Visualizing reaction pathways in photoactive yellow protein from nanoseconds to seconds

被引:219
作者
Ihee, H [1 ]
Rajagopal, S
Srajer, V
Pahl, R
Anderson, S
Schmidt, M
Schotte, F
Anfinrud, PA
Wulff, M
Moffat, K
机构
[1] Korea Adv Inst Sci & Technol, Dept Chem, Taejon 305701, South Korea
[2] Korea Adv Inst Sci & Technol, Sch Mol Sci, Taejon 305701, South Korea
[3] Univ Chicago, Dept Biochem & Mol Biol, Chicago, IL 60637 USA
[4] Univ Chicago, Ctr Adv Radiat Sources, Chicago, IL 60637 USA
[5] Univ Chicago, Inst Biophys Dynam, Chicago, IL 60637 USA
[6] Tech Univ Munich, Phys Dept E17, D-85747 Garching, Germany
[7] NIH, Bethesda, MD 20982 USA
[8] European Synchrotron Radiat Facil, F-38043 Grenoble, France
关键词
intermediates; mechanism; signal transduction; time-resolved crystallography; singular value decomposition;
D O I
10.1073/pnas.0409035102
中图分类号
O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];
学科分类号
07 ; 0710 ; 09 ;
摘要
Determining 3D intermediate structures during the biological action of proteins in real time under ambient conditions is essential for understanding how proteins function. Here we use timer-esolved Laue crystallography to extract short-lived intermediate structures and thereby unveil signal transduction in the blue light photoreceptor photoactive yellow protein (PYP) from Halorhodospira halophila. By analyzing a comprehensive set of Laue data during the PYP photocycle (forty-seven time points from one nanosecond to one second), we track all atoms in PYP during its photocycle and directly observe how absorption of a blue light photon by its p-coumaric acid chromophore triggers a reversible photocycle. We identify a complex chemical mechanism characterized by five distinct structural intermediates. Structural changes at the chromophore in the early, red-shifted intermediates are transduced to the exterior of the protein in the late, blue-shifted intermediates through an initial "volume-conserving" isomerization of the chromophore and the progressive disruption of hydrogen bonds between the chromophore and its surrounding binding pocket. These results yield a comprehensive view of the PYP photocycle when seen in the light of previous biophysical studies on the system.
引用
收藏
页码:7145 / 7150
页数:6
相关论文
共 49 条
  • [1] Structural heterogeneity of cryotrapped intermediates in the bacterial blue light photoreceptor, photoactive yellow protein
    Anderson, S
    Srajer, V
    Moffat, K
    [J]. PHOTOCHEMISTRY AND PHOTOBIOLOGY, 2004, 80 (01) : 7 - 14
  • [2] Short hydrogen bonds in photoactive yellow protein
    Anderson, S
    Crosson, S
    Moffat, K
    [J]. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 2004, 60 : 1008 - 1016
  • [3] Chromophore conformation and the evolution of tertiary structural changes in photoactive yellow protein
    Anderson, S
    Srajer, V
    Pahl, R
    Rajagopal, S
    Schotte, F
    Anfinrud, P
    Wulff, M
    Moffat, K
    [J]. STRUCTURE, 2004, 12 (06) : 1039 - 1045
  • [4] ANDERSON S, 2003, THESIS U CHICAGO CHI
  • [5] COMPLETE CHEMICAL-STRUCTURE OF PHOTOACTIVE YELLOW PROTEIN - NOVEL THIOESTER-LINKED 4-HYDROXYCINNAMYL CHROMOPHORE AND PHOTOCYCLE CHEMIST
    BACA, M
    BORGSTAHL, GEO
    BOISSINOT, M
    BURKE, PM
    WILLIAMS, DR
    SLATER, KA
    GETZOFF, ED
    [J]. BIOCHEMISTRY, 1994, 33 (48) : 14369 - 14377
  • [6] THE CCP4 SUITE - PROGRAMS FOR PROTEIN CRYSTALLOGRAPHY
    BAILEY, S
    [J]. ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 1994, 50 : 760 - 763
  • [7] Time-resolved crystallographic studies of light-induced structural changes in the photosynthetic reaction center
    Baxter, RHG
    Ponomarenko, N
    Srajer, V
    Pahl, R
    Moffat, K
    Norris, JR
    [J]. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2004, 101 (16) : 5982 - 5987
  • [8] 1.4 ANGSTROM STRUCTURE OF PHOTOACTIVE YELLOW PROTEIN, A CYTOSOLIC PHOTORECEPTOR - UNUSUAL FOLD, ACTIVE-SITE, AND CHROMOPHORE
    BORGSTAHL, GEO
    WILLIAMS, DR
    GETZOFF, ED
    [J]. BIOCHEMISTRY, 1995, 34 (19) : 6278 - 6287
  • [9] pH dependence of the photocycle kinetics of the E46Q mutant of photoactive yellow protein:: Protonation equilibrium between I1 and I2 intermediates, chromophore deprotonation by hydroxyl uptake, and protonation relaxation of the dark state
    Borucki, B
    Otto, H
    Joshi, CP
    Gasperi, C
    Cusanovich, MA
    Devanathan, S
    Tollin, G
    Heyn, MP
    [J]. BIOCHEMISTRY, 2003, 42 (29) : 8780 - 8790
  • [10] Kinetics of proton uptake and dye binding by photoactive yellow protein in wild type and in the E46Q and E46A mutants
    Borucki, B
    Devanathan, S
    Otto, H
    Cusanovich, MA
    Tollin, G
    Heyn, MP
    [J]. BIOCHEMISTRY, 2002, 41 (31) : 10026 - 10037