. We confirmed the existence of a pB' intermediate in the pR to pB transition of the photocycle. In addition, we were able to show that the pR to pB' transition is reversible, which explains the previously observed biexponential character of the pR-to-pB photocycle step. Also, the absorption spectrum of pB' is slightly red-shifted with respect to pB. The recovery of the pG state is accompanied by an inverse kinetic deuterium isotope effect. Our interpretation of this is that before the chromophore can be isomerized, it is deprotonated by a hydroxide ion from solution. From this we propose a new photocycle intermediate, pB(deprot), from which pG is recovered and which is in equilibrium with pB. This is supported in our data through the combination of the observed pOH and pH dependence, together with the kinetic deuterium isotope effect.
Collapse
Affiliation(s)
- Johnny Hendriks
- Department of Biochemistry and Molecular Biology, Faculty of Sciences, Vrije Universiteit, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | | | | |
Collapse
|
123
|
|
124
|
Hellingwerf KJ, Hendriks J, Gensch T. Photoactive Yellow Protein, A New Type of Photoreceptor Protein: Will This “Yellow Lab” Bring Us Where We Want to Go? J Phys Chem A 2003. [DOI: 10.1021/jp027005y] [Citation(s) in RCA: 248] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Klaas J. Hellingwerf
- Laboratory for Microbiology, Swammerdam Institute for Life Sciences (SILS), BioCentrum, University of Amsterdam, Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands, and Institute of Biological Information Processing 1, Research Centre Jülich, D-52425 Jülich, Germany
| | - Johnny Hendriks
- Laboratory for Microbiology, Swammerdam Institute for Life Sciences (SILS), BioCentrum, University of Amsterdam, Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands, and Institute of Biological Information Processing 1, Research Centre Jülich, D-52425 Jülich, Germany
| | - Thomas Gensch
- Laboratory for Microbiology, Swammerdam Institute for Life Sciences (SILS), BioCentrum, University of Amsterdam, Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands, and Institute of Biological Information Processing 1, Research Centre Jülich, D-52425 Jülich, Germany
| |
Collapse
|
125
|
Imamoto Y, Kataoka M, Liu RSH. Mechanistic pathways for the photoisomerization reaction of the anchored, tethered chromophore of the photoactive yellow protein and its mutants. Photochem Photobiol 2002; 76:584-9. [PMID: 12511037 DOI: 10.1562/0031-8655(2002)076<0584:mpftpr>2.0.co;2] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
We show by way of physical organic reasoning that the currently known photochemical results of the chromophore of photoactive yellow protein (PYP) are consistent with that expected of a least volume-demanding process for an anchored, tethered chromophore. The primary photoreaction, interestingly, does not appear to involve a hula-twist process. However, the latter might be involved during subsequent transition of dark intermediates. Absorption data of intermediates obtained from a microsecond time-resolved spectroscopic study of three PYP mutants (E46Q, T50V and R52Q) are consistent with the above analyses.
Collapse
Affiliation(s)
- Yasushi Imamoto
- Graduate School of Materials Science, Nara Institute of Science and Technology, Ikoma, Nara, Japan
| | | | | |
Collapse
|
126
|
Changenet-Barret P, Espagne A, Katsonis N, Charier S, Baudin JB, Jullien L, Plaza P, Martin MM. Excited-state relaxation dynamics of a PYP chromophore model in solution: influence of the thioester group. Chem Phys Lett 2002. [DOI: 10.1016/s0009-2614(02)01480-x] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
127
|
Bratos S, Mirloup F, Vuilleumier R, Wulff M. Time-resolved x-ray diffraction: Statistical theory and its application to the photo-physics of molecular iodine. J Chem Phys 2002. [DOI: 10.1063/1.1477923] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
128
|
Spörlein S, Carstens H, Satzger H, Renner C, Behrendt R, Moroder L, Tavan P, Zinth W, Wachtveitl J. Ultrafast spectroscopy reveals subnanosecond peptide conformational dynamics and validates molecular dynamics simulation. Proc Natl Acad Sci U S A 2002; 99:7998-8002. [PMID: 12060746 PMCID: PMC123009 DOI: 10.1073/pnas.122238799] [Citation(s) in RCA: 185] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2002] [Accepted: 04/22/2002] [Indexed: 11/18/2022] Open
Abstract
Femtosecond time-resolved spectroscopy on model peptides with built-in light switches combined with computer simulation of light-triggered motions offers an attractive integrated approach toward the understanding of peptide conformational dynamics. It was applied to monitor the light-induced relaxation dynamics occurring on subnanosecond time scales in a peptide that was backbone-cyclized with an azobenzene derivative as optical switch and spectroscopic probe. The femtosecond spectra permit the clear distinguishing and characterization of the subpicosecond photoisomerization of the chromophore, the subsequent dissipation of vibrational energy, and the subnanosecond conformational relaxation of the peptide. The photochemical cis/trans-isomerization of the chromophore and the resulting peptide relaxations have been simulated with molecular dynamics calculations. The calculated reaction kinetics, as monitored by the energy content of the peptide, were found to match the spectroscopic data. Thus we verify that all-atom molecular dynamics simulations can quantitatively describe the subnanosecond conformational dynamics of peptides, strengthening confidence in corresponding predictions for longer time scales.
Collapse
Affiliation(s)
- Sebastian Spörlein
- Lehrstuhl für BioMolekulare Optik, Oettingenstrasse 67, Ludwig-Maximilians-Universität München, 80538 Munich, Germany
| | | | | | | | | | | | | | | | | |
Collapse
|
129
|
Gensch T, Gradinaru C, van Stokkum I, Hendriks J, Hellingwerf K, van Grondelle R. The primary photoreaction of photoactive yellow protein (PYP): anisotropy changes and excitation wavelength dependence. Chem Phys Lett 2002. [DOI: 10.1016/s0009-2614(02)00344-5] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
130
|
Metzler DE, Metzler CM, Sauke DJ. Light and Life. Biochemistry 2001. [DOI: 10.1016/b978-012492543-4/50026-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|