Structural changes during the formation of early intermediates in the bacteriorhodopsin photocycle

Biophysical Journal

Volumn 83, Issue 3, 2002, Pages 1281-1297

  Hayashi, Shigehiko ^a   Tajkhorshid, Emad ^b   Schulten, Klaus ^a,b  

^a UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

^b NONE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIORHODOPSIN; PROTON PUMP; SCHIFF BASE; PROTON;

ARTICLE; CONFORMATIONAL TRANSITION; HYDROGEN BOND; ISOMER; MOLECULAR DYNAMICS; MOLECULAR MECHANICS; PHOTOREACTIVITY; PROTON TRANSPORT; QUANTUM MECHANICS; REACTION ANALYSIS; STRUCTURE ANALYSIS; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; LIGHT; METABOLISM; PHOTOSYNTHESIS; PHYSIOLOGY; PROTEIN CONFORMATION; PROTEIN SECONDARY STRUCTURE; RETINA; THERMODYNAMICS; X RAY CRYSTALLOGRAPHY;

BACTERIORHODOPSINS; COMPUTER SIMULATION; CRYSTALLOGRAPHY, X-RAY; HYDROGEN BONDING; LIGHT; MODELS, CHEMICAL; MODELS, MOLECULAR; PHOTOSYNTHESIS; PROTEIN CONFORMATION; PROTEIN STRUCTURE, SECONDARY; PROTONS; RETINA; THERMODYNAMICS;

EID: 0036708439     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(02)73900-3     Document Type: Article

References (92)

1. Application of Raman spectroscopy to retinal proteins
2. Fourier transform infrared difference spectroscopy of bacteriorhodopsin and its photoproducts
3. Molecular dynamics study of bacteriorhodopsin and the purple membrane
4. A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: The RESP model
5. Protein, lipid and water organization in bacteriorhodopsin crystals: A molecular view of the purple membrane at 1.9 angstrom resolution
6. Quantum dynamics of retinal's femtosecond photoisomerization in bacteriorhodopsin
7. Molecular dynamics with coupling to an external bath
8. Energy storage in the primary step of the photocycle of bacteriorhodopsin
9. A spectroscopic, photocalorimetric, and theoretical investigation of the quantum efficiency of the primary event in bacteriorhodopsin
10. Resonance Raman spectra of bacteriorhodopsin's primary photoproduct: Evidence for a distorted 13-cis retinal chromophore
11. Vibrational spectroscopy of bacteriorhodopsin mutants-light-driven proton transport involves protonation changes of aspartic-acid residue-85, residue-96, and residue-212
12. Glutamic acid 204 is the terminal proton release group at the extracellular surface of bacteriorhodopsin
13. The projection structure of the low temperature K intermediate of the bacteriorhodopsin photocycle determined by electron diffraction
14. Hydration of counterion of the Schiff base in the chloride-transporting mutant of bacteriorhodopsin: FTIR and FT-Raman studies on the effects of anion binding when Asp85 is replaced with a neutral residue
15. A second generation force field for the simulation of protein, nucleic acids, and organic molecules
16. 15N shift anisotropy
17. Two bathointermediates of the bacteriorhodopsin photocycle, distinguished by nanosecond timeresolved FTIR spectroscopy at room temperature
18. Picosecond time-resolved resonance Raman spectroscopy of bacteriorhodopsin's J, K, and KL intermediates
19. High-resolution X-ray structure of an early intermediate in the bacteriorhodopsin photocycle
20. Structure of an early intermediate in the M-state phase of the bacteriorhodopsin photocycle
21. A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations
22. Detection of a water molecule in the active-site of bacteriorhodopsin: Hydrogen bonding changes during the primary photoreaction
23. Energy components of aqueous solution: Insight from hybrid QM/MM simulations using a polarizable solvent model
24. A priori evaluation of aqueous polarization effects through Monte Carlo QM-MM simulations
25. + protonated Schiff base: An ab initio minimal model for retinal photoisomerization
26. Photoisomerization path for a realistic retinal chromophore model: The nonatetraenimium cation
27. Role of aspartate-96 in proton translocation by bacteriorhodopsin
28. New developments in applying quantum mechanics to proteins
29. Computational evidence in favor of a two-state, two-mode model of the retinal chromophore photoisomerization
30. Electron-crystallographic refinement of the structure of bacteriorhodopsin
31. Protein dynamics in the bacteriorhodopsin photocycle: A nanosecond step-scan FTIR investigation of the KL to L transition
32. Control of the pump cycle in bacteriorhodopsin: Mechanisms elucidated by solid-state NMR of the D85N mutant
33. Proton transfer in bacteriorhodopsin: Structure, excitation, IR spectra, and potential energy surface analyses by an ab initio QM/MM method
34. Structural determinants of spectral tuning in retinal proteins-bacteriorhodopsin vs sensory rhodopsin II
35. Three dimensional model of purple membrane obtained by electron microscopy
36. NMR probes of vectoriality in the proton-motive photocycle of bacteriorhodopsin: Evidence for an 'electrostatic steering' mechanism
37. Study of the opsin shift of bacteriorhodopsin: In-sight from QM/MM calculations with electronic polarization effects of the protein environment
38. 15N solid-state NMR study of the L photointermediate
39. VMD-visual molecular dynamics
40. Three electronic state model of the primary phototransformation of bacteriorhodopsin
41. Vibrational frequency and dipolar orientation of the protonated Schiff base in bacteriorhodopsin before and after photoisomerization
42. Protein structural changes in bacteriorhodopsin upon photoisomerization as revealed by polarized FTIR spectroscopy
43. Cysteine S-H as a hydrogen-bonding probe in proteins
44. Structural change of threonine 89 upon photoisomerization in bacteriorhodopsin as revealed by polarized FTIR spectroscopy
45. Local and distant protein structural changes on photoisomerization of the retinal in bacteriorhodopsin
46. Direct observation of the bridged water stretching vibrations inside a protein
47. Water-mediated proton transfer in proteins: An FTIR study of bacteriorhodopsin
48. Tight Asp-85-Thr-89 association during the pump switch of bacteriorhodopsin
49. A new energy decomposition scheme for molecular interactions within the Hartree-Fock approximation
50. Molecular dynamics study of the dark-adaptation process in bacteriorhodopsin
51. Bacteriorhodopsin: A light-driven proton pump in Halobacterium halobium
52. Proton transfer pathways in bacteriorhodopsin at 2.3 angstrom resolution
53. Coupling photoisomerization of retinal to directional transport in bacteriorhodopsin
54. Crystal structure of sensory rhodopsin II at 2.4 Å: Insights into color tuning and transducer interaction
55. Structure of bacteriorhodopsin at 1.55 angstrom resolution
56. Structural changes in bacteriorhodopsin during ion transport at 2 angstrom resolution
57. Interaction of aspartate-85 with a water molecule and the protonated Schiff base in the L intermediate of bacteriorhodopsin: A Fourier transform infrared spectroscopic study
58. IMOMM: A new ab initio + molecular mechanics geometry optimization scheme of equilibrium structures and transition states
59. A study of small water clusters using the effective fragment potential (EFP) method
60. Raster3D: Photorealistic molecular graphics
61. The structure of bacteriorhodopsin at 3.0 Å resolution based on electron crystallography: Implication of the charge distribution
62. Characterization of a conical intersection between the ground and first excited state for a retinal analog
63. Functional interaction in bacteriorhodopsin: A theoretical analysis of retinal hydrogen bonding with water
64. Rhodopsin-like protein from the purple membrane of Halobacterium halobium
65. Resonance Raman study of the primary photochemistry of bacteriorhodopsin
66. Lipidic cubic phase crystallization of bacteriorhodopsin and cryotrapping of intermediates: Towards resolving a resolving photocycle
67. X-ray structure of bacteriorhodopsin at 2.5 angstroms from microcrystals grown in lipidic cubic phases
68. Diyamical fluctuating charge force fields: Application to liquid water
69. Infrared evidence that the Schiff base of bacteriorhodopsin is protonated: bR570 and K intermediates
70. Fourier transform infrared spectroscopic evidence for the existence of two conformations of the bacteriorhodopsin primary photoproduct at low temperature
71. Helix deformation is coupled to vectorial proton transport in the photocycle of bacteriorhodopsin
72. X-ray structure of sensory rhodopsin II at 2.1 Å resolution
73. Complete identification of C=O stretching vibrational bands of protonated aspartic acid residues in the difference infrared spectra of M and N intermediate versus bacteriorhodopsin
74. Time-resolved infrared spectral analysis of the KL-to-L conversion in the photocycle of bacteriorhodopsin
75. Nanosecond time-resolved infrared spectroscopy distinguishes two K species in the bacteriorhodopsin photocycle
76. Structural alterations for proton translocation in the M state of wild-type bacteriorhodopsin
77. Absorption spectra of intermediates of bacteriorhodopsin measured by lase photolysis at room temperatures
78. Molecular dynamics studies of bacteriorhodopsin's photocycles
79. Molecular dynamics study of the nature and origin of retinal's twisted structure in bacteriorhodopsin
80. α control of the retinal Schiff base: A density functional study
81. Influence of the methyl groups on the structure, charge distribution, and proton affinity of the retinal Schiff base
82. The origin of hydrogen bonding: An energy decomposition study
83. Nature of the surface crossing process in bacteriorhodopsin: Computer simulations of the quantum dynamics of the primary photochemical event
84. The dynamics of the primary event in rhodopsins revisited
85. Theoretical studies of enzymatic reactions: Dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme
86. Time-resolved step-scan FT-IR investigations of the transition from KL to L in the bacteriorhodopsin photocycle: Identification of chromophore twists by assigning hydrogen-out-of-plane (HOOP) bending vibrations
87. Molecular dynamics study of early picosecond events in the bacteriorhodopsin photocycle: Dielectric response, vibrational cooling and the J, K intermediates
88. Does the KL intermediate exist in the photocycle of bacteriorhodopsin?
89. Molecular dynamics simulation of the excited-state dynamics of bacteriorhodopsin
90. Molecular dynamics study of the proton pump cycle of bacteriorhodopsin