| 1. |
- Andersson, Magnus, et al.
(författare)
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Structural Dynamics of Light-Driven Proton Pumps
- 2009
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Ingår i: Structure. - : Elsevier BV. - 0969-2126 .- 1878-4186. ; 17:9, s. 1265-1275
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Tidskriftsartikel (refereegranskat)abstract
- Bacteriorhodopsin and proteorhodopsin are simple heptahelical proton pumps containing a retinal chromophore covalently bound to helix G via a protonated Schiff base. Following the absorption of a photon, all-trans retinal is isomerized to a 13-cis conformation, initiating a sequence of conformational changes driving vectorial proton transport. In this study we apply time-resolved wide-angle X-ray scattering to visualize in real time the helical motions associated with proton pumping by bacteriorhodopsin and proteorhodopsin. Our results establish that three conformational states are required to describe their photocycles. Significant motions of the cytoplasmic half of helix F and the extracellular half of helix C are observed prior to the primary proton transfer event, which increase in amplitude following proton transfer. These results both simplify the structural description to emerge from intermediate trapping studies of bacteriorhodopsin and reveal shared dynamical principles for proton pumping.
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| 2. |
- Daranciang, Dan, et al.
(författare)
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Ultrafast Photovoltaic Response in Ferroelectric Nanolayers
- 2012
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Ingår i: Physical Review Letters. - 1079-7114. ; 108:8
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Tidskriftsartikel (refereegranskat)abstract
- We show that light drives large-amplitude structural changes in thin films of the prototypical ferroelectric PbTiO3 via direct coupling to its intrinsic photovoltaic response. Using time-resolved x-ray scattering to visualize atomic displacements on femtosecond time scales, photoinduced changes in the unit-cell tetragonality are observed. These are driven by the motion of photogenerated free charges within the ferroelectric and can be simply explained by a model including both shift and screening currents, associated with the displacement of electrons first antiparallel to and then parallel to the ferroelectric polarization direction.
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| 3. |
- Davidsson, Jan, et al.
(författare)
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Structural determination of a transient isomer of CH2I2 by picosecond x-ray diffraction
- 2005
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Ingår i: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 94:24
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Tidskriftsartikel (refereegranskat)abstract
- Ultrafast time-resolved spectroscopic studies of complex chemical reactions in solution are frequently hindered by difficulties in recovering accurate structural models for transient photochemical species. Time-resolved x-ray and electron diffraction have recently emerged as techniques for probing the structural dynamics of short lived photointermediates. Here we determine the structure of a transient isomer of photoexcited CH2I2 in solution and observe the downstream reactions of the initial photoproducts. Our results illustrate how geminate recombination proceeds via the formation of a transient covalent bond onto the iodine atom remaining with the parent molecule. Further intramolecular rearrangements are thus required for the CH2I-I isomer to return to CH2I2. The generation of I-3(-) from those iodine radicals escaping the solvent cage is also followed with time.
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| 4. |
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| 5. |
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| 6. |
- Lemke, Henrik T., et al.
(författare)
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Coherent structural trapping through wave packet dispersion during photoinduced spin state switching
- 2017
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 8
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Tidskriftsartikel (refereegranskat)abstract
- The description of ultrafast nonadiabatic chemical dynamics during molecular photo-transformations remains challenging because electronic and nuclear configurations impact each other and cannot be treated independently. Here we gain experimental insights, beyond the Born-Oppenheimer approximation, into the light-induced spin-state trapping dynamics of the prototypical [Fe(bpy) 3 ] 2+ compound by time-resolved X-ray absorption spectroscopy at sub-30-femtosecond resolution and high signal-to-noise ratio. The electronic decay from the initial optically excited electronic state towards the high spin state is distinguished from the structural trapping dynamics, which launches a coherent oscillating wave packet (265 fs period), clearly identified as molecular breathing. Throughout the structural trapping, the dispersion of the wave packet along the reaction coordinate reveals details of intramolecular vibronic coupling before a slower vibrational energy dissipation to the solution environment. These findings illustrate how modern time-resolved X-ray absorption spectroscopy can provide key information to unravel dynamic details of photo-functional molecules.
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| 7. |
- Malmerberg, Erik, 1980, et al.
(författare)
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Time-Resolved WAXS Reveals Accelerated Conformational Changes in Iodoretinal-Substituted Proteorhodopsin.
- 2011
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Ingår i: Biophysical journal. - : Elsevier BV. - 1542-0086 .- 0006-3495. ; 101:6, s. 1345-53
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Tidskriftsartikel (refereegranskat)abstract
- Time-resolved wide-angle x-ray scattering (TR-WAXS) is an emerging biophysical method which probes protein conformational changes with time. Here we present a comparative TR-WAXS study of native green-absorbing proteorhodopsin (pR) from SAR86 and a halogenated derivative for which the retinal chromophore has been replaced with 13-desmethyl-13-iodoretinal (13-I-pR). Transient absorption spectroscopy differences show that the 13-I-pR photocycle is both accelerated and displays more complex kinetics than native pR. TR-WAXS difference data also reveal that protein structural changes rise and decay an order-of-magnitude more rapidly for 13-I-pR than native pR. Despite these differences, the amplitude andnature of the observed helical motions are not significantly affected by the substitution of the retinal's C-20 methyl group with an iodine atom. Molecular dynamics simulations indicate that a significant increase in free energy is associated with the 13-cis conformation of 13-I-pR, consistent with our observation that the transient 13-I-pR conformational state is reached more rapidly. We conclude that although the conformational trajectory is accelerated, the major transient conformation of pR is unaffected by the substitution of an iodinated retinal chromophore.
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| 8. |
- Orädd, Fredrik, 1994-
(författare)
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Determining the effects of regulatory parameters on the structural dynamics of P-type ATPase membrane transporters
- 2024
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Proteins are macromolecular machines with roles in all cellular activities and structures. The functional properties of each protein is the result of its combination of 3D-structure and inherent dynamics, and a wealth of structural and dynamic mechanisms have evolved to regulate protein activity. P-type ATPases are membrane transport proteins that hydrolyze ATP to move cations across membranes. These proteins are involved in important biological functions such as Ca2+ signaling and Cu+ homeostasis, making proper regulation critical. Adenylate kinase (AdK) is a small, soluble protein that plays a role in energy homeostasis by interconverting ATP, AMP, and ADP, which are bound by two substrate binding domains. In this thesis, the effect of regulatory parameters on the structural dynamics of Cu+-ATPases and the sarcoplasmic/endoplasmic Ca2+-ATPase (SERCA) was investigated, together with the reaction dynamics of AdK.In Paper III, the human Cu+-ATPase ATP7B was simulated with (holo) and without (apo) Cu+ bound to the regulatory metal binding domains (MBDs, with MBD-1 closest to the core protein). In the holo state, the MBD chain was more dynamic and extended, and MBD-2 approached the membrane Cu+ entry site. In Paper IV, the stability of the interaction between MBD-2 and the Cu+-entry site was evaluated using MD simulations, showing that the interaction was stable in the cytosol-open E1 state, but not in the lumen-facing E2P state. An interaction site between MBD-3 and the cytoplasmic domains was also found, where MBD-3 might inhibit activity by interfering with functional motions. Finally, in Paper II, Cu+ entry into the membrane high-affinity Cu+-binding site was simulated, showing that a proposed initial binding site was transient and that the Cu+ ion could move deeper into the membrane domain. In Paper I, we used time-resolved X-ray solution scattering (TR-XSS) to show a simultaneous closing of the substrate binding domains in AdK, which included a partial unfolding and refolding event in the ATP-binding domain. Paper VI demonstrated that a novel time-resolved setup based on detector readout at the MAX IV beamline CoSAXS could trigger and detect AdK structural dynamics.In Paper V, TR-XSS experiments showed that the rate-limiting step in skeletal-muscle SERCA1a was an E1-to-E2P intermediate at both low and high Ca2+ concentrations. An inhibitory effect at high Ca2+ concentration was explained by a fraction of SERCA molecules stalling in the ATP-binding/phosphorylation step. In Paper VII, TR-XSS experiments showed that the housekeeping isoform SERCA2b, which is slower but has higher Ca2+ affinity than the other SERCA isoforms, shared the same rate-limiting step as the SERCA1a isoform, but with a longer rise-time. Deletion of the SERCA2b luminal extension (LE) shifted the rate-limiting step to ATP-binding/phosphorylation, possibly because of LE-stabilization of the ATP-bound structure. These papers demonstrated the capability of TR-XSS to detect changes in rate-limiting steps and to investigate how protein structural dynamics respond to mutations and inhibitory conditions.
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