Protein Dynamics Control the Kinetics of Initial Electron Transfer in Photosynthesis

Li, Ang; Lin, Su; Allen, James P.; Williams, Joann; Blankert, Sean; Laser, Christa; Woodbury, Neal W.

doi:10.1126/science.1140030

Cited by 228 publications

(319 citation statements)

References 23 publications

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“…2a and Supplementary Fig. 1a), Ae À ðt=tÞ b (A, amplitude; t, decay time constant; and b, stretched parameter), due to the modulation of ET by active-site solvation on similar timescales [11][12][13]19,20 . Using t h i ¼ ðt=bÞGð1=bÞ and knowing the deactivation lifetimes (t LT ) in nanoseconds in the absence of substrate (Supplementary Fig.…”

Section: Resultsmentioning

confidence: 99%

“…The ER after repair is in the Marcus inverted region ( À DG 0 Zl). The mutations considerably alter not only the free energy changes, that is, the reduction potentials of the cofactor or the substrate, but also the reorganization energies 20,25,26 and thus significantly modulate all three ET reactions. The derived large reorganization energies mainly come from the contributions of the different structural distortions of FADH À and FADH (refs 25,27).…”

Section: Discussionmentioning

confidence: 99%

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The molecular origin of high DNA-repair efficiency by photolyase

Tan

Liu

et al. 2015

Nat Commun

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The primary dynamics in photomachinery such as charge separation in photosynthesis and bond isomerization in sensory photoreceptor are typically ultrafast to accelerate functional dynamics and avoid energy dissipation. The same is also true for the DNA repair enzyme, photolyase. However, it is not known how the photoinduced step is optimized in photolyase to attain maximum efficiency. Here, we analyse the primary reaction steps of repair of ultraviolet-damaged DNA by photolyase using femtosecond spectroscopy. With systematic mutations of the amino acids involved in binding of the flavin cofactor and the cyclobutane pyrimidine dimer substrate, we report our direct deconvolution of the catalytic dynamics with three electron-transfer and two bond-breaking elementary steps and thus the fine tuning of the biological repair function for optimal efficiency. We found that the maximum repair efficiency is not enhanced by the ultrafast photoinduced process but achieved by the synergistic optimization of all steps in the complex repair reaction.

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Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

The molecular origin of high DNA-repair efficiency by photolyase

Tan

Liu

et al. 2015

Nat Commun

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“…A whole cell cycle takes about 1 d (Granier and Tardieu, 1998;Granier et al, 2000), changes in cell wall properties take minutes to hours (Chazen and Neumann, 1994), and hydraulic processes occur over seconds to minutes (Ye and Steudle, 2006;Tang and Boyer, 2008;Parent et al, 2009). While analysis of time constants is a common method to identify the most likely mechanisms affecting time courses in physics (Kim et al, 2008;Knowles et al, 2009) or enzymology (Schweizer et al, 1998;Wang et al, 2007;Zheng et al, 2013), it is less common in studies of growth or of genomics applied to responses to environmental conditions. The progress of phenotyping now allows one to obtain a large number of time courses of LER, transpiration, and environmental conditions with a time step of minutes (Sadok et al, 2007), thereby making possible the use of this method.…”

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confidence: 99%

A Hydraulic Model Is Compatible with Rapid Changes in Leaf Elongation under Fluctuating Evaporative Demand and Soil Water Status

et al. 2014

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Plants are constantly facing rapid changes in evaporative demand and soil water content, which affect their water status and growth. In apparent contradiction to a hydraulic hypothesis, leaf elongation rate (LER) declined in the morning and recovered upon soil rehydration considerably quicker than transpiration rate and leaf water potential (typical half-times of 30 min versus 1–2 h). The morning decline of LER began at very low light and transpiration and closely followed the stomatal opening of leaves receiving direct light, which represent a small fraction of leaf area. A simulation model in maize (Zea mays) suggests that these findings are still compatible with a hydraulic hypothesis. The small water flux linked to stomatal aperture would be sufficient to decrease water potentials of the xylem and growing tissues, thereby causing a rapid decline of simulated LER, while the simulated water potential of mature tissues declines more slowly due to a high hydraulic capacitance. The model also captured growth patterns in the evening or upon soil rehydration. Changes in plant hydraulic conductance partly counteracted those of transpiration. Root hydraulic conductivity increased continuously in the morning, consistent with the transcript abundance of Zea maize Plasma Membrane Intrinsic Protein aquaporins. Transgenic lines underproducing abscisic acid, with lower hydraulic conductivity and higher stomatal conductance, had a LER declining more rapidly than wild-type plants. Whole-genome transcriptome and phosphoproteome analyses suggested that the hydraulic processes proposed here might be associated with other rapidly occurring mechanisms. Overall, the mechanisms and model presented here may be an essential component of drought tolerance in naturally fluctuating evaporative demand and soil moisture.

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“…24,[29][30][31][32] In particular, for the latter case, there has been growing interest in the study of fast photo-induced reaction dynamics that can occur during time scales comparable to those of molecular relaxation and dephasing dynamics. [33][34][35] For these, currently available QFPE or QSE are not well suited. Thus, generalization of QFPE to include nonMarkovian and nonequilibrium effects remains an important and interesting theoretical issue to be addressed.…”

Section: Introductionmentioning

confidence: 99%

Generalized quantum Fokker-Planck equation for photoinduced nonequilibrium processes with positive definiteness condition

Jang

2016

The Journal of Chemical Physics

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This work provides a detailed derivation of a generalized quantum Fokker-Planck equation (GQFPE) appropriate for photo-induced quantum dynamical processes. The path integral method pioneered by Caldeira and Leggett (CL) [Caldeira and Leggett, Physica A 121, 587 (1983)] is extended for a nonequilibrium influence functional, which has been obtained for general cases where the ground and the excited electronic state baths can be different. Both nonequilibrium and nonMarkovian effects are accounted for consistently by expanding the paths in the exponents of the influence functional with respect to time up to the second order. This procedure results in approximations involving only single time integrations for the exponents of the influence functional but with additional time dependent boundary terms that have been ignored in previous works. The boundary terms complicate the derivation of a time evolution equation, but do not affect position dependent physical observables or the dynamics in the steady state limit. For an effective density operator with the boundary terms factored out, a time evolution equation is derived through short time expansion of the effective action followed by Gaussian integrations in analytically continued complex domain of space. This leads to a compact form of GQFPE with time dependent kernels and additional terms, which make the resulting equation the Dekker form [H. Dekker, Phys. Rep. 80, 1 (1981)]. Major terms of the equation are analyzed for the case of Ohmic spectral density with Drude cutoff, which shows that the new GQFPE satisfies the positive definiteness condition in medium to high temperature limit.

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Protein Dynamics Control the Kinetics of Initial Electron Transfer in Photosynthesis

Cited by 228 publications

References 23 publications

The molecular origin of high DNA-repair efficiency by photolyase

The molecular origin of high DNA-repair efficiency by photolyase

A Hydraulic Model Is Compatible with Rapid Changes in Leaf Elongation under Fluctuating Evaporative Demand and Soil Water Status

Generalized quantum Fokker-Planck equation for photoinduced nonequilibrium processes with positive definiteness condition

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